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Background: Brugada syndrome (BrS) is a cardiac arrhythmia disorder that causes sudden death in young adults. Rare genetic variants in the SCN5A gene encoding the Na v 1.5 sodium channel and common noncoding variants at this locus are robustly associated with the condition. BrS is particularly prevalent in Southeast Asia but the underlying ancestry-specific factors remain largely unknown., Methods: Genome sequencing of BrS probands and population-matched controls from Thailand was performed to identify rare noncoding variants at the SCN5A-SCN10A locus that were enriched in patients with BrS. A likely causal variant was prioritized by computational methods and introduced into human induced pluripotent stem cell (hiPSC) lines using CRISPR-Cas9. The effect of the variant on SCN5A expression and Na v 1.5 sodium channel current was then assessed in hiPSC-derived cardiomyocytes (hiPSC-CMs)., Results: A rare noncoding variant in an SCN5A intronic enhancer region was highly enriched in patients with BrS (detected in 3.9% of cases with a case-control odds ratio of 45.2). The variant affects a nucleotide conserved across all mammalian species and predicted to disrupt a Mef2 transcription factor binding site. Heterozygous introduction of the enhancer variant in hiPSC-CMs caused significantly reduced SCN5A expression from the variant-containing allele and a 30% reduction in Na v 1.5-mediated sodium current density compared with isogenic controls, confirming its pathogenicity. Patients with the variant had severe phenotypes, with 89% experiencing cardiac arrest., Conclusions: This is the first example of a functionally validated rare noncoding variant at the SCN5A locus and highlights how genome sequencing in understudied populations can identify novel disease mechanisms. The variant partly explains the increased prevalence of BrS in this region and enables the identification of at-risk variant carriers to reduce the burden of sudden cardiac death in Thailand.

Purpose: To compare AngioTool (AT) vascular parameters (VP) between MacTel2 eyes and normal eyes. Secondary outcome measures were to correlate VP with BCVA and to analyze VP between various grades of Simple MacTel Classification., Methods: This is a retrospective study. SD OCTA images of the superficial vascular complex (SVC) and deep capillary complex (DVC) were exported into Image J and AT. The explant area (EA), vessel area (VA), vessel percentage area (VPA), total number of junctions (TNJ), junction density (JD), total vessel length (TVL), average vessel length (AVL), total number of endpoints (TNE) and mean E lacunarity (MEL) were studied., Results: Group 1 had 120 MacTel2 eyes. Group 2 had 60 age-matched normal eyes. All VP were significantly different between the two groups except EA and TNE in both complexes. None of the VP had a correlation with BCVA. Interquadrant analysis (IQA) in SVC and DVC showed statistical significance in VPA, AVL and JD and in AVL, TNE, JD, VPA respectively. Post hoc analysis in SVC and DVC showed statistical significance in TNJ, JD, TVL and AVL between grade 1 and grade 3, and in VA, VPA, TNJ, JD, TVL and MEL between grade 0 and grade 3 respectively., Conclusion: VP were affected in MacTel2 eyes. VP did not correlate with BCVA. Occurrence of pigmentation is an important event in the progression of disease. AT may provide quantitative markers to measure disease progression., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

