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1.
Nat Biotechnol ; 2020 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-32152598

RESUMO

Crosstalk between neighboring cells underlies many biological processes, including cell signaling, proliferation and differentiation. Current single-cell genomic technologies profile each cell separately after tissue dissociation, losing information on cell-cell interactions. In the present study, we present an approach for sequencing physically interacting cells (PIC-seq), which combines cell sorting of physically interacting cells (PICs) with single-cell RNA-sequencing. Using computational modeling, PIC-seq systematically maps in situ cellular interactions and characterizes their molecular crosstalk. We apply PIC-seq to interrogate diverse interactions including immune-epithelial PICs in neonatal murine lungs. Focusing on interactions between T cells and dendritic cells (DCs) in vitro and in vivo, we map T cell-DC interaction preferences, and discover regulatory T cells as a major T cell subtype interacting with DCs in mouse draining lymph nodes. Analysis of T cell-DC pairs reveals an interaction-specific program between pathogen-presenting migratory DCs and T cells. PIC-seq provides a direct and broadly applicable technology to characterize intercellular interaction-specific pathways at high resolution.

2.
J Contam Hydrol ; 231: 103630, 2020 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-32169749

RESUMO

Sand column experiments were performed under saturated conditions to investigate impact of humic acid (HA) on attachment of nC60 nanoparticles (NPs) in NaCl and CaCl2 at ionic strengths (ISs) from 1 mM to 100 mM and subsequent detachment via reducing solution IS. The attachment increased with increasing IS due to reduced repulsive Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energy and accordingly increased retention in primary energy wells. More attachments occurred in CaCl2 compared to NaCl because Ca2+ exhibited greater charge screen ability and served as a bridging agent between the NPs and sand surfaces. The presence of HA significantly reduced nC60 NPs attachment on sand surfaces (especially on nanoscale physical heterogeneities) in 10 mM NaCl and 1 mM CaCl2 because of enhanced electrostatic and steric repulsions. Interestingly, although the HA did not cause reduction of attachment in 100 mM NaCl and 10 mM CaCl2 compared to the case in absence of HA, the HA caused weak attachment of nC60 on sand surfaces and then much more significant detachment by decreasing IS. The HA did not alter both attachment and detachment in 100 mM CaCl2, because the Ca2+ at the high concentration caused formation of very stable complex of HA and NPs, and strong interaction of the complex with the sand surfaces via cation bridge. Our study highlighted that the HA can not only enhance the transport of NPs by inhibiting attachment as revealed in the literature, but also by the continuous capture and release of the NPs from surfaces in subsurface environments.

3.
Folia Primatol (Basel) ; : 1-19, 2020 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-32126549

RESUMO

With 60% of all primate species now threatened with extinction and many species only persisting in small populations in forest fragments, conservation action is urgently needed. But what type of action? Here we argue that restoration of primate habitat will be an essential component of strategies aimed at conserving primates and preventing the extinctions that may occur before the end of the century and propose that primates can act as flagship species for restoration efforts. To do this we gathered a team of academics from around the world with experience in restoration so that we could provide examples of why primate restoration ecology is needed, outline how primates can act as flagship species for restoration efforts of tropical forest, review what little is known about how primate populations respond to restoration efforts, and make specific recommendations of the next steps needed to make restoration of primate populations successful. We set four priorities: (1) academics must effectively communicate both the value of primates and the need for restoration; (2) more research is needed on how primates contribute to forest restoration; (3) more effort must be put into Masters and PhD level training for tropical country nationals; and finally (4) more emphasis is needed to monitor the responses of regenerating forest and primate populations where restoration efforts are initiated. We are optimistic that populations of many threatened species can recover, and extinctions can be prevented, but only if concerted large-scale efforts are made soon and if these efforts include primate habitat restoration.

