Comprehensive Sequence Analysis Research Articles

Comprehensive sequence and structure analysis of algal lipid catabolic enzyme Triacylglycerol lipase: an in silico study to vitalize the development of optimum engineered strains with high lipid productivity

Microalgae as an alternative renewable resource for biofuel production have captured much significance. Nonetheless, its economic viability is a field of major concern for researchers. Unraveling the lipid catabolic pathway and gaining insights into the sequence-structural features of its primary functioning enzyme, Triacylglycerol lipase, will impart valuable information to target microalgae for augmented lipid content. In the present study, a genome-wide comparative study on putative Triacylglycerol lipase (TAGL) enzyme from algal species belonging to varied phylogenetic lineages was performed. The comprehensive sequence analysis revealed that TAGL comprises of three distinct conserved domains, such as, Patatin, Class III Lipase, and Abhydro_lipase, and also confirmed the ubiquitous presence of GXSXG motif in the sequences analyzed. In the absence of a crystal structure of algal TAGL till date, we developed the first 3D model of patatin domain of TAGL from an oleaginous microalga, Phaedactylum tricornutum, employing homology modeling, docking and molecular dynamic simulations methods. The domain-substrate complex having the low-ranking docking score revealed the binding of palmitic acid to the TAGL patatin domain surface with strong hydrogen bond interactions. The simulation results implied that the substrate-complexed patatin domain and the free enzyme adopted a more stable conformation after 40 ns. This is the first ever attempt to provide in-silico insights into the structural and dynamical insights on catalytic mechanism of the TAGL patatin domain. Subsequently, these findings aided our understanding on their structural stability, folding mechanism and protein-substrate interactions, which could be further utilized to design site-specific mutagenic experiments for engineering microalgal strains. Communicated by Ramaswamy H. Sarma

Assembly and annotation of whole-genome sequence of Fusarium equiseti

Fusarium equiseti is a plant pathogen with a wide range of hosts and diverse effects, including probiotic effects. However, the molecular mechanisms underlying these effects remain unclear, hindering its effective utilization. The final assembly included 16 scaffolds of contiguous sequence without gaps. The total sequence length was 40,776,005 bp, and the GC content of 48.01%. In total, we annotated the putative function of 13,134 genes, accounting for 94.97% of the candidate genes. We identified two and 23 candidate genes that are likely involved in the production of mycotoxins zearalenone and trichothecene, respectively. A comparative genomic analysis supported the high quality of the F. equiseti assembly. Our comprehensive analysis of whole-genome sequence will serve as a valuable resource for future studies of expression, regulation, function and evolution of the genes of F. equiseti as well as studies into disease prevention and control.

Acquisition of an Additional NF-κB Site Allows HIV-1 Subtype C to Evade Restriction by Nuclear PYHIN Proteins

Subtype C is the most prevalent clade of HIV-1 worldwide. The reasons for this are poorly understood. Here, we demonstrate that a characteristic additional third NF-κB binding site in the LTR promoter allows subtype C HIV-1 strains to evade restriction by nuclear PYHIN proteins, which sequester the transcription factor Sp1. We also show that other LTR alterations are responsible for rare PYHIN resistance of subtype B viruses. Resistance-conferring mutations generally reduce the dependency of HIV-1 on Sp1 for virus production and render LTR transcription highly responsive to stimulation by NF-κB/p65. A third NF-κB binding site increased infectious virus yield in primary CD4+ T cells in an IFI16 dependent manner. Comprehensive sequence analyses suggest that the frequency of circulating PYHIN-resistant HIV-1 strains is increasing. Our finding that an additional NF-κB binding site in the LTR confers resistance to nuclear PYHIN proteins helps to explain the dominance of clade C HIV-1 strains.

Conserved functional motifs of the nuclear receptor superfamily as potential pharmacological targets

Nuclear receptors (NRs) are one of the most diverse and well-reported family of proteins. They are involved in numerous cellular processes as they play pivotal roles in cell signaling and the cell cycle. The participation of NRs in various applications in medicine and biology has greatly attracted the interest of the pharmaceutical industry for the discovery of novel and/or improved drugs for the treatment of several diseases, including cancer, diabetes or infertility. In the present study, in an effort to elucidate the molecular function of this superfamily and to identify novel pharmacological targets, a comprehensive sequence and structural analysis was performed using all available information from a repertoire of depositories. Functional conserved motifs were identified and analyzed with regards to their potential roles and implications in a number of biological processes. The essential differences among them were also addressed and discussed. In addition, these motifs were characterized in the main groups of the NRs, such as that of the steroid hormone receptors.

