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  • Cell & Developmental Biology
  • Chemical Engineering
  • Genetics
  • Physical Chemistry
  • 2015-2019  (114)
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Year
  • 1
    Publication Date: 2021-05-19
    Description: One of the main tasks of modern genetics is the study of the genetic diversity of organisms of different taxonomic levels. Such genome studies can serve as a tool for solving problems associated with identifying the evolutionary mechanisms by which genetic diversity has emerged. Discussions are still ongoing on micro- and macroevolutionary processes that can lead to a variety of genes and taxonomic diversity in the species of the Prussian carp Carassius auratus gibelio Bloch. It should also be noted that these studies have started relatively recently, and many questions concerning the genetic research of carp are still open.
    Description: Одной из основных задач современной генетики является изучение генетического разнообразия организмов различного таксономического уровня. Такие исследования геномов могут послужить инструментом для решения проблем, связанных с выявлением эволюционных механизмов, с помощью которых появилось генетическое разнообразие. До сих пор ведутся дискуссии относительно микро- и макроэволюционных процессов, которые могут приводить к разнообразию генов и таксономическому разнообразию у видов серебряного карася Carassius auratus gibelio Bloch. Также нужно отметить то, что данные исследования начались относительно недавно, и многие вопросы, касающиеся генетических исследований карася, остаются открытыми.
    Description: Published
    Keywords: Carassius auratus gibelio ; Genetics ; Prussian carp ; Evolution ; Taxonomy
    Repository Name: AquaDocs
    Type: Conference Material , Non Refereed
    Format: pp.228-232
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  • 2
    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 Capotondi, A., Jacox, M., Bowler, C., Kavanaugh, M., Lehodey, P., Barrie, D., Brodie, S., Chaffron, S., Cheng, W., Dias, D. F., Eveillard, D., Guidi, L., Iudicone, D., Lovenduski, N. S., Nye, J. A., Ortiz, I., Pirhalla, D., Buil, M. P., Saba, V., Sheridan, S., Siedlecki, S., Subramanian, A., de Vargas, C., Di Lorenzo, E., Doney, S. C., Hermann, A. J., Joyce, T., Merrifield, M., Miller, A. J., Not, F., & Pesant, S. Observational needs supporting marine ecosystems modeling and forecasting: from the global ocean to regional and coastal systems. Frontiers in Marine Science, 6, (2019): 623, doi:10.3389/fmars.2019.00623.
    Description: Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem state on sub-seasonal to interannual timescales is gaining increasing attention. Depending on the application, forecasts may be sought for variables and indicators spanning physics (e.g., sea level, temperature, currents), chemistry (e.g., nutrients, oxygen, pH), and biology (from viruses to top predators). Many components of the marine ecosystem are known to be influenced by leading modes of climate variability, which provide a physical basis for predictability. However, prediction capabilities remain limited by the lack of a clear understanding of the physical and biological processes involved, as well as by insufficient observations for forecast initialization and verification. The situation is further complicated by the influence of climate change on ocean conditions along coastal areas, including sea level rise, increased stratification, and shoaling of oxygen minimum zones. Observations are thus vital to all aspects of marine forecasting: statistical and/or dynamical model development, forecast initialization, and forecast validation, each of which has different observational requirements, which may be also specific to the study region. Here, we use examples from United States (U.S.) coastal applications to identify and describe the key requirements for an observational network that is needed to facilitate improved process understanding, as well as for sustaining operational ecosystem forecasting. We also describe new holistic observational approaches, e.g., approaches based on acoustics, inspired by Tara Oceans or by landscape ecology, which have the potential to support and expand ecosystem modeling and forecasting activities by bridging global and local observations.
    Description: This study was supported by the NOAA’s Climate Program Office’s Modeling, Analysis, Predictions, and Projections (MAPP) Program through grants NA17OAR4310106, NA17OAR4310104, NA17OAR4310108, NA17OAR4310109, NA17OAR4310110, NA17OAR4310111, NA17OAR4310112, and NA17OAR4310113. This manuscript is a product of the NOAA/MAPP Marine Prediction Task Force. The Tara Oceans consortium acknowledges support from the CNRS Research Federation FR2022 Global Ocean Systems Ecology and Evolution, and OCEANOMICS (grant agreement ‘Investissement d’Avenir’ ANR-11-BTBR-0008). This is article number 95 of the Tara Oceans consortium. MK and SD acknowledge support from NASA grant NNX14AP62A “National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)” funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), and the NOAA Integrated Ocean Observing System (IOOS) Program Office. WC, IO, and AH acknowledge partial support from the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA15OAR4320063, Contribution No. 2019-1029. This study received support from the European H2020 International Cooperation project MESOPP (Mesopelagic Southern Ocean Prey and Predators), grant agreement no. 692173.
    Keywords: Marine ecosystems ; Modeling and forecasting ; Seascapes ; Genetics ; Acoustics
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
    Publication Date: 2021-05-19
    Description: PCR-denaturing gradient gel electrophoresis (DGGE) and canonical correspondence analysis (CCA) were used to explore the relationship between eukaryotic plankton community succession and environmental factors in two aquaculture pond models with gibel carp Carassius auratus gibelio. The main culture species of pond 1 were gibel carp and grass carp, and the combined density was 46224 fingerling/ha (gibel carp/grass carp/silver carp/bighead carp, 17:4:6:1). The main culture species of pond 2 was gibel carp, and the combined density was 37551 fingerling/ha (Gibel carp/silver carp/bighead carp, 52:1:1). Water samples were collected monthly. The results showed that the annual average concentrations of TP and PO4-P in pond 1were significantly higher than pond 2 (p〉0.05). The concentration of chlorophyll a (chl a) has no significantly difference between pond 1 and pond 2. DGGE profiles of 18S rRNA gene fragments from the two ponds revealed that the diversity of eukaryotic plankton assemblages was highly variable. 91 bands and 71 bands were detected in pond 1 and pond 2, respectively. The average Shannon–Wiener index of pond 1 was significantly higher than pond 2. Canonical correspondence analysis (CCA) revealed that temperature played a key role in the structure of the eukaryotic plankton community in both ponds, but the nutrient concentration did not affect it. Our results suggest that DGGE method is a cost-effective way to gain insight into seasonal dynamics of eukaryotic plankton communities in culture ponds, and the increase in the number of filter-feeding silver carp and bighead carp could increase the diversity of the eukaryotic plankton community.
    Description: Published
    Keywords: Genetics ; 18S rRNA genes ; PCR-denaturing gradient gel electrophoresis ; CCA ; Eukaryotic plankton community ; Environmental factors
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.1540-1555
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  • 4
    Publication Date: 2021-05-19
    Description: Molecular comparison of two parasites Lernaea cyprinacea and Lernaea ctenopharyngodoni was carried out using RAPD (Random Amplified Polymorphic DNA) technique. A total of 43 Lernaea specimens belonging to the two species were collected from the Guilan and Khouzestan Provinces. DNA was extracted using the Phenol-chloroform method. The quality and quantity of DNA was assessed using 1% Agarose gel electrophoresis and spectrophotometer. Polymerase Chain Reaction (PCR) was conducted on the target DNA under specific conditions and PCR products were subjected to electrophoresis on polyacrylamide gels (6%). Polyacrylamide gels were stained using silver nitrate and DNA bands were analyzed with BioCapt software. The genetic analysis was conducted using POP GEN 32 software. Forty two primers, 10 nucleotides each were used for PCR reaction. Totally, 397 RAPD loci were counted on polyacrylamide gel where 349 identical loci were polymorphic of which some bands may be used as genetic markers for the identification of both Lernaea species. Data analysis on PCR products showed higher genetic variation (1.15%) of L. Ctenopharyngodon in the Guilan Province as compared to that of the Khouzestan (0.0%). However, genetic variation (27.46%) of L. cyprinacea in the Khouzestan province was 7.26 times higher than that of the Guilan province (3.78%). The two species showed a genetic differentiation of approximately 88%. Based on the observed molecular differences, we state that L. ctenopharyngodoni is a genetically independent species from L. cyprinacea.
    Description: Published
    Keywords: Parasites ; Polymerase chain reaction ; Primers ; Nucleotides ; Lernaea ctenopharyngodoni ; Lernaea cyprinacea ; Molecular structure ; Genetics ; DNA ; Freshwater
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.19-28
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  • 5
    Publication Date: 2021-05-19
    Description: This study represents a large-scale population genetic analysis of the stellate sturgeon, Acipenser stellatus, in the Caspian Sea. In total, 192 samples of adult stellate sturgeon were collected from four commercial catch stations in the Northern (Volga and Ural Rivers) and Southern Caspian Sea (estuary of Sefidrud and Gorganrod Rivers-Iran). Fifteen sets of microsatellite primers developed from lake sturgeon (Acipenser fulvescens) and shovelnose sturgeon (Scaphirhynchus platorynchus) were tested on genomic DNA. Ten primer sets (LS-19, 34, 54, 68, Spl-105, 104, 163, 170, 173, 113) revealing polymorphic loci were used to analyze the genetic variation found in adults of the stellate sturgeon populations. Analyses revealed that the average number of alleles per locus was 13.05 (range 8 to 18 alleles per locus in regions, Ne= 7.86). All sampled regions contained private alleles. The average observed and expected heterozygosities were 0.665 and 0.862, respectively. Deviations from Hardy-Weinberg equilibrium were seen in most cases. Average of Fis, Fit and Nm were 0.230, 0.261 and 7.498, respectively. Pairwise Population FST Values ranged from 0.019 to 0.035. FST, RST, and gene flow estimates in AMOVA indicated significant genetic differentiation among and regions, indicating that the populations were divergent. The genetic distance between populations indicates that the genetic difference among the studied populations is pronounced. These results together with highly significant RST of genotypic differences between these pairs of collections support the existence of different genetic populations along the Caspian Sea coast.
