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BMC Research Notes Mar 2024Male infertility accounts for approximately 30% of cases of reproductive failure. The characterization of genetic variants using cytogenomic techniques is essential for...
OBJECTIVES
Male infertility accounts for approximately 30% of cases of reproductive failure. The characterization of genetic variants using cytogenomic techniques is essential for the adequate clinical management of these patients. We aimed to conduct a cytogenetic investigation of numerical and structural rearrangements and a genomic study of Y chromosome microdeletions/microduplications in infertile men derived from a single centre with over 14 years of experience.
RESULTS
We evaluated 151 infertile men in a transversal study using peripheral blood karyotypes and 15 patients with normal karyotypes through genomic investigation by multiplex ligation-dependent probe amplification (MLPA) or polymerase chain reaction of sequence-tagged sites (PCR-STS) techniques. Out of the 151 patients evaluated by karyotype, 13 presented chromosomal abnormalities: two had numerical alterations, and 11 had structural chromosomal rearrangements. PCR-STS detected a BPY2 gene region and RBMY2DP pseudogene region microdeletion in one patient. MLPA analysis allowed the identification of one patient with CDY2B_1 and CDY2B_2 probe duplications (CDY2B and NLGN4Y genes) and one patient with BPY2_1, BPY2_2, and BPY2_4 probe duplications (PRY and RBMY1J genes).
Topics: Humans; Male; Brazil; Genomics; Infertility, Male; Genetic Services; Karyotyping; Multiplex Polymerase Chain Reaction
PubMed: 38444014
DOI: 10.1186/s13104-024-06710-1 -
PLoS Genetics Mar 2024The honey bee trypanosomatid parasite, Lotmaria passim, contains two genes that encode the flagellar calcium binding protein (FCaBP) through tandem duplication in its...
The honey bee trypanosomatid parasite, Lotmaria passim, contains two genes that encode the flagellar calcium binding protein (FCaBP) through tandem duplication in its genome. FCaBPs localize in the flagellum and entire body membrane of L. passim through specific N-terminal sorting sequences. This finding suggests that this is an example of protein subcellular relocalization resulting from gene duplication, altering the intracellular localization of FCaBP. However, this phenomenon may not have occurred in Leishmania, as one or both of the duplicated genes have become pseudogenes. Multiple copies of the FCaBP gene are present in several Trypanosoma species and Leptomonas pyrrhocoris, indicating rapid evolution of this gene in trypanosomatid parasites. The N-terminal flagellar sorting sequence of L. passim FCaBP1 is in close proximity to the BBSome complex, while that of Trypanosoma brucei FCaBP does not direct GFP to the flagellum in L. passim. Deletion of the two FCaBP genes in L. passim affected growth and impaired flagellar morphogenesis and motility, but it did not impact host infection. Therefore, FCaBP represents a duplicated gene with a rapid evolutionary history that is essential for flagellar structure and function in a trypanosomatid parasite.
Topics: Bees; Animals; Calcium-Binding Proteins; Parasites; Leishmania; Flagella; Cilia
PubMed: 38437202
DOI: 10.1371/journal.pgen.1011195 -
Bioinformatics (Oxford, England) Mar 2024Large-scale gene expression studies allow gene network construction to uncover associations among genes. To study direct associations among genes, partial...
MOTIVATION
Large-scale gene expression studies allow gene network construction to uncover associations among genes. To study direct associations among genes, partial correlation-based networks are preferred over marginal correlations. However, FDR control for partial correlation-based network construction is not well-studied. In addition, currently available partial correlation-based methods cannot take existing biological knowledge to help network construction while controlling FDR.
RESULTS
In this paper, we propose a method called Partial Correlation Graph with Information Incorporation (PCGII). PCGII estimates partial correlations between each pair of genes by regularized node-wise regression that can incorporate prior knowledge while controlling the effects of all other genes. It handles high-dimensional data where the number of genes can be much larger than the sample size and controls FDR at the same time. We compare PCGII with several existing approaches through extensive simulation studies and demonstrate that PCGII has better FDR control and higher power. We apply PCGII to a plant gene expression dataset where it recovers confirmed regulatory relationships and a hub node, as well as several direct associations that shed light on potential functional relationships in the system. We also introduce a method to supplement observed data with a pseudogene to apply PCGII when no prior information is available, which also allows checking FDR control and power for real data analysis.
AVAILABILITY AND IMPLEMENTATION
R package is freely available for download at https://cran.r-project.org/package=PCGII.