Genomic Determinants Encode the Reactivity and Regioselectivity of Flavin-Dependent Halogenases in Bacterial Genomes and Metagenomes.

ABSTRACTHalogenases create diverse natural products by utilizing halide ions and are of great interest in the synthesis of potential pharmaceuticals and agrochemicals. An increasing number of halogenases discovered in microorganisms are annotated as flavin-dependent halogenases (FDHs), but their chemical reactivities are markedly different and the genomic contents associated with such functional distinction have not been revealed yet. Even though the reactivity and regioselectivity of FDHs are essential in the halogenation activity, these FDHs are annotated inaccurately in the protein sequence repositories without characterizing their functional activities. We carried out a comprehensive sequence analysis and biochemical characterization of FDHs. Using a probabilistic model that we built in this study, FDHs were discovered from 2,787 bacterial genomes and 17 sediment metagenomes. We analyzed the essential genomic determinants that are responsible for substrate binding and subsequent reactions: four flavin adenine dinucleotide-binding, one halide-binding, and four tryptophan-binding sites. Compared with previous studies, our study utilizes large-scale genomic information to propose a comprehensive set of sequence motifs that are related to the active sites and regioselectivity. We reveal that the genomic patterns and phylogenetic locations of the FDHs determine the enzymatic reactivities, which was experimentally validated in terms of the substrate scope and regioselectivity. A large portion of publicly available FDHs needs to be reevaluated to designate their correct functions. Our genomic models establish comprehensive links among genotypic information, reactivity, and regioselectivity of FDHs, thereby laying an important foundation for future discovery and classification of novel FDHs.IMPORTANCE Halogenases are playing an important role as tailoring enzymes in biosynthetic pathways. Flavin-dependent tryptophan halogenases (Trp-FDHs) are among the enzymes that have broad substrate scope and high selectivity. From bacterial genomes and metagenomes, we found highly diverse halogenase sequences by using a well-trained profile hidden Markov model built from the experimentally validated halogenases. The characterization of genotype, steady-state activity, substrate scope, and regioselectivity has established comprehensive links between the information encoded in the genomic sequence and reactivity of FDHs reported here. By constructing models for accurate and detailed sequence markers, our work should guide future discovery and classification of novel FDHs.

Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns

The prevailing COVID-19 pandemic has drawn the attention of the scientific community to study the evolutionary origin of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). This study is a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses (HCoVs) to decipher the nucleotide sequence variability and codon usage patterns. It is essential to understand the survival ability of the viruses, their adaptation to hosts, and their evolution.The current analysis revealed a high abundance of the relative dinucleotide (odds ratio), GC and CT pairs in the first and last two codon positions, respectively, as well as a low abundance of the CG pair in the last two positions of the codon, which might be related to the evolution of the viruses. A remarkable level of variability of GC content in the third position of the codon among the seven coronaviruses was observed. Codons with high RSCU values are primarily from the aliphatic and hydroxyl amino acid groups, and codons with low RSCU values belong to the aliphatic, cyclic, positively charged, and sulfur-containing amino acid groups. In order to elucidate the evolutionary processes of the seven coronaviruses, a phylogenetic tree (dendrogram) was constructed based on the RSCU scores of the codons. The severe and mild categories CoVs were positioned in different clades. A comparative phylogenetic study with other coronaviruses depicted that SARS-CoV-2 is close to the CoV isolated from pangolins (Manis javanica, Pangolin-CoV) and cats (Felis catus, SARS(r)-CoV). Further analysis of the effective number of codon (ENC) usage bias showed a relatively higher bias for SARS-CoV and MERS-CoV compared to SARS-CoV-2. The ENC plot against GC3 suggested that the mutational bias might have a role in determining the codon usage variation among candidate viruses.A codon adaptability study on a few human host parasites (from different kingdoms), including CoVs, showed a diverse adaptability pattern. SARS-CoV-2 and SARS-CoV exhibit relatively lower but similar codon adaptability compared to MERS-CoV.

Distribution of ε-Poly-l-Lysine Synthetases in Coryneform Bacteria Isolated from Cheese and Human Skin.

