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  • General Chemistry  (12,729)
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  • Fisheries
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  • 1
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    Yemaya No. 63, May 2021 (2022)
    The International Collective in Support of Fishworkers (ICSF) | India
    Details
    Publication Date: 2022-02-21
    Description: Yemaya No. 63, dated May 2021, features articles from US, The Netherlands, Myanmar, Senegal, and an article on women in fisheries and human rights. The article from the US by Linda Behnken argues that a growing coalition of small-scale, community-based fishers is calling for the recognition and protection of Alaska’s invaluable coastal fisheries during COVID-19. The article from the Netherlands by Cornelie Quist looks at the challenges facing women engaged in small-scale fishing and supplying fish through retailers and how they found new ways to directly reach consumers. The conversation between Miranda Bout and Cornelie Quist focuses on how they combined new product development with the use of social media to contact their customer base during the pandemic-induced disruption of traditional marketing chains. The article by Elena Finkbeiner, Juno Fitzpatrick and Whitney Yadao-Evans looks at recent media revelations and scientific research that have brought increased attention to human-rights violations and the myriad social issues facing fisheries, but with a disproportionate focus on labour-rights violations at sea and in industrial fishing operations. The systemic inequalities combined with the effects of COVID-19 exacerbated vulnerabilities of women to health risks, food and livelihood security. The article from Senegal by Aby Dia from Lumière Synergie pour le Développement (LSD), in collaboration with WoMin African Alliance, South Africa, narrates the story of traditional women fish processors from the Bargny who have been, for more than a decade, struggling against development projects that jeopardise their environment, health and livelihoods. In order to preserve their livelihoods, women processors in Senegal have come together to oppose the Tosyali steel project. The European Network of Women in Fisheries and Aquaculture in Europe (AKTEA) urges the Office of the Commissioner for the Environment, Oceans and Fisheries to integrate gender into all aspects of European fishing policy. The Profile column looks at how Linda Behnken became a fisher in Alaska and how fishing has shaped her individuality and work. Natalie Sattler says that fishing for halibut, sablefish and salmon from the sparkling waters of the Pacific along with her children and at the same time passion for working with the Alaska Longline Fishermen’s Association and the Alaska Sustainable Fisheries Trust is an immense challenge.
    Description: Published
    Description: Refereed
    Keywords: Fishing Communities ; Women in fisheries ; Gender ; Small-scale fisheries ; Aquaculture ; Fisheries
    Repository Name: AquaDocs
    Type: Book/Monograph/Conference Proceedings
    Format: 12p.
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  • 2
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    Sitios de agregación reproductiva de pargos (Lutjanidae) en el Parque Nacional Cayos de San Felipe, Cuba. (2022)
    Details
    Publication Date: 2022-06-28
    Description: Las pesquerías basadas en las agregaciones reproductivas pueden amenazar a especies como los pargos que tienen conductas gregarias durante el período reproductivo. Esta nota ofrece elementos que sugieren la existencia de sitios de agregación no registrados previamente y no protegidos en el Parque Nacional Cayos de San Felipe (PNCSF), región suroccidental de Cuba. La información tradicional obtenida de pescadores locales y trabajadores del parque se corroboró con muestreos cualitativos y cuantitativos de peces de arrecifes y datos de pesquerías locales del 2014. En la época de reproducción de pargos (mayo a julio) se observaron grupos de entre 40-100 ejemplares de Lutjanus cyanopterus, Lutjanus synagris y Lutjanus jocu en los arrecifes de la zona occidental del PNCSF (camellones entre 15-30 m de profundidad cerca del borde de la plataforma). Dentro de esa área, se señalan dos sitios que parecen ser utilizados para agregaciones de predesove, por lo que requieren protección y ser estudiados. Los censos cuantitativos confirmaron que en mayo y junio la zona occidental tiene densidad alta de pargos adultos. También, el pico de captura de estas especies ocurrió en la época reproductiva. Se comprobó que las pesquerías se realizaron durante las migraciones de peces hacia el borde de la plataforma en áreas de la zona occidental del PNCSF, y que más del 60% de los individuos tuvieron gónadas maduras (antes de desovar). Esta información debe incentivar el estudio de las agregaciones de desove en esta región de Cuba, la protección de especies amenazadas y áreas de alta significación ecológica y la implementación de pesquerías sostenibles.
    Description: Fisheries based on reproductive aggregations can threaten species such as snappers that have gregarious behavior during the reproductive period. This note provides evidence to support the existence of aggregation sites, not previously registered and unprotected, in the National Park San Felipe Keys (NPSFK), southwestern region of Cuba. Traditionalinformation obtained from local fishermen and from the park staff was complemented with qualitative and quantitative fish reef censuses and local fisheries data in 2014. In the reproductive season of snappers (May to July) groups of between 40-100 specimens of Lutjanus cyanopterus, Lutja- nus synagris and Lutjanus jocu were observed in the western area of the NPSFK on the reefs (spoor and grove between 20-30 m deep close to the platform edge). Within that area two sites are indicated that can be used for prespawning aggregation, so they require protection and study. Quanti- tative censuses confirmed that in May and June the western zone has high density of adult snappers. Also, the peak of capture of these snapper species occurred in the reproduc- tive season. It was found that fisheries carried out during fish migrations to the edge of the shelf in areas of the western area of the NPSFK and more than 60% of the individuals had mature gonads (before spawning). This information should promote the study of spawning aggregations in this region of Cuba, the protection of threatened species and areas of high ecological significance and the implementation of sustainable fisheries.
    Description: Published
    Description: Refereed
    Keywords: Región suroccidental de Cuba ; Desove ; Pesquerías ; Migration routes ; Spawning ; Fisheries ; Rutas migraciones
    Repository Name: AquaDocs
    Type: Journal Contribution
    Format: pp.54-65
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  • 3
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    Workshop on ICES Reference Points (WKREF2) (2022)
    International Council for the Exploration of the Sea | Copenhagen, Denmark
    Details
    Publication Date: 2022-09-14
    Description: The ICES Workshop on ICES reference points (WKREF2) was tasked review the WKREF1 report and based on the outcome develop updated guidelines for the ICES reference points system and recommendations for ACOM consideration. The WKREF1 report has suggested 5 key recom- mendations to simplify and harmonise the ICES reference points framework representing a ma- jor change to the current guidelines. At WKREF2, we detailed discussions and four key concerns were raised about the proposed approach. The first related to the simplification of rules to define Blim. Around two thirds of category 1 stocks would end up as WKREF1 “Blim Type 2” where Blim would be set as a fraction of B0. The Allee effect or “depensation” maybe more important than previously thought and should be furthered explored for ICES stocks since it has important consequences for Blim. A number of challenges and issues around defining Blim using the current guidelines were documented. Some suggestions on improvement criteria were discussed including using classifiers to define spas- modic stocks and using change point algorithms to address non-stationary productivity regimes. However, further work is need to make these approaches operational and there was no consen- sus that the WKREF1 Blim types should replace the current guidelines. WKREF1 recommended that the FMSY proxy should be based on a biological proxies and should be less than the deterministic FMSY. It was pointed out that the stochastic FMSY estimated in EqSim for example, is lower than the deterministic FMSY and that the current guidelines ensure that the FMSY should not pose a more than 5% risk to Blim. A large amount of work described in WD 1 was carried out to develop an MSE framework to consistency and robustness test a candidate refer- ence point system for North East Atlantic stocks. However, WKREF2 recommended that further work needs to be carried out to condition and test the simulation framework before the conclu- sions could be adopted by ICES and incorporated into the guidelines. A number of considerations for defining MSY related reference points were discussed including using model validation and prediction skill to ensure that ICES provide robust and credible ad- vice. There is evidence that density dependence (DD) is important in the majority of ICES stocks (68% in recruitment and 54% in growth). The correct prediction of the shape and strength of density-dependence in productivity is key to predicting future stock development and providing the best possible long-term fisheries management advice. A suggested approach to use surplus production models (SPMs) to account for DD in FMSY was suggested and discussed but there was no consensus on whether that approach was appropriate. There was consensus that the FECO approach as a means of adapting target fishing mortality to medium-term changes in productiv- ity should be included in the guidelines subject to a benchmark and ACOM approval. While WKREF1 and 2 focused mainly on Category 1 stocks ToR c) called for a “simplified and harmonised set of guidelines for estimating MSY and precautionary reference points applicable in the advice framework across various ICES stock categories.” Ideally the ICES assessment cat- egories should provide equivalent risk across all stocks. This issue was discussed but no recom- mendations emerged. There was no consensus a revised reference point framework was proposed at WKREF2. How- ever, it was agreed that it should be presented here for further discussion at ACOM and other fora. The key feature of the suggested approach is that the stock status evaluation is treated in- dependent of the Advice Rule (AR). The main feature of the system is that the biomass trigger is not linked to a stock status evaluation, it is linked to the expected biomass when fishing at the target fishing mortality, in contrast to the current ICES approach. It also entailed that FMSY would also become an upper limit of fishing mortality and that the advised fishing mortality would be set at or lower than that level. WKREF2 did not discuss what to do in situations where SSB〈 Blim or alternative forms of HCR for the advice rule. Building community understanding and con- sensus around simplified and harmonised guidelines has yet to be achieved. A further workshop WKREF3 will be required to achieve that aim. The report includes 6 recommendations for ACOM consideration.
    Description: ICES
    Description: The main objective of the workshop was to review the recommendations of WKREF1 and con- sider how these might feed into a new reference points framework and guidelines for ICES. There were a number of presentations on the wider issues of best practice for reference points, the Allee effect, density dependence and the WKIRISH approach. The starting point was to try and develop a set of simplified and harmonised guidelines based on the WKREF1 report rather than evolving the current guidelines to include the WKREF1 conclusions. A key aspect of the meeting was to allow for discussions in order to build a shared understanding of the strengths and weakness of the current framework and of the new framework emerging from WKREF1.
    Description: Published
    Description: Non Refereed
    Keywords: ICES ; Reference points ; Management advice ; Fisheries ; Fishery management reference points
    Repository Name: AquaDocs
    Type: Report
    Format: 103pp
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  • 4
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    The economic tradeoffs and ecological impacts associated with a potential mesopelagic fishery in the California Current (2022)
    Ecological Society of America
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dowd, S., Chapman, M., Koehn, L., & Hoagland, P. The economic tradeoffs and ecological impacts associated with a potential mesopelagic fishery in the California Current. Ecological Applications, 32(4), (2022): e2578, https://doi.org/10.1002/eap.2578.
    Description: The ocean's mesopelagic zone (200–1000 m) remains one of the most understudied parts of the ocean despite knowledge that mesopelagic fishes are highly abundant. Apex predators from the surface waters are known to consume these fishes, constituting an important ecological interaction. Some countries have begun exploring the potential harvest of mesopelagic fishes to supply fishmeal and fish oil markets due to the high fish abundance in the mesopelagic zone compared with overfished surface waters. This study explored the economic and ecological implications of a moratorium on the harvest of mesopelagic fishes such as lanternfish off the US West Coast, one of the few areas where such resources are managed. We adapted a bioeconomic decision model to examine the tradeoffs between the values gained from a hypothetical mesopelagic fishery with the potential values lost from declines in predators of mesopelagic fishes facing a reduced prey resource. The economic rationale for a moratorium on harvesting mesopelagics was sensitive both to ecological relationships and the scale of the nonmarket values attributed to noncommercial predators. Using a California Current-based ecological simulation model, we found that most modeled predators of mesopelagic fishes increased in biomass even under high mesopelagic harvest rates, but the changes (either increases or decreases) were small, with relatively few predators responding with more than a 10% change in their biomass. While the ecological simulations implied that a commercial mesopelagic fishery might not have large biomass impacts for many species in the California Current system, there is still a need to further explore the various roles of the mesopelagic zone in the ocean.
    Description: Sally Dowd acknowledges sponsorship from the WHOI Summer Student Fellowship and the Rausser College of Natural Resources Honors Program at UC Berkeley. This project would not have been possible without the guidance provided by Kama Thieler and Carl Boettiger. Porter Hoagland acknowledges funding from the Audacious Project, a collaborative endeavor, housed at TED and the J. Seward Johnson Fund in support of the Marine Policy Center at WHOI.
    Keywords: Bioeconomic model ; Fisheries ; Mesopelagic fishes ; Moratorium ; Nonmarket value ; Predators ; Rpath ; Willingness-to-pay values
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
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    The ocean twilight zone’s role in climate change (2022)
    Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-27
    Description: Buesseler, K., Jin, D., Kourantidou, M., Levin, D., Ramakrishna, K., Renaud, P., Ausubel, J., Baltes, K., Gjerde, K., Holland, M., Kostel, K., LaCapra, V., Martin, A., Sosik, H., Thorrold, S., Tierney, T., Joyce, K., Renier, N., Taylor, E. (2022). The Ocean Twilight Zone’s Role in Climate Change. Woods Hole Oceanographic Institution, 32 pp.
    Description: The ocean twilight zone (more formally known as the mesopelagic zone) plays a fundamental role in global climate. It is the mid-ocean region roughly 100 to 1000 meters below the surface, encompassing a half-mile deep belt of water that spans more than two-thirds of our planet. The top of the ocean twilight zone only receives 1% of incident sunlight and the bottom level is void of sunlight. Life in the ocean twilight zone helps to transport billions of metric tons (gigatonnes) of carbon annually from the upper ocean into the deep sea, due in part to processes known as the biological carbon pump. Once carbon moves below roughly 1000 meters depth in the ocean, it can remain out of the atmosphere for centuries to millennia. Without the benefits of the biological carbon pump, the atmospheric CO 2 concentration would increase by approximately 200 ppm 1 which would significantly amplify the negative effects of climate change that the world is currently trying to curtail and reverse. Unfortunately, existing scientific knowledge about this vast zone of the ocean, such as how chemical elements flow through its living systems and the physical environment, is extremely limited, jeopardizing the efforts to improve climate predictions and to inform fisheries management and ocean policy development.
    Description: Funding is: The Audacious Project housed at TED
    Keywords: Climate ; Mesopelagic ; Twilight Zone ; Fisheries ; Carbon Dioxide Removal ; Ocean ; Biological Carbon Pump ; Solubility Pump ; Carbon ; Marine Snow
    Repository Name: Woods Hole Open Access Server
    Type: Other
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  • 6
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    Equitable allocations in northern fisheries: bridging the divide for Labrador Inuit (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kourantidou, M., Hoagland, P., Dale, A., & Bailey, M. Equitable allocations in northern fisheries: bridging the divide for Labrador Inuit. Frontiers in Marine Science, 8, (2021): 590213, https://doi.org/10.3389/fmars.2021.590213.
    Description: Canada has undertaken commitments to recognize the rights of Indigenous Peoples in fisheries through policies and agreements, including Integrated Fishery Management Plans, the Reconciliation Strategy, and Land Claim Agreements (LCAs). In addition to recognizing rights, these commitments were intended to respect geographic adjacency principles, to enhance the economic viability of Indigenous communities, and to be reflective of community dependence on marine resources. We examined the determinants of quota allocations in commercial fisheries involving Nunatsiavut, Northern Labrador, the first self-governing region for the Inuit peoples in Canada. It has been argued that current fishery allocations for Nunatsiavut Inuit have not satisfied federal commitments to recognize Indigenous rights. Indicators that measure equity in commercial allocations for the turbot or Greenland halibut (Reinhardtius hippoglossoides) and northern shrimp (Pandalus borealis) fisheries were identified and assessed. In these two cases, historical allocations continue to predominate for allocations based upon equity or other social or economic considerations. We illustrate equity-enhancing changes in the quota distribution under scenarios of different levels of inequality aversion, and we make qualitative assessments of the effects of these allocations to Nunatsiavut for socioeconomic welfare. This approach could benefit fisheries governance in Northern Labrador, where federal commitments to equity objectives continue to be endorsed but have not yet been integrated fully into quota allocations.
    Description: This research was undertaken with funding from the Canada First Research Excellence Fund through the Ocean Frontier Institute (MK and MB) and the Johnson Endowment of the Woods Hole Oceanographic Institution’s (WHOI) Marine Policy Center (PH).
    Keywords: Fisheries ; Allocations ; Equity ; Indigenous rights ; Access
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Experiments on the induced spawning and larval rearing of the milkfish, Chanos chanos (Forsskal) in 1979 (2021)
    In:  aqdchief@seafdec.org.ph | http://aquaticcommons.org/id/eprint/18569 | 2002 | 2015-11-15 16:06:30 | 18569 | Southeast Asian Fisheries Development Center, Aquaculture Department
    Details
    Publication Date: 2022-08-02
    Description: This paper summarizes the results of the experiments on the induced breeding and larval rearing of milkfish (Chanos chanos) during the 1979 season. Milkfish larvae could be reared successfully without the use of trochophore larvae of oysters as feed during the first few days. In order to induce the ovulation of wild adult milkfish a higher dose of human chorionic gonadotropin hormone is required.
    Keywords: Fisheries ; Chanos chanos ; ISEW ; Philippines ; marine environment ; Brood stocks ; Fish culture ; Fish larvae ; Food organisms ; Induced breeding ; Larval development ; Sex hormones
    Repository Name: AquaDocs
    Type: article
    Format: application/pdf
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    Format: 1-3
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  • 8
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    Knowing Asian aquaculture and fisheries. Part 1 (2021)
    In:  library@seafdec.org.ph | http://aquaticcommons.org/id/eprint/20100 | 17342 | 2016-02-24 22:18:26 | 20100 | Southeast Asian Fisheries Development Center, Aquaculture Department
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    Publication Date: 2022-08-02
    Description: An outline is given of aquaculture and fisheries in Asia, providing information of use to students whose work can influence laws, rules, policy and regulations on aquaculture and fisheries, with the view in mind to sustainable aquaculture. In this issue, the following countries are examined: China, Indonesia, and Bangladesh.
