High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response

How human genetic variation contributes to vaccine effectiveness in infants is unclear, and data are limited on these relationships in populations with African ancestries. We undertook genetic analyses of vaccine antibody responses in infants from Uganda (n = 1391), Burkina Faso (n = 353) and South Africa (n = 755), identifying associations between human leukocyte antigen (HLA) and antibody response for five of eight tested antigens spanning pertussis, diphtheria and hepatitis B vaccines. In addition, through HLA typing 1,702 individuals from 11 populations of African ancestry derived predominantly from the 1000 Genomes Project, we constructed an imputation resource, fine-mapping class II HLA-DR and DQ associations explaining up to 10% of antibody response variance in our infant cohorts. We observed differences in the genetic architecture of pertussis antibody response between the cohorts with African ancestries and an independent cohort with European ancestry, but found no in silico evidence of differences in HLA peptide binding affinity or breadth. Using immune cell expression quantitative trait loci datasets derived from African-ancestry samples from the 1000 Genomes Project, we found evidence of differential HLA-DRB1 expression correlating with inferred protection from pertussis following vaccination. This work suggests that HLA-DRB1 expression may play a role in vaccine response and should be considered alongside peptide selection to improve vaccine design.

A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization

Genetic screens in cancer cell lines inform gene function and drug discovery. More comprehensive screen datasets with multi-omics data are needed to enhance opportunities to functionally map genetic vulnerabilities. Here, we construct a second-generation map of cancer dependencies by annotating 930 cancer cell lines with multi-omic data and analyze relationships between molecular markers and cancer dependencies derived from CRISPR-Cas9 screens. We identify dependency-associated gene expression markers beyond driver genes, and observe many gene addiction relationships driven by gain of function rather than synthetic lethal effects. By combining clinically informed dependency-marker associations with protein-protein interaction networks, we identify 370 anti-cancer priority targets for 27 cancer types, many of which have network-based evidence of a functional link with a marker in a cancer type. Mapping these targets to sequenced tumor cohorts identifies tractable targets in different cancer types. This target prioritization map enhances understanding of gene dependencies and identifies candidate anti-cancer targets for drug development.

Transcriptomics and chromatin accessibility in multiple African population samples

Mapping the functional human genome and impact of genetic variants is often limited to European-descendent population samples. To aid in overcoming this limitation, we measured gene expression using RNA sequencing in lymphoblastoid cell lines (LCLs) from 599 individuals from six African populations to identify novel transcripts including those not represented in the hg38 reference genome. We used whole genomes from the 1000 Genomes Project and 164 Maasai individuals to identify 8,881 expression and 6,949 splicing quantitative trait loci (eQTLs/sQTLs), and 2,611 structural variants associated with gene expression (SV-eQTLs). We further profiled chromatin accessibility using ATAC-Seq in a subset of 100 representative individuals, to identity chromatin accessibility quantitative trait loci (caQTLs) and allele-specific chromatin accessibility, and provide predictions for the functional effect of 78.9 million variants on chromatin accessibility. Using this map of eQTLs and caQTLs we fine-mapped GWAS signals for a range of complex diseases. Combined, this work expands global functional genomic data to identify novel transcripts, functional elements and variants, understand population genetic history of molecular quantitative trait loci, and further resolve the genetic basis of multiple human traits and disease.

Africa-specific human genetic variation near CHD1L associates with HIV-1 load

HIV-1 remains a global health crisis1, highlighting the need to identify new targets for therapies. Here, given the disproportionate HIV-1 burden and marked human genome diversity in Africa2, we assessed the genetic determinants of control of set-point viral load in 3,879 people of African ancestries living with HIV-1 participating in the international collaboration for the genomics of HIV3. We identify a previously undescribed association signal on chromosome 1 where the peak variant associates with an approximately 0.3 log10-transformed copies per ml lower set-point viral load per minor allele copy and is specific to populations of African descent. The top associated variant is intergenic and lies between a long intergenic non-coding RNA (LINC00624) and the coding gene CHD1L, which encodes a helicase that is involved in DNA repair4. Infection assays in iPS cell-derived macrophages and other immortalized cell lines showed increased HIV-1 replication in CHD1L-knockdown and CHD1L-knockout cells. We provide evidence from population genetic studies that Africa-specific genetic variation near CHD1L associates with HIV replication in vivo. Although experimental studies suggest that CHD1L is able to limit HIV infection in some cell types in vitro, further investigation is required to understand the mechanisms underlying our observations, including any potential indirect effects of CHD1L on HIV spread in vivo that our cell-based assays cannot recapitulate.

