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1.
Nucleic Acids Res ; 51(D1): D1312-D1324, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36300629

RESUMO

With the exponential growth of multi-omics data, its integration and utilization have brought unprecedented opportunities for the interpretation of gene regulation mechanisms and the comprehensive analyses of biological systems. IAnimal (https://ianimal.pro/), a cross-species, multi-omics knowledgebase, was developed to improve the utilization of massive public data and simplify the integration of multi-omics information to mine the genetic mechanisms of objective traits. Currently, IAnimal provides 61 191 individual omics data of genome (WGS), transcriptome (RNA-Seq), epigenome (ChIP-Seq, ATAC-Seq) and genome annotation information for 21 species, such as mice, pigs, cattle, chickens, and macaques. The scale of its total clean data has reached 846.46 TB. To better understand the biological significance of omics information, a deep learning model for IAnimal was built based on BioBERT and AutoNER to mine 'gene' and 'trait' entities from 2 794 237 abstracts, which has practical significance for comprehending how each omics layer regulates genes to affect traits. By means of user-friendly web interfaces, flexible data application programming interfaces, and abundant functional modules, IAnimal enables users to easily query, mine, and visualize characteristics in various omics, and to infer how genes play biological roles under the influence of various omics layers.


Assuntos
Bases de Dados Genéticas , Animais , Regulação da Expressão Gênica , Genoma , Bases de Conhecimento , Software , Multiômica
2.
J Am Chem Soc ; 145(23): 12532-12540, 2023 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-37249908

RESUMO

An asymmetric three-component carbosulfonylation of alkenes is presented here. The reaction, involving the simultaneous formation of a C-C and a C-S bond across the π-system, uses a dual nickel/photoredox catalytic system to produce both ß-aryl and ß-alkenyl sulfones in high yields and with excellent levels of stereocontrol (up to 99:1 er). This protocol exhibits a broad substrate scope and excellent functional group tolerance and its synthetic potential has been demonstrated by successful applications toward pharmacologically relevant molecules. A broad array of control experiments supports the involvement of a secondary alkyl radical intermediate generated through radical addition of a sulfonyl radical to the double bond. Moreover, stoichiometric and cross-over experiments further suggest an underlying Ni(0)/Ni(I)/Ni(III) pathway operative in these transformations.

3.
Reprod Domest Anim ; 58(7): 955-964, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37151112

RESUMO

Testicular development and spermatogenesis play critical roles in male fertility and sexual maturation. To explore the genetic basis and key genes related to sexual maturity, we measured serum testosterone content and analysed testis tissue sections of Large White (LW) and Tongcheng (TC) boars at an immature age. We then screened differentially expressed genes (DEGs) in testis development in both breeds using RNA-seq. Finally, we analysed the selection signatures of both breeds to investigate which DEGs were subjected to positive selection. Our findings showed that serum testosterone contents in TC pigs (~4 ng/mL) were much higher than those in LW pigs (<0.95 ng/mL). Haematoxylin and eosin staining of testicular sections showed that the cross-sectional areas and perimeters of the seminiferous tubules in TC testes were larger and longer than those in LW pigs. A total of 5068 DEGs were selected by filtering criteria of q value <0.05 and |log2 (fold change)| ≥ 1. Gene Ontology analysis revealed that 250 genes were enriched in 11 biological process categories involved in sexual maturity. Most candidate genes, including TRIP13, NR6A1, STRA8, PCSK4, ACRBP, TSSK1B and TSSK6, were under positive selection. These results provide a better understanding of the genetic basis for testicular maturation and are useful for enhancing boar reproductive traits through molecular breeding.