ε-Poly-l-lysine is a potent antimicrobial produced through fermentation of Streptomyces and used in many Asian countries as a food preservative. It is synthesized and excreted by a special nonribosomal peptide synthetase (NRPS)-like enzyme called Pls. In this study, we discovered a gene from cheese bacterium Corynebacterium variabile that showed high similarity to the Pls from Streptomyces in terms of domain architecture and gene context. By cloning it into Streptomyces coelicolor with a Streptomyces albulus Pls promoter, we confirmed that its product is indeed ε-poly-l-lysine. A comprehensive sequence analysis suggested that Pls genes are widely spread among coryneform actinobacteria isolated from cheese and human skin; 14 out of 15 Brevibacterium isolates and 10 out of 12 Corynebacterium isolates contain it in their genomes. This finding raises the possibility that ε-poly-l-lysine as a bioactive secondary metabolite might be produced and play a role in the cheese and skin ecosystems.IMPORTANCE Every year, microbial contamination causes billions of tons of food wasted and millions of cases of illness. ε-Poly-l-lysine has potent, wide-spectrum inhibitory activity and is heat stable and biodegradable. It has been approved for food preservation by an increasing number of countries. ε-Poly-l-lysine is produced from soil bacteria of the genus Streptomyces, also producers of various antibiotic drugs and toxins and not considered to be a naturally occurring food component. The frequent finding of pls in cheese and skin bacteria suggests that ε-poly-l-lysine may naturally exist in cheese and on our skin, and ε-poly-l-lysine producers are not limited to filamentous actinobacteria.

Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs.

Gluten-specific CD4+ T cells are drivers of celiac disease (CeD). Previous studies of gluten-specific T-cell receptor (TCR) repertoires have found public TCRs shared across multiple individuals, biased usage of particular V-genes and conserved CDR3 motifs. The CDR3 motifs within the gluten-specific TCR repertoire, however, have not been systematically investigated. In the current study, we analyzed the largest TCR database of gluten-specific CD4+ T cells studied so far consisting of TCRs of 3122 clonotypes from 63 CeD patients. We established a TCR database from CD4+ T cells isolated with a mix of HLA-DQ2.5:gluten tetramers representing four immunodominant gluten epitopes. In an unbiased fashion we searched by hierarchical clustering for common CDR3 motifs among 2764 clonotypes. We identified multiple CDR3α, CDR3β, and paired CDR3α:CDR3β motif candidates. Among these, a previously known conserved CDR3β R-motif used by TRAV26-1/TRBV7-2 TCRs specific for the DQ2.5-glia-α2 epitope was the most prominent motif. Furthermore, we identified the epitope specificity of altogether 16 new CDR3α:CDR3β motifs by comparing with TCR sequences of 231 T-cell clones with known specificity and TCR sequences of cells sorted with single HLA-DQ2.5:gluten tetramers. We identified 325 public TCRα and TCRβ sequences of which 145, 102 and 78 belonged to TCRα, TCRβ and paired TCRαβ sequences, respectively. While the number of public sequences was depended on the number of clonotypes in each patient, we found that the proportion of public clonotypes from the gluten-specific TCR repertoire of given CeD patients appeared to be stable (median 37%). Taken together, we here demonstrate that the TCR repertoire of CD4+ T cells specific to immunodominant gluten epitopes in CeD is diverse, yet there is clearly biased V-gene usage, presence of public TCRs and existence of conserved motifs of which R-motif is the most prominent.

Genetic Diversity and Comprehensive Phylodynamic Analysis of Whole Corona Viruses Genomes

Covid-19 is a rapidly emerging viral respiratory disease. The infection of corona virus disease (COVID-19) is initiated by the strains of severe acute respiratory syndrome. Corona virus 2 (SARS-CoV-2), is a highly transmittable viral infection that was first emerged in the of Wuhan, a city of China and ultimately extent in whole world. The World health organization (WHO) affirmed this infection as a global public health disaster. Genomic analysis showing that this novel SARSCoV-2 is hereditarily linked with severe acute respiratory syndrome-like (SARS-like) bat viruses indicating that bats might be the primary source of this epidemic infection. In this review we have summarized a comprehensive phylodynamic analysis of whole corona virus genome sequences in order to analyze the pathogenicity and emergence of novel COVID-19 infection and previous human coronaviruses. Our main objective is to describe the genetic relationships of the 2019-nCoV with other genera of coronavirus and to find out supposed recombination contained by sarbecovirus subgenus. Keywords: COVID-19, Phylogeny, SARS-CoV, MERS-CoV, Coding Sequence (CDS).