This research paper explores the impact of social media-based interventions on adolescent reproductive health education, acknowledging the digital residency of today's youth. Utilizing a Solomon Four Group Design, the study assesses the efficacy of tailored interventions on various digital platforms, emphasizing the value, impact, and relevance of innovative educational approaches, particularly those employed by social media. The paper highlights adolescents' pervasive presence on social media, including platforms such as Instagram, Twitter, and Facebook as integral components of their online experiences. Leveraging these platforms for health education is considered crucial, aligning with adolescents' digital behaviors and preferences. Ethical challenges in the digital health domain are discussed, underscoring the importance of privacy, consent, and responsible content creation. To tailor interventions effectively, the research explores platform-specific preferences, recognizing the diverse usage patterns among adolescents. The paper concludes with a comprehensive analysis of the intervention's impact, revealing significant improvements in reproductive health knowledge among participants exposed to social media-based education. In essence, the paper advocates for the integration of health education into the digital spaces where adolescents naturally reside, recognizing the transformative potential of social media in enhancing reproductive health knowledge., Cette étude examine l'impact des interventions en santé reproductive pour les adolescents basées sur les médias sociaux, tenant compte de la résidence numérique de la jeunesse d'aujourd'hui. En utilisant un modèle de conception à quatre groupes de Solomon, l'étude évalue l'efficacité des interventions personnalisées sur différentes plateformes numériques, mettant l'accent sur la valeur, l'impact et la pertinence des approches pédagogiques innovantes, en particulier celles utilisées par les médias sociaux. Le document met en évidence la présence omniprésente des adolescents sur les médias sociaux, y compris des plateformes telles qu'Instagram, Twitter et Facebook, en tant que composants intégraux de leurs expériences en ligne. L'utilisation de ces plates-formes pour l'éducation à la santé est considérée comme cruciale, s'alignant sur les comportements numériques et les préférences des adolescents. Les défis éthiques dans le domaine de la santé numérique sont discutés, soulignant l'importance de la confidentialité, du consentement et de la création responsable de contenu. Pour adapter efficacement les interventions, la recherche explore les préférences spécifiques à chaque plateforme, reconnaissant les différents schémas d'utilisation chez les adolescents. Le document se termine par une analyse complète de l'impact de l'intervention, révélant des améliorations significatives des connaissances en santé reproductive parmi les participants exposés à l'éducation basée sur les médias sociaux. En essence, le document plaide en faveur de l'intégration de l'éducation à la santé dans les espaces numériques où les adolescents résident naturellement, reconnaissant le potentiel transformateur des médias sociaux dans l'amélioration des connaissances en santé reproductive., Competing Interests: The Authors declared no conflict of interest, (African Journal of Reproductive Health © 2024.)

Statement of the Problem: The common causes of obstructive sleep apnea (OSA) are identified as anatomic and/or functional abnormality in the oral cavity, oropharynx, velopharynx, and hypopharynx leading to compromised airway space and increased collapsibility., Purpose: This study was conducted to evaluate the effect of implant-supported mandibular complete denture in improving the airway space among completely edentulous patients with OSA and compare it with conventional complete denture., Materials and Method: In this observational study, completely edentulous individuals were screened with snoring, tiredness, observed apnea, high blood pressure, body mass index, age, neck circumference, and gender (STOP-Bang) questionnaire to evaluate the incidence of OSA. Ten mild-moderate patients were included as study participants. Lateral cephalograms (L1) made at the edentulous state was considered baseline. They were rehabilitated with complete denture prosthesis. One week after denture insertion, two implants were placed in the edentulous mandibular arch. Delayed loading protocol was followed. Lateral cephalogram (L2) was made 6 months after complete denture insertion and 6 months after implant-supported prosthesis (L3). Cephalometric tracings were used to evaluate change in upper airway space (UAS), middle airway space (MAS), and lower airway space (LAS). Repeated measures ANOVA was used to evaluate statistical significance in the airway measurements made at the three intervals. Post hoc Tukey HSD and Bonferroni test were used to assess if the differences obtained were truly significant., Results: Statistical analysis revealed significant differences in UAS, MAS and LAS between L1, L2 and L3 ( p < 0.05). Post hoc Tukey HSD indicated that UAS increased significantly at all three intervals followed by LAS and MAS respectively (α=.05). Post hoc Bon-ferroni test indicated that implant-supported mandibular complete dentures had a significant improvement in airway space when compared to conventional complete dentures (α=.05)., Conclusion: Implant-supported mandibular complete denture could be effective in edentulous patients with mild-moderate OSA., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright: © Journal of Dentistry.)

The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom's 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia., (© 2022. The Author(s).)