    Description: Published
    Keywords: Genetics ; Genetic variability ; Genetic differentiation ; Acipenser stellatus ; Microsatellite markers
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.687-700
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  • 6
    Publication Date: 2021-05-19
    Description: Understanding the scale at which wild stocks of Persian sturgeon (Acipenser persicus) are genetically discrete is necessary for effective management of this commercially important species. Disomic DNA microsatellite markers are among the best tools for determining stock structure in fishes. As all sturgeon species have a polyploid ancestry of all sturgeons, most gene loci exhibit more than two alleles per individual, limiting the use of powerful analytical methods that commonly assume disomic inheritance. We scored products from 38 sets of microsatellite primers developed in lake (Acipenser fulvescens) and Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) to determine whether they would amplify disomic loci in Persian sturgeon. Samples of 45 individuals were detected.Thirty six loci (95%) were amplified successfully in Persian sturgeon. We identified a single monomorphic locus, 12 disomic, 19 tetrasomic, three octosomic, and one locus that was ambiguous. This is the first report on development of disomic single-locus DNA microsatellite markers in Persian sturgeon. These loci could be used to characterize variation in geographically discrete populations of the Persian sturgeon in their native ecosystem including in the Caspian Sea.
    Description: Published
    Keywords: Genetics ; Persian sturgeon ; Acipenser oxyrinchus oxyrinchus ; Acipenser fulvescens ; Acipenser persicus ; Single-locus DNA microsatellite markers ; DNA
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.389-397
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  • 7
    Publication Date: 2021-05-19
    Description: Genetic diversity as an important marker of the ecological status of aquatic ecosystems is considered a unique and powerful tool to evaluate biological communities. In order to evaluate the genetic diversity among golden mullet species (Liza aurata) in the southeast and southwest coasts of the Caspian Sea by D-Loop gene sequencing, a total of 23 fin specimens of golden mullet were collected from the Gilan (Anzali area) and Golestan (Gomishan area) provinces. Total DNA from the samples was extracted by ammonium acetate method and the quality and quantity of the extracted DNA were assessed by spectrophotometery and electrophoresis. Polymerase Chain Reaction (PCR) was conducted on the target DNA and then DNA sequencing was carried out. D- loop region in mitochondrial DNA (mtDNA) of golden mullet contained 900 base pairs (bp). Phylogenetic relationships among golden mullet were calculated by MEGA software version 5.05 and divergence time was estimated using Tahjima's test. The results obtained from this study revealed that there were high genetic differences among two regions in the Gilan and Golestan provinces. Kimura 2-parameter was used for genetic distance analysis and the genetic distance recorded between Gilan and Golestan Provinces was calculated at 0.259. The high levels of FsT were observed between Gilan and Golestan Provinces which indicates that genetic differences exist among present populations (p≤.05). Based on the results obtained from the south Caspian Sea, probably two different populations of Liza aurata are living in the Gilan and Golestan Provinces.
    Description: Published
    Keywords: Genetics ; Genetic diversity ; Liza aurata ; mtDNA ; Genetic distance ; Population
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.216-227
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  • 8
    Publication Date: 2021-05-19
    Description: Apolipoprotein A-I is the most abundant protein in Cyprinus carpio plasma that plays an important role in lipid transport and protection of the skin by means of its antimicrobial activity. A 527 bp cDNA fragment encoding C terminus part of apoA-I from the skin mucosa of common carp was isolated using RT-PCR. After GenBank database searching, a partial sequence containing a coding sequence (CDS) relating to this gene was found. Overlapping of the cDNA fragment with this CDS allowed us to obtain the full-length sequence including non-coding regions. This sequence has 1170bp including a polyA tail of 18 bp plus 45 and 354 bp at the 3'- and 5'-untranslatedregions, respectively. The complete sequence contained an open reading frame of 256 amino containing 5 amino acid propeptides with a predicted molecular mass of 29.967 kDa and theoretical pI of 6.13.The signal peptide of common carp apoA-I was predicted to have the most likely cleavage site between amino acid positions 17 and 18. Domain analysis of common carp apoA-I showed the conserved domain of Apolipoprotein A1/A4/E between amino acid resides 67 to 251. The similarity search indicated that common carp apoA-I matched apoA protein from the group of fish with 45-77% similarity, but showed relatively low levels of similarity to its mammalian counterparts (20-28%).It was shown that the secondary structure of C. carpio apoA-I consisted of a-helical predominantly amphipathic in nature and was characterized by the presence of thirteen conserved repeats.
    Description: Published
    Keywords: Genetics ; Apolipoprotein A-I ; Common carp ; Cyprinus carpio ; Epidermal mucus ; Full-length sequence ; Molecular ; Characterization
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.366-381
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  • 9
    Publication Date: 2021-05-19
    Description: The aim of the present study was the genetic analysis of the Dniester population of sterlet Acipenser ruthenus and comparison of it to five other sterlet populations, in order to develop a population recovery plan. The genetic analysis of six sterlet populations from Eurasian rivers (Dniester, Dnieper, Danube, Volga, Kama and Ob) was carried out using microsatellite DNA markers. The genetic variation and genetic distance between studied populations were evaluated. Significant genetic differentiation was detected between the analyzed populations through the pairwise genetic differentiation index (Fst) test. The DA measure of genetic distance between pairs of populations indicated that the shortest genetic distance (in relation to the Dniester population) was between the Dniester and the Dnieper populations (0.184). The results obtained represent a starting point of sterlet conservation program in Dniester River.
    Description: Published
    Keywords: Genetics ; Acipenser ruthenus ; Aquaculture ; Genetic analysis ; Microsatellite DNA ; Restitution ; Populations
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.634-645
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  • 10
    Publication Date: 2021-05-19
    Description: This study reports on the molecular identification of fish species from processed products which had a priori been classified as belonging to 5 important species in Iran for human consumption. DNA barcoding using direct sequencing of an approximately 650bp of mitochondrial Cytochrome oxidase subunit I (COI) gene revealed incorrect labeling of Narrow-barred Spanish mackerel samples. High occurrence of fraudulent fishery products, if left unchecked, can pose a negative impact on the economy. This investigation adds further concern on the trading of processed fish products in Iran from both health and conservation points of view.
    Description: Published
    Keywords: Genetics ; Food traceability ; Forensic genetics ; DNA barcoding ; Fish product ; Species ; Identification
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.783-791
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  • 11
    Publication Date: 2021-05-19
    Description: Use of different pesticides in the agriculture sector, in order to boost crop yield within a short time period and low labor, has been tremendously increased since the last decade. Pesticide use has elevated crop yield but has produced a number of pronounced problems regarding environmental and health safety. The continuously deteriorating toxicological effects of these pesticides are not only hazardous to humans and land animals but also to economically important aquatic organisms such as fish. One of these extensively used pesticides is an organochlorine insecticide, endosulfan. Experiments conducted in the past have shown the deleterious effects of endosulfan on different aspects of various fish species but its genetic toxicity has not been well studied. The present study was conducted to diagnose the DNA damage induced by endosulfan in peripheral blood erythrocytes of an economically important teleost fish rohu, Labeo rohita (Hamilton, 1822) using comet assay. The fish were exposed to three different sub lethal concentrations (1, 1.5 and 2 µg L-1) of endosulfan for 7, 14, 21 and 28 days. Rohu showed different extents of DNA damage at different concentrations and time, in terms of genetic damage index (GDI), percentage of damaged cells (% damaged cell) and cumulative tail length (µm) of the comets. Increase in DNA damage was observed to be concentration and time-dependent. The current study revealed the severe genotoxic effects of endosulfan in rohu, Labeo rohita. Therefore its discriminate use should be avoided as it can contribute to the decline of rohu in natural habitats. Also it should be considered as a hazardous threat for human consumption.
    Description: Published
    Keywords: Genetics ; Endosulfan ; DNA damage ; Erythrocyte ; Comet assay ; Rohu
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.138-149
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  • 12
    Publication Date: 2021-05-19
    Description: In order to have a sustainable management on Persian sturgeon as a highly commercial species in the South Caspian Sea, we need to identify its population structure and the level as well as its conservation status in their natural habitat. To develop a conservation program for this all Caspian Sea' sturgeon species it requires knowledge of its genetic diversity using reliable molecular marker to study population genetic structure. For these purposes, an enriched library was prepared based on a modified biotin-capture method. Approximately 1800 positive clones were screened for microsatellites in an Acipenser persicus genomic library. Of these 350 positively hybridizing clones were sequenced, and 81 clones were identified as having microsatellites with adequate flanking regions. We developed and tested 68 microsatellite primer pairs for Persian sturgeon. Out of 68 primer pairs developed, 11 pairs resulted in poor or no amplification, 13 were ambiguous, 6 were monomorphic, 20 were tetrasomic and 18 were octosomic in Persian sturgeon. While none of the markers showed disomic inheritance in Persian sturgeon and Russian sturgeon (A. gueldenstaedtii). Several of the markers appeared useful for studies stellate sturgeon (A. stellatus), ship sturgeon (A.nudiventris) and beluga (Huso huso). Nearly all the polymorphic pattern for ship, stellate and beluga displayed the simple banding patterns characteristic of disomic loci, while those for Russian sturgeon displayed banding patterns characteristic of tetraploid or higher polyploid levels. These markers may prove useful in a variety of future sturgeon population genetic studies in the Caspian Sea.
