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1.
Gene ; 806: 145928, 2022 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-34455027

RESUMO

Cytochrome P450 Family 19 (CYP19) is a crucial enzyme to catalyze the conversion of androgens to estrogens. However, the regulatory mechanism of goose CYP19 gene remains poorly understood. The present study attempted to obtain the full-length coding sequence (CDS) and 5'-flanking sequence of CYP19 gene, to investigate its expression and distribution profiles in different sized follicles, and to analyze the transcriptional regulatory mechanism of CYP19 gene in goose. Results showed that its CDS consisted of 1512 nucleotides and the encoded amino acid sequence contained a classical P450 structural domain. Homology analysis showed that there were high homologies of nucleotide and amino acid sequences between goose and other avian species. Its promoter sequence spanned from -1925 bp to the transcription start site (ATG) and several transcriptional factors were predicted in this region. Further analysis from luciferase assay showed that the luciferase activity was the highest spanning from -118 to -1 bp by constructing deletion promoter reporter vector. In addition, result from quantitative real-time polymerase chain reaction indicated that the mRNA level of CYP19 gene were highly expressed in theca layer of the fifth largest follicle, and the cellular location was in the theca externa cells by immunohistochemistry. Taken together, it could be concluded that the transcription activity of CYP19 gene was activated by transcriptional factors in its proximal region of promoter to promote the synthesis of estrogens, regulating the selection of pre-hierarchical into hierarchical follicle in goose.


Assuntos
Proteínas Aviárias/genética , Família 19 do Citocromo P450/genética , Gansos/genética , Regulação Enzimológica da Expressão Gênica , RNA Mensageiro/genética , Transcrição Genética , Sequência de Aminoácidos , Animais , Proteínas Aviárias/metabolismo , Família 19 do Citocromo P450/metabolismo , Feminino , Gansos/classificação , Regulação da Expressão Gênica no Desenvolvimento , Folículo Ovariano/citologia , Folículo Ovariano/crescimento & desenvolvimento , Folículo Ovariano/metabolismo , Filogenia , Regiões Promotoras Genéticas , RNA Mensageiro/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Sítio de Iniciação de Transcrição
2.
Nat Commun ; 12(1): 5205, 2021 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-34471128

RESUMO

Molecular mechanisms associated with human germ cell aplasia in infertile men remain undefined. Here we perform single-cell transcriptome profiling to highlight differentially expressed genes and pathways in each somatic cell type in testes of men with idiopathic germ cell aplasia. We identify immaturity of Leydig cells, chronic tissue inflammation, fibrosis, and senescence phenotype of the somatic cells, as well markers of chronic inflammation in the blood. We find that deregulated expression of parentally imprinted genes in myoid and immature Leydig cells, with relevant changes in the ratio of Lamin A/C transcripts and an active DNA damage response in Leydig and peritubular myoid cells are also indicative of senescence of the testicular niche. This study offers molecular insights into the pathogenesis of idiopathic germ cell aplasia.


Assuntos
Envelhecimento/fisiologia , Dano ao DNA , Inflamação , Testículo/metabolismo , Envelhecimento/genética , Comunicação Celular , Quimiocinas , Perfilação da Expressão Gênica , Células Germinativas , Humanos , Inflamação/patologia , Células Intersticiais do Testículo , Masculino , Fenótipo , Alinhamento de Sequência , Espermatogênese/genética , Espermatogênese/fisiologia , Espermatogônias/metabolismo , Transcriptoma
3.
Nat Commun ; 12(1): 5216, 2021 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-34471137

RESUMO

Bacterial biosensors, or bactosensors, are promising agents for medical and environmental diagnostics. However, the lack of scalable frameworks to systematically program ligand detection limits their applications. Here we show how novel, clinically relevant sensing modalities can be introduced into bactosensors in a modular fashion. To do so, we have leveraged a synthetic receptor platform, termed EMeRALD (Engineered Modularized Receptors Activated via Ligand-induced Dimerization) which supports the modular assembly of sensing modules onto a high-performance, generic signaling scaffold controlling gene expression in E. coli. We apply EMeRALD to detect bile salts, a biomarker of liver dysfunction, by repurposing sensing modules from enteropathogenic Vibrio species. We improve the sensitivity and lower the limit-of-detection of the sensing module by directed evolution. We then engineer a colorimetric bactosensor detecting pathological bile salt levels in serum from patients having undergone liver transplant, providing an output detectable by the naked-eye. The EMeRALD technology enables functional exploration of natural sensing modules and rapid engineering of synthetic receptors for diagnostics, environmental monitoring, and control of therapeutic microbes.


