Effects of spaced k-mers on alignment-free genotyping.

MOTIVATION: Alignment-free, k-mer based genotyping methods are a fast alternative to alignment-based methods and are particularly well suited for genotyping larger cohorts. The sensitivity of algorithms, that work with k-mers, can be increased by using spaced seeds, however, the application of spaced seeds in k-mer based genotyping methods has not been researched yet. RESULTS: We add a spaced seeds functionality to the genotyping software PanGenie and use it to calculate genotypes. This significantly improves sensitivity and F-score when genotyping SNPs, indels, and structural variants on reads with low (5×) and high (30×) coverage. Improvements are greater than what could be achieved by just increasing the length of contiguous k-mers. Effect sizes are particularly large for low coverage data. If applications implement effective algorithms for hashing of spaced k-mers, spaced k-mers have the potential to become an useful technique in k-mer based genotyping. AVAILABILITY AND IMPLEMENTATION: The source code of our proposed tool MaskedPanGenie is openly available on https://github.com/hhaentze/MaskedPangenie.

Distinct mutations in importin-ß family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding.

Importin-(Imp)ß family nucleocytoplasmic transport receptors (NTRs) are supposed to bind to their cargoes through interaction between a confined interface on an NTR and a nuclear localization or export signal (NLS/NES) on a cargo. Although consensus NLS/NES sequence motifs have been defined for cargoes of some NTRs, many experimentally identified cargoes of those NTRs lack those motifs, and consensus NLSs/NESs have been reported for only a few NTRs. Crystal structures of NTR-cargo complexes have exemplified 3D structure-dependent binding of cargoes lacking a consensus NLS/NES to different sites on an NTR. Since only a limited number of NTR-cargo interactions have been studied, whether most cargoes lacking a consensus NLS/NES bind to the same confined interface or to various sites on an NTR is still unclear. Addressing this issue, we generated four mutants of transportin-(Trn)SR, of which many cargoes lack a consensus NLS, and eight mutants of Imp13, where no consensus NLS has been defined, and we analyzed their binding to as many as 40 cargo candidates that we previously identified by a nuclear import reaction-based method. The cargoes bind differently to the NTR mutants, suggesting that positions on an NTR contribute differently to the binding of respective cargoes.

Long non-coding RNA 2310069B03Rik functions as a suppressor of Ucp1 expression under prolonged cold exposure in murine beige adipocytes.

Specific conditions, such as exposure to cold, can induce the production of brown-like adipocytes in white adipose tissue. These adipocytes express high levels of uncoupling protein 1 (UCP1) and energy expended by generating heat. Thus, these are a potential target for the prevention or treatment of obesity. The present study involved a comprehensive analysis of the adipose tissue to understand the relationship between long non-coding RNA (lncRNA) 2310069B03Rik and UCP1. Cold exposure increased both lncRNA 2310069B03Rik and Ucp1 expression in inguinal white adipose tissue (iWAT). However, overexpression of lncRNA 2310069B03Rik suppressed the Ucp1 mRNA expression and the promoter activity of UCP1 in the iWAT primary adipocytes. In addition, compared to the early induction of Ucp1 expression by cold stimulation, the induction of lncRNA 2310069B03Rik expression was later. These results suggest that lncRNA 2310069B03Rik functions as a suppression factor of Ucp1 expression.

Novel lineage-specific transmembrane ß-barrel proteins in the endoplasmic reticulum of Entamoeba histolytica.

