ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Springer  (1,025,393)
  • Cell Press  (101,524)
  • National Academy of Sciences  (67,169)
  • Essen : Verl. Glückauf
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • 2015-2019  (578,295)
  • 2005-2009  (274,024)
  • 1990-1994  (341,771)
Collection
Publisher
Language
Years
Year
  • 1
    Publication Date: 2020-10-22
    Description: The storage concession "Minerbio Stoccaggio" (Bologna, Northern Italy) covers a 69 km 2 area, 65% of hich is located in the Minerbio municipality. Since 1979, a microseismic network for the monitoring of seismicity, eventually induced by gas storage activities, has been installed in this area. The network was operated by Stogit S.p.A, a subsidiary company of Snam, which is the largest storage operator in Italy. In 2016, the microseismic network, consisting of three surface stations and one 100-m-deep borehole sensor with minimum interstation distances of about 3.0 km, was integrated with 12 regional stations installed in an 80 × 80 km 2 area centered on the surface projection of the reservoir. In 2018, the microseismic network was enhanced by adding one surface and three 150-m-deep borehole stations. In this work, we evaluate the detection improvement of the microseismic network, integrated with the regional stations. We define two crustal volumes for earthquake detection: the inner domain of detection, IDD (10 × 10 × 5) km 3 , within which we should ensure the highest network performance, and the extended domain of detection, EDD (22 × 22 × 11) km 3 . By comparing the simulated power spectral density of hypothetical seismic sources located in EDD with the average power spectra of ambient seismic noise observed at each station site, we calculate detection and localization thresholds for the two above-mentioned networks. Under unfavourable noise conditions, we find that the present operative seismic network allows locating earthquakes with M L ≥ 0.8 occurring at the depth of the reservoir and with M L ≥ 1.0 if located within IDD.
    Description: Funding information This study received financial support from BComune di Minerbio^ under the grant BSperimentazione ILG Minerbio^ (grant number 0913.010)
    Description: Published
    Description: 967–977
    Description: 3SR TERREMOTI - Attività dei Centri
    Description: JCR Journal
    Keywords: Induced seismicity ; Earthquake detection ; Ambient seismic noise ; Microseismic monitoring ; MiSE ; oilfield monitoring guidelines
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 2
    Publication Date: 2020-09-07
    Description: This paper presents an original multidisciplinary (geological-structural-geomorphological and seismological) study aimed at investigating the origin of diffused seismic damages affecting several ancient buildings in the Roman port city of Ostia. We also evaluate the possibility to relate these damages to a previously hypothesized ENE-WSW trending fault, bordering the morphological height upon which the Ostia town was founded. Aimed at this scope, we performed seismic noise measures (by using 14 seismic stations) that show no significantly different response and lack of significant ground motion differential amplifications. The coexistence of (i) no local geological heterogeneities and (ii) low amplification of spectral ratios in the recorded seismic signals seems to exclude that the observed seismic damage may be the consequence of significant site effects. When also the large distance from the strongest Apennine’s seismogenic source areas is considered, the possibility that the observed damage may be the consequence of local events should be considered. We discuss the potentiality of the ENE-WSW trending fault as the source of the observed seismic damages, highlighting the supporting evidence as well as the uncertainties of such interpretation.
    Description: Published
    Description: 833–851
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 3
    Publication Date: 2020-09-07
    Description: This work describes the analysis of the strong-motion data from the Engineering Strong Motion database (ESM, http://esm.mi.ingv.it), aimed at: (1) extract a dataset of accelero- metric waveforms recorded during the 2016–2017 Central Italy seismic sequence; (2) iden- tify the recording stations to be used as reference sites for further seismological analysis; (3) select the records to be used as input for seismic microzonation of higher level at 137 municipalities. Firstly, a residual analysis is carried out on the extracted dataset to perform: (1) the quality check of the waveforms recorded by temporary networks installed soon after the occurrence of the rst main shock (M 6.0, 24 August 2016); (2) the estimation of the site-to-site residual term for each recording station with the aim of recognising potential reference rock sites. Finally, the software REXELite, integrated within the ESM website, is adopted to select suites of spectrum-compatible accelerograms, that will be used as input for calculating site ampli cations through 1D and 2D simulations at sites which suf- fered the greatest damage. The results of this work demonstrate the success of the synergy among Italian institutions. The setup of key infrastructures, such as emergency networks and data repositories, together with the knowledge developed during national projects, turned out to be successful in terms of timely intervention during the emergency phase and the planning of the post-emergency.
    Description: Published
    Description: 5533–5551
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 4
    Publication Date: 2019-04-10
    Description: Our knowledge on distribution, habitats and behavior of Southern Ocean fishes living at water depths beyond scuba-diving limits is still sparse, as it is difficult to obtain quantitative data on these aspects of their biology. Here, we report the results of an analysis of seabed images to investigate species composition, behavior, spatial distribution and preferred habitats of demersal fish assemblages in the southern Weddell Sea. Our study was based on a total of 2736 high-resolution images, covering a total seabed area of 11,317 m2, which were taken at 13 stations at water depths between 200 and 750 m. Fish were found in 380 images. A total of 379 notothenioid specimens were recorded, representing four families (Nototheniidae, Artedidraconidae, Bathydraconidae, Channichthyidae), 17 genera and 25 species. Nototheniidae was the most speciose fam- ily, including benthic species (Trematomus spp.) and the pelagic species Pleuragramma antarctica, which was occasionally recorded in dense shoals. Bathydraconids ranked second with six species, followed by artedidraconids and channichthyids, both with five species. Most abundant species were Trematomus scotti and T. lepidorhinus among nototheniids, and Dol- loidraco longedorsalis and Pagetopsis maculatus among artedidraconids and channichthyids, respectively. Both T. lepi- dorhinus and P. maculatus preferred seabed habitats characterized by biogenous debris and rich epibenthic fauna, whereas T. scotti and D. longedorsalis were frequently seen resting on fine sediments and scattered gravel. Several fish species were recorded to make use of the three-dimensional structure formed by epibenthic foundation species, like sponges, for perching or hiding inside. Nesting behavior was observed, frequently in association with dropstones, in species from various families, including Channichthyidae (Chaenodraco wilsoni and Pagetopsis macropterus) and Bathydraconidae (Cygnodraco mawsoni).
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 5
    facet.materialart.
    Unknown
    Springer
    In:  EPIC3The Ecosystem of Kongsfjorden, Svalbard, The Ecosystem of Kongsfjorden, Svalbard, Cham, Springer, 566 p., pp. 537-562, ISBN: 978-3-319-46425-1
    Publication Date: 2020-07-08
    Description: Due to its year-round accessibility and excellent on-site infrastructure, Kongsfjorden and the Ny-Ålesund Research and Monitoring Facility have become established as a primary location to study the impact of environmental change on Arctic coastal ecosystems. Due to its location right at the interface of Arctic and Atlantic oceanic regimes, Kongsfjorden already experiences large amplitudes of variability in physico/chemical conditions and might, thus, be considered as an early warning indicator of future changes, which can then be extrapolated in a pan-Arctic perspective. Already now, Kongsfjorden represents one of the best-studied Arctic fjord systems. However, research conducted to date has concentrated largely on small disciplinary projects, prompting the need for a higher level of integration of future research activities. This contribution, thus, aims at identifying gaps in knowledge and research priorities with respect to ecological and adaptive responses to Arctic ecosystem changes. By doing so we aim to provide a stimulus for the initiation of new international and interdisciplinary research initiatives.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 6
    Publication Date: 2019-11-26
    Description: Modern Society needs interactive public discussion to provide an effective way of focusing on hydrological hazards and their consequences. Embracing a holistic Earth system Science approach, we experiment since 2004 different stimulating educational/communicative model which emotionally involves the participants to raise awareness on the social dimension of the disaster hydrogeological risk reduction, pointing out that human behavior is the crucial factor in the degree of vulnerability and the likelihood of disasters taking place. The implementation of strategies for risk mitigation must include educational aspects, as well as economical and societal ones. Education is the bridge between knowledge and understanding and the key to raise risk perception. Children’s involvement might trigger a chain reaction that reinforce and spread the culture of risk. No matter how heavy was the rain that hit our land in the past and recent seasons, we still are not prepared. If on one hand we need to fight against worsening Global Warming that trigger extreme meteorological events, we should also work on sustainable land use and promote landscape preservation. Since science can work on improving knowledge of phenomena, technology can provide modern tool to reduce the impact of disasters, children and adults education is the flywheel to provide the change. We present here two cases selected among the wide range of educational activities that we have tested and to which more than 2,000 students and adults have participated within a period of 12 years. They include learn-by-playing, hands-on, emotional-learning activities, open questions seminars, learning paths, curiosity-driven approaches, special venues and science outreach.
    Description: Sendai Partnerships 2015-2025
    Description: Published
    Description: Ljubljana (Slovenia)
    Description: 2TM. Divulgazione Scientifica
    Keywords: Natural hazard ; Hydrogeological risk ; Prevention ; Participatory approach ; Awareness raising ; Resilience ; Hydrogeological Risk prevention
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Conference paper
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 7
    Publication Date: 2020-03-23
    Description: The systematic study of biological basis of behavior and of the process involved in economical choices has outlined a new paradigm of research: neuroeconomics. Now the intersection between neuroscience, psychology and economics, neuroeconomics presents itself as an alternative to the neoclassical vision on economics, according to which the homo oeconomicus acts within the bonds of a formalizing rationality tending to the maximization of the anticipated utility. Brain imagining methods have shown that the decision-making processes activate the frontal lobe and the limbic system above all, a big circonvolution running through the callous body on the medial surface of the hemispheres, extending itself down, responsible for the regulation of emotional phenomena. Reinforcing such a tendency, we find the injury paradigm. It was observed that frontal lobe injuries harm the capacity of making advantageous decisions either in one’s own behalf or in others, as well as decisions according to the social conventions. In this paper, we will try to show that if, by the one hand, the neuro visual methods have given us a great amount of data, on the other hand, using them uncritically, with the recurrent confusion between “correlation” and “causal relation”—contemporary microevents indicate only simple correlations, and no cause-effect relation—risks to stress the relevant explanatory gap regarding the abstract ideal of understanding the nature of the brain.
    Description: Published
    Description: 135-141
    Description: 2TM. Divulgazione Scientifica
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 8
    Publication Date: 2019-03-11
    Description: This paper investigates whether and how depressive disorders affect speech and in particular timing strategies for speech pauses (empty and filled pauses, as well as, phoneme lengthening). The investigation is made exploiting read and spontaneous narratives . The collected data are from 24 subjects, divided into two groups (depressed and control) asked to read a tale, as well as, spontaneously report on their daily activities. Ten different frequency and duration measures for pauses and clauses are proposed and have been collected using the PRAAT software on the speech recordings produced by the participants. A T-Student test for independent samples was applied on the collected frequency and duration measures in order to ascertain whether significant differences between healthy and depressed speech measures are observed. In the “spontaneous narrative” condition, depressed patients exhibited significant differences in: the average duration of their empty pauses, the average frequency, and the average duration of their clauses. In the read narratives, only the average pause’s frequency of the clauses was significantly lower in the depressed subjects with respect to the healthy ones. The results suggest that depressive disorders affect speech quality and speech production through pause and clause durations, as well as, clause quantities. In particular, the significant differences in clause quantities (observed both in the read and spontaneous narratives), suggest a strong general effect of depressive symptoms on cognitive and psychomotor functions. Depressive symptoms produce changes in the planned timing of pauses, even when reading, modifying the timing of pausing strategies.
    Description: Published
    Description: 73-82
    Description: 5TM. Informazione ed editoria
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 9
    Publication Date: 2019-04-01
    Description: t The role of riverine freshwater inflow on the Central Mediterranean Overturning Circulation (CMOC) was studied using a high-resolution ocean model with a complete distribution of rivers in the Adriatic and Ionian catchment areas. The impact of river runoff on the Adriatic and Ionian Sea basins was assessed by a twin experiment, with and without runoff, from 1999 to 2012. This study tries to show the connection between the Adriatic as a marginal sea containing the downwelling branch of the anti-estuarine CMOC and the large runoff occurring there. It is found that the multiannual CMOC is a persistent anti-estuarine structure with secondary estuarine cells that strengthen in years of large realistic river runoff. The CMOC is demonstrated to be controlled by wind forcing at least as much as by buoyancy fluxes. It is found that river runoff affects the CMOC strength, enhancing the amplitude of the secondary estuarine cells and reducing the intensity of the dominant anti-estuarine cell. A large river runoff can produce a positive buoyancy flux without switching off the antiestuarine CMOC cell, but a particularly low heat flux and wind work with normal river runoff can reverse it. Overall by comparing experiments with, without and with unrealistically augmented runoff we demonstrate that rivers affect the CMOC strength but they can never represent its dominant forcing mechanism and the potential role of river runoff has to be considered jointly with wind work and heat flux, as they largely contribute to the energy budget of the basin. Looking at the downwelling branch of the CMOC in the Adriatic basin, rivers are demonstrated to locally reduce the volume of Adriatic dense water formed in the Southern Adriatic Sea as a result of increased water stratification. The spreading of the Adriatic dense water into the Ionian abyss is affected as well: dense waters overflowing the Otranto Strait are less dense in a realistic runoff regime, with respect to no runoff experiment, and confined to a narrower band against the Italian shelf with less lateral spreading toward the Ionian Sea center. 1
    Description: Published
    Description: 1675-1703
    Description: 4A. Oceanografia e clima
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 10
    Publication Date: 2019-03-11
    Description: Humans have very high requirements and expectations when communicating through speech, other than simplicity, flexibility and easiness of interaction. This is because voice interactions do not require cognitive efforts, attention, and memory resources. Voice technologies are however still constrained to use cases and scenarios giving the existing limitations of speech synthesis and recognition systems. Which is the status of nonlinear speech processing techniques and the steps made for cross-fertilization among disciplines? This chapter will provide a short overview trying to answer the above question.
    Description: Published
    Description: 5-11
    Description: 5TM. Informazione ed editoria
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 11
    Publication Date: 2019-12-09
    Description: Since the past decade, geodetic techniques are widely used to gain important information for the monitoring and modeling of the deformation of the Earth at different length and time scales. Although the GNSS derived estimates of the Earth crust velocity are becoming more and more reliable, advanced data analysis techniques are needed to recognize geophysical features in the GNSS time-series, e.g., non linear behaviors, discontinuities in the signal and in its derivative, i.e., in the velocity. Unfortunately these phenomena are often hidden in the time-series noise and external information, as seismic events, are not always known. The main focus of this work is the detection of signal discontinuities in GNSS time-series through the use of advanced analysis techniques: the wavelets, the Bayesian and the variational methods. The Mumford and Shah (Commun Pure Appl Math 42:577–685, 1989) and the Blake and Zisserman (Visual reconstruction, 1987) variational models for signal segmentation can detect signal discontinuities in an explicitly way. The Blake and Zisserman (Visual reconstruction, 1987) model can also detect discontinuities of the signal first derivative, i.e., velocity abrupt changes can be detected. At first, to prove and assess the capability to detect discontinuities correctly, the methods have been applied to some Cascadia (North America) time-series, characterized by well known aseismic deformations. A second test area has been taken into account: the Calabrian Arc subduction zone, in southern Italy. The analyzed Italian GNSS time-series are characterized by very weak and noisy signals and the geodynamic of the area is mostly unknown. When present, discontinuities are expected to be very small and compatible with the signal noise. This motivates the use of advanced data analysis techniques to investigate the presence of discontinuities. At the moment, the analysis of the Italian time-series has revealed several discontinuities which nature cannot be labeled easily as geophysical or geodetic.