Assuntos
Bactérias/metabolismo , Biomarcadores/metabolismo , Técnicas Biossensoriais , Proteínas de Transporte/metabolismo , Patologia Molecular/métodos , Bactérias/genética , Ácidos e Sais Biliares/sangue , Técnicas Biossensoriais/métodos , Proteínas de Transporte/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Regulação Bacteriana da Expressão Gênica , Humanos , Transplante de Fígado , Engenharia Metabólica/métodos , Sensibilidade e Especificidade , Alinhamento de Sequência , Vibrio , Vibrioses/diagnóstico
4.
PLoS One ; 16(9): e0252849, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34499652

RESUMO

Reverse vaccinology is an evolving approach for improving vaccine effectiveness and minimizing adverse responses by limiting immunizations to critical epitopes. Towards this goal, we sought to identify immunogenic amino acid motifs and linear epitopes of the SARS-CoV-2 spike protein that elicit IgG in COVID-19 mRNA vaccine recipients. Paired pre/post vaccination samples from N = 20 healthy adults, and post-vaccine samples from an additional N = 13 individuals were used to immunoprecipitate IgG targets expressed by a bacterial display random peptide library, and preferentially recognized peptides were mapped to the spike primary sequence. The data identify several distinct amino acid motifs recognized by vaccine-induced IgG, a subset of those targeted by IgG from natural infection, which may mimic 3-dimensional conformation (mimotopes). Dominant linear epitopes were identified in the C-terminal domains of the S1 and S2 subunits (aa 558-569, 627-638, and 1148-1159) which have been previously associated with SARS-CoV-2 neutralization in vitro and demonstrate identity to bat coronavirus and SARS-CoV, but limited homology to non-pathogenic human coronavirus. The identified COVID-19 mRNA vaccine epitopes should be considered in the context of variants, immune escape and vaccine and therapy design moving forward.


Assuntos
Vacinas contra COVID-19/imunologia , COVID-19/imunologia , Mapeamento de Epitopos , Motivos de Aminoácidos , Sequência de Aminoácidos , Infecções por Coronavirus/imunologia , Humanos , Imunoglobulina G/sangue , SARS-CoV-2/química , SARS-CoV-2/metabolismo , Alinhamento de Sequência , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/metabolismo
5.
J Microbiol ; 59(9): 840-847, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34383247

RESUMO

Endolysin, a peptidoglycan hydrolase derived from bacteriophage, has been suggested as an alternative antimicrobial agent. Many endolysins on staphylococcal phages have been identified and applied extensively against Staphylococcus spp. Among them, LysK-like endolysin, a well-studied staphylococcal endolysin, accounts for most of the identified endolysins. However, relatively little interest has been paid to LysKunlike endolysin and a few of them has been characterized. An endolysin LysSAP33 encoded on bacteriophage SAP33 shared low homology with LysK-like endolysin in sequence by 41% and domain composition (CHAP-unknown CBD). A green fluorescence assay using a fusion protein for LysSAP33_CBD indicated that the CBD domain (157-251 aa) was bound to the peptidoglycan of S. aureus. The deletion of LysSAP33_CBD at the C-terminal region resulted in a significant decrease in lytic activity and efficacy. Compared to LysK-like endolysin, LysSAP33 retained its lytic activity in a broader range of temperature, pH, and NaCl concentrations. In addition, it showed a higher activity against biofilms than LysK-like endolysin. This study could be a helpful tool to develop our understanding of staphylococcal endolysins not belonging to LysK-like endolysins and a potential biocontrol agent against biofilms.


Assuntos
Endopeptidases/metabolismo , Fagos de Staphylococcus/enzimologia , Staphylococcus aureus/virologia , Proteínas Virais/metabolismo , Sequência de Aminoácidos , Parede Celular/metabolismo , Parede Celular/virologia , Endopeptidases/química , Endopeptidases/genética , Peptidoglicano/metabolismo , Alinhamento de Sequência , Fagos de Staphylococcus/química , Fagos de Staphylococcus/genética , Fagos de Staphylococcus/fisiologia , Staphylococcus aureus/metabolismo , Proteínas Virais/química , Proteínas Virais/genética
6.
Nucleic Acids Res ; 49(15): 8796-8810, 2021 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-34379778

