Host cell traversal is important for progression of the malaria parasite through the dermis to the liver

The malaria sporozoite, the parasite stage transmitted by the mosquito, is delivered into the dermis and differentiates in the liver. Motile sporozoites can invade host cells by disrupting their plasma membrane and migrating through them (termed cell traversal), or by forming a parasite-cell junction and settling inside an intracellular vacuole (termed cell infection). Traversal of liver cells, observed for sporozoites in vivo, is thought to activate the sporozoite for infection of a final hepatocyte. Here, using Plasmodium berghei, we show that cell traversal is important in the host dermis for preventing sporozoite destruction by phagocytes and arrest by nonphagocytic cells. We also show that cell infection is a pathway that is masked, rather than activated, by cell traversal. We propose that the cell traversal activity of the sporozoite must be turned on for progression to the liver parenchyma, where it must be switched off for infection of a final hepatocyte.Inst Pasteur, Unite Biol & Genet Paludisme, F-75724 Paris 15, FranceUniversidade Federal de São Paulo, Dept Bioquim, BR-04044020 São Paulo, BrazilUniv Montpellier 2, CNRS, UMR 5539, F-34095 Montpellier 05, FranceMie Univ, Sch Med, Tsu, Mie 5140001, JapanUniversidade Federal de São Paulo, Dept Bioquim, BR-04044020 São Paulo, BrazilWeb of Scienc

Bunje (Novo Selo, Croatie)

Introduction Le chantier de Bunje sur l’île de Brač constitue la première étape d’un programme portant sur les villae de l’Adriatique orientale, conduit par E. Botte, A. Bertrand et K. Jelinčić et intitulé « Recherches sur l’exploitation économique de la Dalmatie à l’époque romaine (IIe s. av. J.-C. – IIe s. apr. J.‑C.) ». L’intention des auteurs de ce projet est de mesurer, à travers des opérations de fouilles et de prospections, l’impact économique de la présence romaine en Dalmatie. La pr..

CDG: an online server proposing biologically closest disease-causing genes and pathologies and its application to primary immunodeficiency

Summary: In analyses of exome data, candidate gene selection can be challenging in the absence of variants in known disease-causing genes. We calculated the putative biologically closest known disease-causing genes for 13,005 human genes not currently reported to be disease-causing. We used these data to construct the Closest Disease-Causing Genes (CDG) server, which can be used to infer the closest associated disease-causing genes and phenotypes for lists of candidate genes. This resource will be a considerable asset for ascertaining the poten-tial relevance of lists of genes to specific diseases of interest

Whole-exome sequencing-based discovery of STIM1 deficiency in a child with fatal classic Kaposi sarcoma

Whole-exome sequencing reveals a homozygous splice-site mutation in the gene encoding STIM1 in a child with classic Kaposi sarcoma

SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data

Human whole-genome-sequencing reveals about 4 000 000 genomic variants per individual. These data are mostly stored as VCF-format files. Although many variant analysis methods accept VCF as input, many other tools require DNA or protein sequences, particularly for splicing prediction, sequence alignment, phylogenetic analysis, and structure prediction. However, there is no existing webserver capable of extracting DNA/protein sequences for genomic variants from VCF files in a user-friendly and efficient manner. We developed the SeqTailor webserver to bridge this gap, by enabling rapid extraction of (i) DNA sequences around genomic variants, with customizable window sizes and options to annotate the splice sites closest to the variants and to consider the neighboring variants within the window; and (ii) protein sequences encoded by the DNA sequences around genomic variants, with built-in SnpEff annotator and customizable window sizes. SeqTailor supports 11 species, including: human (GRCh37/GRCh38), chimpanzee, mouse, rat, cow, chicken, lizard, zebrafish, fruitfly, Arabidopsis and rice. Standalone programs are provided for command-line-based needs. SeqTailor streamlines the sequence extraction process, and accelerates the analysis of genomic variants with software requiring DNA/protein sequences. It will facilitate the study of genomic variation, by increasing the feasibility of sequence-based analysis and prediction. The SeqTailor webserver is freely available at http://shiva.rockefeller.edu/SeqTailor/