A novel homozygous SLC13A5 whole-gene deletion generated by Alu/Alu-mediated rearrangement in an Iraqi family with epileptic encephalopathy.

Biallelic loss-of-function (LoF) of SLC13A5 (solute carrier family 13, member 5) induced deficiency in sodium/citrate transporter (NaCT) causes autosomal recessive developmental epileptic encephalopathy 25 with hypoplastic amelogenesis imperfecta (DEE25; MIM #615905). Many pathogenic SLC13A5 single nucleotide variants (SNVs) and small indels have been described; however, no cases with copy number variants (CNVs) have been sufficiently investigated. We describe a consanguineous Iraqi family harboring an 88.5kb homozygous deletion including SLC13A5 in Chr17p13.1. The three affected male siblings exhibit neonatal-onset epilepsy with fever-sensitivity, recurrent status epilepticus, global developmental delay/intellectual disability (GDD/ID), and other variable neurological findings as shared phenotypical features of DEE25. Two of the three affected subjects exhibit hypoplastic amelogenesis imperfecta (AI), while the proband shows no evidence of dental abnormalities or AI at 2 years of age with apparently unaffected primary dentition. Characterization of the genomic architecture at this locus revealed evidence for genomic instability generated by an Alu/Alu-mediated rearrangement; confirmed by break-point junction Sanger sequencing. This multiplex family from a distinct population elucidates the phenotypic consequence of complete LoF of SLC13A5 and illustrates the importance of read-depth-based CNV detection in comprehensive exome sequencing analysis to solve cases that otherwise remain molecularly unsolved.

Profile of gut flora in hypertensive patients with insufficient sleep duration.

Recently, the contribution of both insufficient sleep duration and gut microbiome dysbiosis to hypertension (HTN) have been revealed, yet the profile of gut flora in hypertensive patients with insufficient sleep duration remains unknown. To examine this condition, the specific shifts in the fecal microbiome of 53 participants with or without HTN were investigated. The patients were divided into those who slept short (≤6 h) or optimal (6-9 h) duration per day. Comprehensive metagenomic sequencing analysis of fecal specimens was performed in healthy controls with sufficient sleep (s-CTR, n = 10), healthy controls with insufficient sleep (ins-CTR, n = 6), hypertensive patients with sufficient sleep (s-HTN, n = 25), and HTNs complicated by short sleep duration (ins-HTN, n = 12). We found that the α-diversity and β-diversity were quite similar between s-HTN and ins-HTN. Similarities were also observed in the enterotype distribution between s-HTN and ins-HTN subjects. In addition, the enrichment of gut bacteria was evident, such as Fusobacterium mortiferum and Roseburia inulinivorans in ins-HTN subjects. Several functional modules that were distinct between s-HTN and ins-HTN subjects were identified, which were unique to hypertensive patients with insufficient sleep duration. Overall, the data demonstrated that the gut microbial features were largely maintained in hypertensive participants with insufficient sleep duration.

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue

The link between the gut microbiota and social behavior has been demonstrated, however the translational impact of a certain microbiota composition on stable behavioral patterns is yet to be elucidated. Here we employed an established social behavior mouse model of dominance (Dom) or submissiveness (Sub). A comprehensive 16S rRNA gene sequence analysis of Dom and Sub mice revealed a significantly different gut microbiota composition that clearly distinguishes between the two behavioral modes. Sub mice gut microbiota is significantly less diverse than that of Dom mice, and their taxa composition uniquely comprised the genera Mycoplasma and Anaeroplasma of the Tenericutes phylum, in addition to the Rikenellaceae and Clostridiaceae families. Conversely, the gut microbiota of Dom mice includes the genus Prevotella of the Bacteriodetes phylum, significantly less abundant in Sub mice. In addition, Sub mice show lower body weight from the age of 2 weeks and throughout their life span, accompanied with lower epididymis white adipose tissue (eWAT) mass and smaller adipocytes together with substantially elevated expression of inflammation and metabolic-related eWAT adipokines. Finally, fecal microbiota transplantation into germ-free mice show that Sub-transplanted mice acquired Sub microbiota and adopted their behavioral and physiological features, including depressive-like and anti-social behaviors alongside reduced eWAT mass, smaller adipocytes, and a Sub-like eWAT adipokine profile. Our findings demonstrate the critical role of the gut microbiome in determining dominance vs. submissiveness and suggest an association between gut microbiota, the eWAT metabolic and inflammatory profile, and the social behavior mode.