RESUMO

During RNA elongation, the influenza A viral (IAV) RNA-dependent RNA polymerase (RdRp) residues in the active site interact with the triphosphate moiety of nucleoside triphosphate (NTP) for catalysis. The molecular mechanisms by which they control the rate and fidelity of NTP incorporation remain elusive. Here, we demonstrated through enzymology, virology and computational approaches that the R239 and K235 in the PB1 subunit of RdRp are critical to controlling the activity and fidelity of transcription. Contrary to common beliefs that high-fidelity RdRp variants exert a slower incorporation rate, we discovered a first-of-its-kind, single lysine-to-arginine mutation on K235 exhibited enhanced fidelity and activity compared with wild-type. In particular, we employed a single-turnover NTP incorporation assay for the first time on IAV RdRp to show that K235R mutant RdRp possessed a 1.9-fold increase in the transcription activity of the cognate NTP and a 4.6-fold increase in fidelity compared to wild-type. Our all-atom molecular dynamics simulations further elucidated that the higher activity is attributed to the shorter distance between K235R and the triphosphate moiety of NTP compared with wild-type. These results provide novel insights into NTP incorporation and fidelity control mechanisms, which lay the foundation for the rational design of IAV vaccine and antiviral targets.


Assuntos
Vírus da Influenza A/enzimologia , RNA Polimerase Dependente de RNA/química , RNA Polimerase Dependente de RNA/metabolismo , Transcrição Genética , Proteínas Virais/química , Proteínas Virais/metabolismo , Substituição de Aminoácidos , Animais , Domínio Catalítico , Cães , Sequenciamento de Nucleotídeos em Larga Escala , Células Madin Darby de Rim Canino , Mutação , RNA Polimerase Dependente de RNA/genética , Alinhamento de Sequência , Proteínas Virais/genética
7.
Commun Biol ; 4(1): 953, 2021 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-34376792

RESUMO

Major Intrinsic Proteins (MIPs) are membrane channels that permeate water and other small solutes. Some trypanosomatid MIPs mediate the uptake of antiparasitic compounds, placing them as potential drug targets. However, a thorough study of the diversity of these channels is still missing. Here we place trypanosomatid channels in the sequence-function space of the large MIP superfamily through a sequence similarity network. This analysis exposes that trypanosomatid aquaporins integrate a distant cluster from the currently defined MIP families, here named aquaporin X (AQPX). Our phylogenetic analyses reveal that trypanosomatid MIPs distribute exclusively between aquaglyceroporin (GLP) and AQPX, being the AQPX family expanded in the Metakinetoplastina common ancestor before the origin of the parasitic order Trypanosomatida. Synteny analysis shows how African trypanosomes specifically lost AQPXs, whereas American trypanosomes specifically lost GLPs. AQPXs diverge from already described MIPs on crucial residues. Together, our results expose the diversity of trypanosomatid MIPs and will aid further functional, structural, and physiological research needed to face the potentiality of the AQPXs as gateways for trypanocidal drugs.


Assuntos
Aquagliceroporinas/genética , Aquaporinas/genética , Proteínas de Protozoários/genética , Trypanosomatina/genética , Sequência de Aminoácidos , Aquagliceroporinas/química , Aquaporinas/química , Proteínas de Protozoários/química , Alinhamento de Sequência , Trypanosomatina/química
8.
Emerg Microbes Infect ; 10(1): 1683-1690, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34348599

RESUMO

At the end of 2019, A new type of beta-CoV, SARS-CoV-2 emerged and triggered the COVID-19 pandemic, which spread overwhelmingly around the world in less than a year. However, the origin and direct ancestral viruses of SARS-CoV-2 remain unknown. RaTG13, a novel coronavirus found in bats in China's Yunnan Province, is the closest relative virus of the SARS-CoV-2 identified so far. In this study, a new SARS-CoV-2 related virus, provisionally named PrC31, was discovered in Yunnan province by retrospectively analyse bat next generation sequencing (NGS) data of intestinal samples collected in 2018. PrC31 shared 90.7% and 92.0% nucleotide identities to the genomes of SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment of PrC31 showed that several genomic regions, especially orf1a and orf8 had the highest homology with those corresponding genomic regions of SARS-CoV-2 than any other related viruses. Phylogenetic analysis indicated that PrC31 shared a common ancestor with SARS-CoV-2 in evolutionary history. The differences between the PrC31 and SARS-CoV-2 genomes were mainly manifested in the spike genes. The amino acid homology between the receptor binding domains of PrC31 and SARS-CoV-2 was only 64.2%. Importantly, recombination analysis revealed that PrC31 underwent multiple complex recombination events (including three recombination breakpoints) involving the SARS-CoV and SARS-CoV-2 sub-lineages, indicating that PrC31 evolved from yet-to-be-identified intermediate recombination strains. Combined with previous studies, it is revealed that the beta-CoVs may possess a more complex recombination mechanism than we thought.