Assuntos
Testículo , Transcriptoma , Suínos/genética , Masculino , Animais , Espermatogênese/genética , Túbulos Seminíferos , Testosterona
4.
Sensors (Basel) ; 23(13)2023 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-37447675

RESUMO

An effective soil moisture retrieval method for FY-3E (Fengyun-3E) GNOS-R (GNSS occultation sounder II-reflectometry) is developed in this paper. Here, the LAGRS model, which is totally oriented for GNOS-R, is employed to estimate vegetation and surface roughness effects on surface reflectivity. Since the LAGRS (land surface GNSS reflection simulator) model is a space-borne GNSS-R (GNSS reflectometry) simulator based on the microwave radiative transfer equation model, the method presented in this paper takes more consideration on the physical scattering properties for retrieval. Ancillary information from SMAP (soil moisture active passive) such as the vegetation water content and the roughness coefficient are investigated for the final algorithm's development. At first, the SR (surface reflectivity) data calculated from GNOS-R is calculated and then calibrated, and then the vegetation roughness factor is achieved and used to eliminate the effects on both factors. After receiving the Fresnel reflectivity, the corresponding soil moisture estimated from this method is retrieved. The results demonstrate good consistency between soil moisture derived from GNOS-R data and SMAP soil moisture, with a correlation coefficient of 0.9599 and a root mean square error of 0.0483 cm3/cm3. This method succeeds in providing soil moisture on a global scale and is based on the previously developed physical LAGRS model. In this way, the great potential of GNOS-R for soil moisture estimation is presented.


Assuntos
Solo , Água , Água/análise , Micro-Ondas
5.
Parasite Immunol ; 44(12): e12950, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36104299

RESUMO

Haemonchus contortus (H. contortus) has caused a huge impact on the animal husbandry economy in the world's tropical and subtropical regions. Innate immunity is the first-line of host defence. The host recognizes pathogen-associated molecular patterns (PAMPs) through a variety of pattern recognition receptors (PRRs) and activates downstream signalling pathways to resist pathogens invasion. Therefore, elucidating the immune interaction between host and pathogen is key to understanding how the host resists the pathogen. We identified 1516 protein-protein interactions (PPIs) between goat innate immune signal pathway proteins and H. contortus excretory-secretory proteins (ESPs) by Recombination-based "Library vs. Library" yeast two-hybrid system (RLL-Y2H) and constructed the PPIs network. Among them, the NLR and IL-17 signalling pathways have the most protein interactions. And there were more interaction proteins between NOD1 and MUC5AC proteins in the pathways. Combined with the differentially expressed genes (DEGs) of susceptible and resistant goats identified in the preliminary work of our laboratory, we selected the intersection genes to construct the PPIs network, and TRAF2 appeared as a key protein of goat innate immune signalling pathway. We initially studied the PPIs between goat and H. contortus ESPs, which provides valuable information for better understanding the immune interaction between the goats and the H. contortus.


Assuntos
Doenças das Cabras , Hemoncose , Haemonchus , Animais , Hemoncose/veterinária , Cabras , Imunidade Inata , Transdução de Sinais
6.
BMC Genomics ; 22(1): 581, 2021 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-34330207

RESUMO

BACKGROUND: The Muscovy duck (Cairina moschata) is an economically important duck species, with favourable growth and carcass composition parameters in comparison to other ducks. However, limited genomic resources for Muscovy duck hinder our understanding of its evolution and genetic diversity. RESULTS: We combined linked-reads sequencing technology and reference-guided methods for de novo genome assembly. The final draft assembly was 1.12 Gbp with 29 autosomes, one sex chromosome and 4,583 unlocalized scaffolds with an N50 size of 77.35 Mb. Based on universal single-copy orthologues (BUSCO), the draft genome assembly completeness was estimated to be 93.30 %. Genome annotation identified 15,580 genes, with 15,537 (99.72 %) genes annotated in public databases. We conducted comparative genomic analyses and found that species-specific and rapidly expanding gene families (compared to other birds) in Muscovy duck are mainly involved in Calcium signaling, Adrenergic signaling in cardiomyocytes, and GnRH signaling pathways. In comparison to the common domestic duck (Anas platyrhynchos), we identified 104 genes exhibiting strong signals of adaptive evolution (Ka/Ks > 1). Most of these genes were associated with immune defence pathways (e.g. IFNAR1 and TLR5). This is indicative of the existence of differences in the immune responses between the two species. Additionally, we combined divergence and polymorphism data to demonstrate the "faster-Z effect" of chromosome evolution. CONCLUSIONS: The chromosome-level genome assembly of Muscovy duck and comparative genomic analyses provide valuable resources for future molecular ecology studies, as well as the evolutionary arms race between the host and influenza viruses.


