A multi-trait approach identified 7 novel genes for back pain.

Introduction: Back pain (BP) is a complex heritable trait with an estimated heritability of 40% to 60%. Less than half of this can be explained by known genetic variants identified in genome-wide association studies.

Objectives: We applied a powerful multi-trait and gene-based approach to association analysis of BP to identify novel genes associated with BP.

Cytogenetic features of intergeneric amphydiploids and genome-substituted forms of wheat.

Synthetic intergeneric amphydiploids and genome-substituted wheat forms are an important source for transferring agronomically valuable genes from wild species into the common wheat (Triticum aestivum L.) genome. They can be used both in academic research and for breeding purposes as an original material for developing wheat-alien addition and substitution lines followed by translocation induction with the aid of irradiation or nonhomologous chromosome pairing.

[Methylation of Long Noncoding RNA Genes SNHG6, SNHG12, and TINCR in Ovarian Cancer].

Ovarian cancer (OC) develops asymptomatically and escapes diagnosis until advanced stages, the feature contributing to a higher mortality rate. New prospects of OC diagnosis and treatment have been opened in studies of the gene regulation mechanisms that involve long noncoding RNAs (lncRNAs) and identification of the lncRNA genes that are inhibited via methylation of the promoter region. A set of 122 samples of primary OC tumors was examined by methylation specific real-time PCR to assess the methylation level of the lncRNA genes PLUT, SNHG1, SNHG6, SNHG12, and TINCR.

Understanding the Past to Preserve the Future: Genomic Insights Into the Conservation Management of a Critically Endangered Waterbird.

To ensure the success of genetic rescue, we must minimise the potential negative effects of outbreeding depression that may arise from selecting source populations. The difficulty in assessing the likelihood of outbreeding depression has hindered its consideration in endangered species conservation. However, genomic research offers feasible indications.

Amyloid Fibrils of the s36 Protein Modulate the Morphogenesis of Eggshell.

is the oldest classic model object in developmental genetics. It may seem that various structures of the fruit fly at all developmental stages have been well studied and described. However, recently we have shown that some specialized structures of the eggshell contain an amyloid fibril network.

GPU-accelerated Kendall distance computation for large or sparse data.

Background: Current experimental practices typically produce large multidimensional datasets. Distance matrix calculation between elements (e.g.

Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors.

We describe an effort ("Codebook") to determine the sequence specificity of 332 putative and largely uncharacterized human transcription factors (TFs), as well as 61 control TFs. Nearly 5,000 independent experiments across multiple and assays produced motifs for just over half of the putative TFs analyzed (177, or 53%), of which most are unique to a single TF. The data highlight the extensive contribution of transposable elements to TF evolution, both in and , and identify tens of thousands of conserved, base-level binding sites in the human genome.

Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.

A DNA sequence pattern, or "motif", is an essential representation of DNA-binding specificity of a transcription factor (TF). Any particular motif model has potential flaws due to shortcomings of the underlying experimental data and computational motif discovery algorithm. As a part of the Codebook/GRECO-BIT initiative, here we evaluated at large scale the cross-platform recognition performance of positional weight matrices (PWMs), which remain popular motif models in many practical applications.

Identification of methylation-sensitive human transcription factors using meSMiLE-seq.

Transcription factors (TFs) are key players in eukaryotic gene regulation, but the DNA binding specificity of many TFs remains unknown. Here, we assayed 284 mostly poorly characterized, putative human TFs using selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq), revealing 72 new DNA binding motifs. To investigate whether some of the 158 TFs for which we did not find motifs preferably bind epigenetically modified DNA (i.

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors.

A long-standing challenge in human regulatory genomics is that transcription factor (TF) DNA-binding motifs are short and degenerate, while the genome is large. Motif scans therefore produce many false-positive binding site predictions. By surveying 179 TFs across 25 families using >1,500 cyclic selection experiments with fragmented, naked, and unmodified genomic DNA - a method we term GHT-SELEX (Genomic HT-SELEX) - we find that many human TFs possess much higher sequence specificity than anticipated.

Extensive binding of uncharacterized human transcription factors to genomic dark matter.

Most of the human genome is thought to be non-functional, and includes large segments often referred to as "dark matter" DNA. The genome also encodes hundreds of putative and poorly characterized transcription factors (TFs). We determined genomic binding locations of 166 uncharacterized human TFs in living cells.