    Description: Published
    Description: 627-634
    Description: 2T. Deformazione crostale attiva
    Keywords: Subduction Zone ; Discontinuity point ; Slow slip event ; signal discontinuity ; Cascadia Subduciton zone
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 12
    Publication Date: 2019-12-02
    Description: Algorithms based on artificial intelligence (AI) have had a strong development in recent years in different research fields of earth science such as seismology and volcanology. In particular, they have been applied to the study of the volcanic eruptive products of the recent activity of Mount Etna volcano. This work presents an application of the self-organizing map (SOM) neural networks to perform a clustering analysis on petrographic patterns of rocks of Somma–Vesuvius and Campi Flegrei volcanoes, in the Neapolitan area. The goal is to highlight possible affinity between the magmatic reservoirs of these two volcanic complexes. The SOM is known for its ability to cluster data by using intrinsic similarity measures without any previous information about their distribution. Moreover, it allows an easy understandable data visualization by using a two-dimensional map. The SOM has been tested on a geochemical dataset of 271 samples, consisting of 134 samples of Campi Flegrei eruptions (named CF), 24 samples of Somma–Vesuvius effusive eruptions (VF), 73 samples of Somma–Vesuvius explosive eruptions (VX), and finally 40 samples of “foreign” eruptions (ET), included to verify the neural net classification capability. After a pre-processing phase, applied to have a more appropriate data representation as input for the SOM, each sample has been encoded through a vector of 23 features, containing information about major bulk components, trace elements, and Sr isotopic ratio. The resulting SOM identifies three main clusters, and in particular, the foreign patterns (ET) are well separated from the other ones being mainly grouped in a single node. In conclusion, the obtained results suggest the ability of SOM neural network to associate volcanic rock suites on the basis of their geochemical imprint and can be consistent with the hypothesis that there might be a common magma source beneath the whole Neapolitan area.
    Description: Published
    Description: 55-60
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 13
    Publication Date: 2020-03-23
    Description: This paper investigates the ability of adolescents (aged 13–15 years) and young adults (aged 20–26 years) to decode affective bursts culturally situated in a different context (Francophone vs. South Italian). The effects of context show that Italian subjects perform poorly with respect to the Francophone ones revealing a significant native speaker advantage in decoding the selected affective bursts. In addition, adolescents perform better than young adults, particularly in the decoding and intensity ratings of affective bursts of happiness, pain, and pleasure suggesting an effect of age related to language expertise.
    Description: Published
    Description: 1TM. Formazione
    Keywords: Affective bursts ; Age and cultural effects
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 14
    Publication Date: 2019-03-04
    Description: Many marine gastropods show species-specific behavioral responses to different predators, but less is known about the mechanisms influencing differences or similarities in specific responses. Herein, we examined whether two limpet species, Scurria viridula (Lamarck, 1819) and Fissurella latimarginata (Sowerby, 1835), show species- and size-specific similarities or differences in their reaction to predatory seastars and crabs. Both S. viridula and F. latimarginata reacted to their main seastar predators with escape responses. In contrast, both limpets did not flee from common crab predators, but, instead, fastened to the rock. All tested size classes of both limpet species reacted in a similar way, escaping from seastars, but clamping onto the rock in response to crabs. Limpets could reach velocities sufficient to outrun their specific seastar predators, but they were not fast enough to escape crabs. Experiments with limpets of different shell conditions (with and without shell damage) indicated that F. latimarginata with a damaged shell showed “accommodation movements” (slow movements away from stimulus) in response to predatory crabs. In contrast, intact F. latimarginata and all S. viridula (intact and damaged) clamped the shell down to the substratum. The response details suggest that the keyhole limpet F. latimarginata is more sensitive to predators (faster reaction time, longer escape distances, and higher proportion of reacting individuals) than S. viridula, possibly because the morphology of F. latimarginata (the relationship of its shell size and structure to its total body size) makes this species more vulnerable to predation. Our study suggests that chemically mediated effects of seastar and crab predators result in contrasting behavioral responses of both limpet species, independent of their habitat and morphology. Despite the different characteristics of the limpet species and the identity of predators, the limpets react in comparable ways to similar predator types.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 15
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 115(52), (2018): E12275-E12284. doi: 10.1073/pnas.1805243115.
    Description: Diatoms are prominent eukaryotic phytoplankton despite being limited by the micronutrient iron in vast expanses of the ocean. As iron inputs are often sporadic, diatoms have evolved mechanisms such as the ability to store iron that enable them to bloom when iron is resupplied and then persist when low iron levels are reinstated. Two iron storage mechanisms have been previously described: the protein ferritin and vacuolar storage. To investigate the ecological role of these mechanisms among diatoms, iron addition and removal incubations were conducted using natural phytoplankton communities from varying iron environments. We show that among the predominant diatoms, Pseudo-nitzschia were favored by iron removal and displayed unique ferritin expression consistent with a long-term storage function. Meanwhile, Chaetoceros and Thalassiosira gene expression aligned with vacuolar storage mechanisms. Pseudo-nitzschia also showed exceptionally high iron storage under steady-state high and low iron conditions, as well as following iron resupply to iron-limited cells. We propose that bloom-forming diatoms use different iron storage mechanisms and that ferritin utilization may provide an advantage in areas of prolonged iron limitation with pulsed iron inputs. As iron distributions and availability change, this speculated ferritin-linked advantage may result in shifts in diatom community composition that can alter marine ecosystems and biogeochemical cycles.
    Description: We thank the captain and crew of the R/V Melville and the CCGS J. P. Tully as well as the participants of the IRNBRU (MV1405) cruise for the California-based data, particularly K. Ellis [University of North Carolina (UNC)], T. Coale (University of California, San Diego), F. Kuzminov (Rutgers), H. McNair [University of California, Santa Barbara (UCSB)], and J. Jones (UCSB). W. Burns (UNC), S. Haines (UNC), and S. Bargu (Louisiana State University) assisted with sample processing and analysis. This work was funded by the National Science Foundation Grants OCE-1334935 (to A.M.), OCE-1334632 (to B.S.T.), OCE-1333929 (to K.T.), OCE-1334387 (to M.A.B.), OCE-1259776 (to K.W.B), and DGE-1650116 (Graduate Research Fellowship to R.H.L).
    Description: 2019-06-11
    Keywords: phytoplankton ; iron limitation ; Pseudo-nitzschia ; ferritin ; metatranscriptomics
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 16
    Publication Date: 2019-10-23
    Description: Knowledge on basic biological functions of organisms is essential to understand not only the role they play in the ecosystems but also to manage and protect their populations. The study of biological processes, such as growth, reproduction and physiology, which can be approached in situ or by collecting specimens and rearing them in aquaria, is particularly challenging for deep-sea organisms like cold-water corals. Field experimental work and monitoring of deep-sea populations is still a chimera. Only a handful of research institutes or companies has been able to install in situ marine observatories in the Mediterranean Sea or elsewhere, which facilitate a continuous monitoring of deep-sea ecosystems. Hence, today’s best way to obtain basic biological information on these organisms is (1) working with collected samples and analysing them post-mortem and / or (2) cultivating corals in aquaria in order to monitor biological processes and investigate coral behaviour and physiological responses under different experimental treatments. The first challenging aspect is the collection process, which implies the use of oceanographic research vessels in most occasions since these organisms inhabit areas between ca. 150 m to more than 1000 m depth, and specific sampling gears. The next challenge is the maintenance of the animals on board (in situations where cruises may take weeks) and their transport to home laboratories. Maintenance in the home laboratories is also extremely challenging since special conditions and set-ups are needed to conduct experimental studies to obtain information on the biological processes of these animals. The complexity of the natural environment from which the corals were collected cannot be exactly replicated within the laboratory setting; a fact which has led some researchers to question the validity of work and conclusions drawn from such undertakings. It is evident that aquaria experiments cannot perfectly reflect the real environmental and trophic conditions where these organisms occur, but: (1) in most cases we do not have the possibility to obtain equivalent in situ information and (2) even with limitations, they produce relevant information about the biological limits of the species, which is especially valuable when considering potential future climate change scenarios. This chapter includes many contributions from different authors and is envisioned as both to be a practical “handbook” for conducting cold-water coral aquaria work, whilst at the same time offering an overview on the cold-water coral research conducted in Mediterranean laboratories equipped with aquaria infrastructure. Experiences from Atlantic and Pacific laboratories with extensive experience with cold-water coral work have also contributed to this chapter, as their procedures are valuable to any researcher interested in conducting experimental work with cold-water corals in aquaria. It was impossible to include contributions from all laboratories in the world currently working experimentally with cold-water corals in the laboratory, but at the conclusion of the chapter we attempt, to our best of our knowledge, to supply a list of several laboratories with operational cold-water coral aquaria facilities.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 17
    facet.materialart.
    Unknown
    Springer
    In:  EPIC3Energy Transfers in Atmosphere and Ocean, Energy Transfers in Atmosphere and Ocean, Springer, 1, pp. 87-125, ISBN: 978-3-030-05704-6, ISSN: 2524-4264
    Publication Date: 2020-04-20
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 18
    Publication Date: 2023-11-16
    Description: The paper presents the results of 5 case studies on complex site e ects selected within the project for the level 3 seismic microzonation of several municipalities of Central Italy dam- aged by the 2016 seismic sequence. The case studies are characterized by di erent geo- logical and morphological con gurations: Monte San Martino is located along a hill slope, Montedinove and Arquata del Tronto villages are located at ridge top whereas Capitignano and Norcia lie in correspondence of sediment- lled valleys. Peculiarities of the sites are constituted by the presence of weathered/jointed rock mass, fault zone, shear wave veloc- ity inversion, complex surface and buried morphologies. These factors make the de ni- tion of the subsoil model and the evaluation of the local response particularly complex and di cult to ascertain. For each site, after the discussion of the subsoil model, the results of site response numerical analyses are presented in terms of ampli cation factors and acceleration response spectra in selected points. The physical phenomena governing the site response have also been investigated at each site by comparing 1D and 2D numerical analyses. Implications are deduced for seismic microzonation studies in similar geological and morphological conditions.
    Description: Published
    Description: 5741–5777
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Seismic microzonation ; Ampli cation factors ; Response spectra ; Numerical analyses ; site response
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 19
    Publication Date: 2023-11-21
    Description: This paper describes the seismological analyses performed within the framework of the seismic microzonation study for the reconstruction of 138 municipalities damaged by the 2016–2017 sequence in Central Italy. Many waveforms were recorded over approximately 15 years at approximately 180 instrumented sites equipped with permanent or temporary stations in an area that includes all the damaged localities. Site response was assessed using earthquake and noise recordings at the selected stations through different parameters, such as spectral amplification curves, fundamental resonance frequencies, site-specific response spectra, and average amplification factors. The present study was a collaboration of many different institutions under the coordination of the Italian Center for Seismic Microzonation and its applications. The results were homogenized and gathered into site-specific forms, which represent the main deliverable for the benefit of Italian Civil Protection. It is remarkable that the bulk of this study was performed in a very short period (approximately 2 months) to provide quantitative information for detailed microzonation and future reconstruction of the damaged municipalities.
    Description: Published
    Description: 5553–5593
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 20
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17666-17672. doi:10.1073/pnas.1907871116.
    Description: The conditions of methane (CH4) formation in olivine-hosted secondary fluid inclusions and their prevalence in peridotite and gabbroic rocks from a wide range of geological settings were assessed using confocal Raman spectroscopy, optical and scanning electron microscopy, electron microprobe analysis, and thermodynamic modeling. Detailed examination of 160 samples from ultraslow- to fast-spreading midocean ridges, subduction zones, and ophiolites revealed that hydrogen (H2) and CH4 formation linked to serpentinization within olivine-hosted secondary fluid inclusions is a widespread process. Fluid inclusion contents are dominated by serpentine, brucite, and magnetite, as well as CH4(g) and H2(g) in varying proportions, consistent with serpentinization under strongly reducing, closed-system conditions. Thermodynamic constraints indicate that aqueous fluids entering the upper mantle or lower oceanic crust are trapped in olivine as secondary fluid inclusions at temperatures higher than ∼400 °C. When temperatures decrease below ∼340 °C, serpentinization of olivine lining the walls of the fluid inclusions leads to a near-quantitative consumption of trapped liquid H2O. The generation of molecular H2 through precipitation of Fe(III)-rich daughter minerals results in conditions that are conducive to the reduction of inorganic carbon and the formation of CH4. Once formed, CH4(g) and H2(g) can be stored over geological timescales until extracted by dissolution or fracturing of the olivine host. Fluid inclusions represent a widespread and significant source of abiotic CH4 and H2 in submarine and subaerial vent systems on Earth, and possibly elsewhere in the solar system.
    Description: We are indebted to J. Eckert for his support with FE-EMPA; to K. Aquinho and E. Codillo for providing samples from Zambales; to K. Aquinho for Raman analysis of some of the samples from Zambales and Mt. Dent; to H. Dick for providing access to his thin section collection; to the curators of the IODP core repositories for providing access to Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) samples; and to the captains and crews of the many cruises without whom the collection of these samples would not have been possible. Reviews by Peter Kelemen and an anonymous referee greatly improved this manuscript. This study is supported with funds provided by the National Science Foundation (NSF-OCE Award 1634032 to F.K. and J.S.S.).
    Description: 2020-02-19
    Keywords: Abiotic methane ; Fluid inclusions ; Serpentinization ; Methane seeps ; Carbon cycling
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 21
    Publication Date: 2022-10-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 116(20), (2019):9925-9930, doi:10.1073/pnas.1818349116.
    Description: Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (〉30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.
    Description: We thank John Baross and Rika Anderson for helpful discussions and feedback on this project. We also thank the chief scientists of the research cruise, Al Devol and Bess Ward, as well as the captain and crew of the R/V Thomas G. Thompson. This work was supported through a NASA Earth and Space Sciences Graduate Research Fellowship to J.K.S. and National Science Foundation Grant OCE-1138368 (to G.R.).
    Description: 2019-10-29
    Keywords: Oxygen deficient zones ; Arsenic ; Chemoautotrophy ; Dissimilatory arsenate reduction ; Marine metagenome
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 22
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (24), (2019):11646-11651, doi:10.1073/pnas.1900371116.
    Description: Measurements show large decadal variability in the rate of CO2 accumulation in the atmosphere that is not driven by CO2 emissions. The decade of the 1990s experienced enhanced carbon accumulation in the atmosphere relative to emissions, while in the 2000s, the atmospheric growth rate slowed, even though emissions grew rapidly. These variations are driven by natural sources and sinks of CO2 due to the ocean and the terrestrial biosphere. In this study, we compare three independent methods for estimating oceanic CO2 uptake and find that the ocean carbon sink could be responsible for up to 40% of the observed decadal variability in atmospheric CO2 accumulation. Data-based estimates of the ocean carbon sink from pCO2 mapping methods and decadal ocean inverse models generally agree on the magnitude and sign of decadal variability in the ocean CO2 sink at both global and regional scales. Simulations with ocean biogeochemical models confirm that climate variability drove the observed decadal trends in ocean CO2 uptake, but also demonstrate that the sensitivity of ocean CO2 uptake to climate variability may be too weak in models. Furthermore, all estimates point toward coherent decadal variability in the oceanic and terrestrial CO2 sinks, and this variability is not well-matched by current global vegetation models. Reconciling these differences will help to constrain the sensitivity of oceanic and terrestrial CO2 uptake to climate variability and lead to improved climate projections and decadal climate predictions.
