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Bioinformatics Research

14:46 EST 12th December 2018 | BioPortfolio

Integrative analysis of DNA methylation and gene expression identify a six epigenetic driver signature for predicting prognosis in hepatocellular carcinoma.

DNA methylation is a crucial regulator of gene transcription in the etiology and pathogenesis of hepatocellular carcinoma (HCC). Thus, it is reasonable to identify DNA methylation-related prognostic markers. Currently, we aimed to make an integrative epigenetic analysis of HCC to identify the effectiveness of epigenetic drivers in predicting prognosis for HCC patients. By the software pipeline TCG...

The 3D Cancer Nucleus.

Research into the three-dimensional (3D) organization of the cancer cell genome started over 100 years ago. We follow an exciting avenue of research in this field, from Hansemann's early observations of aberrant mitoses and nuclei in cancer cells in the late 19 century to Boveri's theory of the cancer cell in the early 20 century, to current views of nuclear organization and its changes in cancer....

Cucumis metuliferus reduces Meloidogyne incognita virulence against the Mi1.2 resistance gene in a tomato-melon rotation sequence.

The susceptible tomato cv. Durinta, ungrafted or grafted onto cv. Aligator resistant rootstock, both followed by the susceptible melon cv. Paloma, ungrafted or grafted onto Cucumis metuliferus BGV11135, and in reverse order, were cultivated from 2015 to 2017 in the same plots in a plastic greenhouse, infested or not with Meloidogyne incognita. For each crop, the soil nematode densities, galling in...

Heart transplantation in two adolescents with Danon disease.

Danon disease (DD) is an X-linked dominant disorder caused by a mutation in the lysosomal-associated membrane protein-2 (LAMP-2) gene coding for the LAMP-2 protein. We report two cases of successful heart transplantation (HT) in adolescent brothers with DD, including one who was bridged to HT for 34 days with a HeartWare left ventricular assist device. In both patients, the post-transplant course...

Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation.

Despite decades of studies meant to analyse the bacterial response to carbon limitation, we still miss a high-resolution overview of the situation. All gene expression changes observed in such conditions cannot solely be accounted for by the global regulator Crp either free or bound to its effector, cyclic AMP. Here, for the first time, we evaluated the response of both CDS (protein-coding sequenc...

Time-resolved Interaction Proteomics of the GIGANTEA Protein Under Diurnal Cycles in Arabidopsis.

The plant-specific protein GIGANTEA (GI) controls many developmental and physiological processes, mediating rhythmic post-translational regulation. GI physically binds several proteins implicated in the circadian clock, photoperiodic flowering, and abiotic stress responses. To understand GI's multifaceted function, we aimed to comprehensively and quantitatively identify potential interactors of GI...

Gene-environment interactions and colorectal cancer risk: an umbrella review of systematic reviews and meta-analyses of observational studies.

The cause of colorectal cancer (CRC) is multifactorial, involving both genetic variants and environmental risk factors. We systematically searched the MEDLINE, EMBASE, China National Knowledge Infrastructure (CNKI) and Wanfang databases from inception to December 2016, to identify systematic reviews and meta-analyses of observational studies that investigated gene-environment (G × E) interact...

Multiple factors bias chromosome micronucleation.

Chromatin dynamics governed by a set of nuclear structural proteins.

During the past three decades, the study of nuclear and chromatin organization has become of great interest. The organization and dynamics of chromatin are directly responsible for many functions including gene regulation, genome replication, and maintenance. In order to better understand the details of these mechanisms, we need to understand the role of specific proteins that take part in these p...

Tamoxifen therapy benefit predictive signature combining with prognostic signature in surgical-only ER-positive breast cancer.

Tamoxifen treatment is important assistant for estrogen-receptor-positive breast cancer (BRCA) after resection. This study aimed to identify signatures for predicting the prognosis of patients with BRCA after tamoxifen treatment. Data of gene-specific DNA methylation (DM), as well as the corresponding clinical data for the patients with BRCA, were obtained from The Cancer Genome Atlas and followed...

Developing a highly efficient and wildly adaptive CRISPR-SaCas9 toolset for plant genome editing.

The CRISPR- Streptococcus pyogenes Cas9 (SpCas9) system offers a rapid, simple and flexible genome editing approach. However, the targeting scope of the SpCas9 system is limited by the canonical NGG PAM. To broaden the editing range of the CRISPR system, several Cas orthologs recognized different PAM were isolated from diverse microbes and were engineered as powerful genome editing tools in eukary...

Draft genome sequence of Candida versatilis and osmotolerance ability analysis in soy sauce fermentation.

The salt tolerant yeast strain C.versatilis usually is added in the high-salt liquid-state soy sauce fermentation. The genome of C.versatilis was sequenced in our previous study, but the reason of high-osmolarity ability was not clear.

YHp as a highly stable, hyper-copy, hyper-expression plasmid constructed using a full 2 μm circle sequence in cir0 strains of Saccharomyces cerevisiae.