4.
Ann Bot ; 2020 Mar 17.
Artigo em Inglês | MEDLINE | ID: mdl-32179920

RESUMO

BACKGROUND AND AIMS: Light interception is closely related to canopy architecture. Few studies based on multi-view photography have been conducted in a field environment, particularly studies that link 3D plant architecture with a radiation model to quantify the dynamic canopy light interception. In this study, we combined realistic 3D plant architecture with a radiation model to quantify and evaluate the effect of differences in planting patterns and row orientations on canopy light interception. METHODS: The three-dimensional architecture of maize and soybean plants were reconstructed for sole crops and intercrops based on multi-view images obtained at five growth dates in the field. We evaluated the accuracy of the calculated leaf length, maximum leaf width, plant height and leaf area according to the measured data. The light distribution within the 3D plant canopy was calculated with a 3D radiation model. Finally, we evaluated canopy light interception in different row orientations. KEY RESULTS: There was good agreement between the measured and calculated phenotypic traits, with an R2>0.97. The light distribution was more uniform for intercropped maize and more concentrated for sole maize. At the maize silking stage, 85% of radiation was intercepted by approximately 55% of the upper canopy region for maize and by approximately 33% of the upper canopy region for soybean. There was no significant difference in daily light interception between the different row orientations for the entire intercropping and sole systems. However, for intercropped maize, near east-west orientations showed approximately 19% higher daily light interception than near south-north orientations. For intercropped soybean, daily light interception showed the opposite trend. It was approximately 49% higher for near south-north orientations than for near east-west orientations. CONCLUSIONS: The accurate reconstruction of 3D plants grown in the field based on multi-view images provides the possibility for high-throughput 3D phenotyping in the field and allows a better understanding of the relationship between canopy architecture and the light environment.

5.
Sci Rep ; 10(1): 480, 2020 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-31949226

RESUMO

Collective decision-making is important for coordination and synchronization of the activities among group-living animals and the mechanisms guiding such procedure involve a great variety of characteristics of behavior and motivation. This study provides some evidence investigating collective movement initiation in a multi-level social band of the golden snub-nosed monkeys (Rhinopithecus roxellana) located in the Mts. Qinling, China. We collect 1223 datum records relevant to decision initiation from six OMUs. The results indicate that collective movement initiation could be divided into two continual but relatively independent processes: decisions on moving direction and movement implementation. In both processes, adult individuals are more likely to initiate the decision-making, while other adults vote on initiator's preference, with a threshold, a supporting number required for a success. Thus, voting behavior and quorum fulfillment contribute to a successful decision-making. Adult individuals play important role in making decisions for moving direction and implementation. For a successful collective movement initiation, the individuals being more central in grooming network initiate decisions more frequently than the others, and attract voters more easily. Furthermore, following the initiation, at least four positive voters are required for a direction decision and at least three positive voters are needed for the decision on movement implementation, which could be considered as the threshold of quorum numbers required for a successful decision. This study has provided some very interesting information and scientific evidence in understanding social structure and behaviors of the nonhuman primates with a social structure very similar to humans'. Thus, some results can directly be referred to the comprehension of human social structure and behavior.

6.
Environ Pollut ; 259: 113924, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31926396

RESUMO

Microalgal aggregation is a key to many ecosystem functions in aquatic environments. Yet mechanistic understanding of microalgae aggregation, especially the interactions with ubiquitous bacteria populations, remains elusive. We reported an experimental study illustrating how the emerging bacterial populations interacted with a model microalga (Chlamydomonas microsphaera) cells and the consequent aggregation patterns. Results showed that the emergence of bacterial populations significantly stimulated C. microsphaera aggregation. Both bacterial and C. microsphaera motilities were remarkably excited upon coculturing, with the mean cell velocity being up to 2.67 and 1.80 times of those of separate bacterial and C. microsphaera cultures, respectively. The stimulated bacterial and C. microsphaera cell velocity upon coculturing would likely provide a mechanism for enhanced probability of cell-cell collisions that led to amplified aggregation of C. microsphaera population. Correlation analysis revealed that bacterial resource foraging (for polysaccharides) was likely a candidate mechanism for stimulated cell motility in an organic carbon source-limited environment, whereby C. microsphaera-derived polysaccharides serve as the sole organic carbon source for heterotrophic bacteria which in turns facilitates bacteria-C. microsphaera aggregation. Additional analysis showed that bacterial populations capable of successive decomposing algal-derived organic matters dominated the cocultures, with the top five abundant genera of Brevundimonas (24.78%), Shinella (17.94%), Sphingopyxis (11.62%), Dongia (5.82%) and Hyphomicrobium (5.45%). These findings provide new insights into full understanding of microalgae-bacteria interactions and consequent microbial aggregation characteristics in aquatic ecosystems.