    Description: Published
    Keywords: Russian sturgeon ; A. gueldenstaedtii ; Persian sturgeon ; Acipenser persicus ; Caspian Sea ; Microsatellite ; Population genetic ; Genetics ; Population ; Structure ; Species
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.548-558
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  • 13
    Publication Date: 2021-05-19
    Description: Genetic diversity of six populations of bartail flathead (Platycephalus indicus Linnaeus, 1758) was investigated using amplified fragment length polymorphism (AFLP). A total of 118 reproducible bands amplified with ten AFLP primer combinations were obtained from 42 fishes that were collected from six different locations in the northern part of the Persian Gulf. The percentage of polymorphic bands was 57.06%. Nei’s genetic diversity was 0.1808±0.2074 - 0.2164±0.1903, and Shannon’s index was 0.2675±0.2949 - 0.3280±0.2727. The results of AMOVA analysis indicated that 66% and 34% of the genetic variation occurred within and among the populations and gene flow was 0.6454. The estimated level of population differentiation as measured by average Fst value across all loci was 0.327. Analyses revealed significant genetic differentiation with low gene flow among the six locations, indicating at least six separate populations of bartail flathead in the northern part of the Persian Gulf.
    Description: Published
    Keywords: Genetics ; Genetic diversity ; Bartail flathead. ; Platycephalus indicus ; AFLP ; Genetic ; Populations ; Fish
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.924-936
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  • 14
    Publication Date: 2021-05-19
    Description: The present study was carried out during 2006-2007 along the southern Caspian Sea. The species composition showed that the common kilka, Clupeonella cultriventris caspia, is dominant species with 89% and then anchovy, C. engrauliformis, has shown only 8.7% while it was already dominant species in the past decades. The overall results indicated that common kilka was replaced with anchovy kilka as previous dominant kilka species due to invasion of Mnemiopsis leidyi to the southern Caspian Sea. Anchovy suffered greatly from M. leidyi so that the total catch dropped from 95000 mt in 1999 to less than 20000 mt in 2007. In our survey, 1415 fish specimens were collected randomly, including 221 anchovy, 281 bigeye and 913 common kilka. The mean length of anchovy was 117.8 ± 0.27 mm, while it was about 93.0 mm during 1995 to 1998 before the invasion of M. leidyi. Analysis of age classes indicated the mean age of 4.5 ± 0.04 years for anchovy, 3.6 ± 0.03 for common kilka and 4.6 ± 0.08 for big eye C. grimmi. According to the age and the length structure of the specimens in this study, it could be concluded that in recent years, young fish population of anchovy has been decreased in comparison with the last decade. The results showed that some biological characteristics of kilka population were affected by M. leidyi. Recently fishing activities take place in shallow waters where schools of kilka are in suitable density for fishing. According to our results, ctenophore occupied the anchovy habitat where it was mainly more than 50 m depth. The fishing has moved to areas with depths less than 50 meters where it was the main reason to change in species composition.
    Description: Published
    Keywords: Age structure ; Clupeonella ; Species composition ; Mnemiopsis leidyi ; Genetics
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.559-569
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  • 15
    Publication Date: 2021-05-19
    Description: Black pomfret Parastromateus niger is a commercially important fishery resource in the Persian Gulf but harvesting its stocks lacks genetic identification of populations. AFLP technique was applied to analyze genetic diversity and population structure of 32 fish from coastal waters of Bandar Abbas, Bushehr and Abadan with 7 EcoRI/MseI primer pair combinations. In total, 381 bands were produced of which, 46 were polymorphic (12.07%). Percentage of polymorphic bands was higher in Bushehr samples (91.30%) than in Abadan (84.78%) and Bandar Abbas (73.91%) samples. The highest level of heterozygosity based on Nei’s coefficient and Shannon’s index was observed in Bushehr fish (0.38±0.16 and 0.54±0.21). Observed and effective alleles ranged from 1.73±0.44 and 1.53±0.40 in Bandar Abbas samples to 1.91±0.28 and 1.70±0.34 in Bushehr samples. The average Fst was 0.19 indicating high genetic differentiation among the three locations. Gene flow with mean of 1.93 was the lowest level between Bandar Abbas and Abadan (1.24). Nei's genetic identity revealed the least genetic similarity between the samples of Bandar Abbas and Abadan (0.77). AMOVA analysis demonstrated 81% of the genetic variation within populations and 19% among populations. The UPGMA dendrogram clustered all 32 individuals into 3 groups. In some cases individuals from the same region were grouped together but in most cases, gene exchange was observed to be common among the groups. Analyses provided evidence for genetic differentiation among the three locations, indicating separate populations of black pomfret in the northern Persian Gulf.
    Description: Published
    Keywords: Genetics ; Black pomfret ; Parastromateus niger ; AFLP molecular markers ; Population structure ; Genetic ; Populations
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.857-875
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  • 16
    Publication Date: 2021-05-19
    Description: Esox lucius is an economically important freshwater species. Mitochondrial cytb, 12SrRNA, and 16SrRNA gene sequences were used in order to clarify the genetic variation and population structure in three E. Lucius populations, i.e., one Wild population (W) and two hatchery populations (Hatchery Population I-HPI and Hatchery Population II-HPII). A total of 55 individuals, with 19 from wild and 18 from each hatchery population, were sequenced. The results are as follows: 1) cytb. Eleven variable sites defined eight distinct haplotypes, with 1137 base pairs (bp) complete cytb sequences. The nucleotide diversity (π) values were W 0.009%, HPI 0.075% and HPII 0.068%, respectively. Genetic distances within and between populations were both between 0 and 0.1%. Analysis of molecular variance (AMOVA) analysis revealed that variation within populations accounts for 98.49% of total variation. 2) 12SrRNA. We obtained 380 bp consensus 12SrRNA sequence and found little variation among the 55 sequences. 3) 16SrRNA. Twelve variable sites defined seven haplotypes, with 519 bp consensus 16SrRNA sequence. The π values were W 0.041%, HPI 0.310% and HPII 0.021%, respectively. Genetic distances were between 0 and 0.3% within populations and from 0 to 0.2% between populations. AMOVA disclosed that variation within populations accounts for 91.79% of total variation. Variation within populations is the main source of total variation. The results suggest that low genetic variation can be found in both wild and hatchery populations of E. lucius, and the effect of genetic drift and adaptation to culture conditions gradually emerged under only two generations’ artificial cultivation.
    Description: Published
    Keywords: Genetics ; Northern pike ; Esox lucius ; Mitochondrial DNA ; Genetic diversity ; Genetic variability ; Hatchery ; Populations
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.792-801
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  • 17
    Publication Date: 2021-05-19
    Description: The effects of starvation and subsequent re-feeding on compensatory growth performance, blood serum metabolites and IGF-ImRNA expression in liver and muscle were investigated in juvenile Persian sturgeon. Growth indices including body weight, SGR, CF, and HSI significantly decreased after starvation. However, after re-feeding sturgeons that were starved for 1 week reached the same weight as the control, indicating that complete compensatory growth had occurred. Conversely, sturgeon in longer periods of starvation showed only partial growth compensation. HSI values decreased significantly during starvation, although they returned to the control fish levels after re-feeding. Plasma levels of glucose and insulin during starvation and re-feeding did not significantly change. This suggests that sturgeon is able to maintain glycaemia during starvation, probably due to their non-carbohydrates source dietary. Plasma total lipid level in un-fed treatments, however, was found to increase, possibly as a mechanism to utilise lipids as a fuel during starvation. IGF-I mRNA expression in liver and muscle increased during starvation and decreased after re-feeding. However, changes in the IGF-ImRNA expression were not significantly different among treatments. These results indicate that a periodic short-term starvation in Persian sturgeon does not adversely sacrifice overall fish weight gain and sturgeon can realise compensatory growth.
    Description: Published
    Keywords: Genetics ; Acipenser persicus ; Persian sturgeon ; Feeding regime ; Compensatory growth ; Blood metabolite ; Plasma ; Dietary
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.465-483
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  • 18
    Publication Date: 2021-05-19
    Description: A Gram-negative, rod-shaped, motile and halophilic bacterium identified as Vibrio harveyi was isolated from hatchery-reared larval of Iran Shrimp Research Centerfollowing mass mortality . Seven isolates of Vibrio spp.were collected from nauplii of Litopenaeus vannamei and then were evaluated for characteristics including morphology, physiology and biochemistry. The results indicated that the isolates belonged to a single species that grew on Thiosulfate citrate- Bile Sucrose agar and in 1.5 to 6% NaCl, positive lysine and ornithine decarboxylation and susceptible to O/129 disk. Identification of Vibrio harveyi strainIS01 (1 of 7 isolates) was confirmed by Polymerase Chain Reaction assay for Vibrio harveyi (expected amplicon 1493 bp). The 16S ribosomal DNA sequence (National Center for Biotechnology Information, GenBank accession number GU974342.1) gave 99% sequence identity to V. harveyi ATCC: 35084 (GenBank accession number EU130475.1).
    Description: Published
    Keywords: Genetics ; Vibriosis ; Shrimp diseases ; Litopenaeus vannamei ; 16S rDNA sequencing ; Molecular
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.384-393
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  • 19
    Publication Date: 2021-05-19
    Description: An experiment was undertaken to develop a suitable seed production technique for Sperata aor in captivity. Naturally produced fry of aor was reared at different densities in nine nursery ponds 0.012 ha in size with an average depth of 0.8 m each. Three stocking densities tested, each of which was triplicated. Fry of aor stocked at 100,000/ha was designated as treatment-1 (T1), 150,000/ha as treatment-2 (T2) and 200,000/ha as treatment-3 (T3). All stocked fry were from the same age group with mean length and weight of 1.78 ± 0.28 cm and 0.24 ± 0.05 g, respectively. Fry in all the treatments were fed with SABINCO nursery feed (32.06% crude protein) for the first 14 days and starter-I (31.53% crude protein) for days 15 to 56. Physico-chemical parameters and plankton population of pond water were within the optimal level being better in T1 than those in T2 and T3. Growth in terms of final weight and length, weight and length gain, specific growth rate, daily growth rate, and survival of fingerlings were significantly higher in T1 followed by T2 and T3. Food conversion rate was significantly lower in T1 than in T2 and T3. Significantly higher number of fingerlings was produced in T3 than those in T2 and T1. Despite this, consistently higher net benefits were achieved from T1 than from T2 and T3. This is the first time report that stocking of 100,000 fry/ha appears to be the most suitable density for rearing of aor fingerlings in nursery ponds.