    Keywords: Aquaculture ; Fisheries ; Fishery management ; Aquaculture development ; Aquaculture regulations ; Marine aquaculture ; Freshwater aquaculture ; Fishery industry ; Asia ; Bangladesh ; China
    Repository Name: AquaDocs
    Type: article
    Format: application/pdf
    Format: application/pdf
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  • 9
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    Knowing Asian aquaculture and fisheries. Part 4 (2021)
    In:  library@seafdec.org.ph | http://aquaticcommons.org/id/eprint/20067 | 2002 | 2016-03-04 15:16:24 | 20067 | Southeast Asian Fisheries Development Center, Aquaculture Department
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    Publication Date: 2022-08-02
    Keywords: Fisheries ; Aquaculture ; Vietnam ; Sri Lanka ; Sri Lanka ; Vietnam ; brackishwater environment ; freshwater environment ; marine environment ; Aquaculture ; Aquaculture techniques ; Brackishwater aquaculture ; Feed ; Fish culture ; Fish diseases ; Fisheries ; Fishery data ; Food organisms ; Freshwater aquaculture ; Marine aquaculture ; Marine fisheries ; Mollusc culture ; Pond culture ; Seaweed culture ; Shrimp culture
    Repository Name: AquaDocs
    Type: article
    Format: application/pdf
    Format: application/pdf
    Format: pp.9-10, 27
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  • 10
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    Knowing Asian aquaculture and fisheries (2021)
    In:  library@seafdec.org.ph | http://aquaticcommons.org/id/eprint/20055 | 2002 | 2016-03-03 11:33:32 | 20055 | Southeast Asian Fisheries Development Center, Aquaculture Department
    Details
    Publication Date: 2022-08-02
    Keywords: Fisheries ; Aquaculture ; Asia ; Cambodia ; India ; Asia ; Cambodia ; India ; Myanmar ; Myanmar ; brackishwater environment ; freshwater environment ; marine environment ; Aquaculture ; Aquaculture development ; Aquaculture economics ; Aquaculture techniques ; Brackishwater aquaculture ; Catching methods ; Culture effects ; Environmental impact ; Fish culture ; Fisheries ; Fishery development ; Fishery resources ; Fishery statistics ; Freshwater aquaculture ; Marine aquaculture ; Shrimp culture ; Sustainability ; Trade
    Repository Name: AquaDocs
    Type: article
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  • 11
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    Regional survey of heavy metals in fish and fish products: Indonesia (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26291 | 23782 | 2019-04-08 09:42:05 | 26291 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
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    Publication Date: 2022-08-02
    Keywords: Fisheries ; Pollution ; Indonesia ; Heavy metals ; Chemical pollution ; Pollution monitoring
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  • 12
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    Regional survey of heavy metals in fish and fish products: Myanmar (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26293 | 23782 | 2019-03-22 03:49:21 | 26293 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
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    Publication Date: 2022-08-02
    Keywords: Fisheries ; Myanmar ; Heavy metals ; Cadmium ; Lead ; Mercury ; Biological sampling ; Fish ; Fishery products ; Seafood
    Repository Name: AquaDocs
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    Format: 38-46
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  • 13
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    Round scad exploration by purse seine in the South China Sea, Area III: Western Philippines (2021)
    Secretariat, Southeast Asian Fisheries Development Center | Bangkok, Thailand
    In:  http://aquaticcommons.org/id/eprint/26259 | 2002 | 2019-03-01 05:56:06 | 26259 | Southeast Asian Fisheries Development Center, Secretariat
    Details
    Publication Date: 2022-08-02
    Description: Round scad exploration by purse seine in the waters of western Philippines was conducted from April 22 to May 7, 1998 for a period of five (5) fishing days with a total catch of 7.3 tons and an average of 1.5 tons per setting. Dominant species caught were Decapterus spp. having 70.09% of the total catch, followed by Selar spp. at 12.66% and Rastrelliger spp. 10.70%. Among the Decapterus spp. caught, D. macrosoma attained the highest total catch composition by species having 68.81% followed by D. kurroides and D.russelli with 0.31% and 1.14% respectively. The round scad fishery stock was composed mainly of juvenile fish (less than 13 cm) and Age group II (13 cm to 14 cm). Few large round scad at Age group IV and V (20 cm to 28 cm) stayed at the fishery. Other fishes caught were: Auxis rochei (0.85%), A. thazard (0.12%), Caranx spp. (0.45%), Emmilichthys nitidus (0.58%), Euthynnus affinis (0.42%), Leiognathus ruconius (0.58%), Loligo sp. (0.31%), Megalaspis cordyla (0.09%), Rastrelliger spp. (10.70%), Sardinella longiceps (0.03%), Scomberoides lysan (0.24%), Selar spp. (12.66%), Sphyraena spp. (0.90%), Thunnus albacares (0.96%) and others (1.02%). Tuna and tuna like fishes such as yellowfin tuna, eastern little tuna, bullet tuna, frigate tuna and oceanic squid are distributed in the upper latitudes of the survey area. On the other hand, round scads, big-eyed scads and Indian mackerels are dominantly present in the lower latitudes of the survey area.
    Keywords: Fisheries ; Exploratory fishing ; Purse seining ; Age composition ; Catch composition ; Fishery surveys ; Carangid fisheries ; South China Sea ; Philippines ; Rastrelliger ; Decapterus
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  • 14
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    Fisheries in Brunei Darussalam (2021)
    Training Department, Southeast Asian Fisheries Development Center | Samut Prakarn, Thailand
    In:  http://aquaticcommons.org/id/eprint/26215 | 17342 | 2019-02-08 06:25:54 | 26215 | Southeast Asian Fisheries Development Center, Training Department
    Details
    Publication Date: 2022-08-02
    Description: Presented in this paper is the status of the fishery industry in Brunei Darussalam. Specifically, it discussed the following topics: fishery management strategies, zonation scheme, licencing, the use of poisons and explosives, the minimum cod-end mesh size for trawlers, closed areas, enhancement of fishing grounds, and the enforcement activities.
    Keywords: Fisheries ; Fishery resources ; Fishery management ; Fisheries ; Ecological zonation ; Licensing ; Fish poisoning ; Catching methods ; Illegal fishing ; Explosive fishing ; Fishing gear ; Season regulations ; Fishing grounds
    Repository Name: AquaDocs
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  • 15
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    Regional survey of heavy metals in fish and fish products: Thailand (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26295 | 23782 | 2019-03-22 08:39:12 | 26295 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
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    Publication Date: 2022-08-02
    Keywords: Fisheries ; Thailand ; Cadmium ; Lead ; Mercury ; Biological sampling ; Fish ; Fishery products ; Seafood
    Repository Name: AquaDocs
    Type: book_section
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    Format: 53-58
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  • 16
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    Regional survey of heavy metals in fish and fish products: Malaysia (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26292 | 23782 | 2019-03-22 03:43:09 | 26292 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Keywords: Fisheries ; Malaysia ; Cadmium ; Lead ; Mercury ; Biological sampling ; Fish ; Fishery products ; Seafood
    Repository Name: AquaDocs
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    Format: application/pdf
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  • 17
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    Tuna resource exploration with longline in the South China Sea, Area III: Western Philippines (2021)
    Secretariat, Southeast Asian Fisheries Development Center | Bangkok, Thailand
    In:  http://aquaticcommons.org/id/eprint/26258 | 2002 | 2019-03-01 06:00:19 | 26258 | Southeast Asian Fisheries Development Center, Secretariat
    Details
    Publication Date: 2022-08-02
    Description: An exploratory tuna longline fishing survey was conducted using the research and training vessels of the Southeast Asian Fisheries Development Center, the 1,178 GT MV SEAFDEC and the Bureau of Fisheries and Aquatic Resources, the 165 GT MV MAYA-MAYA in the South China Sea Waters, West of the Philippines from April to May, 1998. A total of 3,796 hooks was set in sixteen (16) fishing stations. There were no tuna caught during the entire survey but only minor and irrelevant species like the Pacific lancetfish, sharks and an opah species, Lampris guttatus. The important fishing and oceanographic factors during the survey and other research results on longline are described and analyzed. Additional longline studies within and near the Philippines territorial waters are also presented to substantiate the research results of the joint SEAFDEC/BFAR resource exploratory.
    Keywords: Fisheries ; Exploratory fishing ; Catch composition ; Fishery surveys ; Longlining ; Tuna fisheries ; South China Sea ; Philippines
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    Regional survey of pesticide residues in fish and fish products: Malaysia (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26299 | 23782 | 2019-03-27 06:00:01 | 26299 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Keywords: Chemistry ; Fisheries ; Malaysia ; Pesticides ; Biological sampling ; Fish ; Fishery products ; Biochemical analysis ; Lethal limits
    Repository Name: AquaDocs
    Type: book_section
    Format: application/pdf
    Format: application/pdf
    Format: 71-74
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    Regional survey of pesticide residues in fish and fish products: Myanmar (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26300 | 23782 | 2019-03-27 05:58:36 | 26300 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Keywords: Aquaculture ; Chemistry ; Fisheries ; Myanmar ; Pesticides ; Biological sampling ; Fish ; Fishery products ; Lethal limits
    Repository Name: AquaDocs
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    Format: application/pdf
    Format: application/pdf
    Format: 75-83
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    Regional survey of histamine in fish and fish products: Indonesia (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26307 | 23782 | 2019-03-27 03:35:56 | 26307 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Keywords: Fisheries ; Indonesia ; Histamines ; Biological sampling ; Fish ; Fishery products ; Quality control
    Repository Name: AquaDocs
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    Format: application/pdf
    Format: application/pdf
    Format: 116-123
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    Regional survey of pesticide residues in fish and fish products: Thailand (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26303 | 23782 | 2019-03-27 05:51:15 | 26303 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Keywords: Chemistry ; Fisheries ; Thailand ; Pesticides ; Biological sampling ; Fish ; Fishery products ; Dried products ; Lethal limits
    Repository Name: AquaDocs
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    Format: application/pdf
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    Regional survey of histamine in fish and fish products: Myanmar (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26309 | 23782 | 2019-03-27 03:49:31 | 26309 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Keywords: Fisheries ; Myanmar ; Histamines ; Biological sampling ; Biochemical analysis ; Fish ; Fishery products
    Repository Name: AquaDocs
    Type: book_section
    Format: application/pdf
    Format: application/pdf
    Format: 129-133
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    Determination of chemical properties of meat: Determination of K value (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26826 | 23782 | 2019-11-21 00:56:12 | 26826 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: Presented in the paper is the standard procedure in the determination of K value which is an index to measure the enzymatic freshness of fish and squid. Specifically, reagents, apparatus and the analytical procedures needed and the calculations are presented.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Chemical analysis ; Fishery products ; Fish inspection ; Fishery industry ; Food technology ; Standards ; Specifications
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    Determination of chemical properties of meat: Freshness testing paper (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26825 | 23782 | 2019-11-21 00:52:35 | 26825 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: Presented in the paper is the standard procedure in measuring K value in fish meat by means of the freshness testing paper technique.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Chemical analysis ; Fishery products ; Fish inspection ; Fishery industry ; Food technology ; Standards ; Specifications
    Repository Name: AquaDocs
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    Determination of physical properties of meat: Measurement of pH (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26802 | 23782 | 2019-11-12 05:28:20 | 26802 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: Presented in the paper is the standard procedure in the measurement of pH in the fresh fish meat. Specifically, the procedures in sampling and sample preparation, apparatus and reagents required, and the analytical procedures are presented.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Chemical analysis ; Microbiological analysis ; Fishery products ; Processed fishery products ; Fish inspection ; Fishery industry ; Food additives ; Food technology ; Standards ; Specifications ; pH
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    Analysis of additives: Determination of starch (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26842 | 23782 | 2019-11-15 07:54:48 | 26842 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: Starch is commonly used in the production of fish jelly products as an extender and as binding agent. The paper provides the methodology in the determination of starch in fish jelly products. Instructions for sample preparation and the reagents needed are presented. Detailed procedures in the determination of the starch in a sample are provided.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Chemical analysis ; Fishery products ; Fishery industry ; Food technology ; Standards ; Specifications ; Starch ; Additives ; Food additives
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    Red tides and paralytic shellfish poisoning in the Philippines (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26881 | 23782 | 2019-11-05 02:46:02 | 26881 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: Monitoring and investigative work undertaken in the Philippines regarding dinoflagellate blooms are described. Chronological observations of the occurrence of red tides, aerial surveys, spatial distribution of the dinoflagellate and the physical environment are discussed. Fishing and the examination of gut content of fish and mussels and bioassay tests are detailed. Incidents of paralytic shellfish poisoning in the Philippines are considered briefly.
    Keywords: Fisheries ; Health ; Environmental monitoring ; Red tides ; Public health ; Medicine ; Dangerous organisms ; Philippines
    Repository Name: AquaDocs
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    Format: 52-79
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    Red tide and paralytic shellfish poisoning phenomena in Thailand (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26885 | 23782 | 2019-11-05 02:23:34 | 26885 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: A report is made of the first incidence occurring of paralytic shellfish poisoning in Thailand in May 1983, following an extensive bloom of Trichodesmium erythraeum. Investigations undertaken regarding the source of the toxicity are outlined.
    Keywords: Fisheries ; Health ; Biological poisons ; Public health ; Red tides ; Shellfish ; Dangerous organisms ; Thailand
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    Red tide and paralytic shellfish poisoning in Sabah, Malaysia (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26879 | 23782 | 2019-11-05 02:54:38 | 26879 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: A brief account is given of recent cases of paralytic shellfish poisoning in Sabah, Malaysia, and toxicological studies undertaken. Hydrography surveys, underwater observations after the occurrence of the red tides and plankton studies and monitoring of red tides are discussed.
    Keywords: Fisheries ; Health ; Shellfish ; Toxicity tests ; Red tides ; Public health ; Dangerous organisms ; Malaysia
    Repository Name: AquaDocs
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    Format: 35-42
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    Microbiological procedure: Vibrio cholera (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26852 | 23782 | 2019-11-15 07:36:44 | 26852 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: Cholera is an acute specific infection caused by the organism, Vibrio cholera. Diagnosis may be confirmed by the presence of large numbers of the comma-shaped bacilli on direct microscopic examination of a fecal or vomitus smear, and by the isolation of the organism on culture. Fish and shellfish have been identified as vehicles of cholera. Large numbers of V. cholera must usually be ingested to cause cholera. Thus problems often occur when poor handling and inadequate refrigeration have allowed the organism to multiply. Presented in the paper is the methodology of determining the presence of Vibrio cholera in fish and fishery products.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Fishery products ; Fishery industry ; Food technology ; Standards ; Specifications ; Aerobic bacteria ; Microbiological analysis ; Microorganisms ; Pathogenic bacteria ; Pathogens ; Health and safety ; Public health ; Microbial contamination ; Vibrio cholerae
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    Fisheries statistics in Brunei Darussalam (2021)
    Secretariat, Southeast Asian Fisheries Development Center | Bangkok, Thailand
    In:  http://aquaticcommons.org/id/eprint/26890 | 23782 | 2019-11-14 01:01:29 | 26890 | Southeast Asian Fisheries Development Center, Secretariat
    Details
    Publication Date: 2022-08-02
    Description: Fishery statistics in Brunei Darussalam have been collected by the Department of Fisheries since the 1940s. In the early 1980s, a number of statistics were collected, such as catch and effort data of artisanal fishermen, aquaculture statistics, processing statistics as well as data from major wet markets focusing on the amount, prices of marketed fish either from the local fishermen or imported. In 1984, the collection of statistics on commercial fishing was started. The statistics have been used in the formulation of fishery management and development policies as well as for sectoral development. Following a brief account of the responsibility and statistic collections of the Department of Fisheries, an examination is made of employment in the fishery sector, fisheries production, fish marketed and the GDP for the fishery industry. Fisheries in Brunei Darussalam is a very healthy industry, where production is well below the maximum allowable harvestable limit of 20,000 tons at 30%. The Department is embarking to increase production from the capture fishery to reduce the country's dependence on imported fish; the same applies for aquaculture, in order to complement production from the capture fisheries. The processing sector is also increasing in importance, especially with the increase in the number of capture fishery licenses, and the demand for quality and value-added products.