7.
Environ Pollut ; 256: 113482, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31679872

RESUMO

Antibiotics are contaminants of emerging concern due to their potential effect on antibiotic resistance and human health. Antibiotics tend to sorb strongly to organic materials, and biochar, a high efficient agent for adsorbing and immobilizing pollutants, can thus be used for remediation of antibiotic-contaminated soil and water. The effect of ionizable antibiotics on surface characteristics and transport of biochar colloids (BC) in the environment is poorly studied. Column experiments of BC were conducted in 1 mM NaCl solution under three pH (5, 7, and 10) conditions in the presence of sulfamethazine (SMT). Additionally, the adsorption of SMT by BC and the zeta potential of BC were also studied. The experimental results showed that SMT sorption to BC was enhanced at pH 5 and 7, but reduced at pH 10. SMT sorption reduced the surface charge of BC at pH 5 and 7 due to charge shielding, but increased surface charge at pH 10 due to adsorption of the negatively charged SMT species. The mobility of BC was inhibited by SMT under acidic or neutral conditions, while enhanced by SMT under alkaline conditions, which can be well explained by the change of electrostatic repulsion between BC and sand grains. These findings imply that pH conditions played a crucial role in deciding whether the transport of BC would be promoted by SMT or not. Biochar for antibiotics remediation will be more effective under acidic and neutral soil conditions, and the mobility of BC will be less than in alkaline soils.


Assuntos
Carvão Vegetal/química , Coloides/química , Sulfametazina/química , Adsorção , Antibacterianos , Modelos Químicos , Porosidade , Solo , Poluentes do Solo , Eletricidade Estática
8.
Integr Zool ; 15(1): 79-86, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31305022

RESUMO

Following significant developments in technology, alternative devices have been applied in fieldwork for animal and plant surveys. Thermal-image acquisition cameras installed on unmanned aerial vehicles (UAVs) have been used in animal surveys in the wilderness. This article demonstrates an example of how UAVs can be used in high mountainous regions, presenting a case study on the Sichuan snub-nosed monkey with a detection rate of 65.19% for positive individual identification. It also presents a model that can prospectively predict population size for a given animal species, which is based on combined initial work using UAVs and traditional surveys on the ground. A great potential advantage of UAVs is significantly shortening survey procedures, particularly for areas with high mountains and plateaus, such as the Himalayas, the Qinghai-Tibet Plateau, Hengduan Mountains, the Yunnan-Gui Plateau and Qinling Mountains in China, where carrying out a traditional survey is extremely difficult, so that species and population surveys, particularly for critically endangered animals, are largely absent. This lack of data has impacted the management of endangered animals as well as the formulation and amendment of conservation strategies.


Assuntos
Distribuição Animal , Colobinae/fisiologia , Tecnologia de Sensoriamento Remoto/métodos , Aeronaves , Animais , China , Conservação dos Recursos Naturais , Ecossistema , Densidade Demográfica , Tecnologia de Sensoriamento Remoto/instrumentação
9.
Proc Biol Sci ; 286(1916): 20192047, 2019 12 04.
Artigo em Inglês | MEDLINE | ID: mdl-31797732