Base editing screens map mutations affecting interferon-γ signaling in cancer

Interferon-γ (IFN-γ) signaling mediates host responses to infection, inflammation and anti-tumor immunity. Mutations in the IFN-γ signaling pathway cause immunological disorders, hematological malignancies, and resistance to immune checkpoint blockade (ICB) in cancer; however, the function of most clinically observed variants remains unknown. Here, we systematically investigate the genetic determinants of IFN-γ response in colorectal cancer cells using CRISPR-Cas9 screens and base editing mutagenesis. Deep mutagenesis of JAK1 with cytidine and adenine base editors, combined with pathway-wide screens, reveal loss-of-function and gain-of-function mutations, including causal variants in hematological malignancies and mutations detected in patients refractory to ICB. We functionally validate variants of uncertain significance in primary tumor organoids, where engineering missense mutations in JAK1 enhanced or reduced sensitivity to autologous tumor-reactive T cells. We identify more than 300 predicted missense mutations altering IFN-γ pathway activity, generating a valuable resource for interpreting gene variant function.

An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens

A limitation of pooled CRISPR-Cas9 screens is the high false-positive rate in detecting essential genes arising from copy-number-amplified genomics regions. To solve this issue, we previously developed CRISPRcleanR: a computational method implemented as R/python package and in a dockerized version. CRISPRcleanR detects and corrects biased responses to CRISPR-Cas9 targeting in an unsupervised fashion, accurately reducing false-positive signals while maintaining sensitivity in identifying relevant genetic dependencies. Here, we present CRISPRcleanR WebApp , a web application enabling access to CRISPRcleanR through an intuitive interface. CRISPRcleanR WebApp removes the complexity of R/python language user interactions; provides user-friendly access to a complete analytical pipeline, not requiring any data pre-processing and generating gene-level summaries of essentiality with associated statistical scores; and offers a range of interactively explorable plots while supporting a more comprehensive range of CRISPR guide RNAs' libraries than the original package. CRISPRcleanR WebApp is available at https://crisprcleanr-webapp.fht.org/.

Surface Defect Formation and Passivation in Formamidinium Lead Triiodide (FAPbI3) Perovskite Solar Cell Absorbers

Formamidinium lead iodide based hybrid perovskite materials with improved efficiency and stability still lack well-understood surface defect formation mechanisms. Controlling the surface termination and defects has the potential to improve the performance of both conventional 3D and latterly reduced-dimensional perovskites photovoltaics. Here, we characterized the termination and all possible defect formations in FAPbI₃ surface by the first-principles calculations. We found that, among the surfaces we considered, FAI-termination exhibits the most stable surface with a high defect tolerance. The PbI₂-terminated surface is also found to be relatively stable; however, certain defects, such as electron-donating FA-interstitial and Pb-interstitial defects, can create deep-level stable charge-traps, potentially limiting the optoelectronic performance. We further investigate the surface treatment on these deep defects by model small molecule additives. We found that benzene additive with delocalized electron distribution can effectively passivate the deep FA-interstitial and Pb-interstitial defects by electron donating to the surface defect through charge-transfer.

CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens

BACKGROUND

CRISPR-Cas9 genome-wide screens are being increasingly performed, allowing systematic explorations of cancer dependencies at unprecedented accuracy and scale. One of the major computational challenges when analysing data derived from such screens is to identify genes that are essential for cell survival invariantly across tissues, conditions, and genomic-contexts (core-fitness genes), and to distinguish them from context-specific essential genes. This is of paramount importance to assess the safety profile of candidate therapeutic targets and for elucidating mechanisms involved in tissue-specific genetic diseases.

RESULTS

We have developed CoRe: an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens. We demonstrate, through a fully reproducible benchmarking pipeline, that CoRe outperforms state-of-the-art tools, yielding more reliable and biologically relevant sets of core-fitness genes.

CONCLUSIONS

CoRe offers a flexible pipeline, compatible with many pre-processing methods for the analysis of CRISPR data, which can be tailored onto different use-cases. The CoRe package can be used for the identification of high-confidence novel core-fitness genes, as well as a means to filter out potentially cytotoxic hits while analysing cancer dependency datasets for identifying and prioritising novel selective therapeutic targets.