    Keywords: Fisheries ; Marine fisheries ; Fishery statistics ; Aquaculture development ; Aquaculture statistics ; Fish catch statistics ; Marine aquaculture ; Freshwater aquaculture ; Fishery development ; Marine ; Brackish ; Freshwater
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    Analysis of additives: Determination of salt (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26843 | 23782 | 2019-11-15 07:52:55 | 26843 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: Sodium chloride is an important additive for the production of fish jelly products. It extracts the salt soluble protein to give the gel strength of the final product. The paper provides the methodology in the determination of the amount of sodium chloride in fish jelly products. Instructions for sample preparation and the reagents needed are presented. Detailed procedures in the determination of the salt in a sample are provided.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Chemical analysis ; Fishery products ; Fishery industry ; Food technology ; Standards ; Specifications ; Additives ; Food additives ; Salts ; Sodium chloride
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    Microbiological procedure: Vibrio parahaemolyticus (2021)
    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26851 | 23782 | 2019-11-14 01:29:31 | 26851 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Details
    Publication Date: 2022-08-02
    Description: Food poisoning due to Vibrio parahaemolyticus is a food-borne infection resulting from the ingestion of a large number of this organism (about 106-109 viable cells). The major symptoms are diarrhea and abdominal pain with headache, fever, and vomiting also occurring. The organisms are excreted during the acute stage of the illness after which they decrease rapidly. The differentiation of V. parahaemolyticus from other pathogenic species of Vibrio is based mainly on salt tolerance, Voges-Proskauer reaction, fermentation of sucrose, and growth at 43°C. Presented in the paper is the methodology of determining the presence of Vibrio cholera in fish and fishery products.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Fishery products ; Fishery industry ; Food technology ; Standards ; Specifications ; Aerobic bacteria ; Microbiological analysis ; Microorganisms ; Pathogenic bacteria ; Pathogens ; Health and safety ; Public health ; Microbial contamination ; Vibrio parahaemolyticus ; Vibrio cholerae
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    Coots use hatch order to learn to recognize and reject conspecific brood parasitic chicks (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-18
    Description: Avian brood parasites and their hosts provide model systems for investigating links between recognition, learning, and their fitness consequences. One major evolutionary puzzle has continued to capture the attention of naturalists for centuries: why do hosts of brood parasites generally fail to recognize parasitic offspring after they have hatched from the egg, even when the host and parasitic chicks differ to almost comic degrees? One prominent theory to explain this pattern proposes that the costs of mistakenly learning to recognize the wrong offspring make recognition maladaptive. Here we show that American coots, Fulica americana, can recognize and reject parasitic chicks in their brood by using learned cues, despite the fact that the hosts and the brood parasites are of the same species. A series of chick cross-fostering experiments confirm that coots use first-hatched chicks in a brood as referents to learn to recognize their own chicks and then discriminate against later-hatched parasitic chicks in the same brood. When experimentally provided with the wrong reference chicks, coots can be induced to discriminate against their own offspring, confirming that the learning errors proposed by theory can exist. However, learning based on hatching order is reliable in naturally parasitized coot nests because host eggs hatch predictably ahead of parasite eggs. Conversely, a lack of reliable information may help to explain why the evolution of chick recognition is not more common in hosts of most interspecific brood parasites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shizuka, Daizaburo -- Lyon, Bruce E -- England -- Nature. 2010 Jan 14;463(7278):223-6. doi: 10.1038/nature08655. Epub 2009 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA. shizuka@biology.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016486" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birds/*parasitology/*physiology ; British Columbia ; Cues ; Discrimination Learning/*physiology ; Feeding Behavior/physiology ; Genetic Fitness ; Nesting Behavior/*physiology ; Ovum/growth & development ; Pattern Recognition, Visual/physiology ; Survival Rate ; Time Factors ; Wetlands
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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    Reprogramming towards pluripotency requires AID-dependent DNA demethylation (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-23
    Description: Reprogramming of somatic cell nuclei to yield induced pluripotent stem (iPS) cells makes possible derivation of patient-specific stem cells for regenerative medicine. However, iPS cell generation is asynchronous and slow (2-3 weeks), the frequency is low (〈0.1%), and DNA demethylation constitutes a bottleneck. To determine regulatory mechanisms involved in reprogramming, we generated interspecies heterokaryons (fused mouse embryonic stem (ES) cells and human fibroblasts) that induce reprogramming synchronously, frequently and fast. Here we show that reprogramming towards pluripotency in single heterokaryons is initiated without cell division or DNA replication, rapidly (1 day) and efficiently (70%). Short interfering RNA (siRNA)-mediated knockdown showed that activation-induced cytidine deaminase (AID, also known as AICDA) is required for promoter demethylation and induction of OCT4 (also known as POU5F1) and NANOG gene expression. AID protein bound silent methylated OCT4 and NANOG promoters in fibroblasts, but not active demethylated promoters in ES cells. These data provide new evidence that mammalian AID is required for active DNA demethylation and initiation of nuclear reprogramming towards pluripotency in human somatic cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906123/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906123/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhutani, Nidhi -- Brady, Jennifer J -- Damian, Mara -- Sacco, Alessandra -- Corbel, Stephane Y -- Blau, Helen M -- AG009521/AG/NIA NIH HHS/ -- AG024987/AG/NIA NIH HHS/ -- AI007328/AI/NIAID NIH HHS/ -- R01 AG009521/AG/NIA NIH HHS/ -- R01 AG009521-25/AG/NIA NIH HHS/ -- R01 AG024987/AG/NIA NIH HHS/ -- R01 AG024987-05/AG/NIA NIH HHS/ -- T32 AI007328/AI/NIAID NIH HHS/ -- U01 HL100397/HL/NHLBI NIH HHS/ -- England -- Nature. 2010 Feb 25;463(7284):1042-7. doi: 10.1038/nature08752.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Baxter Laboratory for Stem Cell Biology, Institute for Stem Cell Biology and Regenerative Medicine, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305-5175, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20027182" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Division ; Cell Fusion ; Cell Line ; Cells, Cultured ; Cellular Reprogramming/genetics/*physiology ; Chromatin Immunoprecipitation ; Cytidine Deaminase/deficiency/genetics/*metabolism ; DNA/chemistry/genetics/metabolism ; *DNA Methylation ; DNA Replication ; Embryonic Stem Cells/cytology/metabolism ; Fibroblasts/cytology/metabolism ; Gene Expression Regulation ; Gene Knockdown Techniques ; Homeodomain Proteins/genetics ; Humans ; Induced Pluripotent Stem Cells/*cytology/enzymology/*metabolism ; Lung/cytology/embryology ; Mice ; Models, Biological ; Octamer Transcription Factor-3/genetics ; Promoter Regions, Genetic/genetics ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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    The sequence and de novo assembly of the giant panda genome (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-17
    Description: Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951497/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951497/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Ruiqiang -- Fan, Wei -- Tian, Geng -- Zhu, Hongmei -- He, Lin -- Cai, Jing -- Huang, Quanfei -- Cai, Qingle -- Li, Bo -- Bai, Yinqi -- Zhang, Zhihe -- Zhang, Yaping -- Wang, Wen -- Li, Jun -- Wei, Fuwen -- Li, Heng -- Jian, Min -- Li, Jianwen -- Zhang, Zhaolei -- Nielsen, Rasmus -- Li, Dawei -- Gu, Wanjun -- Yang, Zhentao -- Xuan, Zhaoling -- Ryder, Oliver A -- Leung, Frederick Chi-Ching -- Zhou, Yan -- Cao, Jianjun -- Sun, Xiao -- Fu, Yonggui -- Fang, Xiaodong -- Guo, Xiaosen -- Wang, Bo -- Hou, Rong -- Shen, Fujun -- Mu, Bo -- Ni, Peixiang -- Lin, Runmao -- Qian, Wubin -- Wang, Guodong -- Yu, Chang -- Nie, Wenhui -- Wang, Jinhuan -- Wu, Zhigang -- Liang, Huiqing -- Min, Jiumeng -- Wu, Qi -- Cheng, Shifeng -- Ruan, Jue -- Wang, Mingwei -- Shi, Zhongbin -- Wen, Ming -- Liu, Binghang -- Ren, Xiaoli -- Zheng, Huisong -- Dong, Dong -- Cook, Kathleen -- Shan, Gao -- Zhang, Hao -- Kosiol, Carolin -- Xie, Xueying -- Lu, Zuhong -- Zheng, Hancheng -- Li, Yingrui -- Steiner, Cynthia C -- Lam, Tommy Tsan-Yuk -- Lin, Siyuan -- Zhang, Qinghui -- Li, Guoqing -- Tian, Jing -- Gong, Timing -- Liu, Hongde -- Zhang, Dejin -- Fang, Lin -- Ye, Chen -- Zhang, Juanbin -- Hu, Wenbo -- Xu, Anlong -- Ren, Yuanyuan -- Zhang, Guojie -- Bruford, Michael W -- Li, Qibin -- Ma, Lijia -- Guo, Yiran -- An, Na -- Hu, Yujie -- Zheng, Yang -- Shi, Yongyong -- Li, Zhiqiang -- Liu, Qing -- Chen, Yanling -- Zhao, Jing -- Qu, Ning -- Zhao, Shancen -- Tian, Feng -- Wang, Xiaoling -- Wang, Haiyin -- Xu, Lizhi -- Liu, Xiao -- Vinar, Tomas -- Wang, Yajun -- Lam, Tak-Wah -- Yiu, Siu-Ming -- Liu, Shiping -- Zhang, Hemin -- Li, Desheng -- Huang, Yan -- Wang, Xia -- Yang, Guohua -- Jiang, Zhi -- Wang, Junyi -- Qin, Nan -- Li, Li -- Li, Jingxiang -- Bolund, Lars -- Kristiansen, Karsten -- Wong, Gane Ka-Shu -- Olson, Maynard -- Zhang, Xiuqing -- Li, Songgang -- Yang, Huanming -- Wang, Jian -- Wang, Jun -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HG003229-05/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):311-7. doi: 10.1038/nature08696. Epub 2009 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BGI-Shenzhen, Shenzhen 518083, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010809" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; China ; Conserved Sequence/genetics ; Contig Mapping ; Diet/veterinary ; Dogs ; Evolution, Molecular ; Female ; Fertility/genetics/physiology ; Genome/*genetics ; *Genomics ; Heterozygote ; Humans ; Multigene Family/genetics ; Polymorphism, Single Nucleotide/genetics ; Receptors, G-Protein-Coupled/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Synteny/genetics ; Ursidae/classification/*genetics/physiology
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    Phylogenies reveal new interpretation of speciation and the Red Queen (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-17
    Description: The Red Queen describes a view of nature in which species continually evolve but do not become better adapted. It is one of the more distinctive metaphors of evolutionary biology, but no test of its claim that speciation occurs at a constant rate has ever been made against competing models that can predict virtually identical outcomes, nor has any mechanism been proposed that could cause the constant-rate phenomenon. Here we use 101 phylogenies of animal, plant and fungal taxa to test the constant-rate claim against four competing models. Phylogenetic branch lengths record the amount of time or evolutionary change between successive events of speciation. The models predict the distribution of these lengths by specifying how factors combine to bring about speciation, or by describing how rates of speciation vary throughout a tree. We find that the hypotheses that speciation follows the accumulation of many small events that act either multiplicatively or additively found support in 8% and none of the trees, respectively. A further 8% of trees hinted that the probability of speciation changes according to the amount of divergence from the ancestral species, and 6% suggested speciation rates vary among taxa. By comparison, 78% of the trees fit the simplest model in which new species emerge from single events, each rare but individually sufficient to cause speciation. This model predicts a constant rate of speciation, and provides a new interpretation of the Red Queen: the metaphor of species losing a race against a deteriorating environment is replaced by a view linking speciation to rare stochastic events that cause reproductive isolation. Attempts to understand species-radiations or why some groups have more or fewer species should look to the size of the catalogue of potential causes of speciation shared by a group of closely related organisms rather than to how those causes combine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venditti, Chris -- Meade, Andrew -- Pagel, Mark -- England -- Nature. 2010 Jan 21;463(7279):349-52. doi: 10.1038/nature08630. Epub 2009 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6BX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010607" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; *Genetic Speciation ; *Models, Biological ; *Phylogeny ; Selection, Genetic ; Stochastic Processes
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    A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex (2009)
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    Publication Date: 2009-01-14
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340503/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340503/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelly, Bernard T -- McCoy, Airlie J -- Spate, Kira -- Miller, Sharon E -- Evans, Philip R -- Honing, Stefan -- Owen, David J -- 090909/Wellcome Trust/United Kingdom -- MC_U105178845/Medical Research Council/United Kingdom -- England -- Nature. 2008 Dec 18;456(7224):976-79. doi: 10.1038/nature07422.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19140243" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Protein Complex 2/*chemistry/genetics/*metabolism ; Amino Acid Motifs ; Animals ; Antigens, CD4/*chemistry/*metabolism ; Binding Sites ; Conserved Sequence ; *Endocytosis ; Humans ; Leucine/*metabolism ; Mice ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Subunits/chemistry/genetics/metabolism ; Rats
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    No bull: genes for better milk (2009)
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    Publication Date: 2009-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2009 Jan 22;457(7228):369. doi: 10.1038/457369a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158758" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Breeding/economics/*methods ; Cattle/*genetics ; Dairying/economics/*methods ; Female ; Internationality ; Male ; Milk/*secretion/*standards ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; United States ; United States Department of Agriculture
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    Two types of dopamine neuron distinctly convey positive and negative motivational signals (2009)
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    Publication Date: 2009-05-19
    Description: Midbrain dopamine neurons are activated by reward or sensory stimuli predicting reward. These excitatory responses increase as the reward value increases. This response property has led to a hypothesis that dopamine neurons encode value-related signals and are inhibited by aversive events. Here we show that this is true only for a subset of dopamine neurons. We recorded the activity of dopamine neurons in monkeys (Macaca mulatta) during a Pavlovian procedure with appetitive and aversive outcomes (liquid rewards and airpuffs directed at the face, respectively). We found that some dopamine neurons were excited by reward-predicting stimuli and inhibited by airpuff-predicting stimuli, as the value hypothesis predicts. However, a greater number of dopamine neurons were excited by both of these stimuli, inconsistent with the hypothesis. Some dopamine neurons were also excited by both rewards and airpuffs themselves, especially when they were unpredictable. Neurons excited by the airpuff-predicting stimuli were located more dorsolaterally in the substantia nigra pars compacta, whereas neurons inhibited by the stimuli were located more ventromedially, some in the ventral tegmental area. A similar anatomical difference was observed for their responses to actual airpuffs. These findings suggest that different groups of dopamine neurons convey motivational signals in distinct manners.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739096/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739096/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsumoto, Masayuki -- Hikosaka, Okihide -- Z01 EY000415-05/Intramural NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):837-41. doi: 10.1038/nature08028. Epub 2009 May 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892-4435, USA. matsumotom@nei.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19448610" target="_blank"〉PubMed〈/a〉
    Keywords: Air ; Animals ; Appetitive Behavior/physiology ; Conditioning, Classical/physiology ; Dopamine/*metabolism ; Macaca mulatta/*physiology ; Models, Neurological ; *Motivation ; Neurons/*physiology ; Reward
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    Costing the earth (2009)
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    Publication Date: 2009-11-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sukhdev, Pavan -- England -- Nature. 2009 Nov 19;462(7271):277. doi: 10.1038/462277a. Epub 2009 Nov 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Economics of Ecosystems and Biodiversity (TEEB) project, United Nations Campus, Hermann-Ehlers-Strasse 10, 53113 Bonn, Germany. teeb@unep-teeb.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19915547" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Conservation of Natural Resources ; Fresh Water ; Government ; Humans ; Poverty
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    Frequent inactivation of A20 in B-cell lymphomas (2009)
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    Publication Date: 2009-05-05
    Description: A20 is a negative regulator of the NF-kappaB pathway and was initially identified as being rapidly induced after tumour-necrosis factor-alpha stimulation. It has a pivotal role in regulation of the immune response and prevents excessive activation of NF-kappaB in response to a variety of external stimuli; recent genetic studies have disclosed putative associations of polymorphic A20 (also called TNFAIP3) alleles with autoimmune disease risk. However, the involvement of A20 in the development of human cancers is unknown. Here we show, using a genome-wide analysis of genetic lesions in 238 B-cell lymphomas, that A20 is a common genetic target in B-lineage lymphomas. A20 is frequently inactivated by somatic mutations and/or deletions in mucosa-associated tissue lymphoma (18 out of 87; 21.8%) and Hodgkin's lymphoma of nodular sclerosis histology (5 out of 15; 33.3%), and, to a lesser extent, in other B-lineage lymphomas. When re-expressed in a lymphoma-derived cell line with no functional A20 alleles, wild-type A20, but not mutant A20, resulted in suppression of cell growth and induction of apoptosis, accompanied by downregulation of NF-kappaB activation. The A20-deficient cells stably generated tumours in immunodeficient mice, whereas the tumorigenicity was effectively suppressed by re-expression of A20. In A20-deficient cells, suppression of both cell growth and NF-kappaB activity due to re-expression of A20 depended, at least partly, on cell-surface-receptor signalling, including the tumour-necrosis factor receptor. Considering the physiological function of A20 in the negative modulation of NF-kappaB activation induced by multiple upstream stimuli, our findings indicate that uncontrolled signalling of NF-kappaB caused by loss of A20 function is involved in the pathogenesis of subsets of B-lineage lymphomas.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kato, Motohiro -- Sanada, Masashi -- Kato, Itaru -- Sato, Yasuharu -- Takita, Junko -- Takeuchi, Kengo -- Niwa, Akira -- Chen, Yuyan -- Nakazaki, Kumi -- Nomoto, Junko -- Asakura, Yoshitaka -- Muto, Satsuki -- Tamura, Azusa -- Iio, Mitsuru -- Akatsuka, Yoshiki -- Hayashi, Yasuhide -- Mori, Hiraku -- Igarashi, Takashi -- Kurokawa, Mineo -- Chiba, Shigeru -- Mori, Shigeo -- Ishikawa, Yuichi -- Okamoto, Koji -- Tobinai, Kensei -- Nakagama, Hitoshi -- Nakahata, Tatsutoshi -- Yoshino, Tadashi -- Kobayashi, Yukio -- Ogawa, Seishi -- England -- Nature. 2009 Jun 4;459(7247):712-6. doi: 10.1038/nature07969. Epub 2009 May 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genomics Project, Department of Pediatrics, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19412163" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/physiology ; Cell Line ; Cysteine Endopeptidases/*genetics/*metabolism ; DNA-Binding Proteins ; Gene Expression ; *Gene Silencing ; Genome/genetics ; Humans ; Intracellular Signaling Peptides and Proteins/*genetics/*metabolism ; Lymphoma, B-Cell/*genetics/*physiopathology ; Mice ; NF-kappa B/genetics/metabolism ; Nuclear Proteins/*genetics/*metabolism