RESUMO

Research is a highly competitive profession where evaluation plays a central role; journals are ranked and individuals are evaluated based on their publication number, the number of times they are cited and their h-index. Yet such evaluations are often done in inappropriate ways that are damaging to individual careers, particularly for young scholars, and to the profession. Furthermore, as with all indices, people can play games to better their scores. This has resulted in the incentive structure of science increasingly mimicking economic principles, but rather than a monetary gain, the incentive is a higher score. To ensure a diversity of cultural perspectives and individual experiences, we gathered a team of academics in the fields of ecology and evolution from around the world and at different career stages. We first examine how authorship, h-index of individuals and journal impact factors are being used and abused. Second, we speculate on the consequences of the continued use of these metrics with the hope of sparking discussions that will help our fields move in a positive direction. We would like to see changes in the incentive systems, rewarding quality research and guaranteeing transparency. Senior faculty should establish the ethical standards, mentoring practices and institutional evaluation criteria to create the needed changes.

10.
Folia Primatol (Basel) ; : 1-7, 2019 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-31665734

RESUMO

Our study presents the first evidence on how target animacy impacts on manual laterality in the Hylobatidae and contributes to filling the knowledge gap between monkeys and great apes in primate evolution of emotional lateralization. Eleven captive individuals of northern white-cheeked gibbons (Nomascus leucogenys) were chosen as focal subjects. There were significantly more ambipreferent individuals than left/right-handed individuals for both inanimate (χ2(1, n = 11) = 7.364, p = 0.007) and animate (χ2(1, n = 11) = 4.455, p = 0.035) targets, meaning no significant group-level hand preference. The right hand was more frequently used than the left hand for inanimate targets whereas the left hand was more frequently used than the right hand for animate targets, although the interaction between target animacy and hand use was not significant (proportion: F1, 10 = 0.283, p = 0.607; rate: F1, 10 = 0.228, p = 0.643). Our findings in N. leucogenys could not fully support either the tool use theory or the right hemisphere hypothesis.

11.
Gigascience ; 8(8)2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31437279

RESUMO

BACKGROUND: The golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered colobine species endemic to China, which has several distinct traits including a unique social structure. Although a genome assembly for R. roxellana is available, it is incomplete and fragmented because it was constructed using short-read sequencing technology. Thus, important information such as genome structural variation and repeat sequences may be absent. FINDINGS: To obtain a high-quality chromosomal assembly for R. roxellana qinlingensis, we used 5 methods: Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, BioNano optical maps, 10X Genomics link-reads, and high-throughput chromosome conformation capture. The assembled genome was ∼3.04 Gb, with a contig N50 of 5.72 Mb and a scaffold N50 of 144.56 Mb. This represented a 100-fold improvement over the previously published genome. In the new genome, 22,497 protein-coding genes were predicted, of which 22,053 were functionally annotated. Gene family analysis showed that 993 and 2,745 gene families were expanded and contracted, respectively. The reconstructed phylogeny recovered a close relationship between R. rollexana and Macaca mulatta, and these 2 species diverged ∼13.4 million years ago. CONCLUSION: We constructed a high-quality genome assembly of the Qinling golden snub-nosed monkey; it had superior continuity and accuracy, which might be useful for future genetic studies in this species and as a new standard reference genome for colobine primates. In addition, the updated genome assembly might improve our understanding of this species and could assist conservation efforts.


Assuntos
Espécies em Perigo de Extinção , Genoma , Genômica , /genética , Animais , Biologia Computacional/métodos , Ontologia Genética , Genômica/métodos , Anotação de Sequência Molecular , Filogenia , /classificação
12.
Cell ; 178(3): 686-698.e14, 2019 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-31257031

RESUMO

Immune cells residing in white adipose tissue have been highlighted as important factors contributing to the pathogenesis of metabolic diseases, but the molecular regulators that drive adipose tissue immune cell remodeling during obesity remain largely unknown. Using index and transcriptional single-cell sorting, we comprehensively map all adipose tissue immune populations in both mice and humans during obesity. We describe a novel and conserved Trem2+ lipid-associated macrophage (LAM) subset and identify markers, spatial localization, origin, and functional pathways associated with these cells. Genetic ablation of Trem2 in mice globally inhibits the downstream molecular LAM program, leading to adipocyte hypertrophy as well as systemic hypercholesterolemia, body fat accumulation, and glucose intolerance. These findings identify Trem2 signaling as a major pathway by which macrophages respond to loss of tissue-level lipid homeostasis, highlighting Trem2 as a key sensor of metabolic pathologies across multiple tissues and a potential therapeutic target in metabolic diseases.