Assuntos
Quirópteros/virologia , Recombinação Genética , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Sequência de Aminoácidos , Animais , China , Genoma Viral , Filogenia , SARS-CoV-2/classificação , Alinhamento de Sequência , Proteínas Virais/genética
9.
Nat Commun ; 12(1): 4699, 2021 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-34349111

RESUMO

Similarity in T-cell receptor (TCR) sequences implies shared antigen specificity between receptors, and could be used to discover novel therapeutic targets. However, existing methods that cluster T-cell receptor sequences by similarity are computationally inefficient, making them impractical to use on the ever-expanding datasets of the immune repertoire. Here, we developed GIANA (Geometric Isometry-based TCR AligNment Algorithm) a computationally efficient tool for this task that provides the same level of clustering specificity as TCRdist at 600 times its speed, and without sacrificing accuracy. GIANA also allows the rapid query of large reference cohorts within minutes. Using GIANA to cluster large-scale TCR datasets provides candidate disease-specific receptors, and provides a new solution to repertoire classification. Querying unseen TCR-seq samples against an existing reference differentiates samples from patients across various cohorts associated with cancer, infectious and autoimmune disease. Our results demonstrate how GIANA could be used as the basis for a TCR-based non-invasive multi-disease diagnostic platform.


Assuntos
Algoritmos , Receptores de Antígenos de Linfócitos T/classificação , COVID-19/diagnóstico , COVID-19/imunologia , Análise por Conglomerados , Regiões Determinantes de Complementaridade/química , Regiões Determinantes de Complementaridade/imunologia , Diagnóstico Diferencial , Epitopos de Linfócito T/química , Epitopos de Linfócito T/imunologia , Humanos , Esclerose Múltipla/diagnóstico , Esclerose Múltipla/imunologia , Neoplasias/diagnóstico , Neoplasias/imunologia , Receptores de Antígenos de Linfócitos T/química , Receptores de Antígenos de Linfócitos T/imunologia , SARS-CoV-2 , Alinhamento de Sequência
10.
Microbiol Spectr ; 9(1): e0003021, 2021 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-34346753

RESUMO

Monitoring and strategic response to variants in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent a considerable challenge in the current pandemic and for future viral outbreaks. Mutations/deletions of the virion's prefusion Spike protein may have significant impact on vaccines and therapeutics that utilize this key structural protein in their mitigation strategies. In this study, we have demonstrated how dominant energetic landscape mappings ("glue points") based on ab inito all-atom force fields coupled with phylogenetic sequence alignment information can identify key residue mutations and deletions associated with variants. We also found several examples of excellent homology of stabilizing residue glue points across the lineages of betacoronavirus Spike proteins that we have called "sequence homologous glue points." SARS-CoV-2 demonstrates the least number of stabilizing glue points associated with interchain interactions among Down-state protomers across lineages. Additionally, we computationally studied variants among the trimeric Spike protein of SARS-CoV-2 using all-atom molecular dynamics to ascertain structural and energetic changes among variants. We examined both a theoretically based triple mutant and the UK or B.1.1.7 variant. For the theoretical triple mutant, we demonstrated through alanine substitutions that three key residues could cause the transition of Down-to-Up protomer states, where the transition is characterized by the "arm" length of the receptor-binding domain (RBD) rather than the hinge angle. For the B.1.1.7 variant, we demonstrated the critical importance of mutations D614G and N501Y on the structure and binding, respectively, of the Spike protein. We note that these same two key mutations are also found in the South African B.1.351 variant. IMPORTANCE Viral variants represent a major challenge to monitoring viral outbreaks and formulating strategic health care responses. Variants represent transmitting viruses that have specific mutations and deletions associated with their genome. In the case of SARS-CoV-2 and other related viruses (betacoronaviruses), many of these mutations and deletions are associated with the Spike protein that the virus uses to infect cells. Here, we have analyzed both SARS-CoV-2 variants and related viruses, such as Middle Eastern respiratory syndrome coronavirus (MERS-CoV), in order to understand not only differences, but also key similarities between them. Understanding similarities can be as important as differences in determining key functional features of a class of viruses, such as the betacoronaviruses. We have used both phylogenetic analysis, which traces genetic similarities and differences, along with independent biophysics analysis, which adds function or behavior, in order to determine possible functional differences and hence possible transmission and infection differences among variants and lineages.