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    A magnificence to share (2009)
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    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 16;458(7240):808. doi: 10.1038/458808a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19369979" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; *Ecosystem ; International Cooperation/*legislation & jurisprudence ; Travel/*legislation & jurisprudence
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    Pore architecture and ion sites in acid-sensing ion channels and P2X receptors (2009)
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    Publication Date: 2009-07-31
    Description: Acid-sensing ion channels are proton-activated, sodium-selective channels composed of three subunits, and are members of the superfamily of epithelial sodium channels, mechanosensitive and FMRF-amide peptide-gated ion channels. These ubiquitous eukaryotic ion channels have essential roles in biological activities as diverse as sodium homeostasis, taste and pain. Despite their crucial roles in biology and their unusual trimeric subunit stoichiometry, there is little knowledge of the structural and chemical principles underlying their ion channel architecture and ion-binding sites. Here we present the structure of a functional acid-sensing ion channel in a desensitized state at 3 A resolution, the location and composition of the approximately 8 A 'thick' desensitization gate, and the trigonal antiprism coordination of caesium ions bound in the extracellular vestibule. Comparison of the acid-sensing ion channel structure with the ATP-gated P2X(4) receptor reveals similarity in pore architecture and aqueous vestibules, suggesting that there are unanticipated yet common structural and mechanistic principles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845979/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845979/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gonzales, Eric B -- Kawate, Toshimitsu -- Gouaux, Eric -- F32 GM083615/GM/NIGMS NIH HHS/ -- F32 GM083615-01/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 30;460(7255):599-604. doi: 10.1038/nature08218.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19641589" target="_blank"〉PubMed〈/a〉
    Keywords: Acid Sensing Ion Channels ; Animals ; Binding Sites ; CHO Cells ; Cell Line ; Cesium/metabolism ; Chickens/*physiology ; Cricetinae ; Cricetulus ; Crystallization ; Humans ; Ions/metabolism ; *Models, Molecular ; Nerve Tissue Proteins/*chemistry ; Protein Structure, Tertiary ; Receptors, Purinergic P2/*chemistry ; Receptors, Purinergic P2X ; Sodium Channels/*chemistry ; Zebrafish/*physiology
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    A fly by any other name (2009)
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    Publication Date: 2009-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2009 Jan 22;457(7228):368. doi: 10.1038/457368a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158757" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drosophila/*classification ; Drosophila melanogaster/classification ; Species Specificity ; *Terminology as Topic
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    Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay (2009)
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    Publication Date: 2009-03-27
    Description: Toll-like receptors (TLRs) recognize microbial components, and evoke inflammation and immune responses. TLR stimulation activates complex gene expression networks that regulate the magnitude and duration of the immune reaction. Here we identify the TLR-inducible gene Zc3h12a as an immune response modifier that has an essential role in preventing immune disorders. Zc3h12a-deficient mice suffered from severe anaemia, and most died within 12 weeks. Zc3h12a(-/-) mice also showed augmented serum immunoglobulin levels and autoantibody production, together with a greatly increased number of plasma cells, as well as infiltration of plasma cells to the lung. Most Zc3h12a(-/-) splenic T cells showed effector/memory characteristics and produced interferon-gamma in response to T-cell receptor stimulation. Macrophages from Zc3h12a(-/-) mice showed highly increased production of interleukin (IL)-6 and IL-12p40 (also known as IL12b), but not TNF, in response to TLR ligands. Although the activation of TLR signalling pathways was normal, Il6 messenger RNA decay was severely impaired in Zc3h12a(-/-) macrophages. Overexpression of Zc3h12a accelerated Il6 mRNA degradation via its 3'-untranslated region (UTR), and destabilized RNAs with 3'-UTRs for genes including Il6, Il12p40 and the calcitonin receptor gene Calcr. Zc3h12a contains a putative amino-terminal nuclease domain, and the expressed protein had RNase activity, consistent with a role in the decay of Il6 mRNA. Together, these results indicate that Zc3h12a is an essential RNase that prevents immune disorders by directly controlling the stability of a set of inflammatory genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsushita, Kazufumi -- Takeuchi, Osamu -- Standley, Daron M -- Kumagai, Yutaro -- Kawagoe, Tatsukata -- Miyake, Tohru -- Satoh, Takashi -- Kato, Hiroki -- Tsujimura, Tohru -- Nakamura, Haruki -- Akira, Shizuo -- P01 AI070167/AI/NIAID NIH HHS/ -- England -- Nature. 2009 Apr 30;458(7242):1185-90. doi: 10.1038/nature07924. Epub 2009 Mar 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19322177" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/genetics/metabolism ; Anemia/complications/genetics ; Animals ; Autoantibodies/blood/immunology ; Autoimmune Diseases/complications/immunology ; Cell Line ; Cytokines/biosynthesis/genetics ; Fetal Diseases/immunology ; Humans ; Immunity/*genetics/*immunology ; Inflammation Mediators/metabolism ; Interleukin-6/genetics ; Macrophages, Peritoneal/immunology/metabolism ; Mice ; Plasma Cells/cytology ; *RNA Stability ; Ribonucleases/deficiency/genetics/*metabolism ; T-Lymphocytes/immunology
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    NOAA chief ready to tackle climate (2009)
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    Publication Date: 2009-04-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- Witze, Alexandra -- England -- Nature. 2009 Mar 26;458(7237):396. doi: 10.1038/458396a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19334300" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ecosystem ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; Leadership ; Marine Biology ; United States ; United States Government Agencies/*organization & administration
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    Linking the p53 tumour suppressor pathway to somatic cell reprogramming (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-08-12
    Description: Reprogramming somatic cells to induced pluripotent stem (iPS) cells has been accomplished by expressing pluripotency factors and oncogenes, but the low frequency and tendency to induce malignant transformation compromise the clinical utility of this powerful approach. We address both issues by investigating the mechanisms limiting reprogramming efficiency in somatic cells. Here we show that reprogramming factors can activate the p53 (also known as Trp53 in mice, TP53 in humans) pathway. Reducing signalling to p53 by expressing a mutated version of one of its negative regulators, by deleting or knocking down p53 or its target gene, p21 (also known as Cdkn1a), or by antagonizing reprogramming-induced apoptosis in mouse fibroblasts increases reprogramming efficiency. Notably, decreasing p53 protein levels enabled fibroblasts to give rise to iPS cells capable of generating germline-transmitting chimaeric mice using only Oct4 (also known as Pou5f1) and Sox2. Furthermore, silencing of p53 significantly increased the reprogramming efficiency of human somatic cells. These results provide insights into reprogramming mechanisms and suggest new routes to more efficient reprogramming while minimizing the use of oncogenes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735889/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735889/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawamura, Teruhisa -- Suzuki, Jotaro -- Wang, Yunyuan V -- Menendez, Sergio -- Morera, Laura Batlle -- Raya, Angel -- Wahl, Geoffrey M -- Izpisua Belmonte, Juan Carlos -- 5 R01 CA061449/CA/NCI NIH HHS/ -- 5 R01 CA100845/CA/NCI NIH HHS/ -- R01 CA061449/CA/NCI NIH HHS/ -- R01 CA061449-30/CA/NCI NIH HHS/ -- R01 CA100845/CA/NCI NIH HHS/ -- R01 CA100845-05/CA/NCI NIH HHS/ -- R33 HL088293/HL/NHLBI NIH HHS/ -- R33 HL088293-03/HL/NHLBI NIH HHS/ -- England -- Nature. 2009 Aug 27;460(7259):1140-4. doi: 10.1038/nature08311. Epub 2009 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19668186" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cells, Cultured ; Cellular Reprogramming/*physiology ; Cyclin-Dependent Kinase Inhibitor p21/deficiency/genetics/metabolism ; Down-Regulation ; Embryo, Mammalian/cytology ; Female ; Fibroblasts/cytology/metabolism ; Humans ; Keratinocytes ; Male ; Mice ; Mice, Inbred C57BL ; Pluripotent Stem Cells/*cytology/*metabolism ; Tumor Suppressor Protein p53/deficiency/genetics/*metabolism
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    Adaptive immune features of natural killer cells (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-01-13
    Description: In an adaptive immune response, naive T cells proliferate during infection and generate long-lived memory cells that undergo secondary expansion after a repeat encounter with the same pathogen. Although natural killer (NK) cells have traditionally been classified as cells of the innate immune system, they share many similarities with cytotoxic T lymphocytes. We use a mouse model of cytomegalovirus infection to show that, like T cells, NK cells bearing the virus-specific Ly49H receptor proliferate 100-fold in the spleen and 1,000-fold in the liver after infection. After a contraction phase, Ly49H-positive NK cells reside in lymphoid and non-lymphoid organs for several months. These self-renewing 'memory' NK cells rapidly degranulate and produce cytokines on reactivation. Adoptive transfer of these NK cells into naive animals followed by viral challenge results in a robust secondary expansion and protective immunity. These findings reveal properties of NK cells that were previously attributed only to cells of the adaptive immune system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674434/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674434/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Joseph C -- Beilke, Joshua N -- Lanier, Lewis L -- AI068129/AI/NIAID NIH HHS/ -- R01 AI068129/AI/NIAID NIH HHS/ -- R01 AI068129-09/AI/NIAID NIH HHS/ -- England -- Nature. 2009 Jan 29;457(7229):557-61. doi: 10.1038/nature07665. Epub 2009 Jan 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology and the Cancer Research Institute, University of California, San Francisco, California 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19136945" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/deficiency/genetics ; Adoptive Transfer ; Animals ; Cell Proliferation ; Immunologic Memory/*immunology ; Killer Cells, Natural/*cytology/*immunology ; Lymphoid Tissue/immunology ; Mice ; Mice, Congenic ; Mice, Inbred C57BL ; *Models, Immunological ; Muromegalovirus/immunology/physiology ; Phenotype ; T-Lymphocytes, Cytotoxic/immunology
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    Lab hazard (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dance, Amber -- England -- Nature. 2009 Apr 2;458(7238):664-5. doi: 10.1038/nj7238-664a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444985" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Laboratory/immunology ; Asthma/immunology ; Hypersensitivity/epidemiology/*immunology ; Occupational Diseases/epidemiology/*etiology/mortality ; *Occupational Exposure/statistics & numerical data ; *Research Personnel
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    Synthetic biology: The yin and yang of nature (2009)
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    Publication Date: 2009-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gore, Jeff -- van Oudenaarden, Alexander -- K99 GM085279/GM/NIGMS NIH HHS/ -- R00 GM085279/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jan 15;457(7227):271-2. doi: 10.1038/457271a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148089" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Clocks/*physiology ; Circadian Rhythm/*physiology ; Escherichia coli ; *Feedback, Physiological ; Gene Expression Regulation/*genetics ; Genes, Synthetic/*genetics ; Genetic Engineering ; *Models, Biological
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    Elite and stochastic models for induced pluripotent stem cell generation (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-07-03
    Description: Induced pluripotent stem cells offer unprecedented potential for disease research, drug screening, toxicology and regenerative medicine. However, the process of reprogramming is inefficient and often incomplete. Here I consider reasons for bottlenecks in induced pluripotent stem cell generation, and propose a model in which most or all cells have the potential to become pluripotent.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamanaka, Shinya -- England -- Nature. 2009 Jul 2;460(7251):49-52. doi: 10.1038/nature08180.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan. yamanaka@cira.kyoto-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19571877" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Lineage ; *Cellular Reprogramming/genetics ; Epigenesis, Genetic ; Humans ; Mice ; *Models, Biological ; Pluripotent Stem Cells/*cytology/metabolism ; Stochastic Processes ; Transduction, Genetic
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    HMGB proteins function as universal sentinels for nucleic-acid-mediated innate immune responses (2009)
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    Publication Date: 2009-11-06
    Description: The activation of innate immune responses by nucleic acids is crucial to protective and pathological immunities and is mediated by the transmembrane Toll-like receptors (TLRs) and cytosolic receptors. However, it remains unknown whether a mechanism exists that integrates these nucleic-acid-sensing systems. Here we show that high-mobility group box (HMGB) proteins 1, 2 and 3 function as universal sentinels for nucleic acids. HMGBs bind to all immunogenic nucleic acids examined with a correlation between affinity and immunogenic potential. Hmgb1(-/-) and Hmgb2(-/-) mouse cells are defective in type-I interferon and inflammatory cytokine induction by DNA or RNA targeted to activate the cytosolic nucleic-acid-sensing receptors; cells in which the expression of all three HMGBs is suppressed show a more profound defect, accompanied by impaired activation of the transcription factors interferon regulatory factor 3 (IRF3) and nuclear factor (NF)-kappaB. The absence of HMGBs also severely impairs the activation of TLR3, TLR7 and TLR9 by their cognate nucleic acids. Our results therefore indicate a hierarchy in the nucleic-acid-mediated activation of immune responses, wherein the selective activation of nucleic-acid-sensing receptors is contingent on the more promiscuous sensing of nucleic acids by HMGBs. These findings may have implications for understanding the evolution of the innate immune system and for the treatment of immunological disorders.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yanai, Hideyuki -- Ban, Tatsuma -- Wang, ZhiChao -- Choi, Myoung Kwon -- Kawamura, Takeshi -- Negishi, Hideo -- Nakasato, Makoto -- Lu, Yan -- Hangai, Sho -- Koshiba, Ryuji -- Savitsky, David -- Ronfani, Lorenza -- Akira, Shizuo -- Bianchi, Marco E -- Honda, Kenya -- Tamura, Tomohiko -- Kodama, Tatsuhiko -- Taniguchi, Tadatsugu -- England -- Nature. 2009 Nov 5;462(7269):99-103. doi: 10.1038/nature08512.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890330" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cytosol/immunology ; DNA/immunology ; HMGB Proteins/deficiency/genetics/*immunology/*metabolism ; HMGB1 Protein/deficiency/genetics/immunology/metabolism ; HMGB2 Protein/deficiency/genetics/immunology/metabolism ; Immunity, Innate/*immunology ; Interferon Regulatory Factor-3/metabolism ; Mice ; Mice, Inbred C57BL ; Models, Immunological ; NF-kappa B/metabolism ; Nucleic Acids/*immunology ; Nucleotides/chemistry/immunology/metabolism ; RNA/immunology ; Signal Transduction ; Toll-Like Receptors/immunology ; Virus Diseases/immunology/virology
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    Long-range oncogenic activation of Igh-c-myc translocations by the Igh 3' regulatory region (2009)
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    Publication Date: 2009-12-17
    Description: B-cell malignancies, such as human Burkitt's lymphoma, often contain translocations that link c-myc or other proto-oncogenes to the immunoglobulin heavy chain locus (IgH, encoded by Igh). The nature of elements that activate oncogenes within such translocations has been a long-standing question. Translocations within Igh involve DNA double-strand breaks initiated either by the RAG1/2 endonuclease during variable, diversity and joining gene segment (V(D)J) recombination, or by activation-induced cytidine deaminase (AID, also known as AICDA) during class switch recombination (CSR). V(D)J recombination in progenitor B (pro-B) cells assembles Igh variable region exons upstream of mu constant region (Cmu) exons, which are the first of several sets of C(H) exons ('C(H) genes') within a C(H) locus that span several hundred kilobases (kb). In mature B cells, CSR deletes Cmu and replaces it with a downstream C(H) gene. An intronic enhancer (iEmu) between the variable region exons and Cmu promotes V(D)J recombination in developing B cells. Furthermore, the Igh 3' regulatory region (Igh3'RR) lies downstream of the C(H) locus and modulates CSR by long-range transcriptional enhancement of C(H) genes. Transgenic mice bearing iEmu or Igh3'RR sequences fused to c-myc are predisposed to B lymphomas, demonstrating that such elements can confer oncogenic c-myc expression. However, in many B-cell lymphomas, Igh-c-myc translocations delete iEmu and place c-myc up to 200 kb upstream of the Igh3'RR. Here we address the oncogenic role of the Igh3'RR by inactivating it in two distinct mouse models for B-cell lymphoma with Igh-c-myc translocations. We show that the Igh3'RR is dispensable for pro-B-cell lymphomas with V(D)J recombination-initiated translocations, but is required for peripheral B-cell lymphomas with CSR-associated translocations. As the Igh3'RR is not required for CSR-associated Igh breaks or Igh-c-myc translocations in peripheral B-cell lymphoma progenitors, we conclude that this regulatory region confers oncogenic activity by long-range and developmental stage-specific activation of translocated c-myc genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802177/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802177/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gostissa, Monica -- Yan, Catherine T -- Bianco, Julia M -- Cogne, Michel -- Pinaud, Eric -- Alt, Frederick W -- CA92625/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Dec 10;462(7274):803-7. doi: 10.1038/nature08633.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010689" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/*genetics ; Alleles ; Animals ; Cells, Cultured ; Chromosome Breakpoints ; Gene Rearrangement, B-Lymphocyte/*genetics ; Genes, Immunoglobulin Heavy Chain/*genetics ; Genes, myc/*genetics ; Immunoglobulin Class Switching/genetics ; Lymphoma, B-Cell/*genetics/pathology ; Mice ; Mice, Transgenic ; Regulatory Sequences, Nucleic Acid/*genetics ; Translocation, Genetic/*genetics
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    Malaria: The gatekeeper revealed (2009)
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    Publication Date: 2009-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reiff, Sarah B -- Striepen, Boris -- England -- Nature. 2009 Jun 18;459(7249):918-9. doi: 10.1038/459918a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536248" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Humans ; Malaria, Falciparum/drug therapy/*parasitology ; Models, Biological ; Plasmodium falciparum/*metabolism ; Protein Binding ; Protein Transport ; Protozoan Proteins/antagonists & inhibitors/*metabolism ; Vacuoles/metabolism/parasitology
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    Stably maintained dendritic spines are associated with lifelong memories (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-01