Assuntos
Patos , Genômica , Animais , Aves , Cromossomos , Patos/genética , Genoma , Humanos
7.
Genet Sel Evol ; 53(1): 35, 2021 Apr 13.
Artigo em Inglês | MEDLINE | ID: mdl-33849442

RESUMO

BACKGROUND: The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. RESULTS: Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100-11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). CONCLUSIONS: Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.


Assuntos
Domesticação , Patos/genética , Fluxo Gênico , Animais , Proteínas Aviárias/genética , Cromossomos/genética , Patos/classificação , Filogenia , Seleção Genética , Sequenciamento Completo do Genoma
8.
Angew Chem Int Ed Engl ; 60(20): 11384-11390, 2021 05 10.
Artigo em Inglês | MEDLINE | ID: mdl-33605007

RESUMO

Chiral carboxylic acids are important compounds because of their prevalence in pharmaceuticals, natural products and agrochemicals. Asymmetric hydrogenation of α,ß-unsaturated carboxylic acids has been widely recognized as one of the most efficient synthetic approaches to afford such compounds. Although related asymmetric hydrogenation of di- and trisubstituted unsaturated acids with noble metals is well established, asymmetric hydrogenation of challenging tetrasubstituted α,ß-unsaturated carboxylic acids is rarely reported. We demonstrate enantioselective hydrogenation of cyclic and acyclic tetrasubstituted α,ß-unsaturated carboxylic acids via cobalt(II) catalysis. This protocol showed broad substrate scope and gave chiral carboxylic acids in good yields with excellent enantiocontrol (up to 98 % yield and 99 % ee). Combined experimental and computational mechanistic studies support a CoII catalytic cycle involving migratory insertion and σ-bond metathesis processes. DFT calculations reveal that enantioselectivity may originate from the steric effect between the phenyl groups of the ligand and the substrate.

9.
Bioinformatics ; 35(9): 1566-1572, 2019 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-30295699

RESUMO

MOTIVATION: Small non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs), play key roles in many biological processes. However, only a few tools can be used to develop the optimal primer or probe design for the expression profile of small ncRNAs. Here, we developed sRNAPrimerDB, the first automated primer designing and query web service for small ncRNAs. RESULTS: The primer online designing module of sRNAPrimerDB is composed of primer design algorithms and quality evaluation of the polymerase chain reaction (PCR) primer. Five types of primers, namely, generic or specific reverse transcription primers, specific PCR primers pairs, TaqMan probe, double-hairpin probe and hybridization probe for different small ncRNA detection methods, can be designed and searched using this service. The quality of PCR primers is further evaluated using melting temperature, primer dimer, hairpin structure and specificity. Moreover, the sequence and size of each amplicon are also provided for the subsequent experiment verification. At present, 531 306 and 2 941 669 primer pairs exist across 223 species for miRNAs and piRNAs, respectively, according to sRNAPrimerDB. Several primers designed by sRNAPrimerDB are further successfully validated by subsequent experiments. AVAILABILITY AND IMPLEMENTATION: sRNAPrimerDB is a valuable platform that can be used to detect small ncRNAs. This module can be publicly accessible at http://www.srnaprimerdb.com or http://123.57.239.141. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Pequeno RNA não Traduzido/genética , Algoritmos , Primers do DNA , Reação em Cadeia da Polimerase , Software
10.
Reprod Domest Anim ; 55(11): 1554-1564, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32815612

