DNA Sequence Research Articles

InDel mutations within the bovine PER2 gene are significantly associated with reproductive traits.

Functioning as a key regulator of circadian rhythms, the PER2 gene exerts a substantial impact on the reproductive traits of animals. However, the effect of the PER2 gene on ovarian development remains unclear. In order to examine the relationship between bovine reproductive trait and the PER2 gene, a total of 901 ovarian samples were collected, categorized into different oestrus cycles (proestrus, oestrus, post-oestrus, anoestrous), and subjected to analysis for two potential insertion/deletions (InDels) in the PER2 gene. Through agarose gel electrophoresis and DNA sequencing, two polymorphic deletion mutations (P2-D5-bp, P3-D13-bp) were identified. Furthermore, a significant association between mature follicle diameter and P2-D5-bp was found (P < 0.05). Additionally, several significant correlations with ovarian length, width, height, and white body diameter were found for P3-D13-bp (P < 0.05). These findings suggested that the bovine PER2 gene plays an important role in above-mentioned reproductive traits, offering new avenues for improving cow fertility through marker-assisted selection (MAS).

Evidence for the Contribution of the miR-206/BDNF Pathway in the Pathophysiology of Depression.

Depression is a complex disorder with substantial impacts on individual health and has major public health implications. Depression results from complex interactions between genetic and environmental factors. Epigenetic mechanisms, including DNA methylation (DNAm), microRNAs (miRNAs), and histone modifications, can produce heritable phenotypic changes without a change in DNA sequence and have been recently proven to mediate lasting increases in the risk of depression following exposure to adverse life events. Of these, miRNAs are gaining attention for their role in the pathogenesis of many stress-associated mental disorders, including depression. One such miRNA is microRNA-206 (miR-206), which is a critical candidate for increasing the susceptibility to stress. Although miR-206 is thought to be a typical muscle-specific miRNA, it is expressed throughout the brain, particularly in the hippocampus and prefrontal cortex (PFC). Until now, only a few studies have been conducted on rodents to understand its role in stress-related abnormalities in neurogenesis. However, the precise underlying molecular mechanism of miR-206-mediated depression-like behaviours remains largely unknown. Here, we reviewed recent advances in the field of biomedical and clinical research on the role of miR-206 in the pathogenesis of depression from studies using different tissues and various experimental designs, and described how abnormalities in miR-206 expression in these tissues can affect neuronal functions. Moreover, we focused on studies investigating the brain-derived neurotrophic factor (BDNF) as a functional target of miR-206, where miR-206 has been implicated in the pathogenesis of depression by suppressing the expression of the BDNF. In summary, these studies confirm the existence of a tight correlation between the pathogenesis of depression and the miR-206/BDNF pathway.

RFLP-kenzy: a new bioinformatics tool for in silico detection of key restriction enzyme in RFLP technique

Abstract Background Today, several bioinformatics tools are available for analyzing restriction fragment length data. RFLP-kenzy is a new bioinformatic tool for identifying restriction key enzyme that cut at least 1 sequence and a maximum of n-1 sequence. Results This bioinformatic tool helps researchers to select appropriate enzymes that yield different RFLP patterns, especially from overly identical sequences with single nucleotide mutation or other small variations. By using RFLP-kenzy, multiple DNA sequences could be analyzed simultaneously and the key enzymes list is provided. The present paper also demonstrates the ability of RFLP-kenzy to identify the key enzymes through the analysis of 16S rRNA sequences and the complete genome of various genera of microorganisms. Conclusion From the results, several key enzymes were provided indicating the importance of this new tool in the selection of appropriate restriction enzymes.