    Description: Published
    Keywords: Genetics ; Catfish ; Sperata aor ; Fry ; Stocking density ; Fingerling ; Growth ; Production ; First time ; Reported
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.1-14
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  • 20
    Publication Date: 2021-05-19
    Description: Members of Nemacheilidae Family, Turcinoemacheilus genus were subjected to molecular phylogenetic analysis in this study. This genus was reported in 2009 to inhabit in Karoon River drainage, in contrary to previous assumption that it was the endemic species in the Basin of Tigris River. It was sampled from three stations placed in different tributaries in Karoon drainage and evaluated to understand the molecular phylogenetic relationships of Turcinoemacheilus in Iran. The mitochondrial cytochrome b gene (cyt b) and control region were used to infer phylogenetic relationships. PCR amplification of control region was not carried out successfully, possibly due to the high divergence of this sequence in the studied genus. The amplified fragments of cyt b were sequenced then analyzed by the use of phylogenetic software. Only one divergent position was seen in all three samples stations located in amino acid position 365. GTR and p-distances of cytochrome b gene for T. kosswigi computed from different stations of running water in Karoon drainage showed these samples belong to different populations and fall in intraspecific differences. In this study, examination of the molecular phylogeny using Bayesian analysis, maximum parsimony or neighbor-joining define the phylogentics of Turcinoemacheilus genus as a monophyletic clade which is sister-clade of Nemacheilus and Schistura genera. This report is the first report of Turcinoemacheilus molecular data and could describe molecular phylogeny of this genus in loaches.
    Description: Published
    Keywords: Genetics ; Nemacheilidae ; Cypriniformes ; Turcinoemacheilus ; Mitochondrial ; Schistura genera ; Software ; Molecular phylogenetics ; Karoon drainage ; Bayesian analysis ; Maximum parsimony ; Neighbor-joining ; DNA ; Phylogenetics
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.592-604
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  • 21
    Publication Date: 2021-05-19
    Description: Considering the importance of genetic studies to manifest inter population differences in species, samples of Artemia partenogenetica were collected from seven inland lakes including Shoor and Inche-Borun lakes in Golestan Province, Hoze-Soltan and Namak lakes in Qom Province, Maharloo and Bakhteghan lakes in Fars Province and Mighan pool in Markazi Province. A total of 210 samples were subjected to DNA extraction by phenol-chloroform method. Primers were designed on a ribosomal fragment (16SrRNA) of the species' mtDNA sequence and the PCR was conducted on the samples. Digestion of the PCR product with approximately 1584bp lengths by 10 restriction endonuclease (AluI, EcoRI, Eco47I, HaeIII, HindIII, HinfI, MboI, MspI, RsaI, TaqI) showed 12 different haplotypes: 4 haplotypes in Shoor and Inche-Borun, 1 in Namak and Hoze-Soltan, 3 in Mighan pool, 1 in Bakhtegan and Maharloo and 3 in Maharloo. Haplotype diversity values within collected samples varied from zero in Hoze-Soltan, Namak and Bakhteghan samples to 0.7425 in Inche-Borun and Shoor while nucleotide diversity varied from zero in Hoze-Soltan, Namak and Bakhteghan, to 0.0077 in Mighan. The minimum nucleotide diversity among samples was zero between Hoze-Soltan vs. Namak and the maximum was 0.1700 between Inche-Borun and Shoor vs. Mighan. Nucleotide divergences among samples were least in Inche-Borun vs. Shoor (%-0.02) and most in Inche-Borun and Shoor vs. Mighan (%16.18), averaging to %3.40. The evolutionary distances between 12 haplotype showed that the maximum value belonged to Mighan haplotypes vs. Inche-Borun and Shoor haplotypes. Regarding the digestive patterns produced by each enzyme in the studied region, Eco47I is introduced as the population-specific marker of A. partenogenetica in Iran. Test of population differentiation based on haplotype frequencies were statistically significant (P~,0.001) with the exception of Hoze-Soltan vs. Namak and Inche-Borun vs. Shoor. We conclude that there are enough evidences in haplotypic level for dividing A. partenogenetica in Iran into five populations: Hoze-Soltan and Namak, Mighan, Maharloo, Bakhtegan, Incheh-Borun and Shoor.
    Description: Published
    Keywords: RNA ; Nucleotide sequence ; Primers ; Nucleotides ; Artemia partenogenetica ; Population Genetics ; Genetics ; DNA ; Enzymes ; Marine
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.53-68
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  • 22
    Publication Date: 2021-05-19
    Description: In the present study we evaluated the amount and distribution of genetic variation by using RAPD marker variation of 12 markers loci in three broodstock groups of rainbow trout. A total of 47 polymorphic bands were observed in Iranian strain, average number of bands was 10 and average number of polymorphic bands per primer was 3.92. The total detected bands in rainbow trout strain originated from French, was 120 bands with an average number of 10 bands per RAPD primer. A total of 117 amplified were detected in Norwegian population, with an average number of bands and average number of polymorphic bands per primer was 9.75 and 2.58, respectively. Data for observed and effective number of alleles, Nei’s genetic diversity and Shannon’s information index for all the three populations were 1.31, 1.20, 0.120 and 0.170, respectively. The mean coefficient of gene differentiation value and the estimate of gene flow across the populations were found as 0.299 and 0.171, respectively. The Nei measures of genetic distance and identity between pairs of rainbow trout strains indicate that the strain originated from France and Iran has the highest genetic identity, while the fish originated from Norway and France showed the greatest genetic distance.
    Description: Published
    Keywords: Genetics ; Oncorhynchus mykiss ; Molecular ; Genetic variation ; Rainbow trout ; Polymorphism ; RAPD ; Populations
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.511-521
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  • 23
    Publication Date: 2021-05-19
    Description: This study was conducted to produce a high percentage of genetically male tilapia through interspecific hybridization between Nile tilapia, Oreochromis niloticus and Blue tilapia, O. aureus and evaluate sex ratio, productive performance and heterosis of the progeny produced. The results revealed that sex ratios of the progenies of (♀ O. aureus x ♂ O. niloticus) and (♀ O. niloticus x ♂ O. aureus) were 4.28: 1.00 and 3.59: 1.00 and differ (P〈0.05 df =1) significantly from the expected sex ratios of 3.00: 1.00 and 1.00: 0.00, respectively. In addition, the productive performance traits of (♀ O. aureus x ♂ O. niloticus) had significant (P≤0.05) superiority in most of these traits. Moreover, although both hybrids displayed a positive or best heterosis for daily gain, SGR%/day, FCR and PER, the hybrid of (♀ O. aureus x ♂ O. niloticus) showed the highest or best heterosis.
    Description: Published
    Keywords: Genetics ; Oreochromis niloticus ; Genetically male ; Interspecific hybridization ; Nile tilapia ; Blue tilapia ; Productive performance ; Heterosis
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.802-812
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  • 24
    Publication Date: 2021-05-19
    Description: The current study evaluated effects of dietary administration doses of Entrococcus faecium on the hematological factors, and disease resistance of Sander lucioperca against Aeromonas hydrophila infection. Fish were fed with dietary administration containing E. faecium doses including of (1010, 108CFU/ g) for diet A1 and A2, respectively in a commercial diet as basal diet were used for 6 weeks. The control group was basal diet with serum. The hematological and immunity parameters were measured and fish were challenged with A.hydrophila (4.5×108CFU/mL). Fish were monitored daily and the mortality rates were recorded over 8 days post – challenge. The results indicated that HCT in A1 treatment (1010CFU/g) had significantly increased in compare to the control and A2 (108 CFU/g) treatments (p〈0.05). MCV in A1(10 10CFU/g) and control groups were significantly higher than A2 (108 CFU/g) Treatment (p〈0.05). However, other parameters e.g. RBC, HB, MCH, MCHC had no significant different. The serum lysozyme, alternative complement activity (ACH50) and IgM levels were significantly enhanced in dietary administration E. faecium(108,1010CFU/g) in feeding period. Survival rate of fish by dietary administration E. faecium (1010CFU/g) was significantly higher (p〈0.05) than the other groups (86.6%).
    Description: Published
    Keywords: Genetics ; Aeromonas hydrophila ; Entrococcus faecium ; Aeromonas hydrophila ; Hematology ; Immunity ; Parameters ; Sander lucioperca ; Hematological
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.1581-1592
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  • 25
    Publication Date: 2021-05-19
    Description: The population genetic structure of common carp (Cyprinus carpio) was examined on 260 specimens from Tajan and Gorgan Rivers, Gorgan Gulf, Anzali Lagoon and other regions in east, middle and west of south Caspian Sea. DNA was extracted from fin tissue by phenol-chlorophorm method with a concentration of 50-100 nanograms. PCR was performed using ND-3/4 and ND-5/6 genes. The PCR products of samples were digested by 15 restriction endonuclease enzymes. The digested products accompanied with standard marker (50 pb). To measure fragment size, samples were run on a 6% vertical poyacrylamide gel. The fragments were visualized by silver staining of the polyacrylamide gel. Statistical analysis of data was performed by Reap software. We detected 14 and 12 different haplotypes in ND-3/4 and ND-5/6 genes of common carp. The mean values of haplotype diversity among populations were 0.59 and 0.48 and the average nucleotide diversity was 0.06 and 0.03 for ND3/4 and ND5/6 genes. Also, the mean values of nucleotide divergence among populations were 0.05% and 0.02%, respectively. The haplotype distribution was not significantly different between Mazandaran and Guilan coasts, Mazandaran and Golestan coasts, Golestan coast and Gorgan Gulf and Gorgan River (P less than or equal to 0.05), but this divergence was significantly different between Guilan region and Anzali Lagoon, Guilan and Golestan coasts, Tajan and Gorgan Rivers (P less than or equal to 0.05). We found a significant genetic divergence between some of the samples such that three genetic groups of common carp were identified in the southern part of the Caspian Sea.