13.
Mol Aspects Med ; 68: 60-73, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31325458

RESUMO

Endothermy requires a source of endogenous heat production. In birds, this is derived primarily from shivering, but in mammals it is mostly non-shivering thermogenesis (NST). Brown adipose tissue (BAT) is a specialized tissue found in Eutherian mammals that is the source of most NST. Heat production in BAT depends primarily on the activity of uncoupling protein 1 (UCP1), which decouples transport of protons across the inner mitochondrial membrane from synthesis of ATP. UCP1 and hence heat production of BAT is regulated by many factors. In this paper we discuss the main factors activating UCP1 and increasing heat production. Probably the most well-known activator is the catecholamine norepinephrine (NE) which is released from sympathetic nerve endings and binds to adrenergic receptors that are abundantly expressed on BAT. NE stimulates release of free-fatty acids. It was previously thought that such FFAs were essential for activation of UCP1. However recent work has suggested intracellular lipolysis is not essential and FFAs can be derived from extracellular sources. Thyroid hormones also exert impacts on metabolic rate via effects on brown adipocytes which express type 2 deiodinase. Knocking out DIO2 makes mice cold intolerant. Parathyroid hormone appears to also be a potent regulator of BAT activity and may be an important mediator of elevated expenditure during cancer cachexia, although this is disputed by observations that cachexia wasting is not blunted in UCP1 KO mice. Cardiac natriuretic peptides have also been implicated in regulating BAT thermogenesis and the interconversion of beige adipocytes from their white to brown form. Activation of BAT thermogenesis may be an important component of the post-ingestion rise in heat production. Recent work suggests the gut derived hormone secretin may play a key role in this effect, directly linking BAT activation to the alimentary tract. Not only gut hormones but also metabolites derived from gut microbiota such as butyrate may be an important activator of BAT during cold exposure. Additional regulatory factors include bone morphogenic proteins, fibroblast growth factor 21, Vascular endothelial growth factors and transient receptor potential vanilloid receptors which are important components of thermal sensing and hence how brown adipose tissue responds to the cold. In the future the main challenge is to understand how these regulatory factors combine with each other and with inhibitory factors to control heat production from BAT, and what their relative importance is in differing circumstances. Knocking out UCP1 has revealed other sources of heat production in BAT including creatine-dependent cycles and a futile cycle of Ca2+ shuttling into and out of the endoplasmic reticulum via the SERCA and ryanodine receptors.

14.
Zool Res ; 40(5): 449-455, 2019 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-31343856

RESUMO

Investigations on manual laterality in non-human primates can help clarify human evolutionary origins of hand preference and cerebral cognition. Although body posture can influence primate hand preference, investigations on how posture affects hylobatid manual laterality are still in their infancy. This study focused on how spontaneous bipedal behavioral tasks affect hand preference in Hylobatidae. Ten captive northern white-cheeked gibbons (Nomascus leucogenys) were chosen as focal subjects. Unimanual grooming during sitting posture and supported bipedal posture were applied as behavioral tasks. The gibbons displayed a modest tendency on left-hand preference during sitting posture and right-hand preference during supported bipedal posture, although no group-level hand preference was detected for either posture. From the sitting to supported bipedal posture, 70% of individuals displayed different degrees of right-side deviation trends. The strength of manual laterality in the supported bipedal posture was higher than that in the sitting posture. We found significant sex differences in manual laterality during supported bipedal posture but not during sitting posture. Thus, to a certain degree, bipedal posture in N. leucogenys facilitates stronger hand preference, elicits a rightward trend in manual laterality, and produces sex-specific hand preference.