    Description: Changes in synaptic connections are considered essential for learning and memory formation. However, it is unknown how neural circuits undergo continuous synaptic changes during learning while maintaining lifelong memories. Here we show, by following postsynaptic dendritic spines over time in the mouse cortex, that learning and novel sensory experience lead to spine formation and elimination by a protracted process. The extent of spine remodelling correlates with behavioural improvement after learning, suggesting a crucial role of synaptic structural plasticity in memory formation. Importantly, a small fraction of new spines induced by novel experience, together with most spines formed early during development and surviving experience-dependent elimination, are preserved and provide a structural basis for memory retention throughout the entire life of an animal. These studies indicate that learning and daily sensory experience leave minute but permanent marks on cortical connections and suggest that lifelong memories are stored in largely stably connected synaptic networks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724802/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724802/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Guang -- Pan, Feng -- Gan, Wen-Biao -- R01 NS047325/NS/NINDS NIH HHS/ -- England -- Nature. 2009 Dec 17;462(7275):920-4. doi: 10.1038/nature08577. Epub 2009 Nov 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Neurobiology Program, The Helen and Martin Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, Department of Physiology and Neuroscience, New York University School of Medicine, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19946265" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/physiology ; Animals ; Dendritic Spines/metabolism/*physiology ; Forelimb/physiology ; Memory/*physiology ; Mice ; Motor Cortex/cytology/physiology ; Motor Skills/physiology ; Neuronal Plasticity/physiology ; Pyramidal Cells/metabolism ; Synapses/*metabolism ; Time Factors
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    Ancient ivory figurine deserves a more thoughtful label (2009)
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    Publication Date: 2009-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McDonnell, Anna -- England -- Nature. 2009 Jun 18;459(7249):909. doi: 10.1038/459909b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536241" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Female ; Fertility ; History, Ancient ; Humans ; Pregnancy ; Sculpture/*history
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    Crystal structure of the ATP-gated P2X(4) ion channel in the closed state (2009)
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    Publication Date: 2009-07-31
    Description: P2X receptors are cation-selective ion channels gated by extracellular ATP, and are implicated in diverse physiological processes, from synaptic transmission to inflammation to the sensing of taste and pain. Because P2X receptors are not related to other ion channel proteins of known structure, there is at present no molecular foundation for mechanisms of ligand-gating, allosteric modulation and ion permeation. Here we present crystal structures of the zebrafish P2X(4) receptor in its closed, resting state. The chalice-shaped, trimeric receptor is knit together by subunit-subunit contacts implicated in ion channel gating and receptor assembly. Extracellular domains, rich in beta-strands, have large acidic patches that may attract cations, through fenestrations, to vestibules near the ion channel. In the transmembrane pore, the 'gate' is defined by an approximately 8 A slab of protein. We define the location of three non-canonical, intersubunit ATP-binding sites, and suggest that ATP binding promotes subunit rearrangement and ion channel opening.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720809/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720809/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawate, Toshimitsu -- Michel, Jennifer Carlisle -- Birdsong, William T -- Gouaux, Eric -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM075026-04/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 30;460(7255):592-8. doi: 10.1038/nature08198.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19641588" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Gadolinium/metabolism ; Humans ; Ion Channels/antagonists & inhibitors/*chemistry ; Membrane Proteins/chemistry ; *Models, Molecular ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; Purinergic P2 Receptor Antagonists ; Receptors, Purinergic P2/*chemistry ; Receptors, Purinergic P2X4 ; Zebrafish/*physiology ; Zebrafish Proteins/antagonists & inhibitors/*chemistry
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    Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-07-25
    Description: African primates are naturally infected with over 40 different simian immunodeficiency viruses (SIVs), two of which have crossed the species barrier and generated human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2). Unlike the human viruses, however, SIVs do not generally cause acquired immunodeficiency syndrome (AIDS) in their natural hosts. Here we show that SIVcpz, the immediate precursor of HIV-1, is pathogenic in free-ranging chimpanzees. By following 94 members of two habituated chimpanzee communities in Gombe National Park, Tanzania, for over 9 years, we found a 10- to 16-fold higher age-corrected death hazard for SIVcpz-infected (n = 17) compared to uninfected (n = 77) chimpanzees. We also found that SIVcpz-infected females were less likely to give birth and had a higher infant mortality rate than uninfected females. Immunohistochemistry and in situ hybridization of post-mortem spleen and lymph node samples from three infected and two uninfected chimpanzees revealed significant CD4(+) T-cell depletion in all infected individuals, with evidence of high viral replication and extensive follicular dendritic cell virus trapping in one of them. One female, who died within 3 years of acquiring SIVcpz, had histopathological findings consistent with end-stage AIDS. These results indicate that SIVcpz, like HIV-1, is associated with progressive CD4(+) T-cell loss, lymphatic tissue destruction and premature death. These findings challenge the prevailing view that all natural SIV infections are non-pathogenic and suggest that SIVcpz has a substantial negative impact on the health, reproduction and lifespan of chimpanzees in the wild.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872475/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872475/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keele, Brandon F -- Jones, James Holland -- Terio, Karen A -- Estes, Jacob D -- Rudicell, Rebecca S -- Wilson, Michael L -- Li, Yingying -- Learn, Gerald H -- Beasley, T Mark -- Schumacher-Stankey, Joann -- Wroblewski, Emily -- Mosser, Anna -- Raphael, Jane -- Kamenya, Shadrack -- Lonsdorf, Elizabeth V -- Travis, Dominic A -- Mlengeya, Titus -- Kinsel, Michael J -- Else, James G -- Silvestri, Guido -- Goodall, Jane -- Sharp, Paul M -- Shaw, George M -- Pusey, Anne E -- Hahn, Beatrice H -- HHSN266200400088C/PHS HHS/ -- P30 AI 27767/AI/NIAID NIH HHS/ -- P30 AI027767/AI/NIAID NIH HHS/ -- P30 AI027767-21A17134/AI/NIAID NIH HHS/ -- R01 AI058715/AI/NIAID NIH HHS/ -- R01 AI058715-06A1/AI/NIAID NIH HHS/ -- R01 AI50529/AI/NIAID NIH HHS/ -- R01 AI58715/AI/NIAID NIH HHS/ -- R37 AI050529/AI/NIAID NIH HHS/ -- R37 AI050529-06A1/AI/NIAID NIH HHS/ -- RR-00165/RR/NCRR NIH HHS/ -- T32 GM008111/GM/NIGMS NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- U19 AI067854-059010/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 23;460(7254):515-9. doi: 10.1038/nature08200.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19626114" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/pathology ; Africa ; Animals ; Animals, Wild ; CD4-Positive T-Lymphocytes/immunology ; Female ; Humans ; Male ; Molecular Sequence Data ; Pan troglodytes/*virology ; Prevalence ; Simian Acquired Immunodeficiency ; Syndrome/epidemiology/immunology/*mortality/*pathology ; Simian Immunodeficiency Virus/*physiology
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    Polar science: bid for freely accessible biodiversity archive (2009)
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    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Danis, Bruno -- Griffiths, Huw -- England -- Nature. 2009 Apr 16;458(7240):830. doi: 10.1038/458830b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19370008" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; *Archives ; *Biodiversity ; Databases, Factual ; *Internet ; *Marine Biology ; Oceans and Seas
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    Bidirectional plasticity in fast-spiking GABA circuits by visual experience (2009)
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    Publication Date: 2009-11-13
    Description: Experience-dependent plasticity in the brain requires balanced excitation-inhibition. How individual circuit elements contribute to plasticity outcome in complex neocortical networks remains unknown. Here we report an intracellular analysis of ocular dominance plasticity-the loss of acuity and cortical responsiveness for an eye deprived of vision in early life. Unlike the typical progressive loss of pyramidal-cell bias, direct recording from fast-spiking cells in vivo reveals a counterintuitive initial shift towards the occluded eye followed by a late preference for the open eye, consistent with a spike-timing-dependent plasticity rule for these inhibitory neurons. Intracellular pharmacology confirms a dynamic switch of GABA (gamma-aminobutyric acid) impact to pyramidal cells following deprivation in juvenile mice only. Together these results suggest that the bidirectional recruitment of an initially binocular GABA circuit may contribute to experience-dependent plasticity in the developing visual cortex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yazaki-Sugiyama, Yoko -- Kang, Siu -- Cateau, Hideyuki -- Fukai, Tomoki -- Hensch, Takao K -- England -- Nature. 2009 Nov 12;462(7270):218-21. doi: 10.1038/nature08485.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CREST, JST, Toyonaka, Osaka 560-0082, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19907494" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials/*physiology ; Aging/physiology ; Animals ; Dominance, Ocular/*physiology ; Interneurons/metabolism ; Mice ; Mice, Inbred C57BL ; Models, Neurological ; Neuronal Plasticity/*physiology ; Neurons/*metabolism ; Photic Stimulation ; Pyramidal Cells/metabolism ; Receptors, GABA/metabolism ; Visual Cortex/cytology/physiology ; Visual Pathways/physiology ; Visual Perception/*physiology ; gamma-Aminobutyric Acid/*metabolism
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    Obituary: Daniel Carleton Gajdusek (1923-2008) (2009)
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    Publication Date: 2009-02-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goudsmit, Jaap -- England -- Nature. 2009 Jan 22;457(7228):394. doi: 10.1038/457394a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Jaap Goudsmit is in the Research and Development Department of Crucell Holland, PO Box 2048, Leiden, 2301 CA, the Netherlands, and in the Academic Medical Center of the University of Amsterdam. j.goudsmit@crucell.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158783" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; History, 20th Century ; History, 21st Century ; Humans ; Nobel Prize ; Prion Diseases/*history/transmission ; Prions/chemistry/*history/metabolism
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    CBP/p300-mediated acetylation of histone H3 on lysine 56 (2009)
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    Publication Date: 2009-03-10
    Description: Acetylation within the globular core domain of histone H3 on lysine 56 (H3K56) has recently been shown to have a critical role in packaging DNA into chromatin following DNA replication and repair in budding yeast. However, the function or occurrence of this specific histone mark has not been studied in multicellular eukaryotes, mainly because the Rtt109 enzyme that is known to mediate acetylation of H3K56 (H3K56ac) is fungal-specific. Here we demonstrate that the histone acetyl transferase CBP (also known as Nejire) in flies and CBP and p300 (Ep300) in humans acetylate H3K56, whereas Drosophila Sir2 and human SIRT1 and SIRT2 deacetylate H3K56ac. The histone chaperones ASF1A in humans and Asf1 in Drosophila are required for acetylation of H3K56 in vivo, whereas the histone chaperone CAF-1 (chromatin assembly factor 1) in humans and Caf1 in Drosophila are required for the incorporation of histones bearing this mark into chromatin. We show that, in response to DNA damage, histones bearing acetylated K56 are assembled into chromatin in Drosophila and human cells, forming foci that colocalize with sites of DNA repair. Furthermore, acetylation of H3K56 is increased in multiple types of cancer, correlating with increased levels of ASF1A in these tumours. Our identification of multiple proteins regulating the levels of H3K56 acetylation in metazoans will allow future studies of this critical and unique histone modification that couples chromatin assembly to DNA synthesis, cell proliferation and cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756583/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756583/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Das, Chandrima -- Lucia, M Scott -- Hansen, Kirk C -- Tyler, Jessica K -- CA95641/CA/NCI NIH HHS/ -- GM64475/GM/NIGMS NIH HHS/ -- R01 CA095641/CA/NCI NIH HHS/ -- R01 CA095641-07/CA/NCI NIH HHS/ -- R01 GM064475/GM/NIGMS NIH HHS/ -- R01 GM064475-07/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 May 7;459(7243):113-7. doi: 10.1038/nature07861. Epub 2009 Mar 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora Colorado 80045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19270680" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Cell Cycle Proteins/metabolism ; Cell Line ; Chromosomal Proteins, Non-Histone/metabolism ; DNA Damage/physiology ; Drosophila Proteins/metabolism ; Drosophila melanogaster/*enzymology ; HeLa Cells ; Histone Deacetylases/metabolism ; Histones/*metabolism ; Humans ; Lysine/*metabolism ; Molecular Chaperones/metabolism ; Retinoblastoma-Binding Protein 4 ; Sirtuin 1 ; Sirtuin 2 ; Sirtuins/metabolism ; p300-CBP Transcription Factors/*metabolism
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    Riboflavin kinase couples TNF receptor 1 to NADPH oxidase (2009)
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    Publication Date: 2009-07-31
    Description: Reactive oxygen species (ROS) produced by NADPH oxidase function as defence and signalling molecules related to innate immunity and various cellular responses. The activation of NADPH oxidase in response to plasma membrane receptor activation depends on the phosphorylation of cytoplasmic oxidase subunits, their translocation to membranes and the assembly of all NADPH oxidase components. Tumour necrosis factor (TNF) is a prominent stimulus of ROS production, but the molecular mechanisms by which TNF activates NADPH oxidase are poorly understood. Here we identify riboflavin kinase (RFK, formerly known as flavokinase) as a previously unrecognized TNF-receptor-1 (TNFR1)-binding protein that physically and functionally couples TNFR1 to NADPH oxidase. In mouse and human cells, RFK binds to both the TNFR1-death domain and to p22(phox), the common subunit of NADPH oxidase isoforms. RFK-mediated bridging of TNFR1 and p22(phox) is a prerequisite for TNF-induced but not for Toll-like-receptor-induced ROS production. Exogenous flavin mononucleotide or FAD was able to substitute fully for TNF stimulation of NADPH oxidase in RFK-deficient cells. RFK is rate-limiting in the synthesis of FAD, an essential prosthetic group of NADPH oxidase. The results suggest that TNF, through the activation of RFK, enhances the incorporation of FAD in NADPH oxidase enzymes, a critical step for the assembly and activation of NADPH oxidase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yazdanpanah, Benjamin -- Wiegmann, Katja -- Tchikov, Vladimir -- Krut, Oleg -- Pongratz, Carola -- Schramm, Michael -- Kleinridders, Andre -- Wunderlich, Thomas -- Kashkar, Hamid -- Utermohlen, Olaf -- Bruning, Jens C -- Schutze, Stefan -- Kronke, Martin -- England -- Nature. 2009 Aug 27;460(7259):1159-63. doi: 10.1038/nature08206. Epub 2009 Jul 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19641494" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cytochrome b Group/metabolism ; Enzyme Activation ; Fibroblasts ; Flavin Mononucleotide/metabolism ; Flavin-Adenine Dinucleotide/biosynthesis/metabolism ; HeLa Cells ; Humans ; Isoenzymes/chemistry/metabolism ; Membrane Glycoproteins/metabolism ; Mice ; NADH, NADPH Oxidoreductases/metabolism ; NADPH Oxidase/chemistry/*metabolism ; Phosphotransferases (Alcohol Group Acceptor)/deficiency/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Reactive Oxygen Species/metabolism ; Receptors, Tumor Necrosis Factor, Type I/chemistry/*metabolism
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    Predicting new molecular targets for known drugs (2009)
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    Publication Date: 2009-11-03
    Description: Although drugs are intended to be selective, at least some bind to several physiological targets, explaining side effects and efficacy. Because many drug-target combinations exist, it would be useful to explore possible interactions computationally. Here we compared 3,665 US Food and Drug Administration (FDA)-approved and investigational drugs against hundreds of targets, defining each target by its ligands. Chemical similarities between drugs and ligand sets predicted thousands of unanticipated associations. Thirty were tested experimentally, including the antagonism of the beta(1) receptor by the transporter inhibitor Prozac, the inhibition of the 5-hydroxytryptamine (5-HT) transporter by the ion channel drug Vadilex, and antagonism of the histamine H(4) receptor by the enzyme inhibitor Rescriptor. Overall, 23 new drug-target associations were confirmed, five of which were potent (〈100 nM). The physiological relevance of one, the drug N,N-dimethyltryptamine (DMT) on serotonergic receptors, was confirmed in a knockout mouse. The chemical similarity approach is systematic and comprehensive, and may suggest side-effects and new indications for many drugs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784146/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784146/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keiser, Michael J -- Setola, Vincent -- Irwin, John J -- Laggner, Christian -- Abbas, Atheir I -- Hufeisen, Sandra J -- Jensen, Niels H -- Kuijer, Michael B -- Matos, Roberto C -- Tran, Thuy B -- Whaley, Ryan -- Glennon, Richard A -- Hert, Jerome -- Thomas, Kelan L H -- Edwards, Douglas D -- Shoichet, Brian K -- Roth, Bryan L -- R01 DA017204/DA/NIDA NIH HHS/ -- R01 DA017204-04/DA/NIDA NIH HHS/ -- R01 DA017204-05/DA/NIDA NIH HHS/ -- R01 MH061887/MH/NIMH NIH HHS/ -- R01 MH061887-09/MH/NIMH NIH HHS/ -- R01 MH061887-10/MH/NIMH NIH HHS/ -- U19 MH082441/MH/NIMH NIH HHS/ -- U19 MH082441-01/MH/NIMH NIH HHS/ -- U19 MH082441-010001/MH/NIMH NIH HHS/ -- U19 MH082441-019002/MH/NIMH NIH HHS/ -- U19 MH082441-019003/MH/NIMH NIH HHS/ -- U19 MH082441-02/MH/NIMH NIH HHS/ -- U19 MH082441-020001/MH/NIMH NIH HHS/ -- U19 MH082441-029002/MH/NIMH NIH HHS/ -- U19 MH082441-03/MH/NIMH NIH HHS/ -- U19 MH082441-030001/MH/NIMH NIH HHS/ -- U19 MH082441-039002/MH/NIMH NIH HHS/ -- England -- Nature. 2009 Nov 12;462(7270):175-81. doi: 10.1038/nature08506. Epub 2009 Nov 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94143-2550, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19881490" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Computational Biology ; Databases, Factual ; Drug Evaluation, Preclinical/*methods ; Drug-Related Side Effects and Adverse Reactions ; Humans ; Ligands ; Mice ; Mice, Knockout ; Off-Label Use ; Pharmaceutical Preparations/*metabolism ; Receptors, Serotonin/metabolism ; *Substrate Specificity ; United States ; United States Food and Drug Administration
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    Mitochondrial gene replacement in primate offspring and embryonic stem cells (2009)
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    Publication Date: 2009-08-28