Assuntos
Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/metabolismo , Sequência de Bases , COVID-19/virologia , Humanos , Simulação de Dinâmica Molecular , Mutação , Filogenia , Ligação Proteica , Conformação Proteica , SARS-CoV-2/classificação , Alinhamento de Sequência , Glicoproteína da Espícula de Coronavírus/classificação , Reino Unido
11.
Int J Mol Sci ; 22(15)2021 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-34360907

RESUMO

The superfamily of P-loop channels includes various potassium channels, voltage-gated sodium and calcium channels, transient receptor potential channels, and ionotropic glutamate receptors. Despite huge structural and functional diversity of the channels, their pore-forming domain has a conserved folding. In the past two decades, scores of atomic-scale structures of P-loop channels with medically important drugs in the inner pore have been published. High structural diversity of these complexes complicates the comparative analysis of these structures. Here we 3D-aligned structures of drug-bound P-loop channels, compared their geometric characteristics, and analyzed the energetics of ligand-channel interactions. In the superimposed structures drugs occupy most of the sterically available space in the inner pore and subunit/repeat interfaces. Cationic groups of some drugs occupy vacant binding sites of permeant ions in the inner pore and selectivity-filter region. Various electroneutral drugs, lipids, and detergent molecules are seen in the interfaces between subunits/repeats. In many structures the drugs strongly interact with lipid and detergent molecules, but physiological relevance of such interactions is unclear. Some eukaryotic sodium and calcium channels have state-dependent or drug-induced π-bulges in the inner helices, which would be difficult to predict. The drug-induced π-bulges may represent a novel mechanism of gating modulation.


Assuntos
Domínio AAA , Canais de Cálcio/metabolismo , Microscopia Crioeletrônica/métodos , Preparações Farmacêuticas/metabolismo , Canais de Potássio/metabolismo , Receptores Ionotrópicos de Glutamato/metabolismo , Canais de Potencial de Receptor Transitório/metabolismo , Canais de Sódio Disparados por Voltagem/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Canais de Cálcio/química , Biologia Computacional/métodos , Eucariotos/metabolismo , Ligantes , Modelos Moleculares , Canais de Potássio/química , Conformação Proteica em alfa-Hélice , Receptores Ionotrópicos de Glutamato/química , Alinhamento de Sequência , Canais de Potencial de Receptor Transitório/química , Canais de Sódio Disparados por Voltagem/química
12.
Molecules ; 26(15)2021 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-34361767

RESUMO

This study describes the catalytic properties of a GH30_7 xylanase produced by the fungus Talaromyces leycettanus. The enzyme is an ando-ß-1,4-xylanase, showing similar specific activity towards glucuronoxylan, arabinoxylan, and rhodymenan (linear ß-1,3-ß-1,4-xylan). The heteroxylans are hydrolyzed to a mixture of linear as well as branched ß-1,4-xylooligosaccharides that are shorter than the products generated by GH10 and GH11 xylanases. In the rhodymenan hydrolyzate, the linear ß-1,4-xylooligosaccharides are accompanied with a series of mixed linkage homologues. Initial hydrolysis of glucuronoxylan resembles the action of other GH30_7 and GH30_8 glucuronoxylanases, resulting in a series of aldouronic acids of a general formula MeGlcA2Xyln. Due to the significant non-specific endoxylanase activity of the enzyme, these acidic products are further attacked in the unbranched regions, finally yielding MeGlcA2Xyl2-3. The accommodation of a substituted xylosyl residue in the -2 subsite also applies in arabinoxylan depolymerization. Moreover, the xylose residue may be arabinosylated at both positions 2 and 3, without negatively affecting the main chain cleavage. The catalytic properties of the enzyme, particularly the great tolerance of the side-chain substituents, make the enzyme attractive for biotechnological applications. The enzyme is also another example of extraordinarily great catalytic diversity among eukaryotic GH30_7 xylanases.