    Description: We thank Rebecca Wright and Erik Buitenhuis at University of East Anglia, Norwich, for providing updated runs from the NEMO-PlankTOM5 model. T.D. was supported by NSF Grant OCE-1658392. C.L.Q. thanks the UK Natural Environment Research Council for supporting the SONATA Project (Grant NE/P021417/1). P.L. was supported by the Max Planck Society for the Advancement of Science. J.H. was supported under Helmholtz Young Investigator Group Marine Carbon and Ecosystem Feedbacks in the Earth System (MarESys) Grant VH-NG-1301. S.B. and R.S. were supported by the H2020 project CRESCENDO “Coordinated Research in Earth Systems and Climate: Experiments, Knowledge, Dissemination and Outreach,” which received funding from the European Union’s Horizon 2020 research and innovation program under Grant No 641816. SOCAT is an international effort, endorsed by the International Ocean Carbon Coordination Project, the Surface Ocean-Lower Atmosphere Study, and the Integrated Marine Biosphere Research program, to deliver a uniformly quality-controlled surface ocean CO2 database. The many researchers and funding agencies responsible for the collection of data and quality control are thanked for their contributions to SOCAT.
    Description: 2019-11-28
    Keywords: Carbon dioxide ; Ocean carbon sink ; Terrestrial carbon sink ; Climate variability ; Carbon budget
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 23
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17934-17942, doi:10.1073/pnas.1910121116.
    Description: Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.
    Description: We are grateful to Martin Kolisko and Fabien Burki for helpful discussion about and comments on the phylogenetic analysis; and Filip Husnik and Vittorio Boscaro for valuable comments on the manuscript. This work was supported by a grant from the National Science Foundation to R.J.G. and P.J.K. (PLR-1341362) and from the Natural Sciences and Engineering Research Council of Canada to P.J.K. (RGPIN-2014-03994).
    Description: 2020-02-19
    Keywords: plastid endosymbiosis ; kleptoplasty ; dinoflagellates ; plastid integration
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 24
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Diaz, J. M., Plummer, S., Hansel, C. M., Andeer, P. F., Saito, M. A., & McIlvin, M. R. NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica. Proceedings of the National Academy of Sciences of the United States of America, 116 (33), (2019): 16448-16453, doi: 10.1073/pnas.1821233116.
    Description: Reactive oxygen species (ROS) like superoxide drive rapid transformations of carbon and metals in aquatic systems and play dynamic roles in biological health, signaling, and defense across a diversity of cell types. In phytoplankton, however, the ecophysiological role(s) of extracellular superoxide production has remained elusive. Here, the mechanism and function of extracellular superoxide production by the marine diatom Thalassiosira oceanica are described. Extracellular superoxide production in T. oceanica exudates was coupled to the oxidation of NADPH. A putative NADPH-oxidizing flavoenzyme with predicted transmembrane domains and high sequence similarity to glutathione reductase (GR) was implicated in this process. GR was also linked to extracellular superoxide production by whole cells via quenching by the flavoenzyme inhibitor diphenylene iodonium (DPI) and oxidized glutathione, the preferred electron acceptor of GR. Extracellular superoxide production followed a typical photosynthesis-irradiance curve and increased by 30% above the saturation irradiance of photosynthesis, while DPI significantly impaired the efficiency of photosystem II under a wide range of light levels. Together, these results suggest that extracellular superoxide production is a byproduct of a transplasma membrane electron transport system that serves to balance the cellular redox state through the recycling of photosynthetic NADPH. This photoprotective function may be widespread, consistent with the presence of putative homologs to T. oceanica GR in other representative marine phytoplankton and ocean metagenomes. Given predicted climate-driven shifts in global surface ocean light regimes and phytoplankton community-level photoacclimation, these results provide implications for future ocean redox balance, ecological functioning, and coupled biogeochemical transformations of carbon and metals.
    Description: This work was supported by a postdoctoral fellowship from the Ford Foundation (to J.M.D.), the National Science Foundation (NSF) under grants OCE 1225801 (to J.M.D.) and OCE 1246174 (to C.M.H.), a Junior Faculty Seed Grant from the University of Georgia Research Foundation (to J.M.D.), and a National Science Foundation Graduate Research Fellowship (to S.P.). The FIRe was purchased through a NSF equipment improvement grant (1624593).The authors thank Melissa Soule for assistance with LC/MS/MS analysis of peptide samples.
    Keywords: Reactive oxygen species ; Photosynthesis ; Oxidative stress ; Biogeochemistry
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 25
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116(27), (2019): 13233-13238, doi: 10.1073/pnas.1904087116.
    Description: The overturning circulation of the global ocean is critically shaped by deep-ocean mixing, which transforms cold waters sinking at high latitudes into warmer, shallower waters. The effectiveness of mixing in driving this transformation is jointly set by two factors: the intensity of turbulence near topography and the rate at which well-mixed boundary waters are exchanged with the stratified ocean interior. Here, we use innovative observations of a major branch of the overturning circulation—an abyssal boundary current in the Southern Ocean—to identify a previously undocumented mixing mechanism, by which deep-ocean waters are efficiently laundered through intensified near-boundary turbulence and boundary–interior exchange. The linchpin of the mechanism is the generation of submesoscale dynamical instabilities by the flow of deep-ocean waters along a steep topographic boundary. As the conditions conducive to this mode of mixing are common to many abyssal boundary currents, our findings highlight an imperative for its representation in models of oceanic overturning.
    Description: The DynOPO project is supported by the UK Natural Environment Research Council (grants NE/K013181/1 and NE/K012843/1) and the US National Science Foundation (grants OCE-1536453 and OCE-1536779). A.C.N.G. acknowledges the support of the Royal Society and the Wolfson Foundation. S.L. acknowledges the support of award NA14OAR4320106 from the National Oceanic and Atmospheric Administration, US Department of Commerce. The statements, findings, conclusions, and recommendations are those of the authors, and do not necessarily reflect the views of the National Oceanic and Atmospheric Administration, or the US Department of Commerce. We are grateful to the scientific party, crew, and technicians on the RRS James Clark Ross for their hard work during data collection.
    Description: 2019-12-18
    Keywords: Ocean mixing ; Overturning circulation ; Submesoscale instabilities ; Turbulence
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 26
    Publication Date: 2022-06-09
    Description: In this paper we describe the macroseismic effects produced by the long and destructive seismic sequence that hit Central Italy from 24 August 2016 to January 2017. Starting from the procedure adopted in the complex field survey, we discuss the characteristics of the building stock and its classification in terms of EMS-98 as well as the issues associated with the intensity assessment due to the evolution of damage caused by multiple shocks. As a result, macroseismic intensity for about 300 localities has been determined; however, most of the intensities assessed for the earthquakes following the first strong shock on 24 August 2016, represent the cumulative effect of damage during the sequence. The earthquake parameters computed from the macroseismic datasets are compared with the instrumental determinations in order to highlight critical issues related to the assessment of macroseismic parameters of strong earthquakes during a seismic sequence. The results also provide indications on how location and magnitude computation can be strongly biased when dealing with historical seismic sequences.
    Description: Presidenza del Consiglio dei Ministri - Dipartimento della Protezione Civile (DPC)
    Description: Published
    Description: 2407–2431
    Description: 4T. Sismicità dell'Italia
    Description: 1SR TERREMOTI - Sorveglianza Sismica e Allerta Tsunami
    Description: 2SR TERREMOTI - Gestione delle emergenze sismiche e da maremoto
    Description: 5SR TERREMOTI - Convenzioni derivanti dall'Accordo Quadro decennale INGV-DPC
    Description: JCR Journal
    Keywords: Central Italy ; 2016–2017 Earthquake sequence ; Cumulative damage ; EMS-98 ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 27
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schwaha, T., Bernhard, J. M., Edgcomb, V. P., & Todaro, M. A. Aethozooides uraniae, a new deep-sea genus and species of solitary bryozoan from the Mediterranean Sea, with a revision of the Aethozoidae. Marine Biodiversity, 49(4), (2019): 1843-1856, doi: 10.1007/s12526-019-00948-w.
    Description: Bryozoa is a phylum of about 6000 extant species that are almost exclusively colonial. Few species of the uncalcified Gymnolaemata, the ctenostomes, however, show solitary forms that essentially consist of single zooids. Recently, several specimens of a solitary ctenostome bryozoan were encountered for the first time in the deep Mediterranean Sea, at the edge of an anoxic brine lake. Differences in size, tentacle number, and in the variability of cystid appendages set these specimens apart from all other known solitary species. Moreover, additional morphological autapomorphic traits suggest the erection of a novel genus to allocate the new species. Consequently, the new taxon Aethozooides gen. nov. is proposed in virtue of the general resemblance of the Mediterranean specimens with those of the genus Aethozoon Hayward, 1978. Aethozooides uraniae gen. et sp. nov. shows significant variability in the number and location of cystid appendages that range from two on the basal side to one or two on the zooid mid-peristomial position and/or, rarely, on the terminal frontal side. The polypide possesses a distinct, long tentacle crown always carrying 10 tentacles. The prominent retractor muscle consists of numerous bundles that, in contrast to other known gymnolaemates, attach not only to the lophophoral base but also to various parts of the gut. Distally, the aperture shows a set of four apertural muscles including four parieto-vaginal bands. Reviewing the state and diversity of solitary ctenostomes, we propose a revision of the family Aethozoidae to include the genera Franzenella d’Hondt, 1983, Aethozoon, Aethozooides, and two species currently affiliated to the genus Franzenella (F. monniotae and F. radicans) for which we erected the new taxon Solella gen. nov. Keywords
    Description: Open access funding provided by University of Vienna. This study was supported by NSF grants OCE-0849578 to VPE and JMB, OCE-1061391 to JMB and VPE, and The Investment in Science Fund at WHOI.
    Keywords: Ctenostomata ; Lophophore ; Cystid appendages ; Arachnidioidea ; Solella
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 28
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mitchell, S. J., Houghton, B. F., Carey, R. J., Manga, M., Fauria, K. E., Jones, M. R., Soule, S. A., Conway, C. E., Wei, Z., & Giachetti, T. Submarine giant pumice: A window into the shallow conduit dynamics of a recent silicic eruption. Bulletin of Volcanology, 81(7), (2019): 42, doi:10.1007/s00445-019-1298-5.
    Description: Meter-scale vesicular blocks, termed “giant pumice,” are characteristic primary products of many subaqueous silicic eruptions. The size of giant pumices allows us to describe meter-scale variations in textures and geochemistry with implications for shearing processes, ascent dynamics, and thermal histories within submarine conduits prior to eruption. The submarine eruption of Havre volcano, Kermadec Arc, in 2012, produced at least 0.1 km3 of rhyolitic giant pumice from a single 900-m-deep vent, with blocks up to 10 m in size transported to at least 6 km from source. We sampled and analyzed 29 giant pumices from the 2012 Havre eruption. Geochemical analyses of whole rock and matrix glass show no evidence for geochemical heterogeneities in parental magma; any textural variations can be attributed to crystallization of phenocrysts and microlites, and degassing. Extensive growth of microlites occurred near conduit walls where magma was then mingled with ascending microlite-poor, low viscosity rhyolite. Meter- to micron-scale textural analyses of giant pumices identify diversity throughout an individual block and between the exteriors of individual blocks. We identify evidence for post-disruption vesicle growth during pumice ascent in the water column above the submarine vent. A 2D cumulative strain model with a flared, shallow conduit may explain observed vesicularity contrasts (elongate tube vesicles vs spherical vesicles). Low vesicle number densities in these pumices from this high-intensity silicic eruption demonstrate the effect of hydrostatic pressure above a deep submarine vent in suppressing rapid late-stage bubble nucleation and inhibiting explosive fragmentation in the shallow conduit.
    Description: This study was funded primarily through an NSF Ocean grant: OCE-1357443 (SJM, BFH and RJC). MM is supported by NSF EAR 1447559. The μXRT analysis was performed at the Lawrence Berkeley National Lab Advanced Light Source beamline 8.3.2 and the large CT scan by SAS at the University of Texas Austin micro-CT facility. Capillary flow porometry and He-pycnometry were assisted by TG and MRJ at the University of Oregon. Microprobe analysis was conducted at the University of Hawai’i at Mānoa. CEC was supported by post-doctoral research fellowship from the Japan Society for the Promotion of Science (JSPS16788). We would like to thank Kenichiro Tani, Takashi Sano, and Eric Hellebrand for their assistance with geochemical data acquisition, JoAnn Sinton and Wagner Petrographic for thin section preparation, Zachary Langdalen for binary processing of BSE images, Warren M. McKenzie for measuring clast densities, and Dula Parkinson for guidance with the μXRT imaging. We further acknowledge the full scientific team, crew and Jason ROV team (Woods Hole Oceanographic Institute) aboard the R/V Roger Revelle (Scripps Institute of Oceanography) during the MESH expedition in 2015, without whom, this study would not have been possible. Finally, we thank Andrew Harris, Katharine Cashman, Lucia Gurioli and an anonymous reviewer for their insightful and helpful reviews of the manuscript.
    Keywords: Giant pumice ; Submarine volcanism ; Banding ; Tube pumice ; Bubble deformation ; Conduit dynamics
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 29
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kelly, M. R., Jr., Neubert, M. G., & Lenhart, S. Marine reserves and optimal dynamic harvesting when fishing damages habitat. Theoretical Ecology, 12(2), (2019): 131-144, doi:10.1007/s12080-018-0399-7.
    Description: Marine fisheries are a significant source of protein for many human populations. In some locations, however, destructive fishing practices have negatively impacted the quality of fish habitat and reduced the habitat’s ability to sustain fish stocks. Improving the management of stocks that can be potentially damaged by harvesting requires improved understanding of the spatiotemporal dynamics of the stocks, their habitats, and the behavior of the harvesters. We develop a mathematical model for both a fish stock as well as its habitat quality. Both are modeled using nonlinear, parabolic partial differential equations, and density dependence in the growth rate of the fish stock depends upon habitat quality. The objective is to find the dynamic distribution of harvest effort that maximizes the discounted net present value of the coupled fishery-habitat system. The value derives both from extraction (and sale) of the stock and the provisioning of ecosystem services by the habitat. Optimal harvesting strategies are found numerically. The results suggest that no-take marine reserves can be an important part of the optimal strategy and that their spatiotemporal configuration depends both on the vulnerability of habitat to fishing damage and on the timescale of habitat recovery when fishing ceases.
    Description: This manuscript is based upon the work supported by the National Science Foundation under Grant No. DEB-1558904 (to MGN) and also supported by the National Institute for Mathematical and Biological Synthesis, an Institute supported by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville.
    Keywords: Fisheries bioeconomics ; Marine protected areas ; Optimal control ; Destructive fishing ; Ecosystem-based management
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 30
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in , Zakroff, C., Mooney, T.A. & Berumen, M.L. Dose-dependence and small-scale variability in responses to ocean acidification during squid, Doryteuthis pealeii, development. Marine Biology, (2019), 166: 62. doi:10.1007/s00227-019-3510-8.
    Description: Coastal squids lay their eggs on the benthos, leaving them to develop in a dynamic system that is undergoing rapid acidification due to human influence. Prior studies have broadly investigated the impacts of ocean acidification on embryonic squid, but have not addressed the thresholds at which these responses occur or their potential variability. We raised squid, Doryteuthis pealeii (captured in Vineyard Sound, Massachusetts, USA: 41° 23.370N 70° 46.418´W), eggs in three trials across the breeding season (May - September, 2013) in a total of six chronic pCO2 exposures (400, 550, 850, 1300, 1900, and 2200 ppm). Hatchlings were counted and subsampled for mantle length, yolk volume, hatching time, hatching success, and statolith morphology. New methods for analysis of statolith shape, rugosity, and surface degradation were developed and are presented (with code). Responses to acidification (e.g., reduced mantle lengths, delayed hatching, and smaller, more degraded statoliths) were evident at ~ 1300 ppm CO2. However, patterns of physiological response and energy management, based on comparisons of yolk consumption and growth, varied among trials. Interactions between pCO2 and hatching day indicated a potential influence of exposure time on responses, while interactions with culture vessel highlighted the substantive natural variability within a clutch of eggs. While this study is consistent with, and expands upon, previous findings of sensitivity of the early life stages to acidification, it also highlights the plasticity and potential for resilience in this population of squid.