Objective: Pulmonary hypoplasia is common in the perinatal period and causes death in newborn infants. It is commonly associated with a number of malformation syndromes. Various parameters are used to estimate pulmonary hypoplasia at fetal autopsy including Lung Weight Body Weight ratio (LW:BW), Radial Alveolar Count (RAC) and DNA estimation., Material and Method: This study was carried out as a retrospective analysis of 108 lung specimens of fetuses with congenital anomalies for a period of five years. All terminated fetuses with anomalies were received with 10% formalin. An inverted Y-shaped incision was made on the fetus to remove the lungs. Lung weight and body weight were measured and the ratio was calculated. Morphometric estimation of RAC was done microscopically by counting the number of alveoli using the Q capture software. RAC was calculated based on gestational age., Results: Among the restrictive lung diseases, pulmonary hypoplasia by the LW:BW ratio was prevalent in 43% while the same by RAC was 19%. Similarly, pulmonary hypoplasia by the LW:BW ratio was prevalent in 35% while the same by RAC was 26% among cases with non restrictive lung diseases. Oligohydramnios showed the highest prevalence of pulmonary hypoplasia (23.7%), followed by renal anomalies (16.9%) and CNS anomalies (15.2%)., Conclusion: Pulmonary hypoplasia is a common occurrence in many congenital anomalies, premature rupture of membranes, and hydrops fetalis. Identifying the anomaly during the intrauterine period will help to anticipate and accordingly manage the baby in the postpartum period. Early diagnosis of correctable condition like oligohydramnios will also help in the early intervention and prevention of pulmonary hypoplasia.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Cryopreservation of all embryos followed by transfer in subsequent cycles has emerged as an effective alternative to fresh embryo transfer (ET) in order to overcome the negative effect of superovulation on endometrial receptivity., Aims: The aim of this study was to compare the reproductive outcomes between fresh ET and first frozen ET (FET) from "freeze-all" group of embryos., Setting: This study was conducted at a private in vitro fertilization center., Design: This was a retrospective study., Patients and Methods: A total of 503 patients fulfilling the inclusion criteria between 2012 and 2017 were included. Of 503, 386 patients underwent fresh ET and 117 patients underwent FET following cryopreservation of all embryos. The results of only first FET were considered to eliminate the confounding factor of poor-quality embryos in subsequent transfer., Results: FET resulted in statistically significant higher live birth rate (44.44% vs. 33.41%), implantation rate (45.08% vs. 30.22%), and clinical pregnancy rate (57.26% vs. 38.6%) compared to fresh ETs. No difference was observed in the abortion rate between the two groups., Conclusion: Reproductive outcomes were significantly better in the freeze-all group compared to fresh ET suggesting that the altered hormone levels during controlled ovarian stimulation could mediate an asynchrony between the endometrium and the transferred embryos, leading to implantation failure., Competing Interests: There are no conflicts of interest., (Copyright: © 2019 Journal of Human Reproductive Sciences.)

Aim: To examine the impact of 4-nonylphenol (4-NP), on the expression of polycomb repressive complexes and cellular proliferation. Materials & methods: Cell proliferation assays, quantitative PCR, Western blotting, luciferase reporter assay, chromatin immunoprecipitation-quantitative PCR were used for the study. Results: The 4-NP at 100 nM concentration significantly increased proliferation of MCF-7 cells. It enhanced the expression of RNF2-BMI1 and EZH2-SUZ12 and concomitantly increased H2AK119ub1 and H3K27me3 repressive marks at p21 proximal promoter resulting in its reduced expression. Selective inhibition of RNF2 or EZH2 reverted the 4-NP action. The phospho-CREB, SP1 and E2F-1 are enriched at proximal promoter of RNF2 and EZH2 and cyclin D1, but not p21. Conclusion: The 4-NP-mediated upregulation of RNF2 and EZH2 resulted in epigenetic silencing of p21.

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Competing Interests: There are no conflicts of interest

Lung cancer has a relatively poor prognosis with a low survival rate and drugs that target other cell death mechanism like autophagy may help improving current therapeutic strategy. This study investigated the anti-proliferative effect of Licarin A (LCA) from Myristica fragrans in non-small cell lung cancer cell lines-A549, NCI-H23, NCI-H520 and NCI-H460. LCA inhibited proliferation of all the four cell lines in a dose and time dependent manner with minimum IC50 of 20.03 ± 3.12, 22.19 ± 1.37 µM in NCI-H23 and A549 cells respectively. Hence NCI-H23 and A549 cells were used to assess the ability LCA to induce autophagy and apoptosis. LCA treatment caused G1 arrest, increase in Beclin 1, LC3II levels and degradation of p62 indicating activation of autophagy in both NCI-H23 and A549 cells. In addition, LCA mediated apoptotic cell death was confirmed by MMP loss, increased ROS, cleaved PARP and decreased pro-caspase3. To understand the role of LCA induced autophagy and its association with apoptosis, cells were analysed following treatment with a late autophagy inhibitor-chloroquine and also after Beclin 1 siRNA transfection. Data indicated that inhibition of autophagy resulted in reduced anti-proliferative as well as pro-apoptotic ability of LCA. These findings confirmed that LCA brought about autophagy dependent apoptosis in non-small cell lung cancer cells and hence it may serve as a potential drug candidate for non-small cell lung cancer therapy.

Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery of extensive alternative splicing in diatoms, including intron retention and exon skipping, which increase the diversity of transcripts generated in changing environments. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genes. We show that the P. tricornutum genome is enriched in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of transposable elements such as SINE, MITE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Autophagy, or self-eating, is a catabolic process that plays a crucial role in cellular homeostasis by carrying out bulk degradation of defective or superfluous proteins as well as worn-out organelles through a specialized structure, the autophagosome, which in turn fuses with the lysosome. Autophagy also alleviates cellular stress induced by nutrient deprivation, metabolic disturbance, hypoxia, and the like, by recycling intracellular constituents. This role of autophagy, to provide metabolic precursors especially upon starvation, might also contribute to the survival of cancer cells. The role of autophagy in cancer cells is ambiguous given that its downregulation or upregulation has been observed to depend on cancer stage and pathological grade. Autophagy has been found to exhibit a dual effect on tumorigenesis where it functions to suppress tumor progression by eliminating factors that cause genome instability while promoting survival of cancer cells under unfavorable conditions like therapeutic stress. This review aims to explain the mechanism, regulation, and the dual role of autophagy in cancer.

Competing Interests: There are no conflicts of interest.

Fusarium culmorum is a soilborne fungal plant pathogen that causes foot and root rot and Fusarium head blight on small-grain cereals, in particular on wheat and barley. We report herein the draft genome sequence of a 1998 field strain called FcUK99 adapted to the temperate climate found in England., (Copyright © 2016 Urban et al.)

PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Unlabelled: Enterococcus faecalis is the most isolated or detected species from oral infections including marginal periodontitis, infected root canals, periradicular abscesses and also detected in cases of failed endodontic therapy. To prevent endodontic treatment failure irrigation is mandatory for the effective removal of smear layer, pulp tissue, and microorganisms. Cultivation and other traditional identification methods have been demonstrated to have several limitations when it comes to microbiological identification. Polymerase chain reaction was selected because it has an added advantage over traditional microbiological methods., Materials and Methods: Twenty single rooted premolars were taken were taken stored in 0.1% thymol solution at 4°C decoronated to obtain 12 mm length, teeth were autoclaved at 121°C, canals were instrumented up to 35k file (International Organization for Standardization). The samples were randomly divided into three groups Group I - 5.25% sodium hypochlorite (NaOCL) and 17% ethylenediaminetetraacetic acid (EDTA), Group - II 5.25% NaOCL and 2% chlorhexidine (CHX), Group III - 5.25% NaOCL and 17% EDTA and 2% CHX., Results: The results showed that Group III which is 5% NaOCl followed by 17% EDTA and followed by 2% CHX showed maximum antimicrobial activity in all the three different time intervals.

Background: Nanoparticles (Ag NPs) have recently received much attention for their possible applications in biotechnology and biomedical. However, little is known about the toxicity in reproductive organs of animal model following exposure to nanoparticles., Objective: This study therefore, tried to examine the effects of nanoparticles with a diameter range of 5-20 nm on the histology of the testis of wistar rats and correlate it with Transmission Electron Microscopy results., Materials and Methods: Sixteen wistar rats were randomly divided into two groups of 8 rats each. Each group received the following via gavage technique for 90 days: Control Group (Group-1)-tap water; Experimental group (Group 2) - nanoparticles (20ug/kg/day). After ninety days (chronic study), rats were sacrificed and testis tissues was processed for histology and transmission electron microscopic study., Results: There was significant difference between the observations of group-1 and group 2. The changes observed in the testis were disarray of the spermatogenic cells and disorientation of the testis. These changes were observed to have been disappearing from normal histological features. Detailed structural damages were observed with TEM analysis, such as depletion of germ cells, germinal cells necrosis, especially in spermatogonia and Leydig cells had an abnormal fibroblast-like appearance, abnormal space between neighboring sertoli cells, mitochondria, lost cristae and vacuolated (none energized) with those animals exposed to nanoparticles., Conclusion: It seems that nanoparticles have acute and significant effects on spermatogenesis and number of spermatogenic cells. More experimental investigations are necessary to elucidate better conclusion regarding the safety of nanoparticles on male reproduction system.