    Description: Published
    Keywords: Nucleotide sequence ; Polymerase chain reaction ; Coastal lagoons ; Nucleotides ; Rivers ; Data processing ; Statistical analysis ; Computer programs ; Software ; Haplotypes ; Endonuclease ; Cyprinus carpio ; Brackish ; Population genetics ; Genetics ; DNA ; Freshwater fish ; Enzymes ; Lead ; Lagoons ; Mitochondrial DNA ; Coasts
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.89-102
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  • 26
    Publication Date: 2021-05-19
    Description: 0Genetic polymorphism by means of biochemical genetic markers using polyacrylamide gel electrophoresis system in four barbus fish species has been investigated. Species scientific name were Barbus sharpeyi ; Gunther, 1847 , Barbus grypus ; Heckel, 1843, Barbus xanthopterus ; Heckel, 1843 and Barbus esocinus ; Heckel, 1843.Sampling site and location were mainly in the rivers located in Khoozestan province such as Karoon and Karkheh rivers and the Dez dam. Different organs such as blood, muscle, kidney, eye and heart were sampled and analysed for the presence of tf, es, sod and pgm alleles. High polymorphism and presence of different alleles scored, but populations were not in the H-W equilibrium. Considring results, using current and avaiable genetic markers such as microsattelits is recommended for future works.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Chemistry ; Genetics ; Genetics Markers ; Distinguish ; Barbus ; Species ; Barbus sharpeyi ; Barbus xanthopterus ; Barbus esocinus
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 62pp.
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  • 27
    Publication Date: 2021-05-19
    Description: In order to introduce genetic markers of four species of fishes, 80 samples of each species, i.e. Parastromateus niger, Scomberomorus comersoniannus, Trachionotus mookalee and Caranx para were collected. DNA was extracted using phenol- chloroform method . The target gene ( cytochrome b ) was amplified by Thermal cycle (PCR) and the PCR product size estimated 1105 bp. In this research out of 27 DNAase enzymes which were used for PCR product enzyme digesting 8 enzymes(Bam HI, Alw 261, Rsa I, Mbo I, Alu I, Hinf I, Dpn I, Dde I) have cut side on target DNA and three enzymes of them Alu I, Hinf I and Mbo I showed polymorphism genetic differences while other enzymes displayed similar patterns. Variarion of haplotypes from four species are as follows: BAA for P. niger, AAB for T. mookalee, ABA for C. para, and ACA for S. comersonianus. So it is possible to claim that each of the above Haplotypes may be used as genetic markers for each of the species.
    Description: Published
    Keywords: Separation ; Polymerase chain reaction ; Phenotypic variations ; Cytochrome b ; DDE ; Trachionotus mookalee ; Parastromateus niger ; Caranx para ; Carangidae ; Scomberomorus comersoniannus ; Scomberomorus ; Genetics ; DNA ; Enzymes ; Biomarkers ; Identification ; Phenotypes ; Chloroform ; Haplotypes ; Gene polymorphism ; Genetic markers ; Caranx ; Marine
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.1-14
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  • 28
    Publication Date: 2021-05-19
    Description: The number of chromosome and karyotype of Garra rufa (Heckel, 1843) was determined by the conventional preparation and Gimsa staining technique, using gill epithelia and kidney cells. In this investigation, 5 specimens of G. rufa were used which collected from Rodbal River, Firouzabad, Fars Province. Based on 30 chromosome spreads counts, the chromosome number was found to be 2n=50 with arm number NF=84. By using the ratio of long arm to short arm, the karyotype formula of 10 metacentric, 24 sub-metacentric and 16 sub-telocentric (10M +24SM +16St) was obtained.
    Description: Published
    Keywords: Light microscopy ; Karyotypes ; Garra rufa ; Genetics ; Chromosomes ; Freshwater
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.11-18
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  • 29
    Publication Date: 2021-05-19
    Description: In this research, antagonistic activity of two Bacillus species isolated from digestive tract of marine fish and culture pond of sea cucumber was studied. The inhibitory activity of Bacillus spp. isolates against some common pathogenic bacteria of fish was assessed using the agar diffusion method. The strain of B. subtilis G024 exhibited antimicrobial activity against Vibrio anguillarum, V. harveyi, V. vulnificus, Streptococcus sp. and Staphylococcus aureus; the isolate of B. amyloliquefaciens N004 inhibited growth in V. anguillarum, V. campbellii, V. vulnificus, V. parahamolyticus, Edwardsiella tarda, Streptococcus sp., B. cereus. Scanning electron microscopy (SEM) investigation of indicator bacteria showed that cell morphologies were strongly affected by the cell-free supernatant of the two Bacillus spp. isolates. It is determined that the culture filtrates contained inhibitors against growth of some pathogenic bacteria with different degrees of inhibition, although none of the culture filtrates could inhibit the growth of V. fluvialis, V. alginolyticus, V. splendidus. Based upon these characteristics, both of the antagonistic Bacillus spp. isolates could be the potential probiotics used in the aquaculture production.
    Description: Published
    Keywords: Genetics ; Culture pond ; Bacillus ; Antagonistic activity ; Scanning electron microscopy ; Probiotic ; Aquaculture ; Gastrointestinal ; Sediments ; Aquatic ; Growth ; Fish
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.701-714
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  • 30
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 158, doi:10.3389/fmars.2018.00158.
    Description: In autumn 2015, several sources reported observations of large amounts of gelatinous material in a large north Norwegian fjord system, either caught when trawling for other organisms or fouling fishing gear. The responsible organism was identified as a physonect siphonophore, Nanomia cara, while a ctenophore, Beroe cucumis, and a hydromedusa, Modeeria rotunda, were also registered in high abundances on a couple of occasions. To document the phenomena, we have compiled a variety of data from concurrent fisheries surveys and local fishermen, including physical samples, trawl catch, and acoustic data, photo and video evidence, and environmental data. Because of the gas-filled pneumatophore, characteristic for these types of siphonophores, acoustics provided detailed and unique insight to the horizontal and vertical distribution and potential abundances (~0.2–20 colonies·m−3) of N. cara with the highest concentrations observed in the near bottom region at ~320 m depth in the study area. This suggests that these animals were retained and accumulated in the deep basins of the fjord system possibly blooming here because of favorable environmental conditions and potentially higher prey availability compared to the shallower shelf areas to the north. Few cues as to the origin and onset of the bloom were found, but it may have originated from locally resident siphonophores. The characteristics of the deep-water masses in the fjord basins were different compared to the deep water outside the fjord system, suggesting no recent deep-water import to the fjords. However, water-masses containing siphonophores (not necessarily very abundant), may have been additionally introduced to the fjords at intermediate depths, with the animals subsequently trapped in the deeper fjord basins. The simultaneous observations of abundant siphonophores, hydromedusae, and ctenophores in the Lyngen-Kvænangen fjord system are intriguing, but difficult to provide a unified explanation for, as the organisms differ in their biology and ecology. Nanomia and Beroe spp. are holopelagic, while M. rotunda has a benthic hydroid stage. The species also have different trophic ecologies and dietary preferences. Only by combining information from acoustics, trawling, genetics, and local fishermen, were the identity, abundance, and the vertical and horizontal distribution of the physonect siphonophore, N. cara, established.
    Description: The work was funded by the Ministry of Fisheries and Coastal Affairs through the Institute of Marine Research (IMR), while the Research Council of Norway (RCN) is thanked for the financial support through the project The Arctic Ocean Ecosystem—(SI_ARCTIC, RCN 228896). AH was supported by the Norwegian Taxonony Initiative (NTI 70184233) and ForBio Research School funding (RCN 248799 and NTI 70184215).
    Keywords: Jellyfish bloom ; Genetics ; Acoustics ; Nanomia ; North Norwegian fjords ; Gelatinous zooplankton
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 31
    Publication Date: 2021-05-19
    Description: We investigated the generation of gynogenetic common carp (Cyprinus carpio L.) during 1989-1990. After selection of suitable breeders containing special transfferin marker in breeding season, we applied ionizing radiation (60 Co gamma ray) for genetic inactivation of spermatozoa of the fish. We found that in the exposure of the sperm to a range 80-120 Krad irradiation, 100 Krad gave the best results. Application of various cold and heat shocks to the eggs at different time intervals after addition of water to the mixture of milk and eggs generated diploid gynogenetic fish. Cold and hot shock treatments generated significantly different gynogenetic fish (7% and 2,5% respectively), The optimum Shock treatment was found to be 5 minutes after fertilization in Ciipc lasting 50 minutes. For each treatment, 100 fish fingerlings were subjected to electrophoresis which showed the mitotic diploid progenies were all-maternal inherited with BB genotype.