    Description: Mitochondria are found in all eukaryotic cells and contain their own genome (mitochondrial DNA or mtDNA). Unlike the nuclear genome, which is derived from both the egg and sperm at fertilization, the mtDNA in the embryo is derived almost exclusively from the egg; that is, it is of maternal origin. Mutations in mtDNA contribute to a diverse range of currently incurable human diseases and disorders. To establish preclinical models for new therapeutic approaches, we demonstrate here that the mitochondrial genome can be efficiently replaced in mature non-human primate oocytes (Macaca mulatta) by spindle-chromosomal complex transfer from one egg to an enucleated, mitochondrial-replete egg. The reconstructed oocytes with the mitochondrial replacement were capable of supporting normal fertilization, embryo development and produced healthy offspring. Genetic analysis confirmed that nuclear DNA in the three infants born so far originated from the spindle donors whereas mtDNA came from the cytoplast donors. No contribution of spindle donor mtDNA was detected in offspring. Spindle replacement is shown here as an efficient protocol replacing the full complement of mitochondria in newly generated embryonic stem cell lines. This approach may offer a reproductive option to prevent mtDNA disease transmission in affected families.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774772/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774772/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tachibana, Masahito -- Sparman, Michelle -- Sritanaudomchai, Hathaitip -- Ma, Hong -- Clepper, Lisa -- Woodward, Joy -- Li, Ying -- Ramsey, Cathy -- Kolotushkina, Olena -- Mitalipov, Shoukhrat -- P01 HD047675/HD/NICHD NIH HHS/ -- P01 HD047675-01A17045/HD/NICHD NIH HHS/ -- P01 HD047675-04/HD/NICHD NIH HHS/ -- P51 RR000163/RR/NCRR NIH HHS/ -- P51 RR000163-486766/RR/NCRR NIH HHS/ -- P51 RR000163-486775/RR/NCRR NIH HHS/ -- P51 RR000163-486819/RR/NCRR NIH HHS/ -- P51 RR000163-496038/RR/NCRR NIH HHS/ -- P51 RR000163-496045/RR/NCRR NIH HHS/ -- P51 RR000163-496074/RR/NCRR NIH HHS/ -- P51 RR000163-496133/RR/NCRR NIH HHS/ -- P51 RR000163-496134/RR/NCRR NIH HHS/ -- P51 RR000163-496136/RR/NCRR NIH HHS/ -- P51 RR000163-496137/RR/NCRR NIH HHS/ -- R01 HD057121/HD/NICHD NIH HHS/ -- R01 HD057121-01A2/HD/NICHD NIH HHS/ -- R01 NS044330/NS/NINDS NIH HHS/ -- R01 NS044330-05/NS/NINDS NIH HHS/ -- R24 RR013632/RR/NCRR NIH HHS/ -- R24 RR013632-10/RR/NCRR NIH HHS/ -- England -- Nature. 2009 Sep 17;461(7262):367-72. doi: 10.1038/nature08368. Epub 2009 Aug 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Oregon National Primate Research Center, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19710649" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/analysis/*genetics ; Embryo Transfer ; Embryonic Stem Cells/*cytology/*metabolism/transplantation ; Female ; Fertilization in Vitro ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Macaca mulatta/embryology/*genetics ; Male ; Meiosis ; Mitochondrial Diseases/genetics/prevention & control ; Mutation ; Oocytes/cytology/metabolism ; Pregnancy ; *Reproductive Techniques, Assisted
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    Rational design of a structural and functional nitric oxide reductase (2009)
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    Publication Date: 2009-11-27
    Description: Protein design provides a rigorous test of our knowledge about proteins and allows the creation of novel enzymes for biotechnological applications. Whereas progress has been made in designing proteins that mimic native proteins structurally, it is more difficult to design functional proteins. In comparison to recent successes in designing non-metalloproteins, it is even more challenging to rationally design metalloproteins that reproduce both the structure and function of native metalloenzymes. This is because protein metal-binding sites are much more varied than non-metal-containing sites, in terms of different metal ion oxidation states, preferred geometry and metal ion ligand donor sets. Because of their variability, it has been difficult to predict metal-binding site properties in silico, as many of the parameters, such as force fields, are ill-defined. Therefore, the successful design of a structural and functional metalloprotein would greatly advance the field of protein design and our understanding of enzymes. Here we report a successful, rational design of a structural and functional model of a metalloprotein, nitric oxide reductase (NOR), by introducing three histidines and one glutamate, predicted as ligands in the active site of NOR, into the distal pocket of myoglobin. A crystal structure of the designed protein confirms that the minimized computer model contains a haem/non-haem Fe(B) centre that is remarkably similar to that in the crystal structure. This designed protein also exhibits NO reduction activity, and so models both the structure and function of NOR, offering insight that the active site glutamate is required for both iron binding and activity. These results show that structural and functional metalloproteins can be rationally designed in silico.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297211/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297211/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yeung, Natasha -- Lin, Ying-Wu -- Gao, Yi-Gui -- Zhao, Xuan -- Russell, Brandy S -- Lei, Lanyu -- Miner, Kyle D -- Robinson, Howard -- Lu, Yi -- GM062211/GM/NIGMS NIH HHS/ -- R01 GM062211/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 24;462(7276):1079-82. doi: 10.1038/nature08620. Epub 2009 Nov 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940850" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallization ; Iron/metabolism ; Models, Molecular ; Myoglobin/chemistry ; Nitric Oxide/metabolism ; Oxidoreductases/*chemical synthesis/*chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary
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    Journal club. A systems biologist ponders how disparate ideas can sometimes come together beautifully (2009)
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    Details
    Publication Date: 2009-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kell, Douglas -- England -- Nature. 2009 Aug 6;460(7256):669. doi: 10.1038/460669e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The University of Manchester, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661875" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain Chemistry ; Creutzfeldt-Jakob Syndrome/metabolism ; Ferritins/metabolism ; Humans ; Hydroxyl Radical/metabolism ; Iron/chemistry/*metabolism ; PrPSc Proteins/*metabolism ; Prion Diseases/*metabolism ; Scrapie/metabolism ; Systems Biology
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    Forcing cells to change lineages (2009)
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    Publication Date: 2009-12-04
    Description: The ability to produce stem cells by induced pluripotency (iPS reprogramming) has rekindled an interest in earlier studies showing that transcription factors can directly convert specialized cells from one lineage to another. Lineage reprogramming has become a powerful tool to study cell fate choice during differentiation, akin to inducing mutations for the discovery of gene functions. The lessons learnt provide a rubric for how cells may be manipulated for therapeutic purposes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Graf, Thomas -- Enver, Tariq -- MC_U137973817/Medical Research Council/United Kingdom -- England -- Nature. 2009 Dec 3;462(7273):587-94. doi: 10.1038/nature08533.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genomic Regulation and ICREA, 08003 Barcelona, Spain. thomas.graf@crg.es〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19956253" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Lineage/*physiology ; Cellular Reprogramming/*genetics ; *Gene Expression Regulation, Developmental ; Gene Regulatory Networks/physiology ; Humans ; Pluripotent Stem Cells/cytology/*metabolism ; Transcription Factors/*metabolism
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    CCR3 is a target for age-related macular degeneration diagnosis and therapy (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-06-16
    Description: Age-related macular degeneration (AMD), a leading cause of blindness worldwide, is as prevalent as cancer in industrialized nations. Most blindness in AMD results from invasion of the retina by choroidal neovascularisation (CNV). Here we show that the eosinophil/mast cell chemokine receptor CCR3 is specifically expressed in choroidal neovascular endothelial cells in humans with AMD, and that despite the expression of its ligands eotaxin-1, -2 and -3, neither eosinophils nor mast cells are present in human CNV. Genetic or pharmacological targeting of CCR3 or eotaxins inhibited injury-induced CNV in mice. CNV suppression by CCR3 blockade was due to direct inhibition of endothelial cell proliferation, and was uncoupled from inflammation because it occurred in mice lacking eosinophils or mast cells, and was independent of macrophage and neutrophil recruitment. CCR3 blockade was more effective at reducing CNV than vascular endothelial growth factor A (VEGF-A) neutralization, which is in clinical use at present, and, unlike VEGF-A blockade, is not toxic to the mouse retina. In vivo imaging with CCR3-targeting quantum dots located spontaneous CNV invisible to standard fluorescein angiography in mice before retinal invasion. CCR3 targeting might reduce vision loss due to AMD through early detection and therapeutic angioinhibition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712122/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712122/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Takeda, Atsunobu -- Baffi, Judit Z -- Kleinman, Mark E -- Cho, Won Gil -- Nozaki, Miho -- Yamada, Kiyoshi -- Kaneko, Hiroki -- Albuquerque, Romulo J C -- Dridi, Sami -- Saito, Kuniharu -- Raisler, Brian J -- Budd, Steven J -- Geisen, Pete -- Munitz, Ariel -- Ambati, Balamurali K -- Green, Martha G -- Ishibashi, Tatsuro -- Wright, John D -- Humbles, Alison A -- Gerard, Craig J -- Ogura, Yuichiro -- Pan, Yuzhen -- Smith, Justine R -- Grisanti, Salvatore -- Hartnett, M Elizabeth -- Rothenberg, Marc E -- Ambati, Jayakrishna -- AI039759/AI/NIAID NIH HHS/ -- AI45898/AI/NIAID NIH HHS/ -- DK076893/DK/NIDDK NIH HHS/ -- EY010572/EY/NEI NIH HHS/ -- EY015130/EY/NEI NIH HHS/ -- EY015422/EY/NEI NIH HHS/ -- EY017011/EY/NEI NIH HHS/ -- EY017182/EY/NEI NIH HHS/ -- EY017950/EY/NEI NIH HHS/ -- EY018350/EY/NEI NIH HHS/ -- EY018836/EY/NEI NIH HHS/ -- R01 DK076893/DK/NIDDK NIH HHS/ -- R01 EY015422/EY/NEI NIH HHS/ -- R01 EY015422-04/EY/NEI NIH HHS/ -- R01 EY018350/EY/NEI NIH HHS/ -- R01 EY018350-02/EY/NEI NIH HHS/ -- R01 EY018836/EY/NEI NIH HHS/ -- R01 EY018836-02/EY/NEI NIH HHS/ -- England -- Nature. 2009 Jul 9;460(7252):225-30. doi: 10.1038/nature08151. Epub 2009 Jun 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ophthalmology & Visual Science, University of Kentucky, Lexington, Kentucky 40506, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19525930" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Movement ; Cell Proliferation ; Cells, Cultured ; Chemokine CCL11/antagonists & inhibitors/metabolism ; Chemokine CCL24/antagonists & inhibitors/metabolism ; Chemokines, CC/antagonists & inhibitors/metabolism ; Choroid/blood supply/cytology/metabolism ; Choroidal Neovascularization/diagnosis/metabolism ; Disease Models, Animal ; Endothelial Cells/cytology/metabolism ; Humans ; Inflammation ; Leukocytes ; Ligands ; Macular Degeneration/*diagnosis/metabolism/*therapy ; Mice ; Mice, Inbred C57BL ; Quantum Dots ; Receptors, CCR3/analysis/*antagonists & ; inhibitors/genetics/immunology/*metabolism ; Retina/drug effects/pathology ; Vascular Endothelial Growth Factor A/antagonists & inhibitors/immunology
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    MicroRNA-mediated switching of chromatin-remodelling complexes in neural development (2009)
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    Publication Date: 2009-06-30
    Description: One of the most distinctive steps in the development of the vertebrate nervous system occurs at mitotic exit when cells lose multipotency and begin to develop stable connections that will persist for a lifetime. This transition is accompanied by a switch in ATP-dependent chromatin-remodelling mechanisms that appears to coincide with the final mitotic division of neurons. This switch involves the exchange of the BAF53a (also known as ACTL6a) and BAF45a (PHF10) subunits within Swi/Snf-like neural-progenitor-specific BAF (npBAF) complexes for the homologous BAF53b (ACTL6b) and BAF45b (DPF1) subunits within neuron-specific BAF (nBAF) complexes in post-mitotic neurons. The subunits of the npBAF complex are essential for neural-progenitor proliferation, and mice with reduced dosage for the genes encoding its subunits have defects in neural-tube closure similar to those in human spina bifida, one of the most serious congenital birth defects. In contrast, BAF53b and the nBAF complex are essential for an evolutionarily conserved program of post-mitotic neural development and dendritic morphogenesis. Here we show that this essential transition is mediated by repression of BAF53a by miR-9* and miR-124. We find that BAF53a repression is mediated by sequences in the 3' untranslated region corresponding to the recognition sites for miR-9* and miR-124, which are selectively expressed in post-mitotic neurons. Mutation of these sites led to persistent expression of BAF53a and defective activity-dependent dendritic outgrowth in neurons. In addition, overexpression of miR-9* and miR-124 in neural progenitors caused reduced proliferation. Previous studies have indicated that miR-9* and miR-124 are repressed by the repressor-element-1-silencing transcription factor (REST, also known as NRSF). Indeed, expression of REST in post-mitotic neurons led to derepression of BAF53a, indicating that REST-mediated repression of microRNAs directs the essential switch of chromatin regulatory complexes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921580/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921580/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yoo, Andrew S -- Staahl, Brett T -- Chen, Lei -- Crabtree, Gerald R -- 2 T32 HD007249/HD/NICHD NIH HHS/ -- AI060037/AI/NIAID NIH HHS/ -- HD55391/HD/NICHD NIH HHS/ -- NS046789/NS/NINDS NIH HHS/ -- R01 HD055391/HD/NICHD NIH HHS/ -- R01 NS046789/NS/NINDS NIH HHS/ -- R01 NS046789-08/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 30;460(7255):642-6. doi: 10.1038/nature08139. Epub 2009 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, and Department of Developmental Biology, Stanford University, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19561591" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/metabolism ; Actins/genetics/metabolism ; Animals ; CHO Cells ; Cell Line ; Chromatin Assembly and Disassembly/genetics/*physiology ; Chromosomal Proteins, Non-Histone/genetics/metabolism ; Cricetinae ; Cricetulus ; DNA-Binding Proteins/genetics/metabolism ; Dendrites/physiology ; *Gene Expression Regulation, Developmental ; Mice ; Mice, Transgenic ; MicroRNAs/*metabolism ; Mitosis ; Nervous System/cytology/*embryology ; Neurons/cytology ; Repressor Proteins/metabolism ; Stem Cells/metabolism
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    Darwin's bridge between microevolution and macroevolution (2009)
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    Publication Date: 2009-02-13
    Description: Evolutionary biologists have long sought to understand the relationship between microevolution (adaptation), which can be observed both in nature and in the laboratory, and macroevolution (speciation and the origin of the divisions of the taxonomic hierarchy above the species level, and the development of complex organs), which cannot be witnessed because it occurs over intervals that far exceed the human lifespan. The connection between these processes is also a major source of conflict between science and religious belief. Biologists often forget that Charles Darwin offered a way of resolving this issue, and his proposal is ripe for re-evaluation in the light of recent research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reznick, David N -- Ricklefs, Robert E -- England -- Nature. 2009 Feb 12;457(7231):837-42. doi: 10.1038/nature07894.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of California, Riverside, California 92521, USA. gupy@ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212402" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; *Biological Evolution ; Extinction, Biological ; Genetic Speciation
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    Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors (2009)
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    Publication Date: 2009-04-28
    Description: Heart disease is the leading cause of mortality and morbidity in the western world. The heart has little regenerative capacity after damage, leading to much interest in understanding the factors required to produce new cardiac myocytes. Despite a robust understanding of the molecular networks regulating cardiac differentiation, no single transcription factor or combination of factors has been shown to activate the cardiac gene program de novo in mammalian cells or tissues. Here we define the minimal requirements for transdifferentiation of mouse mesoderm to cardiac myocytes. We show that two cardiac transcription factors, Gata4 and Tbx5, and a cardiac-specific subunit of BAF chromatin-remodelling complexes, Baf60c (also called Smarcd3), can direct ectopic differentiation of mouse mesoderm into beating cardiomyocytes, including the normally non-cardiogenic posterior mesoderm and the extraembryonic mesoderm of the amnion. Gata4 with Baf60c initiated ectopic cardiac gene expression. Addition of Tbx5 allowed differentiation into contracting cardiomyocytes and repression of non-cardiac mesodermal genes. Baf60c was essential for the ectopic cardiogenic activity of Gata4 and Tbx5, partly by permitting binding of Gata4 to cardiac genes, indicating a novel instructive role for BAF complexes in tissue-specific regulation. The combined function of these factors establishes a robust mechanism for controlling cellular differentiation, and may allow reprogramming of new cardiomyocytes for regenerative purposes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728356/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728356/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Takeuchi, Jun K -- Bruneau, Benoit G -- C06 RR018928/RR/NCRR NIH HHS/ -- R01 HL085860/HL/NHLBI NIH HHS/ -- R01 HL085860-01/HL/NHLBI NIH HHS/ -- R01HL085860/HL/NHLBI NIH HHS/ -- England -- Nature. 2009 Jun 4;459(7247):708-11. doi: 10.1038/nature08039. Epub 2009 Apr 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158, USA. takeuchi.j.ab@m.titech.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19396158" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cell Differentiation ; Cell Transdifferentiation ; Chromosomal Proteins, Non-Histone ; Embryo, Mammalian ; GATA4 Transcription Factor/metabolism ; Gene Expression Regulation, Developmental ; Heart/*embryology ; Mesoderm/cytology/*embryology ; Mice ; Muscle Proteins ; Myocytes, Cardiac/*cytology/metabolism ; T-Box Domain Proteins/metabolism
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    Cancer: When restriction is good (2009)
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    Publication Date: 2009-04-11
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2822621/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2822621/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brunet, Anne -- R01 AG031198/AG/NIA NIH HHS/ -- R01 AG031198-01A1/AG/NIA NIH HHS/ -- England -- Nature. 2009 Apr 9;458(7239):713-4. doi: 10.1038/458713a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19360073" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/physiology ; *Caloric Restriction ; Humans ; Insulin/physiology ; Neoplasms/*diet therapy ; Phosphatidylinositol 3-Kinases/metabolism ; Signal Transduction/physiology ; Tumor Cells, Cultured
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    Discovery of dual function acridones as a new antimalarial chemotype (2009)
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    Publication Date: 2009-04-10
    Description: Preventing and delaying the emergence of drug resistance is an essential goal of antimalarial drug development. Monotherapy and highly mutable drug targets have each facilitated resistance, and both are undesirable in effective long-term strategies against multi-drug-resistant malaria. Haem remains an immutable and vulnerable target, because it is not parasite-encoded and its detoxification during haemoglobin degradation, critical to parasite survival, can be subverted by drug-haem interaction as in the case of quinolines and many other drugs. Here we describe a new antimalarial chemotype that combines the haem-targeting character of acridones, together with a chemosensitizing component that counteracts resistance to quinoline antimalarial drugs. Beyond the essential intrinsic characteristics common to deserving candidate antimalarials (high potency in vitro against pan-sensitive and multi-drug-resistant Plasmodium falciparum, efficacy and safety in vivo after oral administration, inexpensive synthesis and favourable physicochemical properties), our initial lead, T3.5 (3-chloro-6-(2-diethylamino-ethoxy)-10-(2-diethylamino-ethyl)-acridone), demonstrates unique synergistic properties. In addition to 'verapamil-like' chemosensitization to chloroquine and amodiaquine against quinoline-resistant parasites, T3.5 also results in an apparently mechanistically distinct synergism with quinine and with piperaquine. This synergy, evident in both quinoline-sensitive and quinoline-resistant parasites, has been demonstrated both in vitro and in vivo. In summary, this innovative acridone design merges intrinsic potency and resistance-counteracting functions in one molecule, and represents a new strategy to expand, enhance and sustain effective antimalarial drug combinations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelly, Jane X -- Smilkstein, Martin J -- Brun, Reto -- Wittlin, Sergio -- Cooper, Roland A -- Lane, Kristin D -- Janowsky, Aaron -- Johnson, Robert A -- Dodean, Rozalia A -- Winter, Rolf -- Hinrichs, David J -- Riscoe, Michael K -- England -- Nature. 2009 May 14;459(7244):270-3. doi: 10.1038/nature07937. Epub 2009 Apr 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Portland Veterans Affairs Medical Centre, Portland, Oregon 97239, USA. kellyja@ohsu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19357645" target="_blank"〉PubMed〈/a〉