Modified Lung Ultrasound Score in Evaluating the Severity of Covid-19 Pneumonia

Severe acute respiratory syndrome coronavirus 2 causes coronavirus disease 2019 (Covid-19), which has been declared as a pandemic by the World Health Organization. The aim of the study described here was to determine the severity of pneumonia and the clinical parameters related to a modified lung ultrasound score (mLUS) in patients with COVID-19 pneumonia. The study included 44 patients with proven COVID-19 pneumonia. Patients were divided into three groups on the basis of pneumonia severity: mild/moderate pneumonia (group I), severe pneumonia (group II) and critically ill patients (group III). It was determined that mLUS values in groups I-III were 6.51 ± 4.12, 23.5 ± 5.9 and 24.7 ± 3.9, respectively. mLUS values were significantly higher in group II and III patients than in group I patients. There was a positive relationship between mLUS and age and N-terminal pro-brain natriuretic peptide level and a negative relationship with P_aO₂/F_iO₂ (p = 0.032, β = 0.275 vs. p = 0.012, β = 0.315 vs. p = 0.001, β = -0.520, respectively). In patients with COVID-19 pneumonia, mLUS increases significantly with the severity of the disease.

Integrated cross-study datasets of genetic dependencies in cancer

CRISPR-Cas9 viability screens are increasingly performed at a genome-wide scale across large panels of cell lines to identify new therapeutic targets for precision cancer therapy. Integrating the datasets resulting from these studies is necessary to adequately represent the heterogeneity of human cancers and to assemble a comprehensive map of cancer genetic vulnerabilities. Here, we integrated the two largest public independent CRISPR-Cas9 screens performed to date (at the Broad and Sanger institutes) by assessing, comparing, and selecting methods for correcting biases due to heterogeneous single-guide RNA efficiency, gene-independent responses to CRISPR-Cas9 targeting originated from copy number alterations, and experimental batch effects. Our integrated datasets recapitulate findings from the individual datasets, provide greater statistical power to cancer- and subtype-specific analyses, unveil additional biomarkers of gene dependency, and improve the detection of common essential genes. We provide the largest integrated resources of CRISPR-Cas9 screens to date and the basis for harmonizing existing and future functional genetics datasets.

Breaking a species barrier by enabling hybrid recombination

Hybrid sterility maintains reproductive isolation between species by preventing them from exchanging genetic material¹. Anti-recombination can contribute to hybrid sterility when different species' chromosome sequences are too diverged to cross over efficiently during hybrid meiosis, resulting in chromosome mis-segregation and aneuploidy. The genome sequences of the yeasts Saccharomyces cerevisiae and Saccharomyces paradoxus have diverged by about 12% and their hybrids are sexually sterile: nearly all of their gametes are aneuploid and inviable. Previous methods to increase hybrid yeast fertility have targeted the anti-recombination machinery by enhancing meiotic crossing over. However, these methods also have counteracting detrimental effects on gamete viability due to increased mutagenesis² and ectopic recombination³. Therefore, the role of anti-recombination has not been fully revealed, and it is often dismissed as a minor player in speciation¹. By repressing two genes, SGS1 and MSH2, specifically during meiosis whilst maintaining their mitotic expression, we were able to increase hybrid fertility 70-fold, to the level of non-hybrid crosses, confirming that anti-recombination is the principal cause of hybrid sterility. Breaking this species barrier allows us to generate, for the first time, viable euploid gametes containing recombinant hybrid genomes from these two highly diverged parent species.

Disease Severity Affects Ventricular Repolarization Parameters in Patients With COVID-19

Fundamento:

Não há estudos avaliando o intervalo T_pico-T_fim (Tpe), a relação Tpe/QT e a relação Tpe/QTc para avaliar arritmias cardíacas em pacientes com COVID-19.

Objetivo:

Visamos investigar se há alterações nos intervalos QT, QTc e Tpe e nas relações Tpe/QT e Tpe/QTc em pacientes com COVID-19.

Métodos:

O estudo incluiu 90 pacientes com infecção por COVID-19 e 30 controles saudáveis pareados por sexo e idade. Foram aferidos os intervalos QT, QTc e Tpe e as relações Tpe/QT e Tpe/QTc. Os participantes incluídos no estudo foram divididos nos seguintes 4 grupos: controles saudáveis (grupo I), pacientes com COVID-19 sem pneumonia (grupo II), pacientes com COVID-19 e pneumonia leve (grupo III) e pacientes com COVID-19 e pneumonia grave (grupo IV). Significância estatística foi definida por valor p < 0,05.

Resultados:

Verificou-se que a frequência cardíaca basal, a presença de hipertensão e diabetes, a contagem de leucócitos, o nitrogênio ureico no sangue, a creatinina, o potássio, o aspartato aminotransferase, a alanina aminotransferase, o NT-proBNP, a proteína C reativa de alta sensibilidade, o dímero-D, a TncI-as, o intervalo Tpe, a relação Tpe/QT e a relação Tpe/QTc aumentaram do grupo I para o grupo IV e foram significativamente mais altos em todos os pacientes do grupo IV (p < 0,05). A pressão arterial sistólica, a hemoglobina e os níveis de cálcio eram menores no grupo IV e significativamente menores em comparação com os demais grupos (< 0,05). Os intervalos QT e QTc eram semelhantes entre grupos. Determinou-se que os níveis elevados de frequência cardíaca, cálcio, dímero-D, NT-proBNP e PCR-as eram significativamente relacionados a Tpe, Tpe/QT e Tpe/QTc.