ß-barrel outer membrane proteins (BOMPs) are essential components of outer membranes of Gram-negative bacteria and endosymbiotic organelles, usually involved in the transport of proteins and substrates across the membrane. Based on the analysis of our in silico BOMP predictor data for the Entamoeba histolytica genome, we detected a new transmembrane ß-barrel domain-containing protein, EHI_192610. Sequence analysis revealed that this protein is unique to Entamoeba species, and it exclusively clusters with a homolog, EHI_099780, which is similarly lineage specific. Both proteins possess an N-terminal signal peptide sequence as well as multiple repeats that contain dyad hydrophobic periodicities. Data from immunofluorescence assay of trophozoites expressing the respective candidates showed the absence of colocalization with mitosomal marker, and interestingly demonstrated partial colocalization with endoplasmic reticulum (ER) proteins instead. Integration to organellar membrane was supported by carbonate fractionation assay and immunoelectron microscopy. CD analysis of reconstituted proteoliposomes containing EHI_192610 showed a spectrum demonstrating a predominant ß-sheet structure, suggesting that this protein is ß-strand rich. Furthermore, the presence of repeat regions with predicted transmembrane ß-strand pairs in both EHI_192610 and EHI_099780, is consistent with the hypothesis that BOMPs originated from the amplification of ßß-hairpin modules, suggesting that the two Entamoeba-specific proteins are novel ß-barrels, intriguingly localized partially to the ER membrane.

Estimating genome-wide off-target effects for pyrrole-imidazole polyamide binding by a pathway-based expression profiling approach.

In the search for new pharmaceutical leads, especially with DNA-binding molecules or genome editing methods, the issue of side and off-target effects have always been thorny in nature. A particular case is the investigation into the off-target effects of N-methylpyrrole-N-methylimidazole polyamides, a naturally inspired class of DNA binders with strong affinity to the minor-groove and sequence specificity, but at < 20 bases, their relatively short motifs also insinuate the possibility of non-unique genomic binding. Binding at non-intended loci potentially lead to the rise of off-target effects, issues that very few approaches are able to address to-date. We here report an analytical method to infer off-target binding, via expression profiling, based on probing the relative impact to various biochemical pathways; we also proposed an accompanying side effect prediction engine for the systematic screening of candidate polyamides. This method marks the first attempt in PI polyamide research to identify elements in biochemical pathways that are sensitive to the treatment of a candidate polyamide as an approach to infer possible off-target effects. Expression changes were then considered to assess possible outward phenotypic changes, manifested as side effects, should the same PI polyamide candidate be administered clinically. We validated some of these effects with a series of animal experiments, and found agreeable corroboration in certain side effects, such as changes in aspartate transaminase levels in ICR and nude mice post-administration.

Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis.

BACKGROUND: Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. This data has great potential to illuminate our understanding of biology and medicine, but the data alone is of limited value without computational tools to allow human investigators to visualize and interpret it in the context of their problem of interest. RESULTS: We created a web server called SHOE that provides an interactive, visual presentation of the available evidence of transcriptional regulation and gene co-expression to facilitate its exploration and interpretation. SHOE predicts the likely transcription factor binding sites in orthologous promoters of humans, mice, and rats using the combined information of 1) transcription factor binding preferences (position-specific scoring matrix (PSSM) libraries such as Transfac32, Jaspar, HOCOMOCO, ChIP-seq, SELEX, PBM, and iPS-reprogramming factor), 2) evolutionary conservation of putative binding sites in orthologous promoters, and 3) co-expression tendencies of gene pairs based on 1,714 normal human cells selected from the Gene Expression Omnibus Database. CONCLUSION: SHOE enables users to explore potential interactions between transcription factors and target genes via multiple data views, discover transcription factor binding motifs on top of gene co-expression, and visualize genes as a network of gene and transcription factors on its native gadget GeneViz, the CellDesigner pathway analyzer, and the Reactome database to search the pathways involved. As we demonstrate here when using the CREB1 and Nf-κB datasets, SHOE can reliably identify experimentally verified interactions and predict plausible novel ones, yielding new biological insights into the gene regulatory mechanisms involved. SHOE comes with a manual describing how to run it on a local PC or via the Garuda platform ( www.garuda-alliance.org ), where it joins other popular gadgets such as the CellDesigner pathway analyzer and the Reactome database, as part of analysis workflows to meet the growing needs of molecular biologists and medical researchers. SHOE is available from the following URL http://ec2-54-150-223-65.ap-northeast-1.compute.amazonaws.com A video demonstration of SHOE can be found here: https://www.youtube.com/watch?v=qARinNb9NtE.