    Keywords: Acridones/analysis/metabolism/*pharmacology ; Animals ; Antimalarials/analysis/metabolism/*pharmacology ; *Drug Discovery ; Drug Resistance/drug effects ; Drug Synergism ; Heme/antagonists & inhibitors/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Mutation/genetics ; Plasmodium falciparum/*drug effects/genetics/growth & development/metabolism ; Plasmodium yoelii/drug effects ; Protozoan Proteins/genetics/metabolism ; Quinine/pharmacology ; Quinolines/pharmacology ; Trophozoites/metabolism ; Verapamil/pharmacology
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    Neurotransmission selectively regulates synapse formation in parallel circuits in vivo (2009)
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    Publication Date: 2009-08-21
    Description: Activity is thought to guide the patterning of synaptic connections in the developing nervous system. Specifically, differences in the activity of converging inputs are thought to cause the elimination of synapses from less active inputs and increase connectivity with more active inputs. Here we present findings that challenge the generality of this notion and offer a new view of the role of activity in synapse development. To imbalance neurotransmission from different sets of inputs in vivo, we generated transgenic mice in which ON but not OFF types of bipolar cells in the retina express tetanus toxin (TeNT). During development, retinal ganglion cells (RGCs) select between ON and OFF bipolar cell inputs (ON or OFF RGCs) or establish a similar number of synapses with both on separate dendritic arborizations (ON-OFF RGCs). In TeNT retinas, ON RGCs correctly selected the silenced ON bipolar cell inputs over the transmitting OFF bipolar cells, but were connected with them through fewer synapses at maturity. Time-lapse imaging revealed that this was caused by a reduced rate of synapse formation rather than an increase in synapse elimination. Similarly, TeNT-expressing ON bipolar cell axons generated fewer presynaptic active zones. The remaining active zones often recruited multiple, instead of single, synaptic ribbons. ON-OFF RGCs in TeNT mice maintained convergence of ON and OFF bipolar cells inputs and had fewer synapses on their ON arbor without changes to OFF arbor synapses. Our results reveal an unexpected and remarkably selective role for activity in circuit development in vivo, regulating synapse formation but not elimination, affecting synapse number but not dendritic or axonal patterning, and mediating independently the refinement of connections from parallel (ON and OFF) processing streams even where they converge onto the same postsynaptic cell.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746695/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746695/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerschensteiner, Daniel -- Morgan, Josh L -- Parker, Edward D -- Lewis, Renate M -- Wong, Rachel O L -- EY01730/EY/NEI NIH HHS/ -- EY10699/EY/NEI NIH HHS/ -- R01 EY010699/EY/NEI NIH HHS/ -- R01 EY010699-16/EY/NEI NIH HHS/ -- T32 EY07031/EY/NEI NIH HHS/ -- England -- Nature. 2009 Aug 20;460(7258):1016-20. doi: 10.1038/nature08236.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy and Neurobiology, Washington University School of Medicine, St Louis, Missouri 63110, USA. KerschensteinerD@vision.wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693082" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/metabolism ; Dendrites/metabolism ; Female ; Glutamic Acid/metabolism ; Male ; Mice ; Mice, Transgenic ; Receptors, Kainic Acid/genetics/metabolism ; Retinal Bipolar Cells/cytology/metabolism ; Retinal Ganglion Cells/cytology/metabolism ; Synapses/*metabolism ; Synaptic Transmission/*physiology ; Tetanus Toxin/genetics/metabolism
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    Distinct sensory representations of wind and near-field sound in the Drosophila brain (2009)
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    Publication Date: 2009-03-13
    Description: Behavioural responses to wind are thought to have a critical role in controlling the dispersal and population genetics of wild Drosophila species, as well as their navigation in flight, but their underlying neurobiological basis is unknown. We show that Drosophila melanogaster, like wild-caught Drosophila strains, exhibits robust wind-induced suppression of locomotion in response to air currents delivered at speeds normally encountered in nature. Here we identify wind-sensitive neurons in Johnston's organ, an antennal mechanosensory structure previously implicated in near-field sound detection (reviewed in refs 5 and 6). Using enhancer trap lines targeted to different subsets of Johnston's organ neurons, and a genetically encoded calcium indicator, we show that wind and near-field sound (courtship song) activate distinct populations of Johnston's organ neurons, which project to different regions of the antennal and mechanosensory motor centre in the central brain. Selective genetic ablation of wind-sensitive Johnston's organ neurons in the antenna abolishes wind-induced suppression of locomotion behaviour, without impairing hearing. Moreover, different neuronal subsets within the wind-sensitive population respond to different directions of arista deflection caused by air flow and project to different regions of the antennal and mechanosensory motor centre, providing a rudimentary map of wind direction in the brain. Importantly, sound- and wind-sensitive Johnston's organ neurons exhibit different intrinsic response properties: the former are phasically activated by small, bi-directional, displacements of the aristae, whereas the latter are tonically activated by unidirectional, static deflections of larger magnitude. These different intrinsic properties are well suited to the detection of oscillatory pulses of near-field sound and laminar air flow, respectively. These data identify wind-sensitive neurons in Johnston's organ, a structure that has been primarily associated with hearing, and reveal how the brain can distinguish different types of air particle movements using a common sensory organ.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755041/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755041/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yorozu, Suzuko -- Wong, Allan -- Fischer, Brian J -- Dankert, Heiko -- Kernan, Maurice J -- Kamikouchi, Azusa -- Ito, Kei -- Anderson, David J -- R01 DC002780/DC/NIDCD NIH HHS/ -- T32 GM007737/GM/NIGMS NIH HHS/ -- T32 GM007737-30/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Mar 12;458(7235):201-5. doi: 10.1038/nature07843.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology 216-76, California Institute of Technology, Pasadena, California 91125, USA. yorozu@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19279637" target="_blank"〉PubMed〈/a〉
    Keywords: *Air Movements ; Animals ; Auditory Perception/*physiology ; Behavior, Animal/physiology ; Drosophila melanogaster/*physiology ; Electrophysiological Phenomena/physiology ; Mechanoreceptors/physiology ; Sensory Receptor Cells/*physiology
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    Asymptomatic deer excrete infectious prions in faeces (2009)
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    Publication Date: 2009-09-11
    Description: Infectious prion diseases-scrapie of sheep and chronic wasting disease (CWD) of several species in the deer family-are transmitted naturally within affected host populations. Although several possible sources of contagion have been identified in excretions and secretions from symptomatic animals, the biological importance of these sources in sustaining epidemics remains unclear. Here we show that asymptomatic CWD-infected mule deer (Odocoileus hemionus) excrete CWD prions in their faeces long before they develop clinical signs of prion disease. Intracerebral inoculation of irradiated deer faeces into transgenic mice overexpressing cervid prion protein (PrP) revealed infectivity in 14 of 15 faecal samples collected from five deer at 7-11 months before the onset of neurological disease. Although prion concentrations in deer faeces were considerably lower than in brain tissue from the same deer collected at the end of the disease, the estimated total infectious dose excreted in faeces by an infected deer over the disease course may approximate the total contained in a brain. Prolonged faecal prion excretion by infected deer provides a plausible natural mechanism that might explain the high incidence and efficient horizontal transmission of CWD within deer herds, as well as prion transmission among other susceptible cervids.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3186440/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3186440/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tamguney, Gultekin -- Miller, Michael W -- Wolfe, Lisa L -- Sirochman, Tracey M -- Glidden, David V -- Palmer, Christina -- Lemus, Azucena -- DeArmond, Stephen J -- Prusiner, Stanley B -- AG02132/AG/NIA NIH HHS/ -- P01 AG002132/AG/NIA NIH HHS/ -- P01 AG002132-26/AG/NIA NIH HHS/ -- P01 AG002132-29/AG/NIA NIH HHS/ -- England -- Nature. 2009 Sep 24;461(7263):529-32. doi: 10.1038/nature08289. Epub 2009 Sep 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94143 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741608" target="_blank"〉PubMed〈/a〉
    Keywords: Administration, Oral ; Animals ; Biological Assay ; Brain/metabolism ; Deer/*metabolism ; Feces/*chemistry ; Injections, Intraventricular ; Mice ; Mice, Transgenic ; PrPSc Proteins/isolation & purification/*metabolism/*pathogenicity/radiation ; effects ; Time Factors ; Wasting Disease, Chronic/*metabolism/*transmission
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    Amino-acid imbalance explains extension of lifespan by dietary restriction in Drosophila (2009)
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    Publication Date: 2009-12-04
    Description: Dietary restriction extends healthy lifespan in diverse organisms and reduces fecundity. It is widely assumed to induce adaptive reallocation of nutrients from reproduction to somatic maintenance, aiding survival of food shortages in nature. If this were the case, long life under dietary restriction and high fecundity under full feeding would be mutually exclusive, through competition for the same limiting nutrients. Here we report a test of this idea in which we identified the nutrients producing the responses of lifespan and fecundity to dietary restriction in Drosophila. Adding essential amino acids to the dietary restriction condition increased fecundity and decreased lifespan, similar to the effects of full feeding, with other nutrients having little or no effect. However, methionine alone was necessary and sufficient to increase fecundity as much as did full feeding, but without reducing lifespan. Reallocation of nutrients therefore does not explain the responses to dietary restriction. Lifespan was decreased by the addition of amino acids, with an interaction between methionine and other essential amino acids having a key role. Hence, an imbalance in dietary amino acids away from the ratio optimal for reproduction shortens lifespan during full feeding and limits fecundity during dietary restriction. Reduced activity of the insulin/insulin-like growth factor signalling pathway extends lifespan in diverse organisms, and we find that it also protects against the shortening of lifespan with full feeding. In other organisms, including mammals, it may be possible to obtain the benefits to lifespan of dietary restriction without incurring a reduction in fecundity, through a suitable balance of nutrients in the diet.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798000/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798000/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grandison, Richard C -- Piper, Matthew D W -- Partridge, Linda -- 081394/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2009 Dec 24;462(7276):1061-4. doi: 10.1038/nature08619. Epub 2009 Dec 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Healthy Ageing, Department of Genetics Evolution and Environment, University College London, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19956092" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/*metabolism ; Animals ; *Diet ; Drosophila melanogaster/metabolism/*physiology ; Female ; Insulin/metabolism ; Longevity/*physiology ; Methionine/metabolism ; Oviposition/physiology ; Random Allocation ; Signal Transduction
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    Archaeology: Origins of the female image (2009)
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    Publication Date: 2009-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mellars, Paul -- England -- Nature. 2009 May 14;459(7244):176-7. doi: 10.1038/459176a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444200" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Archaeology ; Female ; Germany ; History, Ancient ; Horns/chemistry ; Humans ; Sculpture/*history ; Sex Characteristics ; Symbolism
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    Journal club. A geneticist views two theories of X-chromosome inactivation in a broad context (2009)
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    Publication Date: 2009-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khalil, Ahmad M -- England -- Nature. 2009 Mar 19;458(7236):263. doi: 10.1038/458263f.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard Medical School, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295563" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Female ; *Models, Genetic ; RNA Interference ; RNA, Long Noncoding ; RNA, Untranslated/*genetics ; Ribonuclease III/deficiency ; X Chromosome Inactivation/*genetics
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    Journal club. A physiologist notes the similarities between animal and plant electricity (2009)
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    Publication Date: 2009-03-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tammaro, Paolo -- England -- Nature. 2009 Mar 5;458(7234):11. doi: 10.1038/458011e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Manchester, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19262629" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Arabidopsis/cytology/genetics/metabolism ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Chloride Channels/*chemistry/genetics/*metabolism ; Chlorides/*metabolism ; Humans ; Ion Transport ; Nitrates/*metabolism
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    Developmental biology: Birth of the blood cell (2009)
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    Publication Date: 2009-02-13
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766277/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766277/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yoshimoto, Momoko -- Yoder, Mervin C -- R01 AI080759/AI/NIAID NIH HHS/ -- R01 AI080759-01/AI/NIAID NIH HHS/ -- England -- Nature. 2009 Feb 12;457(7231):801-3. doi: 10.1038/457801a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212393" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blood Cells/*cytology ; Embryo, Mammalian/cytology/embryology ; Hemangioblasts/*cytology ; Hematopoietic Stem Cells/cytology ; Mice
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    Vision: New light on allergy receptor (2009)
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    Publication Date: 2009-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grant, Maria -- England -- Nature. 2009 Jul 9;460(7252):182-3. doi: 10.1038/460182a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587753" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chemokine CCL11/antagonists & inhibitors/metabolism ; Chemokine CCL24/antagonists & inhibitors/metabolism ; Chemokines, CC/antagonists & inhibitors/metabolism ; Choroid/blood supply/cytology/metabolism ; Choroidal Neovascularization/diagnosis/metabolism ; Humans ; Hypersensitivity/metabolism ; Inflammation ; Macular Degeneration/diagnosis/*metabolism/therapy ; Mice ; Receptors, CCR3/antagonists & inhibitors/immunology/*metabolism ; Vascular Endothelial Growth Factor A/antagonists & inhibitors/metabolism
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    Cheater-resistance is not futile (2009)
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    Publication Date: 2009-10-02
    Description: Cooperative social systems are susceptible to cheating by individuals that reap the benefits of cooperation without incurring the costs. There are various theoretical mechanisms for the repression of cheating and many have been tested experimentally. One possibility that has not been tested rigorously is the evolution of mutations that confer resistance to cheating. Here we show that the presence of a cheater in a population of randomly mutated social amoebae can select for cheater-resistance. Furthermore, we show that this cheater-resistance can be a noble strategy because the resister strain does not necessarily exploit other strains. Thus, the evolution of resisters may be instrumental in preserving cooperative behaviour in the face of cheating.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khare, Anupama -- Santorelli, Lorenzo A -- Strassmann, Joan E -- Queller, David C -- Kuspa, Adam -- Shaulsky, Gad -- England -- Nature. 2009 Oct 15;461(7266):980-2. doi: 10.1038/nature08472. Epub 2009 Sep 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794414" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cooperative Behavior ; Dictyostelium/genetics/*physiology ; Evolution, Molecular ; Genes, Protozoan/genetics ; *Models, Biological ; Mutation/genetics ; Protozoan Proteins/genetics/metabolism ; *Social Behavior ; Spores, Protozoan/physiology
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    Recall of learned information may rely on taking drug again (2009)
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    Publication Date: 2009-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Young, Alice M -- Colpaert, Francis C -- England -- Nature. 2009 Jan 29;457(7229):533. doi: 10.1038/457533a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19177109" target="_blank"〉PubMed〈/a〉
    Keywords: Amphetamines/*administration & dosage/adverse effects/*pharmacology ; Animals ; *Biomedical Enhancement ; Cognition/*drug effects/physiology ; *Health ; Humans ; Mental Recall/*drug effects/*physiology
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    Sex determination: Birds do it with a Z gene (2009)
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    Publication Date: 2009-09-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Graves, Jennifer A Marshall -- England -- Nature. 2009 Sep 10;461(7261):177-8. doi: 10.1038/461177a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741690" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chick Embryo ; Chickens/*genetics/*physiology ; Disorders of Sex Development ; Evolution, Molecular ; Female ; Gene Dosage/genetics ; Humans ; Male ; Models, Genetic ; Ovary/embryology/metabolism ; RNA Interference ; SOX9 Transcription Factor/genetics/metabolism ; Sex Chromosomes/*genetics ; *Sex Determination Processes ; Testis/embryology/metabolism ; Transcription Factors/deficiency/*genetics/*metabolism
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    Being human: love: neuroscience reveals all (2009)
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    Publication Date: 2009-01-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Young, Larry J -- England -- Nature. 2009 Jan 8;457(7226):148. doi: 10.1038/457148a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30322, USA. lyoun03@emory.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19129828" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arvicolinae/genetics/physiology ; Dopamine/metabolism ; Female ; Humans ; *Love ; Male ; Maternal Behavior/physiology ; Oxytocin/*metabolism ; Pair Bond ; Paternal Behavior ; Receptors, Vasopressin/genetics/metabolism ; Sexual Behavior/drug effects/physiology ; Vasopressins/*metabolism
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    Journal club. A molecular cardiologist looks into getting to the heart of his inner fish (2009)
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    Publication Date: 2009-08-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riley, Paul -- England -- Nature. 2009 Aug 27;460(7259):1061. doi: 10.1038/4601061e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University College London.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19713895" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cardiovascular Diseases/therapy ; Fishes/*physiology ; Mice ; Myocardium/*cytology ; Neuregulin-1/*pharmacology ; Regeneration/*drug effects ; Salamandridae/physiology
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    JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin (2009)
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    Publication Date: 2009-09-29