RESUMO

The relationship between the conceptus and the maternal uterine environment is crucial for the successful establishment and maintenance of pregnancy in cattle. Gene expression analysis of the conceptus and maternal reproductive tissues is a favourable method to assess the embryonic maternal interaction. The reliability of the commonly used method reverse transcription-quantitative polymerase chain reaction (RT-qPCR) depends on proper normalization to stable reference genes (RGs). The objective of this study was to determine the expression stability of 10 potential RGs in maternal reproductive tissues and foetal tissues, and to analyse the effect of RG selection on the calculation of the relative expression of target genes. The expression stability of 10 potential RGs was analysed in eight different tissues from three pregnant dairy cows. Three programs-GeNorm, NormFinder and Bestkeeper-were used to identify the best RGs. According to all three programs, the most stable RG was CNOT11, whereas the least stable RGs were GAPDH and HPRT1. GeNorm analysis showed that a combination of five RGs (SDHA, PPIA, CNOT11, RPS9 and RPL19) was necessary for appropriate data normalization. However, NormFinder analysis indicated that the combination of CNOT11 and PPIA was the most suitable. When target genes were normalized to these RGs, the relative expression of the Radical S-adenosyl methionine domain containing 2 gene was not affected by the choice of RGs, whereas a large difference was observed in the expression profile of the Nuclear erythroid2-related factor 2 gene between the most stable and least stable RGs. The results indicate that careful selection of RGs is crucial under different conditions, especially for target genes with relatively small fold changes. Furthermore, the results provide useful information for the selection of RGs for evaluating genes affecting bovine reproduction.


Assuntos
Bovinos/genética , Bovinos/metabolismo , Perfilação da Expressão Gênica/veterinária , Animais , Feminino , Feto , Regulação da Expressão Gênica no Desenvolvimento , Genitália Feminina , Glândulas Mamárias Animais , Gravidez , Reação em Cadeia da Polimerase em Tempo Real/veterinária , Valores de Referência
11.
Trop Anim Health Prod ; 52(4): 1583-1598, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31828571

RESUMO

Haemonchus contortus is a common, intractably pathogenic and economically important gastrointestinal nematode for goat producers worldwide, especially in tropical and subtropical regions. The objective of this study is to identify single nucleotide polymorphisms (SNPs) of 12 candidate goat genes mainly related to the innate immune response associated with fecal egg counts (FECs) of Haemonchus contortus in goat as an indicator of the level of parasite infection. Phenotypic data including FEC and blood traits were recorded in 189 native goats from China and 191 ones from Bangladesh, respectively. Bangladeshi goats had significantly (P < 0.01) lower FEC compared to that of Chinese goats, suggesting higher susceptible and infection rates in Chinese goat populations. FEC was significantly positive correlated with body weight (r = 0.64, P < 0.01) and hemoglobin (r = 0.49, P < 0.01) value, but negative with pack cell volume (r = - 0.63, P < 0.05) in goats. Genotyping of SNPs was performed using a matrix-assisted laser desorption ionization time of flight mass spectrometry assay and a generalized linear model was used to evaluate the association between each SNP and goat FEC trait. Eleven novel SNPs in the NLRC3, NLRC5, HIP1, and LRP8, out of 46 variants from these 12 genes, were significantly associated with FEC of goats with a nominal significance level of P < 0.05. Of these 11 SNPs, linkage disequilibrium were revealed among SNPs in LRP8 (r2 = 0.87 to 1), between SNPs in NLRC3, NLRC5, and HIP1 (r2 = 0.96 to 0.99), respectively. Further, haplotypes within NLRC3, NLRC5, and HIP1 were significantly associated (P < 0.001) with FEC. In artificial challenge trail, quantitative real-time PCR exposed that the relative expression of mRNA was higher in the resistant group for NLRC3 (P < 0.01), LRP8 and HIP1 (P < 0.001) but lower in the resistant group for NLRC5 (P < 0.0001), compared to the susceptible group. The possible SNP markers and genes identified in this study could be potentially used in marker-assisted selection for breeding local goats breeds resistant to gastrointestinal nematode parasite particularly for Haemonchus contortus, and then for improving health and productivity of goat.