A systematic review and meta-analysis of the neural correlates of psychological therapies in major depression.

Longitudinal neuroimaging studies in major depression have revealed cortico-limbic abnormalities which are modulated by treatment. We performed a systematic review and meta-analysis of psychotherapy treatment studies measuring neural function and metabolism using fMRI, PET, SPECT and MRS. Seventeen studies were included in the systematic review, total of 200 major depression participants (mean age 37.6 years), all medication free, and 116 healthy controls (mean age 36.4 years). Neuroimaging assessments were performed prior to initiation of treatment and following course of treatment. Treatment durations were: 16-30 weeks for CBT, 11 weeks for behavioral activation therapy, and up to 15 months for psychodynamic psychotherapy. The meta-analysis consisted of studies in which both groups had same serial scans and comparable tasks; total of 5 studies with visual presentation tasks of emotional stimuli: 55 patients (mean age: 38.7 years) and 55 healthy controls (mean age: 36.3 years). The meta-analysis revealed a significant group by time effect in left rostral anterior cingulate, in which patients showed increased activity following psychotherapy while healthy controls showed a decrease at follow up. Longitudinal treatment effects revealed reduced left precentral cortical activity in major depression. Findings could be indicative of improvements in emotion responsivity that may be achieved following psychotherapy.

EAGLE: Explicit Alternative Genome Likelihood Evaluator.

BACKGROUND: Reliable detection of genome variations, especially insertions and deletions (indels), from single sample DNA sequencing data remains challenging, partially due to the inherent uncertainty involved in aligning sequencing reads to the reference genome. In practice a variety of ad hoc quality filtering methods are employed to produce more reliable lists of putative variants, but the resulting lists typically still include numerous false positives. Thus it would be desirable to be able to rigorously evaluate the degree to which each putative variant is supported by the data. Unfortunately, users who wish to do this, e.g. for the purpose of prioritizing validation experiments, have been faced with limited options. RESULTS: Here we present EAGLE, a method for evaluating the degree to which sequencing data supports a given candidate genome variant. EAGLE incorporates candidate variants into explicit hypotheses about the individual's genome, and then computes the probability of the observed data (the sequencing reads) under each hypothesis. In comparison with methods which rely heavily on a particular alignment of the reads to the reference genome, EAGLE readily accounts for uncertainties that may arise from multi-mapping or local misalignment and uses the entire length of each read. We compared the scores assigned by several well-known variant callers to EAGLE for the task of ranking true putative variants on both simulated data and real genome sequencing based benchmarks. For indels, EAGLE obtained marked improvement on simulated data and a whole genome sequencing benchmark, and modest but statistically significant improvement on an exome sequencing benchmark. CONCLUSIONS: EAGLE ranked true variants higher than the scores reported by the callers and can used to improve specificity in variant calling. EAGLE is freely available at https://github.com/tony-kuo/eagle .

A bioinformatics potpourri.

The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.

Extensive cargo identification reveals distinct biological roles of the 12 importin pathways.

Vast numbers of proteins are transported into and out of the nuclei by approximately 20 species of importin-ß family nucleocytoplasmic transport receptors. However, the significance of the multiple parallel transport pathways that the receptors constitute is poorly understood because only limited numbers of cargo proteins have been reported. Here, we identified cargo proteins specific to the 12 species of human import receptors with a high-throughput method that employs stable isotope labeling with amino acids in cell culture, an in vitro reconstituted transport system, and quantitative mass spectrometry. The identified cargoes illuminated the manner of cargo allocation to the receptors. The redundancies of the receptors vary widely depending on the cargo protein. Cargoes of the same receptor are functionally related to one another, and the predominant protein groups in the cargo cohorts differ among the receptors. Thus, the receptors are linked to distinct biological processes by the nature of their cargoes.

Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome.

Pyrrole-imidazole polyamides are versatile DNA minor groove binders and attractive therapeutic options against oncological targets, especially upon functionalization with an alkylating agent such as seco-CBI. These molecules also provide an alternative for oncogenes deemed "undruggable" at the protein level, where the absence of solvent-accessible pockets or structural crevices prevent the formation of protein-inhibitor ligands; nevertheless, the genome-wide effect of pyrrole-imidazole polyamide binding remain largely unclear to-date. Here we propose a next-generation sequencing-based workflow combined with whole genome expression arrays to address such issue using a candidate anti-cancer alkylating agent, KR12, against codon 12 mutant KRAS. Biotinylating KR12 enables the means to identify its genome-wide effects in living cells and possible biological implications via a coupled workflow of enrichment-based sequencing and expression microarrays. The subsequent computational pathway and expression analyses allow the identification of its genomic binding sites, as well as a route to explore a polyamide's possible genome-wide effects. Among the 3,343 KR12 binding sites identified in the human LS180 colorectal cancer genome, the reduction of KR12-bound gene expressions was also observed. Additionally, the coupled microarray-sequencing analysis also revealed some insights about the effect of local chromatin structure on pyrrole-imidazole polyamide, which had not been fully understood to-date. A comparative analysis with KR12 in a different human colorectal cancer genome SW480 also showed agreeable agreements of KR12 binding affecting gene expressions. Combination of these analyses thus suggested the possibility of applying this approach to other pyrrole-imidazole polyamides to reveal further biological details about the effect of polyamide binding in a genome.

GIW and InCoB, two premier bioinformatics conferences in Asia with a combined 40 years of history.

Knowledge discovery in bioinformatics thrives on joint and inclusive efforts of stakeholders. Similarly, knowledge dissemination is expected to be more effective and scalable through joint efforts. Therefore, the International Conference on Bioinformatics (InCoB) and the International Conference on Genome Informatics (GIW) were organized as a joint conference for the first time in 13 years of coexistence. The Asia-Pacific Bioinformatics Network (APBioNet) and the Japanese Society for Bioinformatics (JSBi) collaborated to host GIW/InCoB2015 in Tokyo, September 9-11, 2015. The joint endeavour yielded 51 research articles published in seven journals, 78 poster and 89 oral presentations, showcasing bioinformatics research in the Asia-Pacific region. Encouraged by the results and reduced organizational overheads, APBioNet will collaborate with other bioinformatics societies in organizing co-located bioinformatics research and training meetings in the future. InCoB2016 will be hosted in Singapore, September 21-23, 2016.

Molecular architecture of the active mitochondrial protein gate.

Mitochondria fulfill central functions in cellular energetics, metabolism, and signaling. The outer membrane translocator complex (the TOM complex) imports most mitochondrial proteins, but its architecture is unknown. Using a cross-linking approach, we mapped the active translocator down to single amino acid residues, revealing different transport paths for preproteins through the Tom40 channel. An N-terminal segment of Tom40 passes from the cytosol through the channel to recruit chaperones from the intermembrane space that guide the transfer of hydrophobic preproteins. The translocator contains three Tom40 ß-barrel channels sandwiched between a central α-helical Tom22 receptor cluster and external regulatory Tom proteins. The preprotein-translocating trimeric complex exchanges with a dimeric isoform to assemble new TOM complexes. Dynamic coupling of α-helical receptors, ß-barrel channels, and chaperones generates a versatile machinery that transports about 1000 different proteins.

Contesting heteronormativity: the fight for lesbian, gay, bisexual and transgender recognition in India and Vietnam.