Conclusões:

Em pacientes com COVID-19 e pneumonia grave, o intervalo Tpe, a relação Tpe/QT e a relação Tpe/QTc, que estão entre os parâmetros de repolarização ventricular, foram aumentados, sem prolongação dos intervalos QT e QTc. A partir deste estudo, não podemos definitivamente concluir que as alterações eletrocardiográficas observadas estão diretamente relacionadas à infecção por COVID-19 ou à inflamação, mas sim associadas a cenários graves de COVID-19, que podem envolver outras causas de inflamação e comorbidades.

Prognostic Factors Determining Morbidity and Mortality in Organophosphate Poisoning

Objective:

Our aim in this retrospective study was to determine the factors affecting poor prognosis and mortality of organophosphate (OP) poisoning by reviewing patient data. We also reviewed present knowledge to make conclusions on certain longstanding debates in light of the literature.

Methods:

In this retrospective descriptive study, patients who were admitted to and hospitalized in the emergency department (ED) or intensive care unit (ICU) of a university hospital with the diagnosis of OP poisoning between December 2010 and December 2015 were evaluated. All the data were obtained from electronic and manual patient files. A total of 80 patients were included in the study.

Results:

The mean age of the study patients was 32.4±15.0 (13-94). Forty-nine (61.2%) patients were female. Twenty-two (27.5%) patients were seriously poisoned and needed mechanical ventilation (MV) support. Low pseudocholinesterase (PChE), high creatinine (Cr), low Glasgow Coma Scale (GCS) scores and long hospitalization durations were all found to be poor prognostics in MV patients. Low PChE and high Cr levels were found to be independent predictors of the hospitalization duration and high Cr was found to be an independent predictor of the intubation duration of MV patients in regression analyses. Ten (45.5%) of the MV patients were unresponsive to medical treatment and Therapeutic plasma exchange (TPE) was performed. Seven patients were discharged healthy. Three patients with low PChE levels and comorbidities died.

Conclusions:

Prolongation of respiratory depression necessitating MV support, comorbidities, long hospital stay, elevated creatinine, low GCS scores and low PcHE levels without regeneration in the first 48 hours of admission are all found to be poor prognostic factors for organophosphate (OP) poisoning.

Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus

Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory.

The evolution and functional impact of human deletion variants shared with archaic hominin genomes

Allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-African introgression from archaic hominins. However, evolution of polymorphic human deletions that are shared with archaic hominin genomes has yet to be studied. We identified 427 polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the Human–Neandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed). Recurrence, incomplete lineage sorting between human and chimp lineages, and hominid-specific insertions constitute the remaining approximately 4% of allele sharing between humans and archaic hominins. We observed that ancient deletions correspond to more than 13% of all common (>5% allele frequency) deletion variation among modern humans. Our analyses indicate that the genomic landscapes of both ancient and introgressed deletion variants were primarily shaped by purifying selection, eliminating large and exonic variants. We found 17 exonic deletions that are shared with archaic hominin genomes, including those leading to three fusion transcripts. The affected genes are involved in metabolism of external and internal compounds, growth and sperm formation, as well as susceptibility to psoriasis and Crohn’s disease. Our analyses suggest that these “exonic” deletion variants have evolved through different adaptive forces, including balancing and population-specific positive selection. Our findings reveal that genomic structural variants that are shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionarily important phenotypes.

ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms

MOTIVATION

RNA-Seq technology is promising to uncover many novel alternative splicing events, gene fusions and other variations in RNA transcripts. For an accurate detection and quantification of transcripts, it is important to resolve the mapping ambiguity for those RNA-Seq reads that can be mapped to multiple loci: >17% of the reads from mouse RNA-Seq data and 50% of the reads from some plant RNA-Seq data have multiple mapping loci. In this study, we show how to resolve the mapping ambiguity in the presence of novel transcriptomic events such as exon skipping and novel indels towards accurate downstream analysis. We introduce ORMAN ( O ptimal R esolution of M ultimapping A mbiguity of R N A-Seq Reads), which aims to compute the minimum number of potential transcript products for each gene and to assign each multimapping read to one of these transcripts based on the estimated distribution of the region covering the read. ORMAN achieves this objective through a combinatorial optimization formulation, which is solved through well-known approximation algorithms, integer linear programs and heuristics.