Assuntos
Doenças das Cabras/parasitologia , Hemoncose/veterinária , Haemonchus , Enteropatias Parasitárias/veterinária , Contagem de Ovos de Parasitas/veterinária , Animais , Peso Corporal/genética , Cruzamento , Fezes/parasitologia , Feminino , Predisposição Genética para Doença , Doenças das Cabras/genética , Cabras/genética , Imunidade Inata , Enteropatias Parasitárias/genética , Enteropatias Parasitárias/parasitologia , Polimorfismo de Nucleotídeo Único
12.
BMC Genomics ; 20(Suppl 3): 296, 2019 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-32039697

RESUMO

BACKGROUND: Chromosomal architecture, which is constituted by chromatin loops, plays an important role in cellular functions. Gene expression and cell identity can be regulated by the chromatin loop, which is formed by proximal or distal enhancers and promoters in linear DNA (1D). Enhancers and promoters are fundamental non-coding elements enriched with transcription factors (TFs) to form chromatin loops. However, the specific cooperation of TFs involved in forming chromatin loops is not fully understood. RESULTS: Here, we proposed a method for investigating the cooperation of TFs in four cell lines by the integrative analysis of DNA sequences, ChIP-Seq and ChIA-PET data. Results demonstrate that the interaction of enhancers and promoters is a hierarchical and dynamic complex process with cooperative interactions of different TFs synergistically regulating gene expression and chromatin structure. The TF cooperation involved in maintaining and regulating the chromatin loop of cells can be regulated by epigenetic factors, such as other TFs and DNA methylation. CONCLUSIONS: Such cooperation among TFs provides the potential features that can affect chromatin's 3D architecture in cells. The regulation of chromatin 3D organization and gene expression is a complex process associated with the hierarchical and dynamic prosperities of TFs.


Assuntos
Sequenciamento de Cromatina por Imunoprecipitação/métodos , Fatores de Transcrição/metabolismo , Redes Reguladoras de Genes , Regiões Promotoras Genéticas/genética
13.
J Am Chem Soc ; 141(51): 20424-20433, 2019 Dec 26.
Artigo em Inglês | MEDLINE | ID: mdl-31791120

RESUMO

The development of catalysts based on earth abundant metals in place of noble metals is becoming a central topic of catalysis. We herein report a cobalt/tetraphosphine complex-catalyzed homogeneous hydrogenation of polar unsaturated compounds using an air- and moisture-stable and scalable precatalyst. By activation with potassium hydroxide, this cobalt system shows both high efficiency (up to 24 000 TON and 12 000 h-1 TOF) and excellent chemoselectivities with various aldehydes, ketones, imines, and even N-heteroarenes. The preference for 1,2-reduction over 1,4-reduction makes this method an efficient way to prepare allylic alcohols and amines. Meanwhile, efficient hydrogenation of the challenging N-heteroarenes is also furnished with excellent functional group tolerance. Mechanistic studies and control experiments demonstrated that a CoIH complex functions as a strong hydride donor in the catalytic cycle. Each cobalt intermediate on the catalytic cycle was characterized, and a plausible outer-sphere mechanism was proposed. Noteworthy, external inorganic base plays multiple roles in this reaction and functions in almost every step of the catalytic cycle.

14.
Genetica ; 147(1): 23-32, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30535819

RESUMO

Despite the insights into retrogene evolution in multiple species provided by trans-traffic retrogenes (trans-retrogenes), cis-traffic retrogenes (cis-retrogenes) are hitherto understudied and thus limit our understanding of genetic novelty. Here we used the pig genome as a model to compare cis- and trans-retrogenes. We found that cis- and trans-retrogenes have similar patterns in terms of excessive X-chromosome representation, testis expression preference, and metabolic functional enrichment. Despite these similarities, lower levels of selective pressure were found in cis- than in trans-retrogenes. The evolutionary dating evidence revealed that more cis-retrogenes have originated after pig-cattle divergence than trans-retrogenes, suggesting a more recent origination of cis-retrogenes. The gene family clustering confirmed that excesses of X-derived cis-retrogenes may be driven by their rapid expansion in the recent times. Thus, the different selective constraints between cis- and trans-retrogenes may be due to different evolutionary time-scales rather than any differential functional importance. Thus, this study highlights the ongoing functional contributions from cis- and trans-traffic retrogenes during the reshaping of pig genome.