Recent public debates about sexuality in India and Vietnam have brought the rights of lesbian, gay, bisexual and transgender people sharply into focus. Drawing on legal documents, secondary sources and ethnographic fieldwork conducted in the urban centres of Delhi and Hanoi, this article shows how the efforts of civil society organisations dedicated to the fight for lesbian, gay, bisexual and transgender rights have had different consequences in these two Asian contexts. The paper considers how these organisations navigated government regulations about their formation and activities, as well as the funding priorities of national and international agencies. The HIV epidemic has had devastating consequences for gay men and other men who have sex with men, and has been highly stigmatising. As a sad irony, the epidemic has provided at the same time a strategic entry point for organisations to struggle for lesbian, gay, bisexual and transgender recognition. This paper examines how the fight for lesbian, gay, bisexual and transgender recognition has been doubly framed through health-based and rights-based approaches and how the struggle for recognition has positioned lesbian, gay, bisexual and transgender people in India and Vietnam differently.

Multimodal functional and structural neuroimaging investigation of major depressive disorder following treatment with duloxetine.

BACKGROUND: Longitudinal neuroimaging studies of major depressive disorder (MDD) have most commonly assessed the effects of antidepressants from the serotonin reuptake inhibitor class and usually reporting a single measure. Multimodal neuroimaging assessments were acquired from MDD patients during an acute depressive episode with serial measures during a 12-week treatment with the serotonin-norepinephrine reuptake inhibitor (SNRI) duloxetine. METHODS: Participants were medication-free MDD patients (n = 32; mean age 40.2 years) in an acute depressive episode and healthy controls matched for age, gender, and IQ (n = 25; mean age 38.8 years). MDD patients received treatment with duloxetine 60 mg daily for 12 weeks with an optional dose increase to 120 mg daily after 8 weeks. All participants had serial imaging at weeks 0, 1, 8, and 12 on a 3 Tesla magnetic resonance imaging (MRI) scanner. Neuroimaging tasks included emotional facial processing, negative attentional bias (emotional Stroop), resting state functional MRI and structural MRI. RESULTS: A significant group by time interaction was identified in the anterior default mode network in which MDD patients showed increased connectivity with treatment, while there were no significant changes in healthy participants. In the emotional Stroop task, increased posterior cingulate activation in MDD patients normalized following treatment. No significant group by time effects were observed for happy or sad facial processing, including in amygdala responsiveness, or in regional cerebral volumes. Reduced baseline resting state connectivity within the orbitofrontal component of the default mode network was predictive of clinical response. An early increase in hippocampal volume was predictive of clinical response. CONCLUSIONS: Baseline resting state functional connectivity was predictive of subsequent clinical response. Complementary effects of treatment were observed from the functional neuroimaging correlates of affective facial expressions, negative attentional bias, and resting state. No significant effects were observed in affective facial processing, while the interaction effect in negative attentional bias and individual group effects in resting state connectivity could be related to the SNRI class of antidepressant medication. The specificity of the observed effects to SNRI pharmacological treatments requires further investigation. TRIAL REGISTRATION: Registered at clinicaltrials.gov ( NCT01051466 ).

A novel Mitosomal ß-barrel Outer Membrane Protein in Entamoeba.

Entamoeba possesses a highly divergent mitochondrion-related organelle known as the mitosome. Here, we report the discovery of a novel protein in Entamoeba, which we name Mitosomal ß-barrel Outer Membrane Protein of 30 kDa (MBOMP30). Initially identified through in silico analysis, we experimentally confirmed that MBOMP30 is indeed a ß-barrel protein. Circular dichroism analysis showed MBOMP30 has a predominant ß-sheet structure. Localization to Entamoeba histolytica mitosomes was observed through Percoll-gradient fractionation and immunofluorescence assay. Mitosomal membrane integration was demonstrated by carbonate fractionation, proteinase K digestion, and immunoelectron microscopy. Interestingly, the deletion of the putative ß-signal, a sequence believed to guide ß-barrel outer membrane protein (BOMP) assembly, did not affect membrane integration, but abolished the formation of a ~240 kDa complex. MBOMP30 represents only the seventh subclass of eukaryotic BOMPs discovered to date and lacks detectable homologs outside Entamoeba, suggesting that it may be unique to Entamoeba mitosomes.