RESULTS

On a simulated RNA-Seq dataset including a random subset of transcripts from the UCSC database, the performance of several state-of-the-art methods for identifying and quantifying novel transcripts, such as Cufflinks, IsoLasso and CLIIQ, is significantly improved through the use of ORMAN. Furthermore, in an experiment using real RNA-Seq reads, we show that ORMAN is able to resolve multimapping to produce coverage values that are similar to the original distribution, even in genes with highly non-uniform coverage.

AVAILABILITY

ORMAN is available at http://orman.sf.net

Transmission disequilibrium of small CNVs in simplex autism

We searched for disruptive, genic rare copy-number variants (CNVs) among 411 families affected by sporadic autism spectrum disorder (ASD) from the Simons Simplex Collection by using available exome sequence data and CoNIFER (Copy Number Inference from Exome Reads). Compared to high-density SNP microarrays, our approach yielded ∼2× more smaller genic rare CNVs. We found that affected probands inherited more CNVs than did their siblings (453 versus 394, p = 0.004; odds ratio [OR] = 1.19) and that the probands' CNVs affected more genes (921 versus 726, p = 0.02; OR = 1.30). These smaller CNVs (median size 18 kb) were transmitted preferentially from the mother (136 maternal versus 100 paternal, p = 0.02), although this bias occurred irrespective of affected status. The excess burden of inherited CNVs among probands was driven primarily by sibling pairs with discordant social-behavior phenotypes (p < 0.0002, measured by Social Responsiveness Scale [SRS] score), which contrasts with families where the phenotypes were more closely matched or less extreme (p > 0.5). Finally, we found enrichment of brain-expressed genes unique to probands, especially in the SRS-discordant group (p = 0.0035). In a combined model, our inherited CNVs, de novo CNVs, and de novo single-nucleotide variants all independently contributed to the risk of autism (p < 0.05). Taken together, these results suggest that small transmitted rare CNVs play a role in the etiology of simplex autism. Importantly, the small size of these variants aids in the identification of specific genes as additional risk factors associated with ASD.

Altered splicing of ATP6AP2 causes X-linked parkinsonism with spasticity (XPDS)

We report a novel gene for a parkinsonian disorder. X-linked parkinsonism with spasticity (XPDS) presents either as typical adult onset Parkinson's disease or earlier onset spasticity followed by parkinsonism. We previously mapped the XPDS gene to a 28 Mb region on Xp11.2-X13.3. Exome sequencing of one affected individual identified five rare variants in this region, of which none was missense, nonsense or frame shift. Using patient-derived cells, we tested the effect of these variants on expression/splicing of the relevant genes. A synonymous variant in ATP6AP2, c.345C>T (p.S115S), markedly increased exon 4 skipping, resulting in the overexpression of a minor splice isoform that produces a protein with internal deletion of 32 amino acids in up to 50% of the total pool, with concomitant reduction of isoforms containing exon 4. ATP6AP2 is an essential accessory component of the vacuolar ATPase required for lysosomal degradative functions and autophagy, a pathway frequently affected in Parkinson's disease. Reduction of the full-size ATP6AP2 transcript in XPDS cells and decreased level of ATP6AP2 protein in XPDS brain may compromise V-ATPase function, as seen with siRNA knockdown in HEK293 cells, and may ultimately be responsible for the pathology. Another synonymous mutation in the same exon, c.321C>T (p.D107D), has a similar molecular defect of exon inclusion and causes X-linked mental retardation Hedera type (MRXSH). Mutations in XPDS and MRXSH alter binding sites for different splicing factors, which may explain the marked differences in age of onset and manifestations.

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes--so-called sporadic or simplex families--we sequenced all coding regions of the genome (the exome) for parent-child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected β-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.

Insights into hominid evolution from the gorilla genome sequence

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

Detection of structural variants and indels within exome data

We report an algorithm to detect structural variation and indels from 1 base pair (bp) to 1 Mbp within exome sequence data sets. Splitread uses one end-anchored placements to cluster the mappings of subsequences of unanchored ends to identify the size, content and location of variants with high specificity and sensitivity. The algorithm discovers indels, structural variants, de novo events and copy number-polymorphic processed pseudogenes missed by other methods.