Methylation and molecular profiles of ependymoma: Influence of patient age and tumor anatomic location

Ependymomas are tumors of the central nervous system that can occur in patients of all ages. Guidelines from the World Health Organization (WHO) for the grading of ependymomas consider patient age, tumor resection range, tumor location and histopathological grade. However, recent studies have suggested that a greater focus on both tumor location and patient age in terms of transcriptomic, genetic, and epigenetic analyses may provide a more accurate assessment of clinical prognosis than the grading system proposed by WHO guidelines. The current study identified the differences and similarities in ependymoma characteristics using three different molecular analyses and methylation arrays. Primary intracranial ependymoma tissues were obtained from 13 Korean patients (9 adults and 4 children), after which whole-exome sequencing (WES), ion-proton comprehensive cancer panel (CCP) analysis, RNA sequencing, and Infinium HumanMethylation450 BeadChip array analysis was performed. Somatic mutations, copy number variations, and fusion genes were identified. It was observed that the methylation status and differentially expressed genes were significantly different according to tumor location and patient age. Several novel gene fusions and somatic mutations were identified, including a yes-associated protein 1 fusion mutation in a child with a good prognosis. Moreover, the methylation microarray revealed that genes associated with neurogenesis and neuron differentiation were hypermethylated in the adult group, whereas genes in the homeobox gene family were hypermethylated in the supratentorial (ST) group. The results confirmed the existence of significantly differentially expressed tumor-specific genes based on tumor location and patient age. These results provided valuable insight into the epigenetic and genetic profiles of intracranial ependymomas and uncovered potential strategies for the identification of location- and age-based ependymoma-related prognostic factors.

A Negative Feedback Model to Explain Regulation of SARS-CoV-2 Replication and Transcription.

BackgroundCoronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a preliminary understanding of the replication and transcription of SARS-CoV-2 has recently emerged, their regulation remains unknown.ResultsBy comprehensive analysis of genome sequence and protein structure data, we propose a negative feedback model to explain the regulation of CoV replication and transcription, providing a molecular basis of the “leader-to-body fusion” model. The key step leading to the proposal of our model was that the transcription regulatory sequence (TRS) motifs were identified as the cleavage sites of nsp15, a nidoviral RNA uridylate-specific endoribonuclease (NendoU). According to this model, nsp15 regulates the synthesis of subgenomic RNAs (sgRNAs), and genomic RNAs (gRNAs) by cleaving TRSs. The expression level of nsp15 controls the relative proportions of sgRNAs and gRNAs, which in turn change the expression level of nsp15 to reach equilibrium between the CoV replication and transcription.ConclusionThe replication and transcription of CoVs are regulated by a negative feedback mechanism that influences the persistence of CoVs in hosts. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, and provide new clues for future studies. One important clue is that nsp15 may be an important and ideal target for the development of drugs (e.g., uridine derivatives) against CoVs.

Insights into the evolutionary history of the virulent factor HBHA of Mycobacterium tuberculosis.

In Mycobacterium tuberculosis, heparin-binding hemagglutinin (HBHAMT) has a relevant role in infection. It is also present in non-virulent mycobacteria and ancient actinobacteria, such as Rhodococcus opacus. To have a better understanding of the underlying mechanisms that shaped the evolutionary divergence of these proteins, we performed a comprehensive phylogenetic analysis of the regulatory sequences that drive the expression of hbha in saprophytic and pathogenic mycobacterial species. The alignment of the hbha loci showed the appearance of intergenic sequences containing regulatory elements upstream the hbha gene; this sequence arrangement is present only in slow-growing pathogenic mycobacteria. The heterologous expression of HBHAMT in oleaginous R. opacus PD630 results in protein binding to lipid droplets, as it happens with HBHA proteins from saprophytic mycobacteria. We hypothesize that mycobacterial hbha gene cluster underwent functional divergence during the evolutionary differentiation of slow-growing pathogenic mycobacteria. We propose here an evolutionary scenario to explain the structural and functional divergence of HBHA in fast and slow-growing mycobacteria.