In the yeast Saccharomyces cerevisiae, the plasmid YEp, containing a partial sequence from a natural 2 μm plasmid, has been frequently used to induce high levels of gene expression. In this study, we used Japanese sake yeast natural cir0 strain as a host for constructing an entire 2 μm plasmid with an expression construct using the three-fragment gap-repair method without Escherichia coli manipu...

Whole-genome sequencing for combatting antibiotic resistance.

An Updated Gene Atlas for Maize Reveals Organ-Specific and Stress-Induced Genes.

Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genoty...

Scavager: a versatile postsearch validation algorithm for shotgun proteomics based on gradient boosting.

Shotgun proteomics workflows for database protein identification typically include a combination of search engines and postsearch validation software based mostly on machine learning algorithms. Here we present a new postsearch validation tool called Scavager employing CatBoost, an open-source gradient boosting library, which shows improved efficiency compared with the other popular algorithms, su...

Linear mixed models for association analysis of quantitative traits with next-generation sequencing data.

We develop linear mixed models (LMMs) and functional linear mixed models (FLMMs) for gene-based tests of association between a quantitative trait and genetic variants on pedigrees. The effects of a major gene are modeled as a fixed effect, the contributions of polygenes are modeled as a random effect, and the correlations of pedigree members are modeled via inbreeding/kinship coefficients. -stati...

Putative contributions of the sex chromosome proteins SOX3 and SRY to neurodevelopmental disorders.

The male-biased prevalence of certain neurodevelopmental disorders and the sex-biased outcomes associated with stress exposure during gestation have been previously described. Here, we hypothesized that genes distinctively targeted by only one or both homologous proteins highly conserved across therian mammals, SOX3 and SRY, could induce sexual adaptive changes that result in a differential risk f...

Pharmacogenetics of angiotensin converting enzyme inhibitor - induced angioedema.

Angioedema is a rare adverse effect of the commonly used angiotensin converting enzyme inhibitors (ACEi) and is reported to occur with a prevalence of 0.1 - 0.7%. Although most ACEi-induced angioedema (ACEi-A) cases are mild, severe cases requiring intensive care and even resulting in death have been reported in the literature. The mechanisms underlying ACEi-A are not yet fully understood, but bra...

Genes known to escape X chromosome inactivation predict co-morbid chronic musculoskeletal pain and posttraumatic stress symptom development in women following trauma exposure.

Co-morbid chronic musculoskeletal pain (CMSP) and posttraumatic stress symptoms (PTSS) are frequent sequelae of motor vehicle collision, are associated with greater disability than either outcome alone, and are more prevalent in women than men. In the current study we assessed for evidence that gene transcripts originating from the X chromosome contribute to sex differences in vulnerability to CMS...

Initiation and Evolution of Early Onset Prostate Cancer.

In this issue of Cancer Cell, Gerhauser et al. analyze early-onset prostate cancers, showing roles for androgen receptor-driven rearrangements, an early APOBEC-driven mutational mechanism, and ESRP1 gene duplication. Through integration of whole-genome, transcriptome, and methylome data, they identify high-risk subgroups and develop an algorithm that may predict molecular evolution.

Genetic loss of proadrenomedullin N-terminal 20 peptide (PAMP) in mice is compatible with survival.

Adrenomedullin (AM) and proadrenomedullin N-terminal 20 peptide (PAMP) are small peptides derived from a common precursor, pre-proadrenomedullin. Although AM and PAMP share hypotensive effects in the cardiovascular system, the peptides also exert diverse and distinct effects on endocrine physiology, innate immunity, cytoskeletal biology and receptor signaling pathways. Tremendous knowledge has bee...

Allogeneic hematopoietic stem cell transplantation, especially haploidentical HSCT, may improve long-term survival for high-risk pediatric patients with Philadelphia chromosome-positive acute lymphoblastic leukemia in the tyrosine kinase inhibitor era.

The role of allogeneic hematopoietic stem cell transplantation (allo-HSCT), particularly haploidentical (haplo)-HSCT, in pediatric patients with Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ALL) in the tyrosine kinase inhibitor (TKI) era is unclear. This study aimed to identify prognostic factors and explore the role of haplo-HSCT in the treatment of Ph+ALL in the TKI era.

Cre-miR914-regulated RPL18 is involved with UV-B adaptation in Chlamydomonas reinhardtii.

UV radiation is a serious threat to life, and algae have developed highly efficient adaptations to UV radiation through the course of evolution. To date, studies investigating the mechanisms of UV adaptation in algae have focused on physiological regulation and associated protein coding genes, with only a few reports on associated protein non-coding genes. In a previous study, we found that Cre-mi...

Silurana Chromosomal Evolution: A New Piece to the Puzzle.

The African clawed frogs of the subgenus Silurana comprise both diploid and tetraploid species. The root of the polyploidization event leading to the extant Xenopus calcaratus, X. mellotropicalis, and X. epitropicalis is not fully understood so far. In X. mellotropicalis, we previously proposed 2 evolutionary scenarios encompassing complete (scenario A) or incomplete (scenario B) translocation of ...

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