Assuntos
Endo-1,4-beta-Xilanases/metabolismo , Proteínas Fúngicas/metabolismo , Talaromyces/enzimologia , Xilanos/metabolismo , Sequência de Aminoácidos , Arabinose/química , Arabinose/metabolismo , Sequência de Carboidratos , Endo-1,4-beta-Xilanases/genética , Proteínas Fúngicas/genética , Expressão Gênica , Glucuronatos/química , Glucuronatos/metabolismo , Hidrólise , Oligossacarídeos/química , Oligossacarídeos/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Talaromyces/química , Talaromyces/genética , Xilanos/química
13.
BMC Bioinformatics ; 22(Suppl 9): 172, 2021 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-34433415

RESUMO

BACKGROUND: DNA sequence alignment is a common first step in most applications of high-throughput sequencing technologies. The accuracy of sequence alignments directly affects the accuracy of downstream analyses, such as variant calling and quantitative analysis of transcriptome; therefore, rapidly and accurately mapping reads to a reference genome is a significant topic in bioinformatics. Conventional DNA read aligners map reads to a linear reference genome (such as the GRCh38 primary assembly). However, such a linear reference genome represents the genome of only one or a few individuals and thus lacks information on variations in the population. This limitation can introduce bias and impact the sensitivity and accuracy of mapping. Recently, a number of aligners have begun to map reads to populations of genomes, which can be represented by a reference genome and a large number of genetic variants. However, compared to linear reference aligners, an aligner that can store and index all genetic variants has a high cost in memory (RAM) space and leads to extremely long run time. Aligning reads to a graph-model-based index that includes all types of variants is ultimately an NP-hard problem in theory. By contrast, considering only single nucleotide polymorphism (SNP) information will reduce the complexity of the index and improve the speed of sequence alignment. RESULTS: The SNP-aware alignment tool (SALT) is a fast, memory-efficient, and SNP-aware short read alignment tool. SALT uses 5.8 GB of RAM to index a human reference genome (GRCh38) and incorporates 12.8M UCSC common SNPs. Compared with a state-of-the-art aligner, SALT has a similar speed but higher accuracy. CONCLUSIONS: Herein, we present an SNP-aware alignment tool (SALT) that aligns reads to a reference genome that incorporates an SNP database. We benchmarked SALT using simulated and real datasets. The results demonstrate that SALT can efficiently map reads to the reference genome with significantly improved accuracy. Incorporating SNP information can improve the accuracy of read alignment and can reveal novel variants. The source code is freely available at https://github.com/weiquan/SALT .


Assuntos
Algoritmos , Polimorfismo de Nucleotídeo Único , Genoma Humano , Humanos , Alinhamento de Sequência , Análise de Sequência de DNA
14.
Int J Mol Sci ; 22(11)2021 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-34198800

RESUMO

COVID-19 pandemic is caused by betacoronavirus SARS-CoV-2. The genome of this virus is composed of a single strand of RNA with 5' and 3'-UTR flanking a region of protein-coding ORFs closely resembling cells' mRNAs. MicroRNAs are endogenous post-transcriptional regulators that target mRNA to modulate protein expression and mediate cellular functions, including antiviral defense. In the present study, we carried out a bioinformatics screening to search for endogenous human microRNAs targeting the 3'-UTR of SARS-CoV-2. Results from the computational techniques allowed us to identify 10 potential candidates. The capacity of 3 of them, together with hsa-miR-138-5p, to target the SARS-CoV-2 3'-UTR was validated in vitro by gene reporter assays. Available information indicates that two of these microRNAs, namely, hsa-miR-3941 and hsa-miR-138-5p, combine effective targeting of SARS-CoV-2 genome with complementary antiviral or protective effects in the host cells that make them potential candidates for therapeutic treatment of most, if not all, COVID-19 variants known to date. All information obtained while conducting the present analysis is available at Open Science Framework repository.


Assuntos
MicroRNAs/metabolismo , SARS-CoV-2/genética , Regiões 3' não Traduzidas , Sequência de Bases , Sítios de Ligação , COVID-19/genética , COVID-19/patologia , COVID-19/virologia , Linhagem Celular , Genes Reporter , Genoma Viral , Humanos , MicroRNAs/química , Fases de Leitura Aberta , SARS-CoV-2/isolamento & purificação , Alinhamento de Sequência
15.
Adv Exp Med Biol ; 1208: 387-453, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34260035