    Description: This material was based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1122374 to CZ. This project was funded by National Science Foundation Grant No. 1220034 to TAM.
    Description: 2020-04-19
    Keywords: cephalopod ; embryo ; hypercapnia ; paralarvae ; statolith ; stress
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 31
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 116(25), (2019):12343-12352, doi:10.1073/pnas.1901080116.
    Description: Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 Å. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.
    Description: We thank Dr. David Nes (Texas Tech University) for providing sterols and Dr. Matthieu Legendre and Dr. Chantal Abergel (CNRS, Marseille) for access to the P. celtis sequences. Drs. Irina Arkhipova, Mark Hahn, Judith Luborsky, and Ann Bucklin commented on the manuscript. The research was supported by a USA-UK Fulbright Scholarship and a Royal Society grant (to D.C.L.), the Boston University Superfund Research Program [NIH Grant 5P42ES007381 (to J.J.S. and J.V.G.) and NIH Grant 5U41HG003345 (to J.V.G.)], the European Regional Development Fund and Welsh Government Project BEACON (S.L.K.), the Woods Hole Center for Oceans and Human Health [NIH Grant P01ES021923 and National Science Foundation Grant OCE-1314642 (to J.J.S.)], and NIH Grant R01GM53753 (to T.L.P.).
    Description: 2019-12-05
    Keywords: cytochrome P450 ; virus ; evolution ; domains of life ; redox partner
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 32
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (35), (2019): 17187-17192, doi:10.1073/pnas.1903067116.
    Description: Mesoscale eddies are critical components of the ocean’s “internal weather” system. Mixing and stirring by eddies exerts significant control on biogeochemical fluxes in the open ocean, and eddies may trap distinctive plankton communities that remain coherent for months and can be transported hundreds to thousands of kilometers. Debate regarding how and why predators use fronts and eddies, for example as a migratory cue, enhanced forage opportunities, or preferred thermal habitat, has been ongoing since the 1950s. The influence of eddies on the behavior of large pelagic fishes, however, remains largely unexplored. Here, we reconstruct movements of a pelagic predator, the blue shark (Prionace glauca), in the Gulf Stream region using electronic tags, earth-observing satellites, and data-assimilating ocean forecasting models. Based on 〉2,000 tracking days and nearly 500,000 high-resolution time series measurements collected by 15 instrumented individuals, we show that blue sharks seek out the interiors of anticyclonic eddies where they dive deep while foraging. Our observations counter the existing paradigm that anticyclonic eddies are unproductive ocean “deserts” and suggest anomalously warm temperatures in these features connect surface-oriented predators to the most abundant fish community on the planet in the mesopelagic. These results also shed light on the ecosystem services provided by mesopelagic prey. Careful consideration will be needed before biomass extraction from the ocean twilight zone to avoid interrupting a key link between planktonic production and top predators. Moreover, robust associations between targeted fish species and oceanographic features increase the prospects for effective dynamic ocean management.
    Description: We thank D. McGillicuddy, G. Lawson, and G. Flierl for helpful discussions while developing this work and 2 anonymous reviewers whose feedback significantly improved the manuscript. We also thank C. Fischer and the OCEARCH team for their support of this research. This work was funded by awards to C.D.B. from the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology; the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution; and the National Aeronatics and Space Administration (NASA) Earth and Space Science Fellowship. C.D.B. and P.G. acknowledge support from the NASA New Investigator Program Award 80NSSC18K0757, and P.G. acknowledges support from NSF Award OCE-1558809. This research is partially supported by funding to S.R.T. as part of the Audacious Project, a collaborative endeavor, housed at TED. We thank donors to the Woods Hole Oceanographic Institution (WHOI) ProjectWHOI crowdfunding campaign: The Secret Lives of Sharks. Computational support was provided by the Amazon Web Services Cloud Credits for Research program. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research.
    Description: 2020-02-06
    Keywords: remote sensing ; oceanographic model ; satellite telemetry ; marine predator ; mesopelagic
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 33
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (35), (2019): 17207-17212, doi:10.1073/pnas.1900325116.
    Description: It has been hypothesized that the overall size of—or efficiency of carbon export from—the biosphere decreased at the end of the Great Oxidation Event (GOE) (ca. 2,400 to 2,050 Ma). However, the timing, tempo, and trigger for this decrease remain poorly constrained. Here we test this hypothesis by studying the isotope geochemistry of sulfate minerals from the Belcher Group, in subarctic Canada. Using insights from sulfur and barium isotope measurements, combined with radiometric ages from bracketing strata, we infer that the sulfate minerals studied here record ambient sulfate in the immediate aftermath of the GOE (ca. 2,018 Ma). These sulfate minerals captured negative triple-oxygen isotope anomalies as low as ∼ −0.8‰. Such negative values occurring shortly after the GOE require a rapid reduction in primary productivity of 〉80%, although even larger reductions are plausible. Given that these data imply a collapse in primary productivity rather than export efficiency, the trigger for this shift in the Earth system must reflect a change in the availability of nutrients, such as phosphorus. Cumulatively, these data highlight that Earth’s GOE is a tale of feast and famine: A geologically unprecedented reduction in the size of the biosphere occurred across the end-GOE transition.
    Description: Olivia M. J. Dagnaud assisted during fieldwork. S. V. Lalonde and E. A. Sperling provided helpful comments on an early version of the manuscript. We thank N. J. Planavsky and an anonymous reviewer for their constructive feedback. M.S.W.H. was supported by an NSERC PGS-D and student research grants from National Geographic, the APS Lewis and Clark Fund, Northern Science Training Program, McGill University Graduate Research Enhancement and Travel Awards, Geological Society of America, Mineralogical Association of Canada, and Stanford University. P.W.C. acknowledges support from the University of Colorado Boulder, the Agouron Institute Geobiology postdoctoral Fellowship program, a Natural Sciences and Engineering Council of Canada Postgraduate Scholarship–Doctoral Program scholarship, and the NSTP. Y.P. was supported by the Strategic Priority Research Program of CAS (XDB26000000). T.J.H. thanks Maureen E. Auro for laboratory assistance and the NSF for supporting isotope research in the NIRVANA Labs.
    Description: 2020-02-12
    Keywords: Proterozoic ; primary productivity ; Great Oxidation Event ; triple-oxygen isotopes ; nutrient limitation
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 34
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116(45), (2019): 22518-22525, doi:10.1073/pnas.1913714116.
    Description: The Ganges–Brahmaputra (G-B) River system transports over a billion tons of sediment every year from the Himalayan Mountains to the Bay of Bengal and has built the world’s largest active sedimentary deposit, the Bengal Fan. High sedimentation rates drive exceptional organic matter preservation that represents a long-term sink for atmospheric CO2. While much attention has been paid to organic-rich fine sediments, coarse sediments have generally been overlooked as a locus of organic carbon (OC) burial. However, International Ocean Discovery Program Expedition 354 recently discovered abundant woody debris (millimeter- to centimeter-sized fragments) preserved within the coarse sediment layers of turbidite beds recovered from 6 marine drill sites along a transect across the Bengal Fan (∼8°N, ∼3,700-m water depth) with recovery spanning 19 My. Analysis of bulk wood and lignin finds mostly lowland origins of wood delivered episodically. In the last 5 My, export included C4 plants, implying that coarse woody, lowland export continued after C4 grassland expansion, albeit in reduced amounts. Substantial export of coarse woody debris in the last 1 My included one wood-rich deposit (∼0.05 Ma) that encompassed coniferous wood transported from the headwaters. In coarse layers, we found on average 0.16 weight % OC, which is half the typical biospheric OC content of sediments exported by the modern G-B Rivers. Wood burial estimates are hampered by poor drilling recovery of sands. However, high-magnitude, low-frequency wood export events are shown to be a key mechanism for C burial in turbidites.
    Description: This work was funded by National Science Foundation Grants OCE-1401217 and COL-T354A55 to S.J.F. and OCE-1400805 to V.G. Graduate student participation in the project received support from University of Southern California Provost’s Fellowship to H.L. Samples were provided by the International Ocean Discovery Program. We are grateful for the efforts of the Expedition 354 Science Party, Carl Johnson, and Zongguang Liu. C.F.-L. and A.G. were supported by IODP-France. We thank Colin Osborne and Maria Vorontsova for helpful discussions.
    Description: 2020-04-21
    Keywords: carbon cycle ; wood ; lignin ; Himalaya ; Bengal Fan
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 35
    facet.materialart.
    Unknown
    Springer
    In:  EPIC3Advances in Polar Ecology, The Ecosystem of Kongsfjorden, Svalbard, Springer, pp. 23-46, ISBN: 978-3-319-46423-7
    Publication Date: 2023-06-21
    Description: The Arctic region is considered to be most sensitive to climate change, with warming in the Arctic occurring considerably faster than the global average due to several positive feedback mechanisms contributing to the “Arctic amplification”. Also the maritime and mountainous climate of Svalbard has undergone changes during the last decades. Here, the focus is set on the current atmospheric boundary conditions for the marine ecosystem in the Kongsfjorden area, discussed in the frame of long-term climatic observations in the larger regional and hemispheric context. During the last century, a general warming is found with temperature increases and precipitation changes varying in strength. During the last decades, a strong seasonality of the warming is observed in the Kongsfjorden area, with the strongest temperature increase occurring during the winter season. The winter warming is related to observed changes in the net longwave radiation. Moreover, changes in the net shortwave are observed during the summer period, attributed to the decrease in reflected radiation caused by the retreating snow cover. Another related aspect of radiation is the intensity of solar ultra-violet radiation that is closely coupled to the abundance of ozone in the column of air overhead. The long term evolution of ozone losses in the Arctic and their connection to climate change are discussed.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 36
    Publication Date: 2019-04-02
    Description: Bacteria are surrounded by a protective exoskeleton, peptidoglycan (PG), a cross-linked mesh-like macromolecule consisting of glycan strands interlinked by short peptides. Because PG completely encases the cytoplasmic membrane, cleavage of peptide cross-links is a prerequisite to make space for incorporation of nascent glycan strands for its successful expansion during cell growth. In most bacteria, the peptides consist of l-alanine, d-glutamate, meso-diaminopimelic acid (mDAP) and d-alanine (d-Ala) with cross-links occurring either between d-Ala and mDAP or two mDAP residues. In Escherichia coli, the d-Ala−mDAP cross-links whose cleavage by specialized endopeptidases is crucial for expansion of PG predominate. However, a small proportion of mDAP−mDAP cross-links also exist, yet their role in the context of PG expansion or the hydrolase(s) capable of catalyzing their cleavage is not known. Here, we identified an ORF of unknown function, YcbK (renamed MepK), as an mDAP−mDAP cross-link cleaving endopeptidase working in conjunction with other elongation-specific endopeptidases to make space for efficient incorporation of nascent PG strands into the sacculus. E. coli mutants lacking mepK and another d-Ala−mDAP–specific endopeptidase (mepS) were synthetic sick, and the defects were abrogated by lack of l,d-transpeptidases, enzymes catalyzing the formation of mDAP cross-links. Purified MepK was able to cleave the mDAP cross-links of soluble muropeptides and of intact PG sacculi. Overall, this study describes a PG hydrolytic enzyme with a hitherto unknown substrate specificity that contributes to expansion of the PG sacculus, emphasizing the fundamental importance of cross-link cleavage in bacterial peptidoglycan synthesis.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 37
    Publication Date: 2019-11-12
    Description: As monofacial, single-junction solar cells approach their fundamental limits, there has been significant interest in tandem solar cells in the presence of concentrated sunlight or tandem bifacial solar cells with back-reflected albedo. The bandgap sequence and thermodynamic efficiency limits of these complex cell configurations require sophisticated numerical calculation. Therefore, the analyses of specialized cases are scattered throughout the literature. In this paper, we show that a powerful graphical approach called the normalized “Shockley–Queisser (S-Q) triangle” (i.e., imp=1−vmp) is sufficient to calculate the bandgap sequence and efficiency limits of arbitrarily complex photovoltaic (PV) topologies. The results are validated against a wide variety of specialized cases reported in the literature and are accurate within a few percent. We anticipate that the widespread use of the S-Q triangle will illuminate the deeper physical principles and design trade-offs involved in the design of bifacial tandem solar cells under arbitrary concentration and series resistance.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 38
    Publication Date: 2019-02-14
    Description: Previous studies have shown that insulin and IGF-1 signaling in the brain, especially the hypothalamus, is important for regulation of systemic metabolism. Here, we develop mice in which we have specifically inactivated both insulin receptors (IRs) and IGF-1 receptors (IGF1Rs) in the hippocampus (Hippo-DKO) or central amygdala (CeA-DKO) by stereotaxic delivery of AAV-Cre into IRlox/lox/IGF1Rlox/loxmice. Consequently, both Hippo-DKO and CeA-DKO mice have decreased levels of the GluA1 subunit of glutamate AMPA receptor and display increased anxiety-like behavior, impaired cognition, and metabolic abnormalities, including glucose intolerance. Hippo-DKO mice also display abnormal spatial learning and memory whereas CeA-DKO mice have impaired cold-induced thermogenesis. Thus, insulin/IGF-1 signaling has common roles in the hippocampus and central amygdala, affecting synaptic function, systemic glucose homeostasis, behavior, and cognition. In addition, in the hippocampus, insulin/IGF-1 signaling is important for spatial learning and memory whereas insulin/IGF-1 signaling in the central amygdala controls thermogenesis via regulation of neural circuits innervating interscapular brown adipose tissue.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 39
    Publication Date: 2019-06-17
    Description: The sunflower family, Asteraceae, comprises 10% of all flowering plant species and displays an incredible diversity of form. Asteraceae are clearly monophyletic, yet resolving phylogenetic relationships within the family has proven difficult, hindering our ability to understand its origin and diversification. Recent molecular clock dating has suggested a Cretaceous origin, but the lack of deep sampling of many genes and representative taxa from across the family has impeded the resolution of migration routes and diversifications that led to its global distribution and tremendous diversity. Here we use genomic data from 256 terminals to estimate evolutionary relationships, timing of diversification(s), and biogeographic patterns. Our study places the origin of Asteraceae at ∼83 MYA in the late Cretaceous and reveals that the family underwent a series of explosive radiations during the Eocene which were accompanied by accelerations in diversification rates. The lineages that gave rise to nearly 95% of extant species originated and began diversifying during the middle Eocene, coincident with the ensuing marked cooling during this period. Phylogenetic and biogeographic analyses support a South American origin of the family with subsequent dispersals into North America and then to Asia and Africa, later followed by multiple worldwide dispersals in many directions. The rapid mid-Eocene diversification is aligned with the biogeographic range shift to Africa where many of the modern-day tribes appear to have originated. Our robust phylogeny provides a framework for future studies aimed at understanding the role of the macroevolutionary patterns and processes that generated the enormous species diversity of Asteraceae.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 40
    Publication Date: 2019-04-15
    Description: There is a gap between how many scientists communicate and how most people understand and interpret messages. This article argues that the extensive science communications literature needs to be joined by the health literacy literature and anthropological work on cultural variations in hearing and understanding messages. Rapid changes and differences in how people in the United States get information are also discussed. Better understanding of how people get and perceive messages, and how access to information and to health services affects their behavior, should be an iterative and interdisciplinary effort. Community involvement in developing communication strategies is strongly encouraged.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 41
    Publication Date: 2019-09-30
    Description: Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question. Like others, we find that convergent amino acid substitutions are not more abundant in echolocating mammals compared to their outgroups. However, we also ask a more informative question about the genomic distribution of convergent substitutions by devising a test to determine which, if any, of more than 4,000 tissue-affecting gene sets is most statistically enriched with convergent substitutions. We find that the gene set most overrepresented (q-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. Conversely, when comparing to nonecholocating outgroups, no significant gene set enrichment exists. For aquatic and high-altitude mammals, our analysis highlights 15 and 16 genes from the gene sets most affected by molecular convergence which regulate skin and lung physiology, respectively. Importantly, our test requires that the most convergence-enriched set cannot also be enriched for divergent substitutions, such as in the pattern produced by inactivated vision genes in subterranean mammals. Showing a clear role for adaptive protein-coding molecular convergence, we discover nearly 2,600 convergent positions, highlight 77 of them in 3 organs, and provide code to investigate other clades across the tree of life.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 42