Error tolerant NMR backbone resonance assignment and automated structure generation

Error tolerant backbone resonance assignment is the cornerstone of the NMR structure determination process. Although a variety of assignment approaches have been developed, none works sufficiently well on noisy fully automatically picked peaks to enable the subsequent automatic structure determination steps. We have designed an integer linear programming (ILP) based assignment system (IPASS) that has enabled fully automatic protein structure determination for four test proteins. IPASS employs probabilistic spin system typing based on chemical shifts and secondary structure predictions. Furthermore, IPASS extracts connectivity information from the inter-residue information and the (automatically picked) (15)N-edited NOESY peaks which are then used to fix reliable fragments. When applied to automatically picked peaks for real proteins, IPASS achieves an average precision and recall of 82% and 63%, respectively. In contrast, the next best method, MARS, achieves an average precision and recall of 77% and 36%, respectively. The assignments generated by IPASS are then fed into our protein structure calculation system, FALCON-NMR, to determine the 3D structures without human intervention. The final models have backbone RMSDs of 1.25Å, 0.88Å, 1.49Å, and 0.67Å to the reference native structures for proteins TM1112, CASKIN, VRAR, and HACS1, respectively. The web server is publicly available at http://monod.uwaterloo.ca/nmr/ipass.

PICKY: a novel SVD-based NMR spectra peak picking method

MOTIVATION

Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly.

RESULTS

We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 A.

AVAILABILITY

PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking.

The genotoxicity and cytotoxicity among patients diagnosed with organophosphate poisoning

The genotoxicity and cytotoxicity were investigated in 40 patients (20 females aged 21.57 +/- 1.42 and 20 males aged 29.35 +/- 3.59) diagnosed at the Emergency Department with organophosphate poisoning. Chromosome aberrations (CAs), sister chromatid exchanges (SCEs), micronucleus (MN), mitotic index (MI), replication index (RI) and nuclear division index (NDI) were evaluated in peripheral bloods of patients. The blood samples were collected from the patients on admission to the emergency department before treatment and after treatment before being discharged from the intensive care unit. The CA, MI and NDI values were increased before the discharge when compared to the levels measured on admission. However, there are no differences in mean SCE, frequency of MN and RI (Tab. 2, Ref. 42).

Trends in acute adult poisoning in a ten-year period in Turkey: factors affecting the hazardous outcome

AIM

The aim of this study was to evaluate the trends in acute adult poisoning data during ten years in university emergency department and determine the factors of hazardous outcome such as severe clinical status, prolonged hospital stay and mortality.

MATERIAL AND METHODS

Medical records of 4569 poisoned patients admitted to Emergency Department (ED) of Qukurova University, School of Medicine in Adana.

RESULTS

The mean age of 2988 females (65.4% of the patients) was 24.5+/-10.1 years, whilst the mean age of 1581 male patients (34.6%) was 29.5+/-13.2 years (p=0.001). Of the poisonings 80.0% were suicidal; 69.4% of the women and 30.6% of the men committed suicide. The most common types of poisonings were ingestion of drugs (58.4%), organophosphates (23.9%) corrosives (3.4%), mushrooms (1.7%), methanol (2.4%), carbon monoxide (2.1%) and unknown (8.1%). Of the total 96.0% were discharged from emergency department, 1.4% transferred to IC and 2.6% died.

CONCLUSIONS

Young people and women are high-risk groups for acute poisoning and drug poisoning was found to be the most common type of poisoning. The poisoning by psychoactive drugs is increasinging in the recent years and organophosphates poisoning seems to be still a serious problem in such an agricultural area. However, while the ratios of prolonged hospitalization and mortality are decreasing, suicidal poisoning is seriously increasing (Tab. 4, Fig. 2, Ref. 34). Full Text (Free, PDF) www.bmj.sk.

Ultrastructural changes in rat thyroid tissue after acute organophosphate poisoning and effects of antidotal therapy with atropine and pralidoxime: A single-blind, ex vivo study

BACKGROUND

Organophosphate (OP) insecticides are widely used in both agricultural and landscape pest control, and the potential for human exposure to these compounds is significant.

OBJECTIVES

The aims of this study were to investigate the effects of acute poisoning with the OP methamidophos and the effects of antidotal therapy with atropine and pralidoxime on rat thyroid tissue ultrastructure.

METHODS

In this single-blind, ex vivo study, male Wistar albino rats weighing 220 to 230 g were divided into 4 treatment groups. Group 1 received a median lethal dose of methamidophos (30 mg/kg) via oral gavage. Group 2 received saline via oral gavage and served as the control group for group 1. Group 3 received methamidophos (30 mg/kg) via oral gavage, and after 8 minutes atropine 0.05 mg/kg and pralidoxime chloride (2-FAM) (40 mg/kg) were administered intraperitoneally (IP). Atropine was titrated to reverse signs of cholinergic excess. Group 4 received saline via oral gavage followed by IP injections and served as the control for group 3. Rat thyroid tissues were examined using electron microscopy, and the histologic changes were examined by a histopathologist who was blinded to treatment. All rats were euthanized by intracardiac blood collection. The rats in groups 1 and 2 were euthanized 8 minutes after treatment. The rats in groups 3 and 4 were euthanized 96 hours after treatment.