Assuntos
Retroelementos , Suínos/genética , Cromossomo X/genética , Animais , Evolução Molecular , Feminino , Masculino , Família Multigênica , Seleção Genética
15.
Curr Issues Mol Biol ; 28: 47-68, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29428910

RESUMO

Precise nucleic acid editing technologies have facilitated the research of cellular function and the development of novel therapeutics, especially the current programmable nucleases-based editing tools, such as the prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated nucleases (Cas). As CRISPR-based therapies are advancing toward human clinical trials, it is important to understand how natural genetic variation in the human population may affect the results of these trials and even patient safety. The development of "base-editing" technique allows the direct, stable transformation of target DNA base into an alternative in a programmable way, without DNA double strand cleavage or a donor template. Genome-editing techniques hold promises for the treatment of genetic disease at the DNA level by blocking the sequences associated with disease from producing disease-causing proteins. Currently, scientists can select the gene they want to modify, use the Cas9 as a "molecular cutter" to cut it out, and transform it into a more desirable version. In this review, we focus on the recent advances of CRISPR/Cas system by outlining the evolutionary and biotechnological implications of current strategies for improving the specificity and accuracy of these genome-editing technologies.


Assuntos
Sistemas CRISPR-Cas/genética , Edição de Genes/métodos , Doenças Genéticas Inatas/terapia , Biotecnologia/tendências , Edição de Genes/tendências , Doenças Genéticas Inatas/genética , Humanos
16.
J Transl Med ; 16(1): 298, 2018 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-30368237

RESUMO

BACKGROUND: Chikungunya virus (CHIKV), causes massive outbreaks of chikungunya infection in several regions of Asia, Africa and Central/South America. Being positive sense RNA virus, CHIKV replication within the host resulting in its genome mutation and led to difficulties in creation of vaccine, drugs and treatment strategies. Vector control strategy has been a gold standard to combat spreading of CHIKV infection, but to eradicate a species from the face of earth is not an easy task. Therefore, alongside vector control, there is a dire need to prevent the infection through vaccine as well as through antiviral strategies. METHODS: This study was designed to find out conserved B cell and T cell epitopes of CHIKV structural proteins through immuno-informatics and computational approaches, which may play an important role in evoking the immune responses against CHIKV. RESULTS: Several conserved cytotoxic T-lymphocyte epitopes, linear and conformational B cell epitopes were predicted for CHIKV structural polyprotein and their antigenicity was calculated. Among B-cell epitopes "PPFGAGRPGQFGDI" showed a high antigenicity score and it may be highly immunogenic. In case of T cell epitopes, MHC class I peptides 'TAECKDKNL' and MHC class II peptides 'VRYKCNCGG' were found extremely antigenic. CONCLUSION: The study led to the discovery of various epitopes, conserved among various strains belonging to different countries. The potential antigenic epitopes can be successfully utilized in designing novel vaccines for combating and eradication of CHIKV disease.


Assuntos
Vírus Chikungunya/imunologia , Simulação de Acoplamento Molecular , Vacinas de Subunidades Antigênicas/imunologia , Alelos , Alérgenos/imunologia , Sequência de Aminoácidos , Sequência Conservada , Epitopos de Linfócito B/química , Epitopos de Linfócito B/imunologia , Epitopos de Linfócito T/química , Epitopos de Linfócito T/imunologia , Antígenos de Histocompatibilidade Classe I/imunologia , Humanos , Filogenia , Vacinas de Subunidades Antigênicas/química
17.
Genetica ; 146(3): 277-285, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29748765

RESUMO

Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression. The overall nucleotides diversities of the mtDNA sequences have been reduced following domestication. Interestingly, the selection efficiencies in both European and Asian domestic pigs are reduced, probably caused by changes in both selection constraints and maternal population size following domestication. This study suggests that de novo assembled mitogenomes can be a great boon to uncover the genetic turnover following domestication. Further investigation is warranted to include more samples from the ever-increasing amounts of NGS data to help us to better understand the process of domestication.