    Description: Activation of Janus kinase 2 (JAK2) by chromosomal translocations or point mutations is a frequent event in haematological malignancies. JAK2 is a non-receptor tyrosine kinase that regulates several cellular processes by inducing cytoplasmic signalling cascades. Here we show that human JAK2 is present in the nucleus of haematopoietic cells and directly phosphorylates Tyr 41 (Y41) on histone H3. Heterochromatin protein 1alpha (HP1alpha), but not HP1beta, specifically binds to this region of H3 through its chromo-shadow domain. Phosphorylation of H3Y41 by JAK2 prevents this binding. Inhibition of JAK2 activity in human leukaemic cells decreases both the expression of the haematopoietic oncogene lmo2 and the phosphorylation of H3Y41 at its promoter, while simultaneously increasing the binding of HP1alpha at the same site. Tauhese results identify a previously unrecognized nuclear role for JAK2 in the phosphorylation of H3Y41 and reveal a direct mechanistic link between two genes, jak2 and lmo2, involved in normal haematopoiesis and leukaemia.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785147/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785147/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dawson, Mark A -- Bannister, Andrew J -- Gottgens, Berthold -- Foster, Samuel D -- Bartke, Till -- Green, Anthony R -- Kouzarides, Tony -- 089957/Wellcome Trust/United Kingdom -- 12765/Cancer Research UK/United Kingdom -- G0800784/Medical Research Council/United Kingdom -- MC_UP_1102/2/Medical Research Council/United Kingdom -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2009 Oct 8;461(7265):819-22. doi: 10.1038/nature08448. Epub 2009 Sep 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19783980" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Animals ; Binding Sites ; Cell Line ; Cell Nucleus/enzymology ; Chromatin/chemistry/*metabolism ; Chromosomal Proteins, Non-Histone/*metabolism ; DNA-Binding Proteins/genetics ; Gene Expression Regulation, Neoplastic ; Hematopoiesis/genetics ; Hematopoietic Stem Cells/cytology/enzymology ; Histones/chemistry/genetics/*metabolism ; Humans ; Janus Kinase 2/antagonists & inhibitors/*metabolism ; LIM Domain Proteins ; Leukemia/enzymology/genetics/metabolism/pathology ; Metalloproteins/genetics ; Mice ; Oncogenes/genetics ; Phosphorylation ; Promoter Regions, Genetic/genetics ; Protein Binding ; Proto-Oncogene Proteins ; Signal Transduction ; Tyrosine/metabolism
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    Biomaterials (2009)
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    Publication Date: 2009-11-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Daw, Rosamund -- Tonzani, Stefano -- England -- Nature. 2009 Nov 26;462(7272):425. doi: 10.1038/462425a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940911" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biocompatible Materials/chemistry/metabolism/therapeutic use ; *Biomedical Research/trends ; Humans
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Fgf8 morphogen gradient forms by a source-sink mechanism with freely diffusing molecules (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-09-11
    Description: It is widely accepted that tissue differentiation and morphogenesis in multicellular organisms are regulated by tightly controlled concentration gradients of morphogens. How exactly these gradients are formed, however, remains unclear. Here we show that Fgf8 morphogen gradients in living zebrafish embryos are established and maintained by two essential factors: fast, free diffusion of single molecules away from the source through extracellular space, and a sink function of the receiving cells, regulated by receptor-mediated endocytosis. Evidence is provided by directly examining single molecules of Fgf8 in living tissue by fluorescence correlation spectroscopy, quantifying their local mobility and concentration with high precision. By changing the degree of uptake of Fgf8 into its target cells, we are able to alter the shape of the Fgf8 gradient. Our results demonstrate that a freely diffusing morphogen can set up concentration gradients in a complex multicellular tissue by a simple source-sink mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Shuizi Rachel -- Burkhardt, Markus -- Nowak, Matthias -- Ries, Jonas -- Petrasek, Zdenek -- Scholpp, Steffen -- Schwille, Petra -- Brand, Michael -- England -- Nature. 2009 Sep 24;461(7263):533-6. doi: 10.1038/nature08391. Epub 2009 Sep 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Developmental Genetics, Biotechnology Center, TUD, Tatzberg 47-49, 01307 Dresden, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741606" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Diffusion ; Embryo, Nonmammalian/*cytology/embryology/*metabolism ; *Endocytosis ; Extracellular Space/metabolism ; Fibroblast Growth Factors/genetics/*metabolism ; Gastrulation ; Green Fluorescent Proteins/genetics/metabolism ; Models, Biological ; Morphogenesis/*physiology ; Receptors, Fibroblast Growth Factor/metabolism ; Zebrafish/*embryology/*metabolism ; Zebrafish Proteins/genetics/*metabolism
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    Role of Jhdm2a in regulating metabolic gene expression and obesity resistance (2009)
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    Publication Date: 2009-02-06
    Description: Recent studies indicate that the methylation state of histones can be dynamically regulated by histone methyltransferases and demethylases. The H3K9-specific demethylase Jhdm2a (also known as Jmjd1a and Kdm3a) has an important role in nuclear hormone receptor-mediated gene activation and male germ cell development. Through disruption of the Jhdm2a gene in mice, here we demonstrate that Jhdm2a is critically important in regulating the expression of metabolic genes. The loss of Jhdm2a function results in obesity and hyperlipidemia in mice. We provide evidence that the loss of Jhdm2a function disrupts beta-adrenergic-stimulated glycerol release and oxygen consumption in brown fat, and decreases fat oxidation and glycerol release in skeletal muscles. We show that Jhdm2a expression is induced by beta-adrenergic stimulation, and that Jhdm2a directly regulates peroxisome proliferator-activated receptor alpha (Ppara) and Ucp1 expression. Furthermore, we demonstrate that beta-adrenergic activation-induced binding of Jhdm2a to the PPAR responsive element (PPRE) of the Ucp1 gene not only decreases levels of H3K9me2 (dimethylation of lysine 9 of histone H3) at the PPRE, but also facilitates the recruitment of Ppargamma and Rxralpha and their co-activators Pgc1alpha (also known as Ppargc1a), CBP/p300 (Crebbp) and Src1 (Ncoa1) to the PPRE. Our studies thus demonstrate an essential role for Jhdm2a in regulating metabolic gene expression and normal weight control in mice.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085783/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085783/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tateishi, Keisuke -- Okada, Yuki -- Kallin, Eric M -- Zhang, Yi -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Apr 9;458(7239):757-61. doi: 10.1038/nature07777. Epub 2009 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194461" target="_blank"〉PubMed〈/a〉
    Keywords: Adipose Tissue, Brown/metabolism ; Animals ; Cells, Cultured ; Energy Metabolism/*physiology ; Gene Expression Profiling ; *Gene Expression Regulation ; Glycerol/metabolism ; Ion Channels/metabolism ; Jumonji Domain-Containing Histone Demethylases ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondrial Proteins/metabolism ; Muscle, Skeletal/metabolism ; Obesity/*metabolism ; Oxidation-Reduction ; Oxidoreductases, N-Demethylating/*genetics/*metabolism ; Phenotype ; Receptors, Adrenergic, beta/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Animal-health facility in Germany leads the way for Europe (2009)
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    Publication Date: 2009-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mettenleiter, Thomas C -- England -- Nature. 2009 Apr 2;458(7238):571. doi: 10.1038/458571d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19340058" target="_blank"〉PubMed〈/a〉
    Keywords: *Academies and Institutes/standards ; Animal Welfare/standards ; Animals ; *Animals, Laboratory ; Biomedical Research ; Germany ; Housing, Animal/*standards/*trends
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    Formyl peptide receptor-like proteins are a novel family of vomeronasal chemosensors (2009)
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    Publication Date: 2009-04-24
    Description: Mammals rely heavily on olfaction to interact adequately with each other and with their environment. They make use of seven-transmembrane G-protein-coupled receptors to identify odorants and pheromones. These receptors are present on dendrites of olfactory sensory neurons located in the main olfactory or vomeronasal sensory epithelia, and pertain to the odorant, trace amine-associated receptor and vomeronasal type 1 (ref. 4) or 2 (refs 5-7) receptor superfamilies. Whether these four sensor classes represent the complete olfactory molecular repertoire used by mammals to make sense of the outside world is unknown. Here we report the expression of formyl peptide receptor-related genes by vomeronasal sensory neurons, in multiple mammalian species. Similar to the four known olfactory receptor gene classes, these genes encode seven-transmembrane proteins, and are characterized by monogenic transcription and a punctate expression pattern in the sensory neuroepithelium. In vitro expression of mouse formyl peptide receptor-like 1, 3, 4, 6 and 7 provides sensitivity to disease/inflammation-related ligands. Establishing an in situ approach that combines whole-mount vomeronasal preparations with dendritic calcium imaging in the intact neuroepithelium, we show neuronal responses to the same molecules, which therefore represent a new class of vomeronasal agonists. Taken together, these results suggest that formyl peptide receptor-like proteins have an olfactory function associated with the identification of pathogens, or of pathogenic states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riviere, Stephane -- Challet, Ludivine -- Fluegge, Daniela -- Spehr, Marc -- Rodriguez, Ivan -- England -- Nature. 2009 May 28;459(7246):574-7. doi: 10.1038/nature08029.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology and Animal Biology, and National Center of Competence Frontiers in Genetics, University of Geneva, 1205 Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19387439" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium Signaling ; Cell Line ; Dendrites/drug effects/metabolism ; *Disease ; Gene Expression Profiling ; Humans ; Inflammation/pathology ; Ligands ; Mice ; Olfactory Perception/drug effects/*physiology ; Olfactory Receptor Neurons/cytology/drug effects/*metabolism ; Organ Specificity ; Receptors, Formyl Peptide/genetics/*metabolism ; Smell/drug effects/*physiology ; Vomeronasal Organ/*cytology/drug effects/physiology
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    Behaviour: Flies on film (2009)
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    Publication Date: 2009-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buchen, Lizzie -- England -- Nature. 2009 Dec 3;462(7273):562-4. doi: 10.1038/462562a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19956235" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Behavior/physiology ; *Behavior, Animal ; Behavioral Research/*instrumentation/methods ; Drosophila melanogaster/*physiology ; Female ; Humans ; Male ; Software ; Video Recording/instrumentation/methods
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    VEGFR1-activity-independent metastasis formation (2009)
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    Publication Date: 2009-09-18
    Description: Molecules such as vascular endothelial growth factor (VEGF) or placental growth factor-critical regulators of tumour angiogenesis-are also thought to mobilize into blood circulation bone marrow-derived cells (BMDCs), which may subsequently be recruited to tumours and facilitate tumour growth and metastasis. A study has suggested that BMDCs form 'metastatic niches' in lungs before arrival of cancer cells, and showed that pharmacological inhibition of VEGF receptor 1 (VEGFR1, also known as Flt1)-cognate receptor for VEGF and placental growth factor-prevented BMDC infiltration in lungs and 'metastatic niche' formation. Here we report that blockade of VEGFR1 activity does not affect the rate of spontaneous metastasis formation in a clinically relevant and widely used preclinical model. Therefore, alternative pathways probably mediate the priming of tissues for metastasis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065241/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065241/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dawson, Michelle R -- Duda, Dan G -- Fukumura, Dai -- Jain, Rakesh K -- P01 CA080124/CA/NCI NIH HHS/ -- P01 CA080124-05/CA/NCI NIH HHS/ -- P01 CA080124-06A2/CA/NCI NIH HHS/ -- P01 CA080124-07/CA/NCI NIH HHS/ -- P01 CA080124-08/CA/NCI NIH HHS/ -- P01 CA080124-09/CA/NCI NIH HHS/ -- R01 CA085140/CA/NCI NIH HHS/ -- R01 CA085140-06/CA/NCI NIH HHS/ -- R01 CA085140-07/CA/NCI NIH HHS/ -- R01 CA085140-08/CA/NCI NIH HHS/ -- R01 CA085140-09/CA/NCI NIH HHS/ -- R01 CA096915/CA/NCI NIH HHS/ -- R01 CA096915-04/CA/NCI NIH HHS/ -- R01 CA096915-05/CA/NCI NIH HHS/ -- R01 CA096915-06A1/CA/NCI NIH HHS/ -- R01 CA096915-07/CA/NCI NIH HHS/ -- R01 CA096915-08/CA/NCI NIH HHS/ -- R01 CA115767/CA/NCI NIH HHS/ -- R01 CA115767-01A1/CA/NCI NIH HHS/ -- R01 CA115767-02/CA/NCI NIH HHS/ -- R01 CA115767-03/CA/NCI NIH HHS/ -- R01 CA115767-04/CA/NCI NIH HHS/ -- R01 CA126642/CA/NCI NIH HHS/ -- R01 CA126642-01A1/CA/NCI NIH HHS/ -- R01 CA126642-02/CA/NCI NIH HHS/ -- R24 CA085140/CA/NCI NIH HHS/ -- R24 CA085140-05/CA/NCI NIH HHS/ -- T32 CA073479/CA/NCI NIH HHS/ -- T32 CA073479-08/CA/NCI NIH HHS/ -- T32 CA073479-09/CA/NCI NIH HHS/ -- T32 CA073479-10/CA/NCI NIH HHS/ -- T32 CA073479-11/CA/NCI NIH HHS/ -- T32 CA073479-12/CA/NCI NIH HHS/ -- England -- Nature. 2009 Sep 17;461(7262):E4; discussion E5. doi: 10.1038/nature08254.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Steele Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759568" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bone Marrow Cells/cytology ; Cell Movement ; Lung/pathology ; Lung Neoplasms/*secondary ; Mice ; Mice, Inbred C57BL ; Neoplasm Transplantation ; Neoplasms/*pathology ; Vascular Endothelial Growth Factor Receptor-1/*antagonists & ; inhibitors/deficiency/*metabolism
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    Direct reprogramming of human neural stem cells by OCT4 (2009)
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    Publication Date: 2009-09-01
    Description: Induced pluripotent stem (iPS) cells have been generated from mouse and human somatic cells by ectopic expression of four transcription factors (OCT4 (also called POU5F1), SOX2, c-Myc and KLF4). We previously reported that Oct4 alone is sufficient to reprogram directly adult mouse neural stem cells to iPS cells. Here we report the generation of one-factor human iPS cells from human fetal neural stem cells (one-factor (1F) human NiPS cells) by ectopic expression of OCT4 alone. One-factor human NiPS cells resemble human embryonic stem cells in global gene expression profiles, epigenetic status, as well as pluripotency in vitro and in vivo. These findings demonstrate that the transcription factor OCT4 is sufficient to reprogram human neural stem cells to pluripotency. One-factor iPS cell generation will advance the field further towards understanding reprogramming and generating patient-specific pluripotent stem cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Jeong Beom -- Greber, Boris -- Arauzo-Bravo, Marcos J -- Meyer, Johann -- Park, Kook In -- Zaehres, Holm -- Scholer, Hans R -- England -- Nature. 2009 Oct 1;461(7264):649-3. doi: 10.1038/nature08436.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Rontgenstrasse 20, 48149 Munster, NRW, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19718018" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomarkers/analysis ; *Cell Dedifferentiation ; Cell Differentiation ; Cell Line ; *Cellular Reprogramming ; DNA Methylation ; Embryonic Stem Cells/cytology/metabolism ; Epigenesis, Genetic ; Fetus/*cytology ; Gene Expression Profiling ; Germ Layers/cytology/metabolism ; Humans ; Mice ; Neurons/*cytology/metabolism ; Octamer Transcription Factor-3/genetics/*metabolism ; Pluripotent Stem Cells/*cytology/*metabolism
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    Specific synapses develop preferentially among sister excitatory neurons in the neocortex (2009)
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    Publication Date: 2009-02-11
    Description: Neurons in the mammalian neocortex are organized into functional columns. Within a column, highly specific synaptic connections are formed to ensure that similar physiological properties are shared by neuron ensembles spanning from the pia to the white matter. Recent studies indicate that synaptic connectivity in the neocortex is sparse and highly specific to allow even adjacent neurons to convey information independently. How this fine-scale microcircuit is constructed to create a functional columnar architecture at the level of individual neurons largely remains a mystery. Here we investigate whether radial clones of excitatory neurons arising from the same mother cell in the developing neocortex serve as a substrate for the formation of this highly specific microcircuit. We labelled ontogenetic radial clones of excitatory neurons in the mouse neocortex by in utero intraventricular injection of enhanced green fluorescent protein (EGFP)-expressing retroviruses around the onset of the peak phase of neocortical neurogenesis. Multiple-electrode whole-cell recordings were performed to probe synapse formation among these EGFP-labelled sister excitatory neurons in radial clones and the adjacent non-siblings during postnatal stages. We found that radially aligned sister excitatory neurons have a propensity for developing unidirectional chemical synapses with each other rather than with neighbouring non-siblings. Moreover, these synaptic connections display the same interlaminar directional preference as those observed in the mature neocortex. These results indicate that specific microcircuits develop preferentially within ontogenetic radial clones of excitatory neurons in the developing neocortex and contribute to the emergence of functional columnar microarchitectures in the mature neocortex.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727717/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727717/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Yong-Chun -- Bultje, Ronald S -- Wang, Xiaoqun -- Shi, Song-Hai -- AS5274/Autism Speaks/ -- R01 DA024681/DA/NIDA NIH HHS/ -- R01 DA024681-01A1/DA/NIDA NIH HHS/ -- R21 MH083624/MH/NIMH NIH HHS/ -- R21 MH083624-01/MH/NIMH NIH HHS/ -- England -- Nature. 2009 Mar 26;458(7237):501-4. doi: 10.1038/nature07722. Epub 2009 Feb 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Developmental Biology Program, Memorial Sloan Kettering Cancer Centre, 1275 York Avenue, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19204731" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Lineage ; Clone Cells/cytology ; Mice ; Neocortex/anatomy & histology/*cytology ; Neurons/*cytology/*metabolism ; Synapses/*metabolism
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    Cytoplasmic functions of the tumour suppressor p53 (2009)
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    Publication Date: 2009-05-02
    Description: The principal tumour-suppressor protein, p53, accumulates in cells in response to DNA damage, oncogene activation and other stresses. It acts as a nuclear transcription factor that transactivates genes involved in apoptosis, cell cycle regulation and numerous other processes. An emerging area of research unravels additional activities of p53 in the cytoplasm, where it triggers apoptosis and inhibits autophagy. These previously unknown functions contribute to the mission of p53 as a tumour suppressor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814168/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814168/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Douglas R -- Kroemer, Guido -- P01 CA069381/CA/NCI NIH HHS/ -- P01 CA069381-140010/CA/NCI NIH HHS/ -- R01 AI040646/AI/NIAID NIH HHS/ -- R01 AI040646-14/AI/NIAID NIH HHS/ -- R01 AI044828/AI/NIAID NIH HHS/ -- R01 AI044828-12/AI/NIAID NIH HHS/ -- R01 AI047891/AI/NIAID NIH HHS/ -- R01 AI047891-11/AI/NIAID NIH HHS/ -- R37 GM052735/GM/NIGMS NIH HHS/ -- R37 GM052735-19/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Apr 30;458(7242):1127-30. doi: 10.1038/nature07986.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA. douglas.green@stjude.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19407794" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Autophagy ; Cell Nucleus/metabolism ; Cytoplasm/*metabolism ; Humans ; Mitochondria/metabolism ; Neoplasms/metabolism/pathology ; Transcription, Genetic ; Tumor Suppressor Protein p53/genetics/*metabolism
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