    Description: Published
    Keywords: Common carp ; Gynogenesis ; Cyprinus carpio L. ; Genetic Manipulation ; Genetics ; Gamma ray
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.183-198
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  • 32
    Publication Date: 2021-05-19
    Description: Certain parasites can cause severe diseases in shrimp. Among these, protozoa are very important. The objective of our study was to describe the signs, prevalence, and intensity of hemocytosis, a new disease in shrimp, Fenneropenaeus indicus. The experimental design included three groups, one treatment as infected shrimp or group B and 2 controls with non-infected but exposure to White Spot Syndrom Virus (WSSV) shrimp as group A and non-infected non- exposure to WSSV shrimp as group C in triplicate. The results revealed that Hemocytosis associated with a decrease in hyalinocytes and large-granulocytes (less than 8%) and a considerable increase in semi-granulocytes in group A and B in contrast to group C that Hyalinocyte increased. This infection made the shrimp susceptible to WSSV disease. It is believed that Hemocytosis causes a condition which can result in a rapid mortality among susceptible species, F. indicus when exposure to WSSV is occurred.
    Description: Published
    Keywords: Genetics ; Shrimp ; Fenneropenaeus indicus ; Hemocytosis ; Intrahemocyte ; Mortality
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.605-619
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  • 33
    Publication Date: 2021-05-19
    Description: Rainbow trout (Oncorhynchus mykiss) is one of the most-widely cultivated cold fresh water fish in the world. Gamasyab River, with a length of about 200 Km, is one of the longest rivers of Iran. The aim of this research is to determine the effects of trout farm effluents on this river water. From a total of 24 trout farms in the area, four farms were randomly selected and three sampling stations were chosen at each selected farm. Measured water quality parameters were temperature (T), total suspended solids (TSS), total dissolved solid (TDS) dissolved oxygen (DO), pH, five-day biochemical oxygen demand (BOD5), chemical oxygen demand (COD), ammonia-nitrogen (NH4-N), nitrate-nitrogen (NO3-N) and phosphates (PO4-P). Based on the laboratory analysis, DO in the river water was more than 6 mg/l in all cases. There were significant differences in six variables of T, BOD, COD, NO3-N, NH4-N, and TSS of all water samples taken from the second sampling stations between dry and wet season. The DO concentration in Gamasiab River decreased between the water inlet (first stations) and outlet (second stations), but increased in third station. Trout farm effluents had significant impact on the TSS content of the river. This significant increase in TSS concentrations is expected to have occurred due to cleaning or harvesting activities on any of the farms. The results of the study showed that, in all of season, the amount of TSS in the second stations was not equal to the standards of the Department of Environment Protection (40 mg/L) for discharging into river systems.
    Description: Published
    Keywords: Genetics ; Aquaculture ; Cold water fish culture ; Rainbow trout ; Water quality
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.1568-1580
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  • 34
    Publication Date: 2021-05-19
    Description: The present study investigated the existing relationship between computer assisted semen motility parameters and gametes motility duration, known to express semen quality and fertilizing capacity in fish. The objective was particularly to identify computer aided semen analysis (CASA) parameters that could be used as potential fertility predictors. Semen samples were collected from the beginning to the end of the spawning season of Barbus barbus callensis, a freshwater fish abundantly distributed throughout North Africa. Semen was simultaneously analyzed using optical microscopy including semen motility duration (SMD) measurement, by the aid of a computer-assisted semen analyzer. The measured CASA parameters were: straight line velocity (VSL), average path velocity (VAP), curvilinear velocity (VCL), beat cross frequency (BCF), amplitude of lateral head displacement (ALH), linearity and straightness. The results showed that motility duration evolved in a similar manner as several CASA parameters. Significant correlation coefficients expressed these relationships with r = 0.74, 0.32, 0.16 and 0.45 for VSL, VAP, VCL and BCF, respectively. No correlations were observed when studying relationships between motility duration, STR, LIN and ALH, with r = 0.08, 0.06 and 0.006, respectively. The present results showed that CASA motility parameters are strongly related to motility duration. VSL was revealed as the main parameter being highly correlated to motility duration (r = 0.74). This quantitatively and objectively measured parameter is revealed to be a useful indicator of semen quality and could serve as a potential indicator of fertility outputs in fish.
    Description: Published
    Keywords: Genetics ; Barbus barbus callensis ; Reproduction season ; Semen motility ; CASA
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.1556-1567
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  • 35
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-03
    Keywords: Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 36
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-17
    Keywords: Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 37
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Description: Developmental enhancers mediate on/off patterns of gene expression in specific cell types at particular stages during metazoan embryogenesis. They typically integrate multiple signals and regulatory determinants to achieve precise spatiotemporal expression. Such enhancers can map quite far—one megabase or more—from the genes they regulate. How remote enhancers relay regulatory information to their target promoters is one of the central mysteries of genome organization and function. A variety of contrasting mechanisms have been proposed over the years, including enhancer tracking, linking, looping, and mobilization to transcription factories. We argue that extreme versions of these mechanisms cannot account for the transcriptional dynamics and precision seen in living cells, tissues, and embryos. We describe emerging evidence for dynamic three-dimensional hubs that combine different elements of the classical models.
    Keywords: Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 38
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    Unknown
    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Keywords: Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 39
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Description: The classical model of cytosine DNA methylation (the presence of 5-methylcytosine, 5mC) regulation depicts this covalent modification as a stable repressive regulator of promoter activity. However, whole-genome analysis of 5mC reveals widespread tissue- and cell type–specific patterns and pervasive dynamics during mammalian development. Here we review recent findings that delineate 5mC functions in developmental stages and diverse genomic compartments as well as discuss the molecular mechanisms that connect transcriptional regulation and 5mC. Beyond the newly appreciated dynamics, regulatory roles for 5mC have been suggested in new biological contexts, such as learning and memory or aging. The use of new single-cell measurement techniques and precise editing tools will enable functional analyses of 5mC in gene expression, clarifying its role in various biological processes.
    Keywords: Genetics
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Keywords: Genetics
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  • 41
    Publication Date: 2018-09-28
    Description: Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays survey only one aspect of cellular biology. Here we describe sci-CAR, a combinatorial indexing–based coassay that jointly profiles chromatin accessibility and mRNA (CAR) in each of thousands of single cells. As a proof of concept, we apply sci-CAR to 4825 cells, including a time series of dexamethasone treatment, as well as to 11,296 cells from the adult mouse kidney. With the resulting data, we compare the pseudotemporal dynamics of chromatin accessibility and gene expression, reconstruct the chromatin accessibility profiles of cell types defined by RNA profiles, and link cis-regulatory sites to their target genes on the basis of the covariance of chromatin accessibility and transcription across large numbers of single cells.
    Keywords: Genetics
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  • 42
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Keywords: Genetics
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  • 43
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-14
    Keywords: Genetics
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  • 44
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-20
    Keywords: Genetics
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  • 45
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-20
    Keywords: Genetics
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  • 46
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-20
    Keywords: Genetics
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  • 47
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-01
    Keywords: Genetics
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  • 48
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-26
    Keywords: Genetics
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  • 49
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Genetics
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  • 50
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Description: Consumer genomics databases have reached the scale of millions of individuals. Recently, law enforcement authorities have exploited some of these databases to identify suspects via distant familial relatives. Using genomic data of 1.28 million individuals tested with consumer genomics, we investigated the power of this technique. We project that about 60% of the searches for individuals of European descent will result in a third-cousin or closer match, which theoretically allows their identification using demographic identifiers. Moreover, the technique could implicate nearly any U.S. individual of European descent in the near future. We demonstrate that the technique can also identify research participants of a public sequencing project. On the basis of these results, we propose a potential mitigation strategy and policy implications for human subject research.
    Keywords: Genetics
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  • 51
    Publication Date: 2018-07-06
    Description: Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
    Keywords: Genetics
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  • 52
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-08
    Keywords: Genetics
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  • 53
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-13
    Keywords: Genetics
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  • 54
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-13
    Keywords: Genetics
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  • 55
    Publication Date: 2018-04-20
    Description: The genetic basis of autism spectrum disorder (ASD) is known to consist of contributions from de novo mutations in variant-intolerant genes. We hypothesize that rare inherited structural variants in cis-regulatory elements (CRE-SVs) of these genes also contribute to ASD. We investigated this by assessing the evidence for natural selection and transmission distortion of CRE-SVs in whole genomes of 9274 subjects from 2600 families affected by ASD. In a discovery cohort of 829 families, structural variants were depleted within promoters and untranslated regions, and paternally inherited CRE-SVs were preferentially transmitted to affected offspring and not to their unaffected siblings. The association of paternal CRE-SVs was replicated in an independent sample of 1771 families. Our results suggest that rare inherited noncoding variants predispose children to ASD, with differing contributions from each parent.
    Keywords: Genetics
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  • 56
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-23
    Keywords: Genetics
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  • 57
    Publication Date: 2018-04-13
    Description: Family trees have vast applications in fields as diverse as genetics, anthropology, and economics. However, the collection of extended family trees is tedious and usually relies on resources with limited geographical scope and complex data usage restrictions. We collected 86 million profiles from publicly available online data shared by genealogy enthusiasts. After extensive cleaning and validation, we obtained population-scale family trees, including a single pedigree of 13 million individuals. We leveraged the data to partition the genetic architecture of human longevity and to provide insights into the geographical dispersion of families. We also report a simple digital procedure to overlay other data sets with our resource.
    Keywords: Genetics
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  • 58
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-08
    Keywords: Genetics
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  • 59
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-10
    Keywords: Genetics
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  • 60
    Publication Date: 2018-02-10
    Description: The predisposition to neuropsychiatric disease involves a complex, polygenic, and pleiotropic genetic architecture. However, little is known about how genetic variants impart brain dysfunction or pathology. We used transcriptomic profiling as a quantitative readout of molecular brain-based phenotypes across five major psychiatric disorders—autism, schizophrenia, bipolar disorder, depression, and alcoholism—compared with matched controls. We identified patterns of shared and distinct gene-expression perturbations across these conditions. The degree of sharing of transcriptional dysregulation is related to polygenic (single-nucleotide polymorphism–based) overlap across disorders, suggesting a substantial causal genetic component. This comprehensive systems-level view of the neurobiological architecture of major neuropsychiatric illness demonstrates pathways of molecular convergence and specificity.