Assuntos
Lateralidade Funcional , Asseio Animal/fisiologia , Hylobates/fisiologia , Postura , Animais , Feminino , Masculino
15.
BMC Bioinformatics ; 20(Suppl 7): 195, 2019 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-31074374

RESUMO

BACKGROUND: Lipid metabolism reprogramming is a hallmark for tumor which contributes to tumorigenesis and progression, but the commonality and difference of lipid metabolism among pan-cancer is not fully investigated. Increasing evidences suggest that the alterations in tumor metabolism, including metabolite abundance and accumulation of metabolic products, lead to local immunosuppression in the tumor microenvironment. An integrated analysis of lipid metabolism in cancers from different tissues using multiple omics data may provide novel insight into the understanding of tumorigenesis and progression. RESULTS: Through systematic analysis of the multiple omics data from TCGA, we found that the most-widely altered lipid metabolism pathways in pan-cancer are fatty acid metabolism, arachidonic acid metabolism, cholesterol metabolism and PPAR signaling. Gene expression profiles of fatty acid metabolism show commonalities across pan-cancer, while the alteration in cholesterol metabolism and arachidonic acid metabolism differ with tissue origin, suggesting tissue specific lipid metabolism features in different tumor types. An integrated analysis of gene expression, DNA methylation and mutations revealed factors that regulate gene expression, including the differentially methylated sites and mutations of the lipid genes, as well as mutation and differential expression of the up-stream transcription factors for the lipid metabolism pathways. Correlation analysis of the proportion of immune cells in the tumor microenvironment and the expression of lipid metabolism genes revealed immune-related differentially expressed lipid metabolic genes, indicating the potential crosstalk between lipid metabolism and immune response. Genes related to lipid metabolism and immune response that are associated with poor prognosis were discovered including HMGCS2, GPX2 and CD36, which may provide clues for tumor biomarkers or therapeutic targets. CONCLUSIONS: Our study provides an integrated analysis of lipid metabolism in pan-cancer, highlights the perturbation of key metabolism processes in tumorigenesis and clarificates the regulation mechanism of abnormal lipid metabolism and effects of lipid metabolism on tumor immune microenvironment. This study also provides new clues for biomarkers or therapeutic targets of lipid metabolism in tumors.


Assuntos
Biomarcadores Tumorais/genética , Metilação de DNA , Regulação Neoplásica da Expressão Gênica , Metabolismo dos Lipídeos/genética , Neoplasias/genética , Neoplasias/metabolismo , Microambiente Tumoral/imunologia , Biologia Computacional/métodos , Perfilação da Expressão Gênica , Humanos , Mutação , Neoplasias/imunologia , Neoplasias/patologia , Transcriptoma , Microambiente Tumoral/genética
16.
Appl Plant Sci ; 7(5): e01244, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31139510

RESUMO

Premise: Rosebay willowherb, or fireweed (Chamerion angustifolium: Onagraceae), has diploid, tetraploid, and hexaploid cytotypes. There are known physiological and ecological differences among the three cytotypes, but genetic differences remain undetermined. We developed simple sequence repeat (SSR) markers for this species. Methods and Results: Leaf samples were collected from three hexaploid C. angustifolium populations. We successfully amplified 16 SSR loci, which were found to be highly polymorphic. The number of alleles, the observed heterozygosity levels, and the expected heterozygosity levels ranged from four to 13, 0.286-0.899, and 0.372-0.871, respectively. Most primers could also be amplified successfully in C. conspersum and the closely related species Epilobium palustre. Conclusions: The 16 polymorphic SSR markers developed here will be useful for genetic studies in C. angustifolium and related species.