    Publication Date: 2019-09-16
    Description: Cilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around are composed of radially bundled doublet microtubules. In this study, we present a near-atomic resolution map of the Tetrahymena doublet microtubule by cryoelectron microscopy. The map demonstrates that the network of microtubule inner proteins weaves into the tubulin lattice and forms an inner sheath. From mass spectrometry data and de novo modeling, we identified Rib43a proteins as the filamentous microtubule inner proteins in the protofilament ribbon region. The Rib43a–tubulin interaction leads to an elongated tubulin dimer distance every 2 dimers. In addition, the tubulin lattice structure with missing microtubule inner proteins (MIPs) by sarkosyl treatment shows significant longitudinal compaction and lateral angle change between protofilaments. These results are evidence that the MIPs directly affect and stabilize the tubulin lattice. It suggests that the doublet microtubule is an intrinsically stressed filament and that this stress could be manipulated in the regulation of ciliary waveforms.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 43
    Publication Date: 2019-07-01
    Description: Aberrant MYC oncogene activation is one of the most prevalent characteristics of cancer. By overlapping datasets of Drosophila genes that are insulin-responsive and also regulate nucleolus size, we enriched for Myc target genes required for cellular biosynthesis. Among these, we identified the aminoacyl tRNA synthetases (aaRSs) as essential mediators of Myc growth control in Drosophila and found that their pharmacologic inhibition is sufficient to kill MYC-overexpressing human cells, indicating that aaRS inhibitors might be used to selectively target MYC-driven cancers. We suggest a general principle in which oncogenic increases in cellular biosynthesis sensitize cells to disruption of protein homeostasis.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 44
    Publication Date: 2019-08-21
    Description: Organic electrosynthesis can transform the chemical industry by introducing electricity-driven processes that are more energy efficient and that can be easily integrated with renewable energy sources. However, their deployment is severely hindered by the difficulties of controlling selectivity and achieving a large energy conversion efficiency at high current density due to the low solubility of organic reactants in practical electrolytes. This control can be improved by carefully balancing the mass transport processes and electrocatalytic reaction rates at the electrode diffusion layer through pulsed electrochemical methods. In this study, we explore these methods in the context of the electrosynthesis of adiponitrile (ADN), the largest organic electrochemical process in industry. Systematically exploring voltage pulses in the timescale between 5 and 150 ms led to a 20% increase in production of ADN and a 250% increase in relative selectivity with respect to the state-of-the-art constant voltage process. Moreover, combining this systematic experimental investigation with artificial intelligence (AI) tools allowed us to rapidly discover drastically improved electrosynthetic conditions, reaching improvements of 30 and 325% in ADN production rates and selectivity, respectively. This powerful AI-enhanced experimental approach represents a paradigm shift in the design of electrified chemical transformations, which can accelerate the deployment of more sustainable electrochemical manufacturing processes.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 45
    Publication Date: 2019-04-08
    Description: In most environments, the visual system is confronted with many relevant objects simultaneously. That is especially true during reading. However, behavioral data demonstrate that a serial bottleneck prevents recognition of more than one word at a time. We used fMRI to investigate how parallel spatial channels of visual processing converge into a serial bottleneck for word recognition. Participants viewed pairs of words presented simultaneously. We found that retinotopic cortex processed the two words in parallel spatial channels, one in each contralateral hemisphere. Responses were higher for attended than for ignored words but were not reduced when attention was divided. We then analyzed two word-selective regions along the occipitotemporal sulcus (OTS) of both hemispheres (subregions of the visual word form area, VWFA). Unlike retinotopic regions, each word-selective region responded to words on both sides of fixation. Nonetheless, a single region in the left hemisphere (posterior OTS) contained spatial channels for both hemifields that were independently modulated by selective attention. Thus, the left posterior VWFA supports parallel processing of multiple words. In contrast, activity in a more anterior word-selective region in the left hemisphere (mid OTS) was consistent with a single channel, showing (i) limited spatial selectivity, (ii) no effect of spatial attention on mean response amplitudes, and (iii) sensitivity to lexical properties of only one attended word. Therefore, the visual system can process two words in parallel up to a late stage in the ventral stream. The transition to a single channel is consistent with the observed bottleneck in behavior.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 46
    Publication Date: 2019-06-24
    Description: Genomic analyses of patients with congenital heart disease (CHD) have identified significant contribution from mutations affecting cilia genes and chromatin remodeling genes; however, the mechanism(s) connecting chromatin remodeling to CHD is unknown. Histone H2B monoubiquitination (H2Bub1) is catalyzed by the RNF20 complex consisting of RNF20, RNF40, and UBE2B. Here, we show significant enrichment of loss-of-function mutations affecting H2Bub1 in CHD patients (enrichment 6.01,P= 1.67 × 10−03), some of whom had abnormal laterality associated with ciliary dysfunction. InXenopus, knockdown ofrnf20andrnf40results in abnormal heart looping, defective development of left–right (LR) asymmetry, and impaired cilia motility. Rnf20, Rnf40, and Ube2b affect LR patterning and cilia synergistically. Examination of global H2Bub1 level inXenopusembryos shows that H2Bub1 is developmentally regulated and requires Rnf20. To examine gene-specific H2Bub1, we performed ChIP-seq of mouse ciliated and nonciliated tissues and showed tissue-specific H2Bub1 marks significantly enriched at cilia genes including the transcription factorRfx3. Rnf20 knockdown results in decreased levels ofrfx3mRNA inXenopus, and exogenousrfx3can rescue the Rnf20 depletion phenotype. These data suggest that Rnf20 functions at theRfx3locus regulating cilia motility and cardiac situs and identify H2Bub1 as an upstream transcriptional regulator controlling tissue-specific expression of cilia genes. Our findings mechanistically link the two functional gene ontologies that have been implicated in human CHD: chromatin remodeling and cilia function.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 47
    Publication Date: 2019-12-16
    Description: Plasticity theory aims at describing the yield loci and work hardening of a material under general deformation states. Most of its complexity arises from the nontrivial dependence of the yield loci on the complete strain history of a material and its microstructure. This motivated 3 ingenious simplifications that underpinned a century of developments in this field: 1) yield criteria describing yield loci location; 2) associative or nonassociative flow rules defining the direction of plastic flow; and 3) effective stress–strain laws consistent with the plastic work equivalence principle. However, 2 key complications arise from these simplifications. First, finding equations that describe these 3 assumptions for materials with complex microstructures is not trivial. Second, yield surface evolution needs to be traced iteratively, i.e., through a return mapping algorithm. Here, we show that these assumptions are not needed in the context of sequence learning when using recurrent neural networks, diverting the above-mentioned complications. This work offers an alternative to currently established plasticity formulations by providing the foundations for finding history- and microstructure-dependent constitutive models through deep learning.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 48
    Publication Date: 2019-08-12
    Description: Two-dimensional monolayer materials, with thicknesses of up to several atoms, can be obtained from almost every layer-structured material. It is believed that the catalogs of known 2D materials are almost complete, with fewer new graphene-like materials being discovered. Here, we report 2D graphene-like monolayers from monoxides such as BeO, MgO, CaO, SrO, BaO, and rock-salt structured monochlorides such as LiCl, and NaCl using first-principle calculations. Two-dimensional materials containing d-orbital atoms such as HfO, CdO, and AgCl are predicted. Adopting the same strategy, 2D graphene-like monolayers from mononitrides such as scandium nitride (ScN) and monoselenides such as cadmium selenide (CdSe) are discovered. Stress engineering is found to help stabilize 2D monolayers, through canceling the imaginary frequency of phonon dispersion relation. These 2D monolayers show high dynamic, thermal, kinetic, and mechanic stabilities due to atomic hybridization, and electronic delocalization.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 49
    Publication Date: 2019-03-08
    Description: Materials that can be switched between low and high thermal conductivity states would advance the control and conversion of thermal energy. Employing in situ time-domain thermoreflectance (TDTR) and in situ synchrotron X-ray scattering, we report a reversible, light-responsive azobenzene polymer that switches between high (0.35 W m−1K−1) and low thermal conductivity (0.10 W m−1K−1) states. This threefold change in the thermal conductivity is achieved by modulation of chain alignment resulted from the conformational transition between planar (trans) and nonplanar (cis) azobenzene groups under UV and green light illumination. This conformational transition leads to changes in the π-π stacking geometry and drives the crystal-to-liquid transition, which is fully reversible and occurs on a time scale of tens of seconds at room temperature. This result demonstrates an effective control of the thermophysical properties of polymers by modulating interchain π-π networks by light.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 50
    Publication Date: 2019-05-01
    Description: The Hippo pathway is involved in regulating contact inhibition of proliferation and organ size control and responds to various physical and biochemical stimuli. It is a kinase cascade that negatively regulates the activity of cotranscription factors YAP and TAZ, which interact with DNA binding transcription factors including TEAD and activate the expression of target genes. In this study, we show that the palmitoylation of TEAD, which controls the activity and stability of TEAD proteins, is actively regulated by cell density independent of Lats, the key kinase of the Hippo pathway. The expression of fatty acid synthase and acetyl-CoA carboxylase involved in de novo biosynthesis of palmitate is reduced by cell density in an Nf2/Merlin-dependent manner. Depalmitoylation of TEAD is mediated by depalmitoylases including APT2 and ABHD17A. Palmitoylation-deficient TEAD4 mutant is unstable and degraded by proteasome through the activity of the E3 ubiquitin ligase CHIP. These findings show that TEAD activity is tightly controlled through the regulation of palmitoylation and stability via the orchestration of FASN, depalmitoylases, and E3 ubiquitin ligase in response to cell contact.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 51
    Publication Date: 2019-02-19
    Description: Foraging is a goal-directed behavior that balances the need to explore the environment for resources with the need to exploit those resources. InDrosophila melanogaster, distinct phenotypes have been observed in relation to theforaginggene (for), labeled the rover and sitter. Adult rovers explore their environs more extensively than do adult sitters. We explored whether this distinction would be conserved in humans. We made use of a distinction from regulatory mode theory between those who “get on with it,” so-called locomotors, and those who prefer to ensure they “do the right thing,” so-called assessors. In this logic, rovers and locomotors share similarities in goal pursuit, as do sitters and assessors. We showed that genetic variation inPRKG1, the human ortholog offor, is associated with preferential adoption of a specific regulatory mode. Next, participants performed a foraging task to see whether genetic differences associated with distinct regulatory modes would be associated with distinct goal pursuit patterns. Assessors tended to hug the boundary of the foraging environment, much like behaviors seen inDrosophilaadult sitters. In a patchy foraging environment, assessors adopted more cautious search strategies maximizing exploitation. These results show that distinct patterns of goal pursuit are associated with particular genotypes ofPRKG1, the human ortholog offor.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 52
    Publication Date: 2019-09-23
    Description: Mutational signatures can reveal properties of underlying mutational processes and are important when assessing signals of selection in cancer. Here, we describe the sequence characteristics of mutations induced by ultraviolet (UV) light, a major mutagen in several human cancers, in terms of extended (longer than trinucleotide) patterns as well as variability of the signature across chromatin states. Promoter regions display a distinct UV signature with reduced TCG 〉 TTG transitions, and genome-wide mapping of UVB-induced DNA photoproducts (pyrimidine dimers) showed that this may be explained by decreased damage formation at hypomethylated promoter CpG sites. Further, an extended signature model encompassing additional information from longer contextual patterns improves modeling of UV mutations, which may enhance discrimination between drivers and passenger events. Our study presents a refined picture of the UV signature and underscores that the characteristics of a single mutational process may vary across the genome.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 53
    Publication Date: 2019-02-27
    Description: Drugs that reverse epigenetic silencing, such as the DNA methyltransferase inhibitor (DNMTi) 5-azacytidine (AZA), have profound effects on transcription and tumor cell survival. AZA is an approved drug for myelodysplastic syndromes and acute myeloid leukemia, and is under investigation for different solid malignant tumors. AZA treatment generates self, double-stranded RNA (dsRNA), transcribed from hypomethylated repetitive elements. Self dsRNA accumulation in DNMTi-treated cells leads to type I IFN production and IFN-stimulated gene expression. Here we report that cell death in response to AZA treatment occurs through the 2′,5′-oligoadenylate synthetase (OAS)-RNase L pathway. OASs are IFN-induced enzymes that synthesize the RNase L activator 2-5A in response to dsRNA. Cells deficient in RNase L or OAS1 to 3 are highly resistant to AZA, as are wild-type cells treated with a small-molecule inhibitor of RNase L. A small-molecule inhibitor of c-Jun NH2-terminal kinases (JNKs) also antagonizes RNase L-dependent cell death in response to AZA, consistent with a role for JNK in RNase L-induced apoptosis. In contrast, the rates of AZA-induced and RNase L-dependent cell death were increased by transfection of 2-5A, by deficiencies in ADAR1 (which edits and destabilizes dsRNA), PDE12 or AKAP7 (which degrade 2-5A), or by ionizing radiation (which induces IFN-dependent signaling). Finally, OAS1 expression correlates with AZA sensitivity in the NCI-60 set of tumor cell lines, suggesting that the level of OAS1 can be a biomarker for predicting AZA sensitivity of tumor cells. These studies may eventually lead to pharmacologic strategies for regulating the antitumor activity and toxicity of AZA and related drugs.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 54
    Publication Date: 2019-09-12
    Description: Analyses of thermal diffusivity data on complex insulators and on strongly correlated electron systems hosted in similar complex crystal structures suggest that quantum chaos is a good description for thermalization processes in these systems, particularly in the high-temperature regime where the many phonon bands and their interactions dominate the thermal transport. Here we observe that for these systems diffusive thermal transport is controlled by a universal Planckian timescale τ∼ℏ/kBT and a unique velocity vE. Specifically, vE≈vph for complex insulators, and vph≲vE≪vF in the presence of strongly correlated itinerant electrons (vph and vF are the phonon and electron velocities, respectively). For the complex correlated electron systems we further show that charge diffusivity, while also reaching the Planckian relaxation bound, is largely dominated by the Fermi velocity of the electrons, hence suggesting that it is only the thermal (energy) diffusivity that describes chaos diffusivity.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 55
    Publication Date: 2019-03-12
    Description: SalmonellaTyphimurium can invade and survive within macrophages where the bacterium encounters a range of host environmental conditions. Like many bacteria,S.Typhimurium rapidly responds to changing environments by the use of second messengers such as cyclic di-GMP (c-di-GMP). Here, we generate a fluorescent biosensor to measure c-di-GMP concentrations in thousands of individual bacteria during macrophage infection and to define the sensor enzymes important to c-di-GMP regulation. Three sensor phosphodiesterases were identified as critical to maintaining low c-di-GMP concentrations generated after initial phagocytosis by macrophages. Maintenance of low c-di-GMP concentrations by these phosphodiesterases was required to promote survival within macrophages and virulence for mice. Attenuation ofS. Typhimurium virulence was due to overproduction of c-di-GMP−regulated cellulose, as deletion of the cellulose synthase machinery restored virulence to a strain lacking enzymatic activity of the three phosphodiesterases. We further identified that the cellulose-mediated reduction in survival was constrained to a slow-replicating persister population ofS.Typhimurium induced within the macrophage intracellular environment. As utilization of glucose has been shown to be required forS.Typhimurium macrophage survival, one possible hypothesis is that this persister population requires the glucose redirected to the synthesis of cellulose to maintain a slow-replicating, metabolically active state.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 56
    Publication Date: 2019-05-24