RESULTS

Thirty-four male rats (aged 16 weeks) were included in the study. The rats were grouped accordingly: group 1 (n = 10); group 2 (n = 7); group 3 (n = 10); and group 4 (n = 7). The mean (SD) pseudocholinesterase (FCE) activity was significantly lower in the methamidophos-treated rats (group 1) compared with the corresponding control group (group 2) (32.6 [17.0] vs 579.4 [59.0] U/L, respectively; P < 0.001). PCE activity was significantly higher in rats treated with atropine and 2-PAM (group 3) (392.5 [39.4] U/L; P < 0.001) compared with those not receiving antidotal therapy (group 1). Group 1 experienced changes in thyrocytes and organelles that were not detected in the antidote-treated rats in group 3. These changes included follicular cell nuclei exhibiting an increase in chromatin content, pyknotic nuclei, mitochondrial degeneration, dilated granular endoplasmic reticulum cisternae, reduced microvilli, and intraluminal cellular debris. Within follicular cells, formation of vacuoles filled with fine granular material was noted.

CONCLUSION

Acute OP poisoning was associated with histopathologic effects in rat thyroid tissue that appeared to be mitigated by antidotal therapy in this small animal study. More extensive studies using immunohistochemical methods are needed.

Latex allergy risk assessment in children and adolescents with type I diabetes mellitus

An increased frequency of allergic reactions to latex has been reported in specific populations with chronic latex exposure. However, relevance of latex allergy to children and adolescents with type I diabetes mellitus (DM1) has not been studied yet. The aim of the studty is to assess latex allergy risk in children and adolescents with DM1. Thirty-nine children with DM1 and 35 controls were enrolled. In a case-control study, we applied to all subjects a standard questionnaire, and specific Immunoglobulin E (IgE) concentrations for latex, common aeroallergens, and food-allergens were measured in serum samples. Latex exposure rates by means of medical procedures, operations, and latex glove usage were not different between DM1 and controls. Symptoms due to latex exposure were not determined in both groups. Three (7.7%) subjects in DM1 tested positive for latex-specific antibodies (LSIE), whereas no subject in controls. Diabetics that tested positive for latex-specific antibodies had the disease for three, 5 and 8 years. Nine (23.1%) of diabetics, and two (5.7%) of controls were atopic (p = 0.04). In our investigation, we found that children and adolescents with DM1 are not a risk group for latex allergy, and LSIE in children with DM1 was not accompanied by symptoms of latex allergy, or, presumably, increased risk of latex anaphylaxis.

taveRNA: a web suite for RNA algorithms and applications

We present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction. It is based on a dynamic programming solution that minimizes the sum of energy density and free energy of an RNA structure. inteRNA is the first RNA-RNA interaction structure prediction web service. It also employs a dynamic programming algorithm to minimize the free energy of the resulting joint structure of the two interacting RNAs. Lastly, pRuNA is an efficient database pruning service; which given a query RNA, eliminates a significant portion of an ncRNA database and returns only a few ncRNAs as potential regulators. taveRNA is available at http://compbio.cs.sfu.ca/taverna.

Comparative QSAR analysis of bacterial, fungal, plant and human metabolites

Several QSAR models have been developed using a linear optimization approach that enabled distinguishing metabolic substances isolated from human-, bacterial-, plant- and fungal- cells. Seven binary classifiers based on a k-Nearest Neighbors method have been created using a variety of 'inductive' and traditional QSAR descriptors that allowed up to 95% accurate recognition of the studied groups of chemical substances. The conducted comparative QSAR analysis based on the above mentioned linear optimization approach helped to identify the extent of overlaps between the groups of compounds, such as cross-recognition of fungal and bacterial metabolites and association between fungal and plant substances. Human metabolites exhibited very different QSAR behavior in chemical space and demonstrated no significant overlap with bacterial-, fungal-, and plant-derived molecules. When the developed QSAR models were applied to collections of conventional human therapeutics and antimicrobials, it was observed that the first group of substances demonstrate the strongest association with human metabolites, while the second group exhibit tendency of 'bacterial metabolite - like' behavior. We speculate that the established 'drugs - human metabolites' and 'antimicrobials - bacterial metabolites' associations result from strict bioavailability requirements imposed on conventional therapeutic substances, which further support their metabolite-like properties. It is anticipated that the study may bring additional insight into QSAR determinants for human-, bacterial-, fungal- and plant metabolites and may help rationalizing design and discovery of novel bioactive substances with improved, metabolite-like properties.