    Keywords: Genetics
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  • 61
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-26
    Keywords: Genetics
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  • 62
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-26
    Keywords: Genetics
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  • 63
    Publication Date: 2018-01-26
    Description: Sequence variants in the parental genomes that are not transmitted to a child (the proband) are often ignored in genetic studies. Here we show that nontransmitted alleles can affect a child through their impacts on the parents and other relatives, a phenomenon we call "genetic nurture." Using results from a meta-analysis of educational attainment, we find that the polygenic score computed for the nontransmitted alleles of 21,637 probands with at least one parent genotyped has an estimated effect on the educational attainment of the proband that is 29.9% ( P = 1.6 x 10 –14 ) of that of the transmitted polygenic score. Genetic nurturing effects of this polygenic score extend to other traits. Paternal and maternal polygenic scores have similar effects on educational attainment, but mothers contribute more than fathers to nutrition- and heath-related traits.
    Keywords: Genetics
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  • 64
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-09
    Description: The faithful inheritance of the epigenome is critical for cells to maintain gene expression programs and cellular identity across cell divisions. We mapped strand-specific DNA methylation after replication forks and show maintenance of the vast majority of the DNA methylome within 20 minutes of replication and inheritance of some hemimethylated CpG dinucleotides (hemiCpGs). Mapping the nascent DNA methylome targeted by each of the three DNA methyltransferases (DNMTs) reveals interactions between DNMTs and substrate daughter cytosines en route to maintenance methylation or hemimethylation. Finally, we show the inheritance of hemiCpGs at short regions flanking CCCTC-binding factor (CTCF)/cohesin binding sites in pluripotent cells. Elimination of hemimethylation causes reduced frequency of chromatin interactions emanating from these sites, suggesting a role for hemimethylation as a stable epigenetic mark regulating CTCF-mediated chromatin interactions.
    Keywords: Genetics
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  • 65
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-16
    Keywords: Genetics
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  • 66
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-16
    Keywords: Genetics
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  • 67
    Publication Date: 2018-03-16
    Description: Genetic association studies often examine features independently, potentially missing subpopulations with multiple phenotypes that share a single cause. We describe an approach that aggregates phenotypes on the basis of patterns described by Mendelian diseases. We mapped the clinical features of 1204 Mendelian diseases into phenotypes captured from the electronic health record (EHR) and summarized this evidence as phenotype risk scores (PheRSs). In an initial validation, PheRS distinguished cases and controls of five Mendelian diseases. Applying PheRS to 21,701 genotyped individuals uncovered 18 associations between rare variants and phenotypes consistent with Mendelian diseases. In 16 patients, the rare genetic variants were associated with severe outcomes such as organ transplants. PheRS can augment rare-variant interpretation and may identify subsets of patients with distinct genetic causes for common diseases.
    Keywords: Genetics
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  • 68
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-09
    Keywords: Genetics
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  • 69
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    Universidade Estadual de Maringá. Centro de Ciências Agrárias. Programa de Pós-Graduação em Zootecnia
    Publication Date: 2021-05-19
    Description: Cryopreservation of genetic material of fish has become a tool essential for preservation of biological materials and production. However, stocking of fish embryos in liquid nitrogen (-196°C) and maintain indefinitely is not yet possible. Recently, developments in research on cryopreservation allowed storing embryos at -8°C for 24 hours. This indicates the possibilityof fish embryo cryopreserving, moreover, the biotechnical cooling for a short time already has practical applications. The present study aimed to evaluate the efficiency of different cryoprotectants to the processes of cryopreservation (freezing, vitrification and cooling) of tambaqui embryos (Colossoma macropomum). Despite not having succeeded in tambaqui embryos cryopreservation important points has been clarified as related to damage to the embryos. Injuries and morphological changes in embryos were identified at all stages of the freezing process, being higher with stabilization at -35°C after being submerged in liquid nitrogen and thawed. At the moment of the seeding besides a lower incidence of injuries, higher percentage of embryos with chorion were observed. The freezing curve protocolstested have not prevented the formation of ice crystals, thus turning unfeasible the embryonic embryos C. macropomum freezing. In the experiment of vitrification the methanol 20% with two-minutes of pre-immersion in exposure to liquid nitrogen, preserved the chorion and some cellular structures. Although it avoided further damage was not sufficient to prevent mortality of embryos, these results open perspectives for continued studies on cryopreservation of fish embryos. Ethylene glycol, glycerol and DMSO were toxic at higher concentrations (20 and30%) not being interesting for the vitrification of embryos C. macropomum. In tests of cooling to at -8°C treatments with ethylene glycol, glycerol and DMSO associated withsucrose did not result in satisfactory answers. To store embryos of C. macropomum at -8°Cfor a period of six hours is suggested cryoprotectant solutions with 17% sucrose combinedwith 10% methanol.
    Description: A criopreservação do material genético de peixes tornou uma ferramenta imprescindível,tanto para conservação de biodiversidade como para produção. No entanto, estocar embriões de peixes em nitrogênio líquido (-196ºC) e conservar por tempo indeterminado ainda não é possível. Recentemente, a evolução nas pesquisas com criopreservação possibilitou estocar embriões a -8ºC, por até 24 horas. Este fato aponta a possibilidade de criopreservar embriões de peixe, e a biotecnia de resfriamento por curto período já tem aplicações práticas. O presente estudo teve como objetivo avaliar a eficiência de diferentes crioprotetores nos processos da criopreservação (congelação, vitrificação e resfriamento) de embriões de tambaqui (Colossoma macropomum). Embora parte dos objetivos propostos tenha sido alcançados, nos testes de criopreservação, somando ao esclarecimento dos aspectos importantes quanto aos danos causados aos embriões, existem ainda muitas etapas para tornar viável a criopreservação de embriões de peixes. Nos testes, foram identificadas injúrias nos embriões em todas as etapas do processo de congelação, sendo a fase com maior incidência na estabilização em -35ºC e após a submissão em nitrogênio líquido e posterior descongelamento. No momento do ?seeding? (indução a cristalização a -7ºC), além de menor ocorrência de injúrias, maior porcentagem de embriões com córion foram verificados. As curvas de resfriamento nos testes de congelação não evitaram a formação de cristais de gelo, o que inviabilizou a congelação dos embriões de C. macropomum. No experimento de vitrificação, o metanol 20% com dois minutos de exposição pré-imersão ao nitrogênio líquido preservou o córion e algumas estruturas celulares. Embora tenha evitado maiores danos não foi suficiente para evitar a mortalidade dos embriões, o que abre perspectivas para continuidade nos estudos em criopreservação de embriões de peixes. Etilenoglicol, DMSO eglicerol foram tóxicos nas concentrações mais elevadas (20 e 30%), não sendo interessante para a vitrificação dos embriões de C. macropomum. Nos testes de resfriamento a -8ºC, os tratamentos com etilenoglicol, glicerol e DMSO associados à sacarose não resultaram em respostas satisfatórias. Para armazenar embriões de C. macropomum a -8°C, por um período de seis horas, sugere-se soluções crioprotetoras com sacarose 17% associada ao metanol 10%.
    Description: PhD
    Keywords: Cryoprotectants ; Conservation ; Animal production ; Genetics ; Tambaqui ; Brazil ; Produção animal ; Genética ; Tambaqui ; Reprodução ; Biotecnologia ; Crioprotetores ; Conservação ; Biotechnology ; Brasil ; Reproduction
    Repository Name: AquaDocs
    Type: Thesis/Dissertation
    Format: 91pp.
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  • 70
    Publication Date: 2021-05-19
    Description: In sturgeon aquaculture, where the main purpose is caviar production, a reliable method is needed to separate fish according to gender. Currently, due to the lack of external sexual dimorphism, the fish are sexed by an invasive surgical examination of the gonads. Development of a non-invasive procedure for sexing fish based on genetic markers is of special interest. In the present study we employed Bulked Segregant Analysis (BSA) methodology to search for DNA markers associated with the sex of the beluga sturgeon (Huso huso). DNA bulks (male and female) were created by combining equal amounts of genomic DNA from 10 fish of both sexes. A total of 101 decamer primers associated with the sex-specific sequences in non-sturgeon species was used for targeted screening of the bulks, resulting in 2846 bands that all of them were present in both sexes. Our results showed that sex chromosomes are weakly differentiated in the sturgeon genome and comprised sequences not complementary to the sex-specific primers in non-sturgeon species.
    Description: Published
    Keywords: Huso huso ; Bulked segregant analysis (BSA) ; Beluga ; Genome ; Sex ; Sex markers ; Genetics
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.185-195
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  • 71
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PeerJ 5 (2017): e3059, doi:10.7717/peerj.3059.
    Description: The True’s beaked whale (Mesoplodon mirus, True 1913) is a poorly known member of the Ziphiidae family. Its distribution in the northern hemisphere is thought to be restricted to the temperate or warm temperate waters of the North Atlantic, while a few stranding records from the southern hemisphere suggest a wider and antitropical distribution, extending to waters from the Atlantic coast of Brazil to South Africa, Mozambique, Australia and the Tasman Sea coast of New Zealand. This paper (i) reports the first molecular confirmation of the occurrence of the True’s beaked whale at the southern limit of its distribution recorded in the northeast Atlantic: the Azores and Canary Islands (macaronesian ecoregion); (ii) describes a new colouration for this species using evidence from a whale with molecular species confirmation; and (iii) contributes to the sparse worldwide database of live sightings, including the first underwater video recording of this species and close images of a calf. Species identification was confirmed in two cases using mitochondrial DNA control region and cytochrome b gene markers: a subadult male True’s beaked whale that stranded in El Hierro, Canary Islands, in November 2012, and a subadult male found floating dead near Faial, the Azores, in July 2004. The whale that stranded in the Canary Islands had a clearly delimited white area on its head, extending posteriorly from the tip of the beak to cover the blowhole dorsally and the gular grooves ventrally. This colouration contrasts with previous descriptions for the species and it may be rare, but it exemplifies the variability of the colouration of True’s beaked whales in the North Atlantic, further confirmed here by live sightings data. The recording of several observations of this species in deep but relatively coastal waters off the Azores and the Canary Islands suggests that these archipelagos may be unique locations to study the behaviour of the enigmatic True’s beaked whale.