Relevance of Infertility, Epigenetics, Nutrient, and Bioactive Components: A Review of the Literature

Background: This review discusses epigenetic mechanisms and the relationship of infertility in men and women in relation to parameters pertaining to nutrition. Methods: A review of the line of the literature was conducted prior to June 2021 through the selected websites, including MEDLINE, Embase, Web of Science, www.ClinicalTrials.gov, Cochrane Central, PubMed, Google Scholar, Science Direct, and the WHO. Results: The prevalence of infertility worldwide is 8-12%, and one out of every 8 couples receives medical treatment. Epigenetic mechanisms, aging, environmental factors, dietary energy and nutrients and non-nutrient compounds; more or less energy intake, and methionine play a role in the onset of infertility. Furthermore, more factors that contribute to infertility include the vitamins B12, D, and B6, biotin, choline, selenium, zinc, folic acid, resveratrol, quercetin, and others.. Discussion: To understand the molecular mechanisms regulating the expression of genes that affect infertility, the environment, the role of genotype, age, health, nutrition, and changes in the individual's epigenotype must first be considered. This will pave the way for the identification of the unknown causes of infertility. Insufficient or excessive intake of energy and certain macro and micronutrients may contribute to the occurrence of infertility as well. In addition, it is reported that 5-10% of body weight loss, moderate physical activity and nutritional interventions for improvement in insulin sensitivity contribute to the development of fertility. Conclusion: Epigenetic processes involve inherited changes but not encoded by the DNA sequence itself. Nutrition is thought to affect the epigenetic mechanisms that play a role in the pathogenesis of many diseases, including infertility. Epigenetic mechanisms of individuals with infertility are different from healthy individuals. Infertility is associated with epigenetic mechanisms, nutrients, bioactive components and numerous other factors.

Strategies to Overcome Antimicrobial Resistance in Nosocomial Infections, A Review and Update.

Nosocomial infections, also known as healthcare-associated infections, are a significant global concern due to their strong association with high mortality and morbidity in both developed and developing countries. These infections are caused by a variety of pathogens, particularly the ESKAPE group of bacteria, which includes the six pathogens Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These bacteria have demonstrated noteworthy resistance to different antibiotics. Antimicrobial resistance mechanisms can manifest in various forms, including restricting drug uptake, modifying drug targets, inactivating drugs, active drug efflux, and biofilm formation. Accordingly, various strategies have been developed to combat antibiotic-resistant bacteria. These strategies encompass the development of new antibiotics, the utilization of bacteriophages that specifically target these bacteria, antimicrobial combination therapy and the use of peptides or enzymes that target the genomes or essential proteins of resistant bacteria. Among promising approaches to overcome antibiotic resistance, the CRISPR/Cas system stands out and offers many advantages. This system enables precise and efficient editing of genetic material at specific locations in the genome. Functioning as a bacterial "adaptive immune system," the CRISPR/Cas system recognizes, degrades, and remembers foreign DNA sequences through the use of spacer DNA segments that are transcribed into CRISPR RNAs (crRNA). This paper has focused on nosocomial infections, specifically the pathogens involved in hospital infections, the mechanisms underlying bacterial resistance, and the strategies currently employed to address this issue. Special emphasis has been placed on the application of CRISPR/Cas technology for overcoming antimicrobial resistance.

Proof of ssDNA degraded from dsDNA for ET recombination

The widely used ET recombination requires an ssDNA product degraded by Rac phage protein E588 from dsDNA for strand invasion. However, proof of the ssDNA product is still elusive. The study provided three levels of proof sequentially. The probable ssDNAs degraded by E588 from the fluorescent plus-, minus-, or double-stranded dsDNA pET28a-xylanase exhibited a half fluorescence intensity of the corresponding dsDNAs, equivalent to the E588 degradation nucleotides half that of the total nucleotides degraded from the corresponding dsDNA. The ssDNA product degraded by E588 from the fluorescent minus-stranded dsDNA was confirmed by gradient gel-electrophoresis and two nuclease degradation reactions. Degraded by E588 from the dsDNA pET28a-xylanase that had a phosphorothioated plus-stranded 5′-terminus, the plus-stranded ssDNA product was separated via gel electrophoresis and recovered via a DNAclean kit. The recovered ssDNA product was proven to have intact 5′- and 3′-ends by DNA sequencing analysis. This study provides a solid foundation for the mechanism of ssDNA invasion.