    Description: IgA is the most abundantly produced antibody in the body and plays a crucial role in gut homeostasis and mucosal immunity. IgA forms a dimer that covalently associates with the joining (J) chain, which is essential for IgA transport into the mucosa. Here, we demonstrate that the marginal zone B and B-1 cell-specific protein (MZB1) interacts with IgA through the α-heavy-chain tailpiece dependent on the penultimate cysteine residue and prevents the intracellular degradation of α-light-chain complexes. Moreover, MZB1 promotes J-chain binding to IgA and the secretion of dimeric IgA. MZB1-deficient mice are impaired in secreting large amounts of IgA into the gut in response to acute inflammation and develop severe colitis. Oral administration of a monoclonal IgA significantly ameliorated the colitis, accompanied by normalization of the gut microbiota composition. The present study identifies a molecular chaperone that promotes J-chain binding to IgA and reveals an important mechanism that controls the quantity, quality, and function of IgA.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 57
    Publication Date: 2019-02-25
    Description: Raindrop impact on infected plants can disperse micron-sized propagules of plant pathogens (e.g., spores of fungi). Little is known about the mechanism of how plant pathogens are liberated and transported due to raindrop impact. We used high-speed photography to observe thousands of dry-dispersed spores of the rust fungus Puccinia triticina being liberated from infected wheat plants following the impact of a single raindrop. We revealed that an air vortex ring was formed during the raindrop impact and carried the dry-dispersed spores away from the surface of the host plant. The maximum height and travel distance of the airborne spores increased with the aid of the air vortex. This unique mechanism of vortex-induced dispersal dynamics was characterized to predict trajectories of spores. Finally, we found that the spores transported by the air vortex can reach beyond the laminar boundary layer of leaves, which would enable the long-distance transport of plant pathogens through the atmosphere.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 58
    Publication Date: 2019-11-18
    Description: The avian predentary is a small skeletal structure located rostral to the paired dentaries found only in Mesozoic ornithuromorphs. The evolution and function of this enigmatic element is unknown. Skeletal tissues forming the predentary and the lower jaws in the basal ornithuromorph Yanornis martini are identified using computed-tomography, scanning electron microscopy, and histology. On the basis of these data, we propose hypotheses for the development, structure, and function of this element. The predentary is composed of trabecular bone. The convex caudal surface articulates with rostromedial concavities on the dentaries. These articular surfaces are covered by cartilage, which on the dentaries is divided into 3 discrete patches: 1 rostral articular cartilage and 2 symphyseal cartilages. The mechanobiology of avian cartilage suggests both compression and kinesis were present at the predentary–dentary joint, therefore suggesting a yet unknown form of avian cranial kinesis. Ontogenetic processes of skeletal formation occurring within extant taxa do not suggest the predentary originates within the dentaries, nor Meckel’s cartilage. We hypothesize that the predentary is a biomechanically induced sesamoid that arose within the soft connective tissues located rostral to the dentaries. The mandibular canal hosting the alveolar nerve suggests that the dentary teeth and predentary of Yanornis were proprioceptive. This whole system may have increased foraging efficiency. The Mesozoic avian predentary apparently coevolved with an edentulous portion of the premaxilla, representing a unique kinetic morphotype that combined teeth with a small functional beak and persisted successfully for ∼60 million years.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 59
    Publication Date: 2019-01-17
    Description: Human feet have evolved to facilitate bipedal locomotion, losing an opposable digit that grasped branches in favor of a longitudinal arch (LA) that stiffens the foot and aids bipedal gait. Passive elastic structures are credited with supporting the LA, but recent evidence suggests that plantar intrinsic muscles (PIMs) within the foot actively contribute to foot stiffness. To test the functional significance of the PIMs, we compared foot and lower limb mechanics with and without a tibial nerve block that prevented contraction of these muscles. Comparisons were made during controlled limb loading, walking, and running in healthy humans. An inability to activate the PIMs caused slightly greater compression of the LA when controlled loads were applied to the lower limb by a linear actuator. However, when greater loads were experienced during ground contact in walking and running, the stiffness of the LA was not altered by the block, indicating that the PIMs’ contribution to LA stiffness is minimal, probably because of their small size. With the PIMs blocked, the distal joints of the foot could not be stiffened sufficiently to provide normal push-off against the ground during late stance. This led to an increase in stride rate and compensatory power generated by the hip musculature, but no increase in the metabolic cost of transport. The results reveal that the PIMs have a minimal effect on the stiffness of the LA when absorbing high loads, but help stiffen the distal foot to aid push-off against the ground when walking or running bipedally.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 60
    Publication Date: 2019-05-08
    Description: Scalable nanomanufacturing enables the commercialization of nanotechnology, particularly in applications such as nanophotonics, silicon photonics, photovoltaics, and biosensing. Nanoimprinting lithography (NIL) was the first scalable process to introduce 3D nanopatterning of polymeric films. Despite efforts to extend NIL’s library of patternable media, imprinting of inorganic semiconductors has been plagued by concomitant generation of crystallography defects during imprinting. Here, we use an electrochemical nanoimprinting process—called Mac-Imprint—for directly patterning electronic-grade silicon with 3D microscale features. It is shown that stamps made of mesoporous metal catalysts allow for imprinting electronic-grade silicon without the concomitant generation of porous silicon damage while introducing mesoscale roughness. Unlike most NIL processes, Mac-Imprint does not rely on plastic deformation, and thus, it allows for replicating hard and brittle materials, such as silicon, from a reusable polymeric mold, which can be manufactured by almost any existing microfabrication technique.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 61
    Publication Date: 2019-12-10
    Description: Electrochemical reduction of CO2to multicarbon products is a significant challenge, especially for molecular complexes. We report here CO2reduction to multicarbon products based on a Ru(II) polypyridyl carbene complex that is immobilized on an N-doped porous carbon (RuPC/NPC) electrode. The catalyst utilizes the synergistic effects of the Ru(II) polypyridyl carbene complex and the NPC interface to steer CO2reduction toward C2 production at low overpotentials. In 0.5 M KHCO3/CO2aqueous solutions, Faradaic efficiencies of 31.0 to 38.4% have been obtained for C2 production at −0.87 to −1.07 V (vs. normal hydrogen electrode) with 21.0 to 27.5% for ethanol and 7.1 to 12.5% for acetate. Syngas is also produced with adjustable H2/CO mole ratios of 2.0 to 2.9. The RuPC/NPC electrocatalyst maintains its activity during 3-h CO2-reduction periods.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 62
    Publication Date: 2019-06-24
    Description: We present a mechanism for the anomalous behavior of the specific heat in low-temperature amorphous solids. The analytic solution of a mean-field model belonging to the same universality class as high-dimensional glasses, the spherical perceptron, suggests that there exists a cross-over temperature above which the specific heat scales linearly with temperature, while below it, a cubic scaling is displayed. This relies on two crucial features of the phase diagram: (i) the marginal stability of the free-energy landscape, which induces a gapless phase responsible for the emergence of a power-law scaling; and (ii) the vicinity of the classical jamming critical point, as the cross-over temperature gets lowered when approaching it. This scenario arises from a direct study of the thermodynamics of the system in the quantum regime, where we show that, contrary to crystals, the Debye approximation does not hold.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 63
    Publication Date: 2019-09-23
    Description: The condensation of half-light half-matter exciton polaritons in semiconductor optical cavities is a striking example of macroscopic quantum coherence in a solid-state platform. Quantum coherence is possible only when there are strong interactions between the exciton polaritons provided by their excitonic constituents. Rydberg excitons with high principal value exhibit strong dipole–dipole interactions in cold atoms. However, polaritons with the excitonic constituent that is an excited state, namely Rydberg exciton polaritons (REPs), have not yet been experimentally observed. Here, we observe the formation of REPs in a single crystal CsPbBr3 perovskite cavity without any external fields. These polaritons exhibit strong nonlinear behavior that leads to a coherent polariton condensate with a prominent blue shift. Furthermore, the REPs in CsPbBr3 are highly anisotropic and have a large extinction ratio, arising from the perovskite’s orthorhombic crystal structure. Our observation not only sheds light on the importance of many-body physics in coherent polariton systems involving higher-order excited states, but also paves the way for exploring these coherent interactions for solid-state quantum optical information processing.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 64
    Publication Date: 2019-06-18
    Description: A major obstacle to vaccination against antigenically variable viruses is skewing of antibody responses to variable immunodominant epitopes. For influenza virus hemagglutinin (HA), the immunodominance of the variable head impairs responses to the highly conserved stem. Here, we show that head immunodominance depends on the physical attachment of head to stem. Stem immunogenicity is enhanced by immunizing with stem-only constructs or by increasing local HA concentration in the draining lymph node. Surprisingly, coimmunization of full-length HA and stem alters stem-antibody class switching. Our findings delineate strategies for overcoming immunodominance, with important implications for human vaccination.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 65
    Publication Date: 2019-10-07
    Description: All cells, including nonexcitable cells, maintain a discrete transmembrane potential (Vmem), and have the capacity to modulate Vmem and respond to their own and neighbors’ changes in Vmem. Spatiotemporal variations have been described in developing embryonic tissues and in some cases have been implicated in influencing developmental processes. Yet, how such changes in Vmem are converted into intracellular inputs that in turn regulate developmental gene expression and coordinate patterned tissue formation, has remained elusive. Here we document that the Vmem of limb mesenchyme switches from a hyperpolarized to depolarized state during early chondrocyte differentiation. This change in Vmem increases intracellular Ca2+ signaling through Ca2+ influx, via CaV1.2, 1 of L-type voltage-gated Ca2+ channels (VGCCs). We find that CaV1.2 activity is essential for chondrogenesis in the developing limbs. Pharmacological inhibition by an L-type VGCC specific blocker, or limb-specific deletion of CaV1.2, down-regulates expression of genes essential for chondrocyte differentiation, including Sox9, Col2a1, and Agc1, and thus disturbs proper cartilage formation. The Ca2+-dependent transcription factor NFATc1, which is a known major transducer of intracellular Ca2+ signaling, partly rescues Sox9 expression. These data reveal instructive roles of CaV1.2 in limb development, and more generally expand our understanding of how modulation of membrane potential is used as a mechanism of developmental regulation.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 66
    Publication Date: 2019-08-19
    Description: An important feature of human cognition is the ability to flexibly and efficiently adapt behavior in response to continuously changing contextual demands. We leverage a large-scale dataset from Lumosity, an online cognitive-training platform, to investigate how cognitive processes involved in cued switching between tasks are affected by level of task practice across the adult lifespan. We develop a computational account of task switching that specifies the temporal dynamics of activating task-relevant representations and inhibiting task-irrelevant representations and how they vary with extended task practice across a number of age groups. Practice modulates the level of activation of the task-relevant representation and improves the rate at which this information becomes available, but has little effect on the task-irrelevant representation. While long-term practice improves performance across all age groups, it has a greater effect on older adults. Indeed, extensive task practice can make older individuals functionally similar to less-practiced younger individuals, especially for cognitive measures that focus on the rate at which task-relevant information becomes available.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 67
    Publication Date: 2019-12-06
    Description: The considerable interest in two-dimensional (2D) materials and complex molecular topologies calls for a robust experimental system for single-molecule studies. In this work, we study the equilibrium properties and deformation response of a complex DNA structure called a kinetoplast, a 2D network of thousands of linked rings akin to molecular chainmail. Examined in good solvent conditions, kinetoplasts appear as a wrinkled hemispherical sheet. The conformation of each kinetoplast is dictated by its network topology, giving it a unique shape, which undergoes small-amplitude thermal fluctuations at subsecond timescales, with a wide separation between fluctuation and diffusion timescales. They deform elastically when weakly confined and swell to their equilibrium dimensions when the confinement is released. We hope that, in the same way that linear DNA became a canonical model system on the first investigations of its polymer-like behavior, kinetoplasts can serve that role for 2D and catenated polymer systems.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 68
    Publication Date: 2019-04-16
    Description: While studying spontaneous mutations at the maize bronze (bz) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate new bz mutations from several Bz stocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stable bz mutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneous wx mutations [Wessler S (1997) The Mutants of Maize, pp 385–386]. Similar mutations were recovered at the closely linked sh locus. These events occurred with a frequency of 2–4 × 10−5 in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, like Hopscotch, Magellan, and Bs2, a Bs1 variant, were described previously; others, like Foto and Focou in 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition of Hopscotch, Magellan, and Bs2 occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 69
    Publication Date: 2019-07-24
    Description: A recently proposed oxidative damage protection mechanism in proteins relies on hole hopping escape routes formed by redox-active amino acids. We present a computational tool to identify the dominant charge hopping pathways through these residues based on the mean residence times of the transferring charge along these hopping pathways. The residence times are estimated by combining a kinetic model with well-known rate expressions for the charge-transfer steps in the pathways. We identify the most rapid hole hopping escape routes in cytochrome P450 monooxygenase, cytochrome c peroxidase, and benzylsuccinate synthase (BSS). This theoretical analysis supports the existence of hole hopping chains as a mechanism capable of providing hole escape from protein catalytic sites on biologically relevant timescales. Furthermore, we find that pathways involving the [4Fe4S] cluster as the terminal hole acceptor in BSS are accessible on the millisecond timescale, suggesting a potential protective role of redox-active cofactors for preventing protein oxidative damage.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 70
    Publication Date: 2019-07-24
    Description: Our understanding of the rotary-coupling mechanism of F1-ATPase has been greatly enhanced in the last decade by advances in X-ray crystallography, single-molecular imaging, and theoretical models. Recently, Volkán-Kacsó and Marcus [S. Volkán-Kacsó, R. A. Marcus, Proc. Natl. Acad. Sci. U.S.A. 112, 14230 (2015)] presented an insightful thermodynamic model based on the Marcus reaction theory coupled with an elastic structural deformation term to explain the observed γ-rotation angle dependence of the adenosine triphosphate (ATP)/adenosine diphosphate (ADP) exchange rates of F1-ATPase. Although the model is successful in correlating single-molecule data, it is not in agreement with the available theoretical results. We describe a revision of the model, which leads to consistency with the simulation results and other experimental data on the F1-ATPase rotor compliance. Although the free energy liberated on ATP hydrolysis by F1-ATPase is rapidly dissipated as heat and so cannot contribute directly to the rotation, we show how, nevertheless, F1-ATPase functions near the maximum possible efficiency. This surprising result is a consequence of the differential binding of ATP and its hydrolysis products ADP and Pi along a well-defined pathway.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 71
    Publication Date: 2019-07-24
    Description: Eukaryotic cells express transcription factor (TF) paralogues that bind to nearly identical DNA sequences in vitro but bind at different genomic loci and perform different functions in vivo. Predicting how 2 paralogous TFs bind in vivo using DNA sequence alone is an important open problem. Here, we analyzed 2 yeast bHLH TFs, Cbf1p and Tye7p, which have highly similar binding preferences in vitro, yet bind at almost completely nonoverlapping target loci in vivo. We dissected the determinants of specificity for these 2 proteins by making a number of chimeric TFs in which we swapped different domains of Cbf1p and Tye7p and determined the effects on in vivo binding and cellular function. From these experiments, we learned that the Cbf1p dimer achieves its specificity by binding cooperatively with other Cbf1p dimers bound nearby. In contrast, we found that Tye7p achieves its specificity by binding cooperatively with 3 other DNA-binding proteins, Gcr1p, Gcr2p, and Rap1p. Remarkably, most promoters (63%) that are bound by Tye7p do not contain a consensus Tye7p binding site. Using this information, we were able to build simple models to accurately discriminate bound and unbound genomic loci for both Cbf1p and Tye7p. We then successfully reprogrammed the human bHLH NPAS2 to bind Cbf1p in vivo targets and a Tye7p target intergenic region to be bound by Cbf1p. These results demonstrate that the genome-wide binding targets of paralogous TFs can be discriminated using sequence information, and provide lessons about TF specificity that can be applied across the phylogenetic tree.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 72