Abstract PS16-31: SKT11 loss drives rapid cancer progression and fatal pulmonary tumor thrombotic microangiopathy (PTTM) in a breast cancer patient: A case report

Abstract Introduction: Pulmonary tumor thrombotic microangiopathy (PTTM) is a rare cancer-associated respiratory complication characterized by widespread tumor cell emboli in small arteries and arterioles of the lung. Breast cancer is the second most common cancer causing PTTM. The pathogenesis and molecular background of PTTM have not been clarified. Here we present a case of breast cancer that experienced early onset of liver metastasis after surgical resection of the primary tumor and rapid progression leading to death due to severe respiratory distress. Autopsy was performed and it revealed that the main cause of her death was PTTM. Comprehensive next generation sequencing (NGS) analysis of the tissue obtained serially during the clinical course was performed. Case Presentation: A 48-year-old woman was diagnosed with invasive ductal carcinoma of the left breast, which was ER positive, PgR negative, and HER2 negative. FEC followed by docetaxel was administered as preoperative chemotherapy. Her tumor dramatically shrunk with chemotherapy and left partial mastectomy with left axillary lymph node dissection was performed. Histopathological analysis of the resected breast tissue revealed that there were a lot of residual cancer cells, which were ER negative, PgR negative, HER2 negative, and the result indicated that response to preoperative chemotherapy was insufficient. Additional two courses of FEC therapy were performed. Postoperative radiation therapy including the left supraclavicular lymph node area was given and adjuvant endocrine therapy with anastrozole started at the same time. At 3 months of anastrozole administration, she presented hepatic dysfunction and abnormal CT findings in the liver. Liver biopsy revealed multiple liver metastasis of breast cancer. Unresponsive to weekly paclitaxel and bevacizumab, she developed rapid respiratory failure leading to her death in two weeks. Postmortem microscopic analysis revealed an intimal fibrocellular proliferation in the pulmonary arterioles regardless of microscopic tumor emboli and extensive sinusoidal metastasis of the whole liver. NGS Analysis: We analyzed four specimens, breast cancer biopsy specimen at diagnosis, surgical resection specimen, liver needle biopsy specimen, and liver specimen obtained at autopsy, with the Ion AmpliSeq Comprehensive Cancer Panel (Thermo Fisher). The results were compared with NGS analysis of her normal lung tissue to exclude single nucleotide polymorphisms. Deep sequencing revealed that only TP53 R213* was detected as an oncogenic mutation in all four specimens. There were no mutations associated with the development of liver metastasis and her death. Comparison of the samples obtained between before and after liver metastasis revealed that STK11 loss and IKBKE amplification were harbored only in the specimens after liver metastasis. RNA sequencing analysis with the samples of initial biopsy and liver biopsy showed that the RNA expression associated with apoptosis and adhesion molecules was strongly suppressed in the liver sample. Conclusion: STK11 encodes a serine/threonine kinase, which organizes cell polarity and inhibits tumor growth. In the present patient, STK11 loss had occurred during the treatment and could induce rapid progression of her disease and PTTM. Citation Format: Fumie Fujisawa, Kei Kunimasa, Rieko Kano, Hiroki Kusama, Minako Nishio, Saki Matsui, Tetsuhiro Yoshinami, Nobuyoshi Kittaka, Shigenori Nagata, Toshinari Yagi, Takahiro Nakayama, Yasuhiro Tamaki, Fumio Imamura. SKT11 loss drives rapid cancer progression and fatal pulmonary tumor thrombotic microangiopathy (PTTM) in a breast cancer patient: A case report [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS16-31.

Improving representations of genomic sequence motifs in convolutional networks with exponential activations.

Deep convolutional neural networks (CNNs) trained on regulatory genomic sequences tend to build representations in a distributed manner, making it a challenge to extract learned features that are biologically meaningful, such as sequence motifs. Here we perform a comprehensive analysis on synthetic sequences to investigate the role that CNN activations have on model interpretability. We show that employing an exponential activation to first layer filters consistently leads to interpretable and robust representations of motifs compared to other commonly used activations. Strikingly, we demonstrate that CNNs with better test performance do not necessarily imply more interpretable representations with attribution methods. We find that CNNs with exponential activations significantly improve the efficacy of recovering biologically meaningful representations with attribution methods. We demonstrate these results generalise to real DNA sequences across several in vivo datasets. Together, this work demonstrates how a small modification to existing CNNs, i.e. setting exponential activations in the first layer, can significantly improve the robustness and interpretabilty of learned representations directly in convolutional filters and indirectly with attribution methods.

Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: an endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations.

Accumulation of mutations within the genome is the primary driving force in viral evolution within an endemic setting. This inherent feature often leads to altered virulence, infectivity and transmissibility, and antigenic shifts to escape host immunity, which might compromise the efficacy of vaccines and antiviral drugs. Therefore, we carried out a genome-wide analysis of circulating SARS-CoV-2 strains to detect the emergence of novel co-existing mutations and trace their geographical distribution within India. Comprehensive analysis of whole genome sequences of 837 Indian SARS-CoV-2 strains revealed the occurrence of 33 different mutations, 18 of which were unique to India. Novel mutations were observed in the S glycoprotein (6/33), NSP3 (5/33), RdRp/NSP12 (4/33), NSP2 (2/33), and N (1/33). Non-synonymous mutations were found to be 3.07 times more prevalent than synonymous mutations. We classified the Indian isolates into 22 groups based on their co-existing mutations. Phylogenetic analysis revealed that the representative strains of each group were divided into various sub-clades within their respective clades, based on the presence of unique co-existing mutations. The A2a clade was found to be dominant in India (71.34%), followed by A3 (23.29%) and B (5.36%), but a heterogeneous distribution was observed among various geographical regions. The A2a clade was highly predominant in East India, Western India, and Central India, whereas the A2a and A3 clades were nearly equal in prevalence in South and North India. This study highlights the divergent evolution of SARS-CoV-2 strains and co-circulation of multiple clades in India. Monitoring of the emerging mutations will pave the way for vaccine formulation and the design of antiviral drugs.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00705-020-04911-0.

Alternative Polyadenylation in response to temperature stress contributes to gene regulation in Populus trichocarpa

BackgroundGenome-wide change of polyadenylation (polyA) sites (also known as alternative polyadenylation, APA) is emerging as an important strategy of gene regulation in response to stress in plants. But little is known in woody perennials that are persistently dealing with multiple abiotic stresses.ResultsHere, we performed a genome-wide profiling of polyadenylation sites under heat and cold treatments in Populus trichocarpa. Through a comprehensive analysis of polyA tail sequences, we identified 25,919 polyA-site clusters (PACs), and revealed 3429 and 3139 genes shifted polyA sites under heat and cold stresses respectively. We found that a small proportion of genes possessed APA that affected the open reading frames; and some shifts were commonly identified. Functional analysis of genes displaying shifted polyA tails suggested that pathways related to RNA metabolism were linked to regulate the APA events under both heat and cold stresses. Interestingly, we found that the heat stress induced a significantly more antisense PACs comparing to cold and control conditions. Furthermore, we showed that a unique cis-element (AAAAAA) was predominately enriched downstream of PACs in P. trichocarpa genes; and this sequence signal was only absent in shifted PACs under the heat condition, indicating a distinct APA mechanism responsive to heat tolerance.ConclusionsThis work provides a comprehensive picture of global polyadenylation patterns in response to temperatures stresses in trees. We show that the frequent change of polyA tail is a potential mechanism of gene regulation responsive to stress, which are associated with distinctive sequence signatures.

Frequency of co-occurrence of chinese characters as an indicator of lexicality (when selecting the vocabulary of chinese military discourse)

Teaching a foreign language in a non-linguistic college or university should be professionally oriented, which brings up the question of selecting the relevant vocabulary of a professional discourse under study. Modern text corpora are too general in subject matter and the time span. Therefore, a specially compiled collection of texts can serve the purpose of selecting the vocabulary. In the case of the Chinese language, the task is complicated by the lack of word segmentation in such texts. Taking into account the fact that most words in Chinese are written in two characters, it is assumed that one of the methods applicable in this situation is a comprehensive frequency analysis of text sequences of two characters – character bigrams. The analysis of frequent bigrams has showed that 70% of the most frequent lexical units are representative of the discourse, including 11% of out-of-vocabulary ones. The remaining part of bigrams pertain to syntactic constructions, including structurally incomplete ones, and fragments of longer lexical units. Thus, the high frequency of character co-occurrence can with a rather high probability (p > 0.7) be considered as an indicator of lexicality in identifying representative vocabulary in an unsegmented the matic collection of texts in Chinese.