Microbial populations vary between the upper and lower respiratory tract, but not within biogeographic regions of the lung of healthy horses

Understanding normal microbial populations within areas of the respiratory tract is essential, as variable regional conditions create different niches for microbial flora, and proliferation of commensal microbes likely contributes to clinical respiratory disease. The objective was to describe microbial population variability between respiratory tract locations in healthy horses. Samples were collected from four healthy adult horses by nasopharyngeal lavage (NPL), transtracheal aspirate (TTA), and bronchoalveolar lavage (BAL) of six distinct regions within the lung. Full-length 16S ribosomal DNA sequencing and microbial profiling analysis was performed. There was a large amount of diversity, with over 1797 ASVs identified, reduced to 94 taxa after tip agglomeration and prevalence filtering. Number of taxa and diversity were highly variable across horses, sample types, and BAL locations. Firmicutes, proteobacteria, and actinobacteria were the predominant phyla. There was a significant difference in richness (Chao1, p=0.02) and phylogenetic diversity (FaithPD, p = 0.01) between NPL, TTA, and BAL. Sample type (p=0.03) and horse (p=0.005) contributed significantly to Bray-Curtis compositional diversity, while Weighted Unifrac metric was only affected by simplified sample type (NPL and TTA vs BAL, p=0.04). There was no significant effect of BAL locations within the lung with alpha or beta diversity statistical tests. Overall findings support diverse microbial populations that were variable between upper and lower respiratory tract locations, but with no apparent difference in microbial populations of the six biogeographic regions of the lung, suggesting that BAL fluid obtained blindly by standard clinical techniques may be sufficient for future studies in healthy horses.

Modulation of dynamic DNA G-quadruplex structures in the hTERT promoter region by ligands.

Small molecules can inhibit cellular processes such as replication and transcription by binding to the promoter regions that are prone to form G-quadruplexes. However, since G-quadruplexes exist throughout the human genome, the G-quadruplex binders suffer from specificity issues. To tackle this problem, a G-quadruplex binder (Pyridostatin, or PDS) is conjugated with a ligand (Polyamide, or PA) that can specifically recognize DNA sequences flanking the G-quadruplex forming region. The binding mechanism of this hybrid ligand to the hTERT promoter region (hTERT 5-12) is then elucidated using optical tweezers. During mechanical unfolding processes, different intermediate structures of hTERT 5-12 in presence of PDS, PA, or PA-PDS conjugateare observed. These intermediate structures are consistent with two folding patterns of G-quadruplexes in the hTERT 5-12 fragment. While the duplex DNA binder PA facilitates the folding of a hairpin-G-quadruplex structure, the PDS assists the formation of two tandem G-quadruplexes. Both replication stop assay in vitro and dual luciferase assay in vivo established the effectiveness of the PA-PDS conjugate for hTERT 5-12 targeting. We expect such a ligand dependent folding dynamics will provide guidelines to the development of drugs that not only target hTERT expressions, but also other oncogenes via interactions with specific G-quadruplex structures formed in their promotor regions.

DNA sequences alignment method using sparse index on pan-genome graph.

The graph of sequences represents the genetic variations of pan-genome concisely and space-efficiently than multiple linear reference genome. In order to accelerate aligning reads to the graph, an index of graph-based reference genomes is used to obtain candidate locations. However, the potential combinatorial explosion of nodes on the sequence graph leads to increasing the index space and maximum memory usage of alignment process considerably, especially for large-scale datasets. For this, existing methods typically attempt to prune complex regions, or extend the length of seeds, which sacrifices the recall of alignment algorithm despite reducing space usage slightly. We present the Sparse-index of Graph (SIG) and alignment algorithm SIG-Aligner, capable of indexing and aligning at the lower memory cost. SIG builds the non-overlapping minimizers index inside nodes of sequence graph and SIG-Aligner filters out most of the false positive matches by the method based on the pigeonhole principle. Compared to Giraffe, the results of computational experiments show that SIG achieves a significant reduction in index memory space ranging from 50% to 75% for the human pan-genome graphs, while still preserving superior or comparable accuracy of alignment and the faster alignment time.