Genome-wide detection of human variants that disrupt intronic branchpoints

The search for candidate variants underlying human disease in massive parallel sequencing data typically focuses on coding regions and essential splice sites, mostly ignoring noncoding variants. The RNA spliceosome recognizes intronic branchpoint (BP) motifs at the beginning of splicing and operates mostly within introns to define the exon-intron boundaries; however, BP variants have been paid little attention. We established a comprehensive genome-wide database and knowledgebase of BP and developed BPHunter for systematic and informative genome-wide detection of intronic variants that may disrupt BP and splicing, together with an effective strategy for prioritizing BP variant candidates. BPHunter not only constitutes an important resource for understanding BP, but should also drive discovery of BP variants in human genetic diseases and traits. Pre-messenger RNA splicing is initiated with the recognition of a single-nucleotide intronic branchpoint (BP) within a BP motif by spliceosome elements. Forty-eight rare variants in 43 human genes have been reported to alter splicing and cause disease by disrupting BP. However, until now, no computational approach was available to efficiently detect such variants in massively parallel sequencing data. We established a comprehensive human genome-wide BP database by integrating existing BP data and generating new BP data from RNA sequencing of lariat debranching enzyme DBR1-mutated patients and from machine-learning predictions. We characterized multiple features of BP in major and minor introns and found that BP and BP-2 (two nucleotides upstream of BP) positions exhibit a lower rate of variation in human populations and higher evolutionary conservation than the intronic background, while being comparable to the exonic background. We developed BPHunter as a genome-wide computational approach to systematically and efficiently detect intronic variants that may disrupt BP recognition. BPHunter retrospectively identified 40 of the 48 known pathogenic BP variants, in which we summarized a strategy for prioritizing BP variant candidates. The remaining eight variants all create AG-dinucleotides between the BP and acceptor site, which is the likely reason for missplicing. We demonstrated the practical utility of BPHunter prospectively by using it to identify a novel germline heterozygous BP variant of STAT2 in a patient with critical COVID-19 pneumonia and a novel somatic intronic 59-nucleotide deletion of ITPKB in a lymphoma patient, both of which were validated experimentally. BPHunter is publicly available from an

Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency

Life-threatening pulmonary influenza can be caused by inborn errors of type I and III IFN immunity. We report a 5-yr-old child with severe pulmonary influenza at 2 yr. She is homozygous for a loss-of-function IRF9 allele. Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-α2b. The transcriptome induced by IFN-α2b in the patient's cells is much narrower than that of control cells; however, induction of a subset of IFN-stimulated gene transcripts remains detectable. In vitro, the patient's cells do not control three respiratory viruses, influenza A virus (IAV), parainfluenza virus (PIV), and respiratory syncytial virus (RSV). These phenotypes are rescued by wild-type IRF9, whereas silencing IRF9 expression in control cells increases viral replication. However, the child has controlled various common viruses in vivo, including respiratory viruses other than IAV. Our findings show that human IRF9- and ISGF3-dependent type I and III IFN responsive pathways are essential for controlling IAV

Genome-wide detection of human intronic AG-gain variants located between splicing branchpoints and canonical splice acceptor sites

Human genetic variants that introduce an AG into the intronic region between the branchpoint (BP) and the canonical splice acceptor site (ACC) of protein-coding genes can disrupt pre-mRNA splicing. Using our genome-wide BP database, we delineated the BP-ACC segments of all human introns and found extreme depletion of AG/YAG in the [BP+8, ACC-4] high-risk region. We developed AGAIN as a genome-wide computational approach to systematically and precisely pinpoint intronic AG-gain variants within the BP-ACC regions. AGAIN identified 350 AG-gain variants from the Human Gene Mutation Database, all of which alter splicing and cause disease. Among them, 74% created new acceptor sites, whereas 31% resulted in complete exon skipping. AGAIN also predicts the protein-level products resulting from these two consequences. We performed AGAIN on our exome/genomes database of patients with severe infectious diseases but without known genetic etiology and identified a private homozygous intronic AG-gain variant in the antimycobacterial gene SPPL2A in a patient with mycobacterial disease. AGAIN also predicts a retention of six intronic nucleotides that encode an in-frame stop codon, turning AG-gain into stop-gain. This allele was then confirmed experimentally to lead to loss of function by disrupting splicing. We further showed that AG-gain variants inside the high-risk region led to misspliced products, while those outside the region did not, by two case studies in genes STAT1 and IRF7. We finally evaluated AGAIN on our 14 paired exome-RNAseq samples and found that 82% of AG-gain variants in high-risk regions showed evidence of missplicing

The adoption of open access scholarly communication in Tanzanian public universities: some Influencing factors

Open access is a means for free availability of scholarly content via the internet. It is an emerging opportunity for wider and unlimited access to scholarly literature. Scholarly communication, through open access journals and self-arching, are the two main approaches of open access publishing. However, this mode of scholarly communication is not widely utilised in developing countries such as Tanzania. This article discusses the factors that influence the adoption of open access for scholarly communication in Tanzanian public universities, based on a study conducted in 2008 using a survey questionnaire. A sample of 544 researchers, selected through stratified random sampling from a population of 1 088 researchers and 69 policymakers at six public universities in Tanzania, provided their views. It was evident from the findings that researchers’ internet usage skills and self-efficacy, social influence, performance expectancy, effort expectancy, and the respondents’ general perceptions about open access were the positive factors likely to facilitate open access adoption. The current poor research conditions and researchers’ low internet self-efficacy (such as inadequate information search skills) were cited as the main hindrances for researchers to use open access outlets to access scholarly content. It is therefore recommended that university policies on scholarly communication should be revised to incorporate the use of open access publishing. Furthermore, universities should accelerate the establishment of institutional repositories, advocacy campaigns and training directed at researchers, policymakers, readers and information managers of scholarly content, and the improvement of internet speed through subscription to more bandwidth, so as to meet the demand from the scholarly communit