    Description: MAS is supported by an FCT-Investigator contract (funded by POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education). ELC was supported for the analysis by a Newton International Fellowship from the Royal Society of London and during writting by the EU-FP7 Marie Curie project ``Behaviour-Connect''. NAS was funded during data collection of this work by the EU-FP7 Marie Curie project SOUNDMAR and during writting by project ECOSOUND within the Horizon 2020 EU Marie Slodowska Curie program.
    Keywords: Ziphiidae ; Cytochrome b ; mtDNA ; Genetics ; Colouration patterns ; Phenotype ; North Atlantic ; Cetacean distribution ; Canary Islands ; Azores
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 72
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Genetics
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  • 73
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-18
    Keywords: Genetics
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  • 74
    Publication Date: 2017-09-01
    Description: Copy number mutations implicate excess production of α-synuclein as a possibly causative factor in Parkinson’s disease (PD). Using an unbiased screen targeting endogenous gene expression, we discovered that the β2-adrenoreceptor (β2AR) is a regulator of the α-synuclein gene ( SNCA ). β2AR ligands modulate SNCA transcription through histone 3 lysine 27 acetylation of its promoter and enhancers. Over 11 years of follow-up in 4 million Norwegians, the β2AR agonist salbutamol, a brain-penetrant asthma medication, was associated with reduced risk of developing PD (rate ratio, 0.66; 95% confidence interval, 0.58 to 0.76). Conversely, a β2AR antagonist correlated with increased risk. β2AR activation protected model mice and patient-derived cells. Thus, β2AR is linked to transcription of α-synuclein and risk of PD in a ligand-specific fashion and constitutes a potential target for therapies.
    Keywords: Genetics
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  • 75
    Publication Date: 2017-08-18
    Description: To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei, termed sci-RNA-seq (single-cell combinatorial indexing RNA sequencing). We applied sci-RNA-seq to profile nearly 50,000 cells from the nematode Caenorhabditis elegans at the L2 larval stage, which provided 〉50-fold "shotgun" cellular coverage of its somatic cell composition. From these data, we defined consensus expression profiles for 27 cell types and recovered rare neuronal cell types corresponding to as few as one or two cells in the L2 worm. We integrated these profiles with whole-animal chromatin immunoprecipitation sequencing data to deconvolve the cell type–specific effects of transcription factors. The data generated by sci-RNA-seq constitute a powerful resource for nematode biology and foreshadow similar atlases for other organisms.
    Keywords: Genetics
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  • 76
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Genetics
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  • 77
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Genetics
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  • 78
    Publication Date: 2017-09-01
    Description: Having the correct number of chromosomes is vital for normal development and health. Sex chromosome trisomy affects 0.1% of the human population and is associated with infertility. We show that during reprogramming to induced pluripotent stem cells (iPSCs), fibroblasts from sterile trisomic XXY and XYY mice lose the extra sex chromosome through a phenomenon we term trisomy-biased chromosome loss (TCL). Resulting euploid XY iPSCs can be differentiated into the male germ cell lineage and functional sperm that can be used in intracytoplasmic sperm injection to produce chromosomally normal, fertile offspring. Sex chromosome loss is comparatively infrequent during mouse XX and XY iPSC generation. TCL also applies to other chromosomes, generating euploid iPSCs from cells of a Down syndrome mouse model. It can also create euploid iPSCs from human trisomic patient fibroblasts. The findings have relevance to overcoming infertility and other trisomic phenotypes.
    Keywords: Genetics
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  • 79
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-02
    Keywords: Genetics
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  • 80
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-16
    Keywords: Genetics
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  • 81
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-02
    Keywords: Genetics
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  • 82
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-02
    Keywords: Genetics
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  • 83
    Publication Date: 2017-06-16
    Description: The mechanistic target of rapamycin complex 1 (mTORC1) is recruited to the lysosome by Rag guanosine triphosphatases (GTPases) and regulates anabolic pathways in response to nutrients. We found that MiT/TFE transcription factors—master regulators of lysosomal and melanosomal biogenesis and autophagy—control mTORC1 lysosomal recruitment and activity by directly regulating the expression of RagD. In mice, this mechanism mediated adaptation to food availability after starvation and physical exercise and played an important role in cancer growth. Up-regulation of MiT/TFE genes in cells and tissues from patients and murine models of renal cell carcinoma, pancreatic ductal adenocarcinoma, and melanoma triggered RagD-mediated mTORC1 induction, resulting in cell hyperproliferation and cancer growth. Thus, this transcriptional regulatory mechanism enables cellular adaptation to nutrient availability and supports the energy-demanding metabolism of cancer cells.
    Keywords: Genetics
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  • 84
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-16
    Keywords: Genetics
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  • 85
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-16
    Keywords: Genetics
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  • 86
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Genetics
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  • 87
    Publication Date: 2017-10-06
    Description: The immune system varies in cell types, states, and locations. The complex networks, interactions, and responses of immune cells produce diverse cellular ecosystems composed of multiple cell types, accompanied by genetic diversity in antigen receptors. Within this ecosystem, innate and adaptive immune cells maintain and protect tissue function, integrity, and homeostasis upon changes in functional demands and diverse insults. Characterizing this inherent complexity requires studies at single-cell resolution. Recent advances such as massively parallel single-cell RNA sequencing and sophisticated computational methods are catalyzing a revolution in our understanding of immunology. Here we provide an overview of the state of single-cell genomics methods and an outlook on the use of single-cell techniques to decipher the adaptive and innate components of immunity.
    Keywords: Genetics
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  • 88
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-10-06
    Description: The stereotyped spatial architecture of the brain is both beautiful and fundamentally related to its function, extending from gross morphology to individual neuron types, where soma position, dendritic architecture, and axonal projections determine their roles in functional circuitry. Our understanding of the cell types that make up the brain is rapidly accelerating, driven in particular by recent advances in single-cell transcriptomics. However, understanding brain function, development, and disease will require linking molecular cell types to morphological, physiological, and behavioral correlates. Emerging spatially resolved transcriptomic methods promise to fill this gap by localizing molecularly defined cell types in tissues, with simultaneous detection of morphology, activity, or connectivity. Here, we review the requirements for spatial transcriptomic methods toward these goals, consider the challenges ahead, and describe promising applications.
    Keywords: Genetics
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  • 89
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-10-06
    Description: Single-cell multi-omics has recently emerged as a powerful technology by which different layers of genomic output—and hence cell identity and function—can be recorded simultaneously. Integrating various components of the epigenome into multi-omics measurements allows for studying cellular heterogeneity at different time scales and for discovering new layers of molecular connectivity between the genome and its functional output. Measurements that are increasingly available range from those that identify transcription factor occupancy and initiation of transcription to long-lasting and heritable epigenetic marks such as DNA methylation. Together with techniques in which cell lineage is recorded, this multilayered information will provide insights into a cell’s past history and its future potential. This will allow new levels of understanding of cell fate decisions, identity, and function in normal development, physiology, and disease.
    Keywords: Genetics
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  • 90
    Publication Date: 2017-11-17
    Description: Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.
    Keywords: Genetics
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  • 91
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-17
    Keywords: Genetics
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  • 92
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-12-22
    Keywords: Genetics
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  • 93
    Publication Date: 2017-12-22
    Description: Puccinia graminis f. sp. tritici ( Pgt ) causes wheat stem rust, a devastating fungal disease. The Sr35 resistance gene confers immunity against this pathogen’s most virulent races, including Ug99. We used comparative whole-genome sequencing of chemically mutagenized and natural Pgt isolates to identify a fungal gene named AvrSr35 that is required for Sr35 avirulence. The AvrSr35 gene encodes a secreted protein capable of interacting with Sr35 and triggering the immune response. We show that the origin of Pgt isolates virulent on Sr35 is associated with the nonfunctionalization of the AvrSr35 gene by the insertion of a mobile element. The discovery of AvrSr35 provides a new tool for Pgt surveillance, identification of host susceptibility targets, and characterization of the molecular determinants of immunity in wheat.
    Keywords: Genetics
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  • 94
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-12
    Keywords: Genetics
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  • 95
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-04-28
    Keywords: Genetics
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  • 96
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-04-28
    Keywords: Genetics
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  • 97
    Publication Date: 2017-04-28
    Description: The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between ~4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs.
    Keywords: Genetics
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  • 98
    Publication Date: 2017-05-05
    Description: Bantu languages are spoken by about 310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial rainforest, before spreading toward eastern and southern Africa. We also found that genetic adaptation of Bantu speakers was facilitated by admixture with local populations, particularly for the HLA and LCT loci. Finally, we identified a major contribution of western central African Bantu speakers to the ancestry of African Americans, whose genomes present no strong signals of natural selection. Together, these results highlight the contribution of Bantu-speaking peoples to the complex genetic history of Africans and African Americans.
    Keywords: Genetics
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  • 99
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-05
    Keywords: Genetics
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  • 100
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-05
    Keywords: Genetics
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