RESUMO

Autophagy is an important and dynamic biological process, and provides an ideal application scenario for bioinformatics to develop new data resources, algorithms, tools and computational or mathematic models for a better understanding of complex regulatory mechanisms in cells. In the past decade, great efforts have been taken on the development of numerous bioinformatics technologies in autophagy research, and a comprehensive summarization of these important studies will provide a timely reference for both biologists and bioinformaticians who are working in the field of autophagy. In this book chapter, we first introduce bioinformatics technologies that allow sequence analysis of autophagy genes. We briefly summarize the mainstream algorithms in sequence alignment for the identification of homologous autophagy genes and emphasize the computational identification of potential orthologs and paralogs, as well as the evolutionary analysis of autophagy gene families. Three methods for the recognition of autophagy-related sequence motifs are introduced: regular expression, position-specific scoring matrix (PSSM) and group-based prediction system (GPS). Second, we carefully summarize recent progress in the analysis of autophagy-related omics data. We discuss how two major types of computational methods, enrichment analysis and network analysis can be used to analyze omics data, including transcriptomics, non-coding RNAomics, epigenomics, proteomics, phosphoproteomics and protein lysine modification (PLM) omics data. Finally, we summarize several important autophagy-related data resources, including both autophagy gene databases and autophagy-related RNA databases. We anticipate that more useful bioinformatics technologies will be developed and play an ever-more-important role in the analysis of autophagy.


Assuntos
Biologia Computacional , Proteômica , Algoritmos , Autofagia/genética , Alinhamento de Sequência
16.
Sensors (Basel) ; 21(12)2021 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-34203682

RESUMO

Localization is one of the essential process in robotics, as it plays an important role in autonomous navigation, simultaneous localization, and mapping for mobile robots. As robots perform large-scale and long-term operations, identifying the same locations in a changing environment has become an important problem. In this paper, we describe a robust visual localization system under severe appearance changes. First, a robust feature extraction method based on a deep variational autoencoder is described to calculate the similarity between images. Then, a global sequence alignment is proposed to find the actual trajectory of the robot. To align sequences, local fragments are detected from the similarity matrix and connected using a rectangle chaining algorithm considering the robot's motion constraint. Since the chained fragments provide reliable clues to find the global path, false matches on featureless structures or partial failures during the alignment could be recovered and perform accurate robot localization in changing environments. The presented experimental results demonstrated the benefits of the proposed method, which outperformed existing algorithms in long-term conditions.


Assuntos
Robótica , Algoritmos , Movimento (Física) , Alinhamento de Sequência
17.
Arch Virol ; 166(9): 2495-2504, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34232400

RESUMO

Short beak and dwarfism syndrome (SBDS) emerged in Cherry Valley duck flocks in China in 2015, and novel goose parvovirus (NGPV) was shown to be the etiological agent of SBDS. To date, it is not known whether SBDS-related NGPV isolates possess common molecular characteristics. In this study, three new NGPV strains (namely, SDHT16, SDJN19, and SDLC19) were isolated from diseased ducks showing typical signs of SBDS and successfully passaged in embryonated goose or Cherry Valley duck eggs. The complete genome sequences of these NGPV strains were 98.9%-99.7% identical to each other but showed slightly less similarity (95.2%-96.1% identity) to classical GPV strains. A total of 16 common amino acid substitutions were present in the VP1 proteins of six NGPV strains (SDHT16, SDJN19, SDLC19, QH, JS1, and SDLC01) compared with the classical Chinese GPV strains, nine of which were identical to those found in European GPV strain B. The non-structural protein Rep1 of the six NGPV strains had 12 common amino acid substitutions compared with the classical GPV strains. Phylogenetic analysis indicated that the Chinese NGPV strains clustered with the European SBDS-related NGPV strains, forming a separate branch that was distinct from the group formed by the classical GPV strains. The present study shows the common molecular characteristics of NGPV isolates and suggests that the Chinese NGPV isolates probably share a common ancestor with European SBDS-related NGPV strains.


Assuntos
Nanismo/veterinária , Nanismo/virologia , Parvovirinae/classificação , Parvovirinae/genética , Filogenia , Doenças das Aves Domésticas/virologia , Animais , China , Patos/virologia , Gansos/virologia , Genoma Viral , Infecções por Parvoviridae/virologia , Parvovirus/genética , Alinhamento de Sequência , Sequenciamento Completo do Genoma
18.
Int J Mol Sci ; 22(14)2021 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-34299001

RESUMO

G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network.