Molecular identification of some species of dragonfly (Odonata: Anisoptera) using COXI gene and DNA barcodes from Basrah Province, Southern Iraq

The taxonomy of the Odonata group is still poorly understood; therefore, molecular identification has been developed to address the shortcomings of traditional taxonomy, such as misidentification and inconsistencies in reference databases. The mtCOXI gene has been used in animal barcoding studies because of its wide range of phylogenetic signals. Odonata, a diverse group of aquatic insects, has been studied at the molecular level to understand the evolutionary relationships between their species and global species. In the current study in Basrah Province, Iraq, we extracted mitochondrial DNA from adult and nymph Dragonflies and designed species-specific primers to distinguish some of the endemic species at the molecular level. This study identified five species, Crocothemis erythraea, Diplacodes trivialis, Orthetrum sabina, Trithemis annulata and Hemianax ephippiger. The DNA sequences were deposited in the NCBI database for the first time. The nucleotide sequences of the mtCOXI genes were analyzed via BLAST. The similarity results ranged from 91.8% to 100%, indicating related species on the basis of the branches of the phylogenetic tree. The molecular identity of the selected species was confirmed, and DNA barcodes for Anisoptera species from Basrah Province were successfully developed and documented in GenBank and IBIN.

Room-temperature mL-to-μL quantitative liquid concentration device for cyclone flow.

Highly sensitive quantitative analysis of liquids is required in various fields. Analytical instruments and devices such as chromatography, spectroscopic analysis, DNA sequencers, immunoassay, mass spectrometry, and microfluidic devices are utilized for this purpose. Typically, the sample volume is at the milliliter scale, while the analysis volume is at the microliter scale. Consequently, most of the sample is discarded. Therefore, a universal volume interface is required to quantitatively concentrate samples from milliliter to microliter volume. This study introduces a liquid quantitative function to the cyclone concentration method using a millimeter-scale channel, which is highly suitable for controlling liquids at the microliter scale due to its high fluidic resistance against cyclone flow. This method enables the effective control of liquid concentration by cyclone flow. The optimum channel structure is investigated, and a 33-fold concentration of aqueous solutions is demonstrated. Finally, the concentration device is applied to measure molybdenum ions in a river.

Are Genomic Language Models All You Need? Exploring Genomic Language Models on Protein Downstream Tasks.

Large language models, trained on enormous corpora of biological sequences, are state-of-the-art for downstream genomic and proteomic tasks. Since the genome contains the information to encode all proteins, genomic language models (gLMs) hold the potential to make downstream predictions not only about DNA sequences, but also about proteins. However, the performance of gLMs on protein tasks remains unknown, due to few tasks pairing proteins with the coding DNA sequences (CDS) that can be processed by gLMs. In this work, we curated five such datasets and used them to evaluate the performance of gLMs and proteomic language models (pLMs). We show that gLMs are competitive and even outperform their pLMs counterparts on some tasks. The best performance was achieved using the retrieved CDS compared to sampling strategies. We found that training a joint genomic-proteomic model outperforms each individual approach, showing that they capture different but complementary sequence representations, as we demonstrate through model interpretation of their embeddings. Lastly, we explored different genomic tokenization schemes to improve downstream protein performance. We trained a new Nucleotide Transformer (50M) foundation model with 3mer tokenization that outperforms its 6mer counterpart on protein tasks while maintaining performance on genomics tasks. The application of gLMs to proteomics offers the potential to leverage rich CDS data, and in the spirit of the central dogma, the possibility of a unified and synergistic approach to genomics and proteomics. We make our inference code, 3mer pre-trained model weights and datasets available. Supplementary data are available at Journal Name online.

Complete genome sequence of a Circovirus pigeon strain in lymphocyte-depleted bursa of Fabricius of a Common Raven (Corvus corax).

A necropsy was performed on a Common Raven (Corvus corax) presenting an opportunistic fungal respiratory infection and a bursal lymphoid depletion with inclusion bodies, suggestive of a circovirus infection. High-throughput sequencing of circular DNA in the bursa of Fabricius revealed a complete genome sequence of a Circovirus pigeon strain.

Direct inhibition of tumor hypoxia response with synthetic transcriptional repressors.