Comparative QSAR- and fragments distribution analysis of drugs, druglikes, metabolic substances, and antimicrobial compounds

A number of binary QSAR models have been developed using methods of artificial neural networks, k-nearest neighbors, linear discriminative analysis, and multiple linear regression and have been compared for their ability to recognize five types of chemical compounds that include conventional drugs, inactive druglikes, antimicrobial substituents, and bacterial and human metabolites. Thus, 20 binary classifiers have been created using a variety of 'inductive' and traditional 2D QSAR descriptors which allowed up to 99% accurate separation of the studied groups of activities. The comparison of the performance by four computational approaches demonstrated that the neural nets result in generally more accurate predictions, followed closely by k-nearest neighbors methods. It has also been demonstrated that complementation of 'inductive' descriptors with conventional QSAR parameters does not generally improve the quality of resulting solutions, conforming high predictive ability of 'inductive' variables. The conducted comparative QSAR analysis based on a novel linear optimization approach has helped to identify the extent of overlapping between the studied groups of compounds, such as cross-recognition of bacterial metabolites and antimicrobial compounds reflecting their immanent resemblance and similar origin. Human metabolites have been characterized as a very distinctive class of substances, separated from all other groups in the descriptors space and exhibiting different QSAR behavior. The analysis of unique structural fragments and substituents revealed inhomogeneous scale-free organization of human metabolites illustrating the fact that certain molecular scaffolds (such as sugars and nucleotides) may be strongly favored by natural evolution. The established scale-free organization of human metabolites has been contemplated as a factor of their unique positioning in the descriptors space and their distinctive QSAR properties. It is anticipated that the study may bring additional insight into QSAR determinants for conventional drugs, inactive chemicals, and metabolic substances and may help in rationalizing design and discovery of novel antimicrobials and human therapeutics with improved, metabolite-like properties.

Distance based algorithms for small biomolecule classification and structural similarity search

MOTIVATION

Structural similarity search among small molecules is a standard tool used in molecular classification and in-silico drug discovery. The effectiveness of this general approach depends on how well the following problems are addressed. The notion of similarity should be chosen for providing the highest level of discrimination of compounds wrt the bioactivity of interest. The data structure for performing search should be very efficient as the molecular databases of interest include several millions of compounds.

RESULTS

In this paper we focus on the k-nearest-neighbor search method, which, until recently was not considered for small molecule classification. The few recent applications of k-nn to compound classification focus on selecting the most relevant set of chemical descriptors which are then compared under standard Minkowski distance L(p). Here we show how to computationally design the optimal weighted Minkowski distance wL(p) for maximizing the discrimination between active and inactive compounds wrt bioactivities of interest. We then show how to construct pruning based k-nn search data structures for any wL(p) distance that minimizes similarity search time. The accuracy achieved by our classifier is better than the alternative LDA and MLR approaches and is comparable to the ANN methods. In terms of running time, our classifier is considerably faster than the ANN approach especially when large data sets are used. Furthermore, our classifier quantifies the level of bioactivity rather than returning a binary decision and thus is more informative than the ANN approach.

Thrombotic thrombocytopenic purpura in southern Turkey: a single-center experience of 29 cases

In this retrospective, nonrandomized study, we describe our experience in the management of 29 consecutive patients with thrombotic thrombocytopenic purpura (TTP) treated with a combined therapy of plasma exchange (PE) and steroids at a single center. We compared the effectiveness of high-dose steroids (20-25 mg/kg methyl prednisolone) as first-line treatment in combination with PE therapy with the combination of standard-dose steroids (1 mg/kg methyl prednisolone) and PE in adult patients with TTP. Clinical, laboratory data and treatment outcomes such as response rate, median time to recovery and survival were evaluated retrospectively. Overall (OR) and complete (CR) response rates were 69 and 52% respectively. Similar response rates were found in patients treated with pulse or conventional dose steroids; however, the median time to response was delayed in the high-dose methyl prednisolone (HDP) group. The median time from the initiation of symptoms to initiation of treatment was approximately 15 days (range: 0-30). Delayed treatment in our patients because of delayed referral to our center resulted in poor response to treatment. In all, four of 14 (27%) complete responders experienced relapses. The predicted relapse rate was 48% at a median of 30 months. All the relapses presented with a combination of thrombocytopenia and microangiopathic hemolytic anemia. This analysis showed that high-dose steroid treatment did not prove to be beneficial for TTP patients as firstline therapy combined with PE. Moreover, pulse steroid interventions might have resulted in delayed responses and our data suggest that initiation of treatment with PE should not be delayed.