Assuntos
Quadruplex G , Proteínas de Plantas/química , Plantas/química , RNA Polimerase II/química , Sequência de Aminoácidos , Arabidopsis/química , Arabidopsis/genética , Arabidopsis/efeitos da radiação , Dicroísmo Circular , Biologia Computacional , Evolução Molecular , Quadruplex G/efeitos da radiação , Regulação da Expressão Gênica de Plantas/genética , Glaucófitas/química , Glaucófitas/genética , Glaucófitas/efeitos da radiação , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/efeitos da radiação , Plantas/genética , Plantas/efeitos da radiação , RNA Polimerase II/genética , Rodófitas/química , Rodófitas/genética , Rodófitas/efeitos da radiação , Alinhamento de Sequência , Raios Ultravioleta
19.
Int J Mol Sci ; 22(14)2021 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-34299011

RESUMO

Osteoporosis is the most common metabolic bone disorder and nitrogen-containing bisphosphonates (BP) are a first line treatment for it. Yet, atypical femoral fractures (AFF), a rare adverse effect, may appear after prolonged BP administration. Given the low incidence of AFF, an underlying genetic cause that increases the susceptibility to these fractures is suspected. Previous studies uncovered rare CYP1A1 mutations in osteoporosis patients who suffered AFF after long-term BP treatment. CYP1A1 is involved in drug metabolism and steroid catabolism, making it an interesting candidate. However, a functional validation for the AFF-associated CYP1A1 mutations was lacking. Here we tested the enzymatic activity of four such CYP1A1 variants, by transfecting them into Saos-2 cells. We also tested the effect of commonly used BPs on the enzymatic activity of the CYP1A1 forms. We demonstrated that the p.Arg98Trp and p.Arg136His CYP1A1 variants have a significant negative effect on enzymatic activity. Moreover, all the BP treatments decreased CYP1A1 activity, although no specific interaction with CYP1A1 variants was found. Our results provide functional support to the hypothesis that an additive effect between CYP1A1 heterozygous mutations p.Arg98Trp and p.Arg136His, other rare mutations and long-term BP exposure might generate susceptibility to AFF.


Assuntos
Citocromo P-450 CYP1A1/genética , Citocromo P-450 CYP1A1/metabolismo , Fraturas do Fêmur/genética , Fraturas do Fêmur/metabolismo , Sequência de Aminoácidos , Linhagem Celular , Linhagem Celular Tumoral , Sobrevivência Celular/genética , Citocromo P-450 CYP1A1/química , Difosfonatos/uso terapêutico , Fraturas do Fêmur/enzimologia , Humanos , Incidência , Mutagênese Sítio-Dirigida , Mutação de Sentido Incorreto , Filogenia , Alinhamento de Sequência
20.
Virus Res ; 302: 198497, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34217778

RESUMO

Porcine deltacoronavirus (PDCoV) is an emerging coronavirus that causes vomiting, diarrhea, dehydration, and even death of piglets, resulting in significant losses to the pig industry worldwide. However, the epitopes of PDCoV remain largely unknown. In this study, a monoclonal antibody (mAb) against the PDCoV nucleocapsid (N) protein, termed 9G1, was prepared using the lymphocyte hybridoma technique, and was identified as a type IgG1 with a κ light chain and reacted with the native N protein of PDCoV. Furthermore, the epitope recognized by the 9G1 mAb was subjected to western blot and an ELISA using truncated recombinant proteins and synthetic polypeptides of the PDCoV N protein. The results indicate that 9G1 mAb recognized the epitope, G59TPIPPSYAFYY70 (EP-9G1), a novel linear B cell epitope of the PDCoV N protein. A comparison analysis revealed that the EP-9G1 epitope was highly conserved among PDCoV strains, in which four residues (G59-F68YY70) were observed among different coronavirus genera. These data demonstrate that the EP-9G1 epitope identified in this study provides some basic information for further characterization of the antigenic structure of the PDCoV N protein and has potential use for developing diagnostic reagents for PDCoV.


Assuntos
Anticorpos Monoclonais/imunologia , Infecções por Coronavirus/veterinária , Deltacoronavirus/imunologia , Epitopos de Linfócito B/imunologia , Proteínas do Nucleocapsídeo/imunologia , Sequência de Aminoácidos , Animais , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/virologia , Deltacoronavirus/genética , Ensaio de Imunoadsorção Enzimática/veterinária , Feminino , Imunoglobulina G/imunologia , Camundongos Endogâmicos BALB C , Proteínas do Nucleocapsídeo/genética , Proteínas Recombinantes , Alinhamento de Sequência , Suínos
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