Many oncogenic transcription factors (TFs) are considered to be undruggable because of their reliance on large protein-protein and protein-DNA interfaces. TFs such as hypoxia-inducible factors (HIFs) and X-box-binding protein 1 (XBP1) are induced by hypoxia and other stressors in solid tumors and bind to unfolded protein response element (UPRE) and hypoxia-induced response element (HRE) motifs to control oncogenic gene programs. Here, we report a strategy to create synthetic transcriptional repressors (STRs) that mimic the basic leucine zipper domain of XBP1 and recognize UPRE and HRE motifs. A lead molecule, STR22, binds UPRE and HRE DNA sequences with high fidelity and competes with both TFs in cells. Under hypoxia, STR22 globally suppresses HIF1α binding to HRE-containing promoters and enhancers, inhibits hypoxia-induced gene expression and blocks protumorigenic phenotypes in triple-negative breast cancer (TNBC) cells. In vivo, intratumoral and systemic STR22 treatment inhibited hypoxia-dependent gene expression, primary tumor growth and metastasis of TNBC tumors. These data validate a novel strategy to target the tumor hypoxia response through coordinated inhibition of TF-DNA binding.

Enhancing Early Cancer Detection: An Investigation of DNA Sequences and Machine Learning

Enhancing Early Cancer Detection: An Investigation of DNA Sequences and Machine Learning

Molecular classification of ovarian high-grade serous/endometrioid carcinomas through multi-omics analysis: JGOG3025-TR2 study.

Considerable interobserver variability exists in diagnosis of ovarian high-grade endometrioid carcinoma (HGEC) and high-grade serous carcinoma (HGSC) due to histopathological similarities. While homologous recombination deficiency (HRD) correlates with drug sensitivity in HGSC, the molecular features of HGEC are unclear. Fresh-frozen samples from 15 ovarian HGECs and 274 ovarian HGSCs in the JGOG-TR2 cohort were submitted to targeted DNA sequencing, RNA sequencing, DNA methylation array, and SNP array. We additionally analyzed 555 ovarian HGSCs from TCGA-OV and 287 endometrial high-grade carcinomas from TCGA-UCEC. Unsupervised clustering using copy number signatures identified four distinct tumor groups (C1, C2, C3 and C4). C1 (n = 41) showed CCNE1 amplification and poor survival. C2 (n = 160) and C3 (n = 59) showed high BRCA1/2 alteration frequency with low and moderate ploidy, respectively. C4 (n = 22) was characterized by favorable outcome, higher HGEC proportion, no BRCA1/2 alteration or CCNE1 amplification, and low levels of HRD score, ploidy, intra-tumoral heterogeneity, cell proliferation rate, and WT1 gene expression. Notably, C4 exhibited a normal endometrium-like DNA methylation profile, thus, defined as "HGEC-type" tumors, which were also identified in TCGA-OV and TCGA-UCEC. Ovarian "HGEC-type" tumors present a non-HRD status, favorable prognosis, and endometrial differentiation, possibly constituting a subset of clinically diagnosed HGSCs.

Unidirectional association of clonal hematopoiesis with atherosclerosis development.

Clonal hematopoiesis, a condition in which acquired somatic mutations in hematopoietic stem cells lead to the outgrowth of a mutant hematopoietic clone, is associated with a higher risk of hematological cancer and a growing list of nonhematological disorders, most notably atherosclerosis and associated cardiovascular disease. However, whether accelerated atherosclerosis is a cause or a consequence of clonal hematopoiesis remains a matter of debate. Some studies support a direct contribution of certain clonal hematopoiesis-related mutations to atherosclerosis via exacerbation of inflammatory responses, whereas others suggest that clonal hematopoiesis is a symptom rather than a cause of atherosclerosis, as atherosclerosis or related traits may accelerate the expansion of mutant hematopoietic clones. Here we combine high-sensitivity DNA sequencing in blood and noninvasive vascular imaging to investigate the interplay between clonal hematopoiesis and atherosclerosis in a longitudinal cohort of healthy middle-aged individuals. We found that the presence of a clonal hematopoiesis-related mutation confers an increased risk of developing de novo femoral atherosclerosis over a 6-year period, whereas neither the presence nor the extent of atherosclerosis affects mutant cell expansion during this timeframe. These findings indicate that clonal hematopoiesis unidirectionally promotes atherosclerosis, which should help translate the growing understanding of this condition into strategies for the prevention of atherosclerotic cardiovascular disease in individuals exhibiting clonal hematopoiesis.