Assuntos
Evolução Molecular , Variação Genética , Genoma Mitocondrial , Genômica , Suínos/classificação , Suínos/genética , Animais , Animais Selvagens , Teorema de Bayes , Biologia Computacional/métodos , Genômica/métodos , Filogenia , Seleção Genética , Sus scrofa
18.
Int J Mol Sci ; 18(4)2017 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-28368324

RESUMO

Gastrointestinal nematodes (GINs) are one of the most economically important parasites of small ruminants and a major animal health concern in many regions of the world. However, the molecular mechanisms of the host response to GIN infections in goat are still little known. In this study, two genetically distinct goat populations, one relatively resistant and the other susceptible to GIN infections, were identified in Yichang goat and then four individuals in each group were chosen to compare mRNA expression profiles using RNA-seq. Field experiment showed lower worm burden, delayed and reduced egg production in the relatively resistant group than the susceptible group. The analysis of RNA-seq showed that 2369 genes, 1407 of which were up-regulated and 962 down-regulated, were significantly (p < 0.001) differentially expressed between these two groups. Functional annotation of the 298 genes more highly expressed in the resistant group yielded a total of 46 significant (p < 0.05) functional annotation clusters including 31 genes (9 in innate immunity, 13 in immunity, and 9 in innate immune response) related to immune biosynthetic process as well as transforming growth factor (TGF)-ß, mitogen-activated protein kinase (MAPK), and cell adhesion molecules (CAMs) pathways. Our findings provide insights that are immediately relevant for the improvement of host resistance to GIN infections and which will make it possible to know the mechanisms underlying the resistance of goats to GIN infections.


Assuntos
Resistência à Doença/genética , Gastroenteropatias/genética , Doenças das Cabras/genética , Hemoncose/genética , Haemonchus/crescimento & desenvolvimento , Análise de Sequência de RNA/métodos , Animais , Análise por Conglomerados , Gastroenteropatias/parasitologia , Gastroenteropatias/veterinária , Perfilação da Expressão Gênica/métodos , Ontologia Genética , Doenças das Cabras/parasitologia , Cabras , Hemoncose/parasitologia , Hemoncose/veterinária , Haemonchus/fisiologia , Interações Hospedeiro-Parasita , Anotação de Sequência Molecular , Reprodutibilidade dos Testes , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Transdução de Sinais/genética
19.
Asian-Australas J Anim Sci ; 30(7): 912-919, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-27165029

RESUMO

OBJECTIVE: Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL)-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. METHODS: By using fixation index (FST ) based method, IL-32 (9375) gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and FST . Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8) in Codeml program of phylogenetic analysis by maximum liklihood. RESULTS: IL-32 is detected under positive selection using the FST simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%), bison (91.97%), camel (58.39%), cat (56.59%), buffalo (56.50%), human (56.13%), dog (50.97%), horse (54.04%), and rabbit (53.41%) respectively. CONCLUSION: This study provides evidence for IL-32 gene as under significant positive selection in goat.

20.
Angew Chem Int Ed Engl ; 55(23): 6671-5, 2016 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-27111001

RESUMO

A complementary set of base metal catalysts has been developed for regiodivergent alkene hydrosilylations: iron complexes of phosphine-iminopyridine are selective for anti-Markovnikov hydrosilylations (linear/branched up to >99:1), while the cobalt complexes bearing the same type of ligands provide an unprecedented high level of Markovnikov selectivity (branched/linear up to >99:1). Both systems exhibit high efficiency and wide functional group tolerance.

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