17.
Mol Ecol Resour ; 19(5): 1240-1253, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31094065

RESUMO

Duplicated loci, for example those associated with major histocompatibility complex (MHC) genes, often have similar DNA sequences that can be coamplified with a pair of primers. This results in genotyping difficulties and inaccurate analyses. Here, we present a method to assign alleles to different loci in amplifications of duplicated loci. This method simultaneously considers several factors that may each affect correct allele assignment. These are the sharing of identical alleles among loci, null alleles, copy number variation, negative amplification, heterozygote excess or heterozygote deficiency, and linkage disequilibrium. The possible multilocus genotypes are extracted from the alleles for each individual and weighted to estimate the allele frequencies. The likelihood of an allele configuration is calculated and is optimized with a heuristic algorithm. Monte-Carlo simulations and three empirical MHC data sets are used as examples to evaluate the efficacy of our method under different conditions. Our new software, mhc-typer V1.1, is freely available at https://github.com/huangkang1987/mhc-typer.


Assuntos
Alelos , Biologia Computacional/métodos , Duplicação Gênica , Loci Gênicos , Genótipo , Software
18.
Mol Ecol Resour ; 19(5): 1218-1229, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31070300

RESUMO

A significant portion of plant species are polyploids, with ploidy levels sometimes varying among individuals and/or populations. Current techniques to determine the individual ploidy, e.g., flow cytometry, chromosome counting or genotyping-by-sequencing, are often cumbersome. Based on the genotypic probabilities for polysomic inheritance under double-reduction, we developed a model to estimate allele frequency and infer the ploidy status of individuals from the allelic phenotypes of codominant genetic markers. The allele frequencies are estimated by an expectation-maximization algorithm in the presence of null alleles, false alleles, negative amplifications and self-fertilization, and the posterior probabilities are used to assign individuals into different levels of ploidy. The accuracy of this method under different conditions is evaluated. Our methods are freely available in a new software package, ploidyinfer, for use by other researchers which can be downloaded from http://github.com/huangkang1987/ploidyinfer.


Assuntos
Técnicas de Genotipagem/métodos , Fenótipo , Plantas/genética , Ploidias , Dosagem de Genes , Frequência do Gene , Genótipo
19.
G3 (Bethesda) ; 9(5): 1693-1706, 2019 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-30910817

RESUMO

Polyploids are organisms whose genomes consist of more than two complete sets of chromosomes. Both autopolyploids and allopolyploids may display polysomic inheritance. A peculiarity of polysomic inheritance is multivalent formation during meiosis resulting in double-reduction, which occurs when sister chromatid fragments segregate into the same gamete. Double-reduction can result in gametes carrying identical-by-descent alleles and slightly increasing homozygosity. This will cause the genotypic frequencies to deviate from expected values and will thus bias the results of standard population genetic analytical methods used in molecular ecology and selective breeding. In this study, we extend existing double-reduction models to account for any even level of ploidy, and derive the symbolic expressions for genotypic frequencies via two methods. Inbreeding coefficients and heterozygosity under double-reduction and inbreeding are also calculated. Numerical solutions obtained by computer simulations are compared with analytical solutions predicted by the model to validate the model.


Assuntos
Alelos , Frequência do Gene , Genótipo , Padrões de Herança , Modelos Genéticos , Poliploidia , Algoritmos , Heterozigoto , Endogamia , Zigoto
20.
Cell Rep ; 26(10): 2720-2737.e5, 2019 03 05.
Artigo em Inglês | MEDLINE | ID: mdl-30840893

RESUMO

The relation between gut microbiota and the host has been suggested to benefit metabolic homeostasis. Brown adipose tissue (BAT) and beige adipocytes facilitate thermogenesis to maintain host core body temperature during cold exposure. However, the potential impact of gut microbiota on the thermogenic process is confused. Here, we evaluated how BAT and white adipose tissue (WAT) responded to temperature challenges in mice lacking gut microbiota. We found that microbiota depletion via treatment with different cocktails of antibiotics (ABX) or in germ-free (GF) mice impaired the thermogenic capacity of BAT by blunting the increase in the expression of uncoupling protein 1 (UCP1) and reducing the browning process of WAT. Gavage of the bacterial metabolite butyrate increased the thermogenic capacity of ABX-treated mice, reversing the deficit. Our results indicate that gut microbiota contributes to upregulated thermogenesis in the cold environment and that this may be partially mediated via butyrate.

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