Cell adhesion molecules (CAMs) are important in prokaryotes and eukaryotes for cell-cell and cell-substratum interactions. The characteristics of adhesive proteins in the model diatom Phaeodactylum tricornutum were investigated by bioinformatic analysis and in vivo characterization. Bioinformatic analysis of the protein coding potential of the P. tricornutum genome used an amino-acid profile that we developed as a new system to identify uncharacterized or novel CAMs. Putative diatom CAMs were identified and seven were characterized in vivo, by generation of transgenic diatom lines overexpressing genes encoding C-terminal yellow fluorescent protein (YFP) fusion proteins. Three of these selected genes encode proteins with weak similarity to characterized proteins, a c-type lectin and two fasciclins, whereas the others are novel. The resultant cell lines were investigated for alterations in their adhesive ability. Whole cell-substratum adhesion strength was measured in a fully turbulent flow chamber, while atomic force microscopy was used to quantify the relative frequency of adhesion, as well as the length and strength of single molecules in the secreted mucilage. Finally, quartz crystal microbalance analysis characterized the visco-elastic properties and interaction of the mucilage-substratum interface. These combined studies revealed a range of phenotypes affecting adhesion, and led to the identification of candidate proteins involved in diatom adhesion. In summary, our study has for the first time combined bioinformatics and molecular physiological studies to provide new insights into diatom adhesive molecules., (© 2014 Phycological Society of America.)

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

Mesenteric lymphangiomas are uncommon benign lesions that usually occur in isolation but rarely may be associated with gastrointestinal (GI) malrotation. Malrotation may cause chronic and recurrent volvulus leading to chronic venous congestion and lymphatic engorgement. Interference with lymphatic drainage may result in formation of a lymphangioma or a chylous mesenteric cyst. In our case, mesenteric lymphangioma was present with partial malrotation of small and large bowel. There was no radiological and surgical evidence of volvulus, favouring the hypothesis that lymphangioma may be a primary congenital association of GI malrotation. Another interesting finding was the counter-clockwise twisting of the superior mesenteric vein around the superior mesenteric artery which has been reported only seven times in the literature.

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.

Over the last decades Phaeodactylum tricornutum has become a model to study diatom biology at the molecular level. Cells have the peculiarity to be pleiomorphic and it is thought that this character is triggered by culture conditions, although few quantitative studies have been performed and nothing is known at the molecular level. Our aim was to quantify the effect of growth conditions on cell morphology of different P. tricornutum strains by quantitative microscopy, cellular imaging, and non-targeted transcriptomics. We show that morphotype changes can be regulated by changing culture conditions, depending on the strain, and show a common trend of increased oval cell abundance as a response to stress. Examination of expressed sequence tags (ESTs) from triradiate cells infers the importance of osmoregulation in the maintenance of this morphotype, whereas ESTs derived from oval cells grown in hyposaline and low temperature conditions show a predominance of genes encoding typical components of stress pathways, especially in signaling, cell homeostasis and lipid metabolism. This work contributes to better understand the importance of the unique capability of morphotype conversion in P. tricornutum and its relevance in acclimation to changing environmental conditions., (Copyright © 2011 Elsevier GmbH. All rights reserved.)

• By comparative analyses we identify lineage-specific diversity in transcription factors (TFs) from stramenopile (or heterokont) genome sequences. We compared a pennate (Phaeodactylum tricornutum) and a centric diatom (Thalassiosira pseudonana) with those of other stramenopiles (oomycetes, Pelagophyceae, and Phaeophyceae (Ectocarpus siliculosus)) as well as to that of Emiliania huxleyi, a haptophyte that is evolutionarily related to the stramenopiles. • We provide a detailed description of diatom TF complements and report numerous peculiarities: in both diatoms, the heat shock factor (HSF) family is overamplified and constitutes the most abundant class of TFs; Myb and C2H2-type zinc finger TFs are the two most abundant TF families encoded in all the other stramenopile genomes investigated; the presence of diatom and lineage-specific gene fusions, in particular a class of putative photoreceptors with light-sensitive Per-Arnt-Sim (PAS) and DNA-binding (basic-leucine zipper, bZIP) domains and an HSF-AP2 domain fusion. • Expression data analysis shows that many of the TFs studied are transcribed and may be involved in specific responses to environmental stimuli. • Evolutionary and functional relevance of these observations are discussed.

Summary *Ten axenic cultures, referred to as Fibrocapsa japonica, were studied for their morphology, pigment composition, toxicity and phylogeny. *Morphologically, all 10 accessions were similar and displayed equivalent pigment contents. We identified chlorophylls a and c, beta-carotene and fucoxanthin as the dominant pigments, together with xanthophyll cycle carotenoids likely to be involved in photoprotection. *All 10 accessions caused brine shrimp, Artemia salina, mortality and displayed haemolytic and haemaglutination activities toward sheep erythrocytes. Our results indicate that haemaglutination activity is a key component of F. japonica toxicity. *Examination of a collection of F. japonica expressed sequence tags (ESTs) has led to the identification of candidate genes involved in F. japonica toxicity and/or growth control.

Background: Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes., Results: We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity., Conclusions: The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.