Climate Response and Radial Growth Dynamics of Pedunculate Oak ( L.) Plus Trees and Their Half-Sib Progeny in Periods of Severe Droughts in the Forest-Steppe Zone of Eastern Europe.

The dendrochronological parameters of 97 pedunculate oak ( L.) trees including 20 plus trees (142-year-old on average) and four half-sib families for four of them were analyzed considering also specifically years of the most severe droughts that were identified using average monthly air temperature and precipitation data. The tree-ring width (TRW) was mostly affected by air temperature that had the largest cross-dating indices (CDI), up to 78% maximum.

47f: Bioadaptation to Low Doses of Xenobiotics in Aquaculture.

Agricultural and industrial activities are increasing pollution of water bodies with low doses of xenobiotics that have detrimental effects on aquaculture. The aim of this work was to determine the possibility of using 47f culture in fish aquaculture under the influence of low doses of xenobiotics as an adaptogen. An increase in the survival of individuals exposed to the xenobiotic bisphenol A solution and fed with the 47f was shown compared to control groups and, at the same time, the cytokine profile in the intestinal tissues of was also investigated.

The Germline-Restricted Chromosome of Male Zebra Finches in Meiotic Prophase I: A Proteinaceous Scaffold and Chromatin Modifications.

Among eukaryotes, there are many examples of partial genome elimination during ontogenesis. A striking example of this phenomenon is the loss of entire avian chromosomes during meiosis, called a germline-restricted chromosome (GRC). The GRC is absent in somatic tissues but present in germ cells.

Analysis of the abundance and diversity of RNA secondary structure elements in RNA viruses using the RNAsselem Python package.

Recent advancements in experimental and computational methods for RNA secondary structure detection have revealed the crucial role of RNA structural elements in diverse molecular processes within living cells. It has been demonstrated that the secondary structure of the entire viral genome is often responsible for performing crucial functions in the viral life cycle and also influences virus evolution. To investigate the role of viral RNA secondary structure, alongside experimental techniques, the use of bioinformatics tools is important for analyzing various secondary structure patterns, including hairpin loops, internal loops, multifurcations, external loops, bulges, stems, and pseudoknots.

A new cancer/testis long noncoding RNA, the OTP-AS1 RNA.

The orthopedia homeobox (OTP) gene encodes a homeodomain-containing transcription factor involved in brain development. OTP is mapped to human chromosome 5q14.1.

Ten Hypermethylated lncRNA Genes Are Specifically Involved in the Initiation, Progression, and Lymphatic and Peritoneal Metastasis of Epithelial Ovarian Cancer.

Our work aimed to evaluate and differentiate the role of ten lncRNA genes (, , , , , , , , , and ) in the development and progression of epithelial ovarian cancer (EOC). A representative set of clinical samples was used: 140 primary tumors from patients without and with metastases and 59 peritoneal metastases. Using MS-qPCR, we demonstrated an increase in methylation levels of all ten lncRNA genes in tumors compared to normal tissues ( < 0.

Initial WNT/β-Catenin or BMP Activation Modulates Inflammatory Response of Mesodermal Progenitors Derived from Human Induced Pluripotent Stem Cells.

Wound healing in adults largely depends on the functional state of multipotent mesenchymal stromal cells (MSCs). Human fetal tissues at the early stages of development are known to heal quickly with a full-quality restoration of the original structure. The differences in the molecular mechanisms that determine the functional activity of mesodermal cells in fetuses and adults remain virtually unknown.

SpliceMutr Enables Pan-Cancer Analysis of Splicing-Derived Neoantigen Burden in Tumors.

SpliceMutr shows that splicing antigenicity changes in response to ICI therapies and that native modulation of the splicing machinery through mutations increases the contribution of splicing to the neoantigen load of some The Cancer Genome Atlas cancer subtypes. Future studies of the relationship between splicing antigenicity and immune checkpoint inhibitor response pan-cancer are essential to establish the interplay between antigen heterogeneity and immunotherapy regimen on patient response.

The Association of the Oral Microbiota with Cognitive Functioning in Adolescence.

: A growing body of research supports the role of the microbial communities residing in the digestive system in the host's cognitive functioning. Most of these studies have been focused on the gut microbiome and its association with clinical phenotypes in middle-aged and older adults. There is an insufficiency of population-based research exploring the association of normative cognitive functioning with the microbiome particularly with the oral microbiota.