    Publication Date: 2019-02-04
    Description: Much contemporary rhetoric regards the prospects and pitfalls of using artificial intelligence techniques to automate an increasing range of tasks, especially those once considered the purview of people alone. These accounts are often wildly optimistic, understating outstanding challenges while turning a blind eye to the human labor that undergirds and sustains ostensibly “automated” services. This long-standing focus on purely automated methods unnecessarily cedes a promising design space: one in which computational assistance augments and enriches, rather than replaces, people’s intellectual work. This tension between human agency and machine automation poses vital challenges for design and engineering. In this work, we consider the design of systems that enable rich, adaptive interaction between people and algorithms. We seek to balance the often-complementary strengths and weaknesses of each, while promoting human control and skillful action. We share case studies of interactive systems we have developed in three arenas—data wrangling, exploratory analysis, and natural language translation—that integrate proactive computational support into interactive systems. To improve outcomes and support learning by both people and machines, we describe the use of shared representations of tasks augmented with predictive models of human capabilities and actions. We conclude with a discussion of future prospects and scientific frontiers for intelligence augmentation research.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 73
    Publication Date: 2019-03-25
    Description: Phosphorylation of histone H2AX is a major contributor to efficient DNA repair. We recently reported neurobehavioral deficits in mice lacking H2AX. Here we establish that this neural failure stems from impairment of mitochondrial function and repression of the mitochondrial biogenesis gene PGC-1α. H2AX loss leads to reduced levels of the major subunits of the mitochondrial respiratory complexes in mouse embryonic fibroblasts and in the striatum, a brain region particularly vulnerable to mitochondrial damage. These defects are substantiated by disruption of the mitochondrial shape in H2AX mutant cells. Ectopic expression of PGC-1α restores mitochondrial oxidative phosphorylation complexes and mitigates cell death. H2AX knockout mice display increased neuronal death in the brain when challenged with 3-nitropronionic acid, which targets mitochondria. This study establishes a role for H2AX in mitochondrial homeostasis associated with neuroprotection.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 74
    Publication Date: 2019-06-18
    Description: BRUCE/Apollon is a membrane-associated inhibitor of apoptosis protein that is essential for viability and has ubiquitin-conjugating activity. On initiation of apoptosis, the ubiquitin ligase Nrdp1/RNF41 promotes proteasomal degradation of BRUCE. Here we demonstrate that BRUCE together with the proteasome activator PA28γ causes proteasomal degradation of LC3-I and thus inhibits autophagy. LC3-I on the phagophore membrane is conjugated to phosphatidylethanolamine to form LC3-II, which is required for the formation of autophagosomes and selective recruitment of substrates. SIP/CacyBP is a ubiquitination-related protein that is highly expressed in neurons and various tumors. Under normal conditions, SIP inhibits the ubiquitination and degradation of BRUCE, probably by blocking the binding of Nrdp1 to BRUCE. On DNA damage by topoisomerase inhibitors, Nrdp1 causes monoubiquitination of SIP and thus promotes apoptosis. However, on starvation, SIP together with Rab8 enhances the translocation of BRUCE into the recycling endosome, formation of autophagosomes, and degradation of BRUCE by optineurin-mediated autophagy. Accordingly, deletion of SIP in cultured cells reduces the autophagic degradation of damaged mitochondria and cytosolic protein aggregates. Thus, by stimulating proteasomal degradation of LC3-I, BRUCE also inhibits autophagy. Conversely, SIP promotes autophagy by blocking BRUCE-dependent degradation of LC3-I and by enhancing autophagosome formation and autophagic destruction of BRUCE. These actions of BRUCE and SIP represent mechanisms that link the regulation of autophagy and apoptosis under different conditions.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 75
    Publication Date: 2019-01-11
    Description: Coordinated dynamics of individual components in active matter are an essential aspect of life on all scales. Establishing a comprehensive, causal connection between intracellular, intercellular, and macroscopic behaviors has remained a major challenge due to limitations in data acquisition and analysis techniques suitable for multiscale dynamics. Here, we combine a high-throughput adaptive microscopy approach with machine learning, to identify key biological and physical mechanisms that determine distinct microscopic and macroscopic collective behavior phases which develop as Bacillus subtilis swarms expand over five orders of magnitude in space. Our experiments, continuum modeling, and particle-based simulations reveal that macroscopic swarm expansion is primarily driven by cellular growth kinetics, whereas the microscopic swarming motility phases are dominated by physical cell–cell interactions. These results provide a unified understanding of bacterial multiscale behavioral complexity in swarms.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 76
    Publication Date: 2019-05-03
    Description: The quantum Hall effect has recently been generalized from transport of conserved charges to include transport of other approximately conserved-state variables, including spin and valley, via spin- or valley-polarized boundary states with different chiralities. Here, we report a class of quantum Hall effect in Bernal- or ABA-stacked trilayer graphene (TLG), the quantum parity Hall (QPH) effect, in which boundary channels are distinguished by even or odd parity under the system’s mirror reflection symmetry. At the charge neutrality point, the longitudinal conductance σxx is first quantized to 4e2/h at a small perpendicular magnetic field B⊥, establishing the presence of four edge channels. As B⊥ increases, σxx first decreases to 2e2/h, indicating spin-polarized counterpropagating edge states, and then, to approximately zero. These behaviors arise from level crossings between even- and odd-parity bulk Landau levels driven by exchange interactions with the underlying Fermi sea, which favor an ordinary insulator ground state in the strong B⊥ limit and a spin-polarized state at intermediate fields. The transitions between spin-polarized and -unpolarized states can be tuned by varying Zeeman energy. Our findings demonstrate a topological phase that is protected by a gate-controllable symmetry and sensitive to Coulomb interactions.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 77
    Publication Date: 2019-02-28
    Description: The Hedgehog-signaling pathway is an important target in cancer research and regenerative medicine; yet, on the cellular level, many steps are still poorly understood. Extensive studies of the bulk behavior of the key proteins in the pathway established that during signal transduction they dynamically localize in primary cilia, antenna-like solitary organelles present on most cells. The secreted Hedgehog ligand Sonic Hedgehog (SHH) binds to its receptor Patched1 (PTCH1) in primary cilia, causing its inactivation and delocalization from cilia. At the same time, the transmembrane protein Smoothened (SMO) is released of its inhibition by PTCH1 and accumulates in cilia. We used advanced, single molecule-based microscopy to investigate these processes in live cells. As previously observed for SMO, PTCH1 molecules in cilia predominantly move by diffusion and less frequently by directional transport, and spend a fraction of time confined. After treatment with SHH we observed two major changes in the motional dynamics of PTCH1 in cilia. First, PTCH1 molecules spend more time as confined, and less time freely diffusing. This result could be mimicked by a depletion of cholesterol from cells. Second, after treatment with SHH, but not after cholesterol depletion, the molecules that remain in the diffusive state showed a significant increase in the diffusion coefficient. Therefore, PTCH1 inactivation by SHH changes the diffusive motion of PTCH1, possibly by modifying the membrane microenvironment in which PTCH1 resides.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 78
    Publication Date: 2019-05-30
    Description: We introduce a mathematical framework that allows one to carry out multiscalar and multigroup spatial exploratory analysis across urban regions. By producing coefficients that integrate information across all scales and that are normalized with respect to theoretical maximally segregated configurations, this framework provides a practical and powerful tool for the comparative empirical analysis of urban segregation. We illustrate our method with a study of ethnic mixing in the Los Angeles metropolitan area.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 79
    Publication Date: 2019-04-19
    Description: Graphene-based nanodevices have been developed rapidly and are now considered a strong contender for postsilicon electronics. However, one challenge facing graphene-based transistors is opening a sizable bandgap in graphene. The largest bandgap achieved so far is several hundred meV in bilayer graphene, but this value is still far below the threshold for practical applications. Through in situ electrical measurements, we observed a semiconducting character in compressed trilayer graphene by tuning the interlayer interaction with pressure. The optical absorption measurements demonstrate that an intrinsic bandgap of 2.5 ± 0.3 eV could be achieved in such a semiconducting state, and once opened could be preserved to a few GPa. The realization of wide bandgap in compressed trilayer graphene offers opportunities in carbon-based electronic devices.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 80
    Publication Date: 2019-01-17
    Description: Shape, size, and composition are the most fundamental design features, enabling highly complex functionalities. Despite recent advances, the independent control of shape, size, and chemistry of macromolecules remains a synthetic challenge. We report a scalable methodology to produce large, well-defined macromolecules with programmable shape, size, and chemistry that combines reactor engineering principles and controlled polymerizations. Specifically, bottlebrush polymers with conical, ellipsoidal, and concave architectures are synthesized using two orthogonal polymerizations. The chemical versatility is highlighted by the synthesis of a compositional asymmetric cone. The strong agreement between predictions and experiments validates the precision that this methodology offers.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 81
    Publication Date: 2019-05-30
    Description: Neural stem cells (NSCs) are primary progenitor cells in the early developmental stage in the brain that initiate a diverse lineage of differentiated neurons and glia. Radial glial cells (RGCs), a type of neural stem cell in the ventricular zone, are essential for nurturing and delivering new immature neurons to the appropriate cortical target layers. Here we report that Anoctamin 1 (ANO1)/TMEM16A, a Ca2+-activated chloride channel, mediates the Ca2+-dependent process extension of RGCs. ANO1 is highly expressed and functionally active in RGCs of the mouse embryonic ventricular zone. Knockdown of ANO1 suppresses RGC process extension and protrusions, whereas ANO1 overexpression stimulates process extension. Among various trophic factors, brain-derived neurotrophic factor (BDNF) activates ANO1, which is required for BDNF-induced process extension in RGCs. More importantly, Ano1-deficient mice exhibited disrupted cortical layers and reduced cortical thickness. We thus conclude that the regulation of RGC process extension by ANO1 contributes to the normal formation of mouse embryonic brain.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 82
    Publication Date: 2019-06-12
    Description: Ion exchange, as a postsynthetic transformation strategy, offers more flexibilities in controlling material compositions and structures beyond direct synthetic methodology. Observation of such transformation kinetics on the single-particle level with rich spatial and spectroscopic information has never been achieved. We report the quantitative imaging of anion exchange kinetics in individual single-crystalline halide perovskite nanoplates using confocal photoluminescence microscopy. We have systematically observed a symmetrical anion exchange pathway on the nanoplates with dependence on reaction time and plate thickness, which is governed by the crystal structure and the diffusion-limited transformation mechanism. Based on a reaction–diffusion model, the halide diffusion coefficient was estimated to be on the order of10−14cm2⋅s−1. This diffusion-controlled mechanism leads to the formation of 2D perovskite heterostructures with spatially resolved coherent interface through the precisely controlled anion exchange reaction, offering a design protocol for tailoring functionalities of semiconductors at the nano-/microscale.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 83
    Publication Date: 2019-02-06
    Description: Successful efforts to activate T cells capable of recognizing weak cancer-associated self-antigens have employed altered peptide antigens to activate T cell responses capable of cross-reacting on native tumor-associated self. A limitation of this approach is the requirement for detailed knowledge about the altered self-peptide ligands used in these vaccines. In the current study we considered allorecognition as an approach for activating CTL capable of recognizing weak or self-antigens in the context of self-MHC. Nonself antigen-presenting molecules typically contain polymorphisms that influence interactions with the bound peptide and TCR interface. Recognition of these nonself structures results in peptide-dependent alloimmunity. Alloreactive T cells target their inducing alloantigens as well as third-party alloantigens but generally fail to target self-antigens. Certain residues located on the alpha-1/2 domains of class I antigen-presenting molecules primarily interface with TCR. These residues are more conserved within and across species than are residues that determine peptide antigen binding properties. Class I variants designed with amino acid substitutions at key positions within the conserved helical structures are shown to provide strong activating signals to alloreactive CD8 T cells while avoiding changes in naturally bound peptide ligands. Importantly, CTL activated in this manner can break self-tolerance by reacting to self-peptides presented by native MHC. The ability to activate self-tolerant T cells capable of cross-reacting on self-peptide-MHC in vivo represents an approach for inducing autoimmunity, with possible application in cancer vaccines.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 84
    Publication Date: 2019-10-09
    Description: Episodic memories hinge upon our ability to process a wide range of multisensory information and bind this information into a coherent, memorable representation. On a neural level, these 2 processes are thought to be supported by neocortical alpha/beta desynchronization and hippocampal theta/gamma synchronization, respectively. Intuitively, these 2 processes should couple to successfully create and retrieve episodic memories, yet this hypothesis has not been tested empirically. We address this by analyzing human intracranial electroencephalogram data recorded during 2 associative memory tasks. We find that neocortical alpha/beta (8 to 20 Hz) power decreases reliably precede and predict hippocampal “fast” gamma (60 to 80 Hz) power increases during episodic memory formation; during episodic memory retrieval, however, hippocampal “slow” gamma (40 to 50 Hz) power increases reliably precede and predict later neocortical alpha/beta power decreases. We speculate that this coupling reflects the flow of information from the neocortex to the hippocampus during memory formation, and hippocampal pattern completion inducing information reinstatement in the neocortex during memory retrieval.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 85
    Publication Date: 2019-10-14
    Description: Human cells express up to 9 active DNA cytosine deaminases with functions in adaptive and innate immunity. Many cancers manifest an APOBEC mutation signature and APOBEC3B (A3B) is likely the main enzyme responsible. Although significant numbers of APOBEC signature mutations accumulate in tumor genomes, the majority of APOBEC-catalyzed uracil lesions are probably counteracted in an error-free manner by the uracil base excision repair pathway. Here, we show that A3B-expressing cells can be selectively killed by inhibiting uracil DNA glycosylase 2 (UNG) and that this synthetic lethal phenotype requires functional mismatch repair (MMR) proteins and p53. UNG knockout human 293 and MCF10A cells elicit an A3B-dependent death. This synthetic lethal phenotype is dependent on A3B catalytic activity and reversible by UNG complementation. A3B expression in UNG-null cells causes a buildup of genomic uracil, and the ensuing lethality requires processing of uracil lesions (likely U/G mispairs) by MSH2 and MLH1 (likely noncanonical MMR). Cancer cells expressing high levels of endogenous A3B and functional p53 can also be killed by expressing an UNG inhibitor. Taken together, UNG-initiated base excision repair is a major mechanism counteracting genomic mutagenesis by A3B, and blocking UNG is a potential strategy for inducing the selective death of tumors.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 86
    Publication Date: 2019-10-07
    Description: Antibiotics induce large and highly variable changes in the intestinal microbiome even at sublethal concentrations, through mechanisms that remain elusive. Using gnotobiotic zebrafish, which allow high-resolution examination of microbial dynamics, we found that sublethal doses of the common antibiotic ciprofloxacin cause severe drops in bacterial abundance. Contrary to conventional views of antimicrobial tolerance, disruption was more pronounced for slow-growing, aggregated bacteria than for fast-growing, planktonic species. Live imaging revealed that antibiotic treatment promoted bacterial aggregation and increased susceptibility to intestinal expulsion. Intestinal mechanics therefore amplify the effects of antibiotics on resident bacteria. Microbial dynamics are captured by a biophysical model that connects antibiotic-induced collapses to gelation phase transitions in soft materials, providing a framework for predicting the impact of antibiotics on the intestinal microbiome.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 87
    Publication Date: 2019-11-11