Improving the odds: Artificial intelligence and the great plate count anomaly.

Next-generation DNA sequencing has shown that the great plate count anomaly, that is, the difference between bacteria present in the environment and those that can be obtained in culture from that environment, is even greater and more persisting than initially thought. This hampers fundamental understanding of bacterial physiology and biotechnological application of the unculture majority. With big sequence data as foundation, artificial intelligence (AI) may be a game changer in bacterial isolation efforts and provide directions for the cultivation media and conditions that are most promising and as such be used to canalize limited human and financial resources. This opinion paper discusses how AI is or can be used to improve the success of bacterial isolation.

Fluorescence In-Situ Hybridization Assessment of Spindle Cell-Rich Testicular Sex Cord Stromal Tumors Demonstrates Multiple Chromosomal Gains Across Histologic Subtypes.

Spindle cell-rich testicular sex cord-stromal tumors (TSCSTs) comprise a group that includes mostly (but not exclusively): myoid gonadal stromal tumor (MGST), adult granulosa cell tumor (AGCT), and unclassified TSCST. These entities demonstrate histopathologic overlap, and prior genomic studies have failed to identify specific oncogenic drivers. Results of DNA sequencing suggest that different types of spindle cell-rich TSCSTs harbor a recurrent pattern of chromosomal gains consistent with a shift in ploidy. However, these results have not been validated by alternative methods and the extent of these changes within individual tumors remains unknown. We used a combination of commercially available fluorescence in-situ hybridization (FISH) probes (3q11.2, 6p24.3, 6q11.1, 6q23, 7q11.21-q11.22, 9p21.3, 11q13.3, 17p11.2) to enumerate a subset of chromosomes identified as altered (gained) in prior studies. We analyzed 10 cases (3 MGST, 4 unclassified TSCST, 3 AGCT), including 7 that had been previously sequenced. FISH demonstrated gains of chromosomes 3, 6, 7, 9, and 11 above the pre-established threshold (25%) in 50%, 80%, 70%, 20%, and 40% of cases, respectively, with gains of chromosome 17 being present in only 1 unclassified TSCST. The proportion of cells with chromosomal gains ranged from 26% to 60%. Tumors with available copy number data from prior genomic analyses showed a partial discordance between FISH and sequencing results. This study demonstrates that spindle-cell rich TSCSTs harbor a recurrent pattern of chromosomal gains, which are present in variable subsets of neoplastic cells. Further studies are needed to determine if these chromosomal changes represent an oncogenic mechanism or a secondary event.

Alterations of gut microbiome in eosinophilic chronic rhinosinusitis.

A growing body of evidence has elucidated that the gut microbiota has a crucial impact on the pathophysiological process of atopic diseases. Eosinophilic chronic rhinosinusitis with nasal polyps (eCRSwNP) is a local atopic disease of the systemic immune response. Alterations in the gut microbiome in eCRSwNP patients remain largely undefined. 16S rRNA gene sequencing was performed in a cross-sectional study of 17 eCRSwNP patients, 9 noneCRSwNP patients and 13 healthy controls, and gut microbiota DNA sequencing between each pair of groups was compared using bioinformatic methods. Compared with that of healthy controls, the gut microbiomes of eCRSwNP patients were characterised by a distinct overall microbial composition. However, no significant differences were found in the alpha diversity of the gut microbiota between patients and healthy controls. The distinct differences in microbial composition were significantly correlated with the severity of disease. At the genus level, the abundance of Faecalibacterium positively correlated with Lund-Mackay CT scores. Similarly, the abundance of Turicibacter positively correlated with the percentage of tissue eosinophils. We found alterations in the gut microbiome in eCRSwNP patients, and the alterations in the gut microbiome were correlated with the severity of disease.