    Description: Receptor-activity–modifying proteins (RAMPs) are single transmembrane-spanning proteins which serve as molecular chaperones and allosteric modulators of G-protein–coupled receptors (GPCRs) and their signaling pathways. Although RAMPs have been previously studied in the context of their effects on Family B GPCRs, the coevolution of RAMPs with many GPCR families suggests an expanded repertoire of potential interactions. Using bioluminescence resonance energy transfer-based and cell-surface expression approaches, we comprehensively screen for RAMP interactions within the chemokine receptor family and identify robust interactions between RAMPs and nearly all chemokine receptors. Most notably, we identify robust RAMP interaction with atypical chemokine receptors (ACKRs), which function to establish chemotactic gradients for directed cell migration. Specifically, RAMP3 association with atypical chemokine receptor 3 (ACKR3) diminishes adrenomedullin (AM) ligand availability without changing G-protein coupling. Instead, RAMP3 is required for the rapid recycling of ACKR3 to the plasma membrane through Rab4-positive vesicles following either AM or SDF-1/CXCL12 binding, thereby enabling formation of dynamic spatiotemporal chemotactic gradients. Consequently, genetic deletion of either ACKR3 or RAMP3 in mice abolishes directed cell migration of retinal angiogenesis. Thus, RAMP association with chemokine receptor family members represents a molecular interaction to control receptor signaling and trafficking properties.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 88
    Publication Date: 2019-10-14
    Description: KRAS mutations occur in ∼35% of colorectal cancers and promote tumor growth by constitutively activating the mitogen-activated protein kinase (MAPK) pathway. KRAS mutations at codons 12, 13, or 61 are thought to prevent GAP protein-stimulated GTP hydrolysis and render KRAS-mutated colorectal cancers unresponsive to epidermal growth factor receptor (EGFR) inhibitors. We report here that KRAS G13-mutated cancer cells are frequently comutated with NF1 GAP but NF1 is rarely mutated in cancers with KRAS codon 12 or 61 mutations. Neurofibromin protein (encoded by the NF1 gene) hydrolyzes GTP directly in complex with KRAS G13D, and KRAS G13D-mutated cells can respond to EGFR inhibitors in a neurofibromin-dependent manner. Structures of the wild type and G13D mutant of KRAS in complex with neurofibromin (RasGAP domain) provide the structural basis for neurofibromin-mediated GTP hydrolysis. These results reveal that KRAS G13D is responsive to neurofibromin-stimulated hydrolysis and suggest that a subset of KRAS G13-mutated colorectal cancers that are neurofibromin-competent may respond to EGFR therapies.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 89
    Publication Date: 2019-11-18
    Description: Oil and gas well leakage is of public concern primarily due to the perceived risks of aquifer contamination and greenhouse gas (GHG) emissions. This study examined well leakage data from the British Columbia Oil and Gas Commission (BC OGC) to identify leakage pathways and initially quantify incident rates of leakage and GHG emissions from leaking wells. Three types of leakage are distinguished: “surface casing vent flow” (SCVF), “outside the surface casing leakage” (OSCL), and “cap leakage” (CL). In British Columbia (BC), the majority of reported incidents involve SCVF of gases, which does not pose a risk of aquifer contamination but does contribute to GHG emissions. Reported liquid leakage of brines and hydrocarbons is rarer. OSCL and CL of gas are more serious problems due to the risk of long-term leakage from abandoned wells; some were reported to be leaking gas several decades after they were permanently abandoned. According to the requirements of provincial regulation, 21,525 have been tested for leakage. In total, 2,329 wells in BC have had reported leakage during the lifetime of the well. This represents 10.8% of all wells in the assumed test population. However, it seems likely that wells drilled and/or abandoned before 2010 have unreported leakage. In BC, the total GHG emission from gas SCVF is estimated to reach about 75,000 t/y based on the existing inventory calculation; however, this number is likely higher due to underreporting.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 90
    Publication Date: 2019-05-29
    Description: The primary cilium permits compartmentalization of specific signaling pathways, including elements of the Hedgehog (Hh) pathway. Hh transcriptional activity is thought to be negatively regulated by constitutively high ciliary cAMP maintained by the Gα(s)-coupled GPCR, GPR161. However, cilia also sequester many other Gα(s)-coupled GPCRs with unknown potential to regulate Hh. Here we used biosensors optimized for ciliary cAMP and strategies to isolate signals in the cilium from the cell body and neighboring cells. We found that ciliary cAMP was not elevated relative to cellular cAMP, inconsistent with constitutive cAMP production. Gα(s)-coupled GPCRs (e.g., the 5-HT6 serotonin and D1R dopamine receptor) had reduced ability to generate cAMP upon trafficking to the ciliary membrane. However, activation of the Hh pathway restored or amplified GPCR function to permit cAMP elevation selectively in the cilium. Hh therefore enables its own local GPCR-dependent cAMP regulatory circuit. Considering that GPCRs comprise much of the druggable genome, these data suggest alternative strategies to modify Hh signaling.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 91
    Publication Date: 2019-09-11
    Description: The elucidation of the detailed mechanism used by F0 to convert proton gradient to torque and rotational motion presents a major puzzle despite significant biophysical and structural progress. Although the conceptual model has advanced our understanding of the working principles of such systems, it is crucial to explore the actual mechanism using structure-based models that actually reproduce a unidirectional proton-driven rotation. Our previous work used a coarse-grained (CG) model to simulate the action of F0. However, the simulations were based on a very tentative structural model of the interaction between subunit a and subunit c. Here, we again use a CG model but with a recent cryo-EM structure of cF1F0 and also explore the proton path using our water flooding and protein dipole Langevin dipole semimacroscopic formalism with its linear response approximation version (PDLD/S-LRA) approaches. The simulations are done in the combined space defined by the rotational coordinate and the proton transport coordinate. The study reproduced the effect of the protomotive force on the rotation of the F0 while establishing the electrostatic origin of this effect. Our landscape reproduces the correct unidirectionality of the synthetic direction of the F0 rotation and shows that it reflects the combined electrostatic coupling between the proton transport path and the c-ring conformational change. This work provides guidance for further studies in other proton-driven mechanochemical systems and should lead (when combined with studies of F1) to a complete energy transduction picture of the F0F1-ATPase system.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 92
    Publication Date: 2019-03-08
    Description: Apicomplexan parasites replicate within a protective organelle, called the parasitophorous vacuole (PV). TheToxoplasma gondiiPV is filled with a network of tubulated membranes, which are thought to facilitate trafficking of effectors and nutrients. Despite being critical to parasite virulence, there is scant mechanistic understanding of the network’s functions. Here, we identify the parasite-secreted kinase WNG1 (With-No-Gly-loop) as a critical regulator of tubular membrane biogenesis. WNG1 family members adopt an atypical protein kinase fold lacking the glycine rich ATP-binding loop that is required for catalysis in canonical kinases. Unexpectedly, we find that WNG1 is an active protein kinase that localizes to the PV lumen and phosphorylates PV-resident proteins, several of which are essential for the formation of a functional intravacuolar network. Moreover, we show that WNG1-dependent phosphorylation of these proteins is required for their membrane association, and thus their ability to tubulate membranes. Consequently, WNG1 knockout parasites have an aberrant PV membrane ultrastructure. Collectively, our results describe a unique family ofToxoplasmakinases and implicate phosphorylation of secreted proteins as a mechanism of regulating PV development during parasite infection.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 93
    Publication Date: 2019-01-23
    Description: Pre-mRNA splicing must occur with extremely high fidelity. Spliceosomes assemble onto pre-mRNA guided by specific sequences (5′ splice site, 3′ splice site, and branchpoint). When splice sites are mutated, as in many hereditary diseases, the spliceosome can aberrantly select nearby pseudo- or “cryptic” splice sites, often resulting in nonfunctional protein. How the spliceosome distinguishes authentic splice sites from cryptic splice sites is poorly understood. We performed aCaenorhabditis elegansgenetic screen to find cellular factors that affect the frequency with which the spliceosome uses cryptic splice sites and identified two alleles in core spliceosome component Prp8 that alter cryptic splicing frequency. Subsequent complementary genetic and structural analyses in yeast implicate these alleles in the stability of the spliceosome’s catalytic core. However, despite a clear effect on cryptic splicing, high-throughput mRNA sequencing of theseprp-8mutantC. elegansreveals that overall alternative splicing patterns are relatively unchanged. Our data suggest the spliceosome evolved intrinsic mechanisms to reduce the occurrence of cryptic splicing and that these mechanisms are distinct from those that impact alternative splicing.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 94
    Publication Date: 2019-08-13
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 95
    Publication Date: 2019-04-08
    Description: Kirigami-inspired metamaterials are attracting increasing interest because of their ability to achieve extremely large strains and shape changes via out-of-plane buckling. While in flat kirigami sheets, the ligaments buckle simultaneously as Euler columns, leading to a continuous phase transition; here, we demonstrate that kirigami shells can also support discontinuous phase transitions. Specifically, we show via a combination of experiments, numerical simulations, and theoretical analysis that, in cylindrical kirigami shells, the snapping-induced curvature inversion of the initially bent ligaments results in a pop-up process that first localizes near an imperfection and then, as the deformation is increased, progressively spreads through the structure. Notably, we find that the width of the transition zone as well as the stress at which propagation of the instability is triggered can be controlled by carefully selecting the geometry of the cuts and the curvature of the shell. Our study significantly expands the ability of existing kirigami metamaterials and opens avenues for the design of the next generation of responsive surfaces as demonstrated by the design of a smart skin that significantly enhances the crawling efficiency of a simple linear actuator.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 96
    Publication Date: 2019-12-16
    Description: Kirigami (cutting and/or folding) offers a promising strategy to reconfigure metamaterials. Conventionally, kirigami metamaterials are often composed of passive cut unit cells to be reconfigured under mechanical forces. The constituent stimuli-responsive materials in active kirigami metamaterials instead will enable potential mechanical properties and functionality, arising from the active control of cut unit cells. However, the planar features of hinges in conventional kirigami structures significantly constrain the degrees of freedom (DOFs) in both deformation and actuation of the cut units. To release both constraints, here, we demonstrate a universal design of implementing folds to reconstruct sole-cuts–based metamaterials. We show that the supplemented folds not only enrich the structural reconfiguration beyond sole cuts but also enable more DOFs in actuating the kirigami metasheets into 3 dimensions (3D) in response to environmental temperature. Utilizing the multi-DOF in deformation of unit cells, we demonstrate that planar metasheets with the same cut design can self-fold into programmable 3D kirigami metastructures with distinct mechanical properties. Last, we demonstrate potential applications of programmable kirigami machines and easy-turning soft robots.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 97
    Publication Date: 2019-12-16
    Description: Studies of the factors governing global patterns of biodiversity are key to predicting community responses to ongoing and future abiotic and biotic changes. Although most research has focused on present-day climate, a growing body of evidence indicates that modern ecological communities may be significantly shaped by paleoclimatic change and past anthropogenic factors. However, the generality of this pattern is unknown, as global analyses are lacking. Here we quantify the phylogenetic and functional trait structure of 515 tropical and subtropical large mammal communities and predict their structure from past and present climatic and anthropogenic factors. We find that the effects of Quaternary paleoclimatic change are strongest in the Afrotropics, with communities in the Indomalayan realm showing mixed effects of modern climate and paleoclimate. Malagasy communities are poorly predicted by any single factor, likely due to the atypical history of the island compared with continental regions. Neotropical communities are mainly codetermined by modern climate and prehistoric and historical human impacts. Overall, our results indicate that the factors governing tropical and subtropical mammalian biodiversity are complex, with the importance of past and present factors varying based on the divergent histories of the world’s biogeographic realms and their native biotas. Consideration of the evolutionary and ecological legacies of both the recent and ancient past are key to understanding the forces shaping global patterns of present-day biodiversity and its response to ongoing and future abiotic and biotic changes in the 21st century.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 98
    Publication Date: 2019-01-24
    Description: Agricultural expansion remains the most prominent proximate cause of tropical deforestation in Latin America, a region characterized by deforestation rates substantially above the world average and extremely high inequality. This paper deploys several multivariate statistical models to test whether different aspects of inequality, within a context of increasing agricultural productivity, promote agricultural expansion (Jevons paradox) or contraction (land-sparing) in 10 Latin American countries over 1990–2010. Here I show the existence of distinct patterns between the instantaneous and the overall (i.e., accounting for temporal lags) effect of increasing agricultural productivity, conditional on the degree of income, land, and wealth inequality. In a context of perfect equality, the instantaneous effect of increases in agricultural productivity is to promote agricultural expansion (Jevons paradox). When temporal lags are accounted for, agricultural productivity appears to be mainly land-sparing. Increases in the level of inequality, in all its forms, promote agricultural expansion, thus eroding the land-sparing effects of increasing productivity. The results also suggest that the instantaneous impact of inequality is larger than the overall effect (accounting for temporal lags) and that the effects of income inequality are stronger than those of land and wealth inequality, respectively. Reaping the benefits of increasing agricultural productivity, and achieving sustainable agricultural intensification in Latin America, requires policy interventions that specifically address inequality.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 99
    Publication Date: 2019-08-01
    Description: The accurate prediction of protein stability upon sequence mutation is an important but unsolved challenge in protein engineering. Large mutational datasets are required to train computational predictors, but traditional methods for collecting stability data are either low-throughput or measure protein stability indirectly. Here, we develop an automated method to generate thermodynamic stability data for nearly every single mutant in a small 56-residue protein. Analysis reveals that most single mutants have a neutral effect on stability, mutational sensitivity is largely governed by residue burial, and unexpectedly, hydrophobics are the best tolerated amino acid type. Correlating the output of various stability-prediction algorithms against our data shows that nearly all perform better on boundary and surface positions than for those in the core and are better at predicting large-to-small mutations than small-to-large ones. We show that the most stable variants in the single-mutant landscape are better identified using combinations of 2 prediction algorithms and including more algorithms can provide diminishing returns. In most cases, poor in silico predictions were tied to compositional differences between the data being analyzed and the datasets used to train the algorithm. Finally, we find that strategies to extract stabilities from high-throughput fitness data such as deep mutational scanning are promising and that data produced by these methods may be applicable toward training future stability-prediction tools.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 100
    Publication Date: 2019-09-09
    Description: Combination chemotherapy can increase treatment efficacy and suppress drug resistance. Knowledge of how to engineer rational, mechanism-based drug combinations, however, remains lacking. Although studies of drug activity have historically focused on the primary drug–target interaction, growing evidence has emphasized the importance of the subsequent consequences of this interaction. Bedaquiline (BDQ) is the first new drug for tuberculosis (TB) approved in more than 40 y, and a species-selective inhibitor of the Mycobacterium tuberculosis (Mtb) ATP synthase. Curiously, BDQ-mediated killing of Mtb lags significantly behind its inhibition of ATP synthase, indicating a mode of action more complex than the isolated reduction of ATP pools. Here, we report that BDQ-mediated inhibition of Mtb’s ATP synthase triggers a complex metabolic response indicative of a specific hierarchy of ATP-dependent reactions. We identify glutamine synthetase (GS) as an enzyme whose activity is most responsive to changes in ATP levels. Chemical supplementation with exogenous glutamine failed to affect BDQ’s antimycobacterial activity. However, further inhibition of Mtb’s GS synergized with and accelerated the onset of BDQ-mediated killing, identifying Mtb’s glutamine synthetase as a collateral, rather than directly antimycobacterial, metabolic vulnerability of BDQ. These findings reveal a previously unappreciated physiologic specificity of ATP and a facet of mode-of-action biology we term collateral vulnerability, knowledge of which has the potential to inform the development of rational, mechanism-based drug combinations.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...