Topics: Gene Regulatory Networks; Algorithms; Computer Simulation; Genes, Plant; Sample Size
PubMed: 38430463
DOI: 10.1093/bioinformatics/btae125 -
Nucleic Acids Research May 2024microRNAs (miRNAs) regulate nearly all physiological processes but our understanding of exactly how they function remains incomplete, particularly in the context of...
microRNAs (miRNAs) regulate nearly all physiological processes but our understanding of exactly how they function remains incomplete, particularly in the context of viral infections. Here, we adapt a biochemical method (CLEAR-CLIP) and analysis pipeline to identify targets of miRNAs in lung cells infected with Respiratory syncytial virus (RSV). We show that RSV binds directly to miR-26 and miR-27 through seed pairing and demonstrate that these miRNAs target distinct gene networks associated with cell cycle and metabolism (miR-27) and antiviral immunity (miR-26). Many of the targets are de-repressed upon infection and we show that the miR-27 targets most sensitive to miRNA inhibition are those associated with cell cycle. Finally, we demonstrate that high confidence chimeras map to long noncoding RNAs (lncRNAs) and pseudogenes in transcriptional regulatory regions. We validate that a proportion of miR-27 and Argonaute 2 (AGO2) is nuclear and identify a long non-coding RNA (lncRNA) as a miR-27 target that is linked to transcriptional regulation of nearby genes. This work expands the target networks of miR-26 and miR-27 to include direct interactions with RSV and lncRNAs and implicate these miRNAs in regulation of key genes that impact the viral life cycle associated with cell cycle, metabolism, and antiviral immunity.
Topics: Humans; Argonaute Proteins; Cell Cycle; Cell Line; Gene Expression Regulation; Gene Regulatory Networks; Host-Pathogen Interactions; MicroRNAs; Respiratory Syncytial Virus Infections; Respiratory Syncytial Virus, Human; Respiratory Syncytial Viruses; RNA, Long Noncoding
PubMed: 38412296
DOI: 10.1093/nar/gkae116 -
Frontiers in Veterinary Science 2024Studies carried out in several species have demonstrated that detection of low-calorie sweeteners in the lumen of the intestine, by the sweet receptor, T1R2-T1R3,...
Studies carried out in several species have demonstrated that detection of low-calorie sweeteners in the lumen of the intestine, by the sweet receptor, T1R2-T1R3, initiates a signaling pathway leading to enhanced expression and activity of intestinal Na/glucose cotransporter 1, SGLT1. This results in an increased gut capacity to absorb glucose, sodium chloride and water, the basis for oral rehydration therapy. Horses express T1R2, T1R3 and downstream signaling elements in the intestinal tissue. As such, the potential of sweetener-stimulation of T1R2-T1R3 leading to upregulation of SGLT1 allows the provision of more glucose (energy) and hydration for horses. This is especially important when the need for glucose increases during strenuous exercise, pregnancy, and lactation. There are significant differences among species in the ability to detect sweeteners. Amino acid substitutions and pseudogenization of taste receptor genes underlie these variations. Nothing is known about the sweetener specificity of horse T1R2-T1R3. Using heterologous expression methodology, we demonstrate that sweeteners sucralose, stevia and neohesperidin dihydrochalcone (NHDC) activate horse T1R2-T1R3, but cyclamate does not. Determination of sweetener specificity of equine sweet receptor is crucial for developing suitable dietary additives to optimize glucose absorption, hydration and avoiding the intestinal disease brought about by microbial fermentation of unabsorbed carbohydrate reaching the large intestine.
PubMed: 38410741
DOI: 10.3389/fvets.2024.1325135 -
Cureus Jan 2024Background In addition to genetic predisposition, occupational and environmental factors are important for the risk of prostate cancer. We investigated the effect of...
Background In addition to genetic predisposition, occupational and environmental factors are important for the risk of prostate cancer. We investigated the effect of single nucleotide polymorphisms (SNPs) on the development of prostate cancer in Japan, including occupational and industrial history as confounding factors in addition to age, smoking, and alcohol drinking. Methods We enrolled 210 prostate cancer patients and 504 male control patients. We conducted four genome-wide association study (GWAS) patterns for prostate cancer development. In the association test, logistic regression models incorporated age, smoking history, alcohol consumption history, and each pattern of industrial/occupational classification. Results No SNPs satisfying the genome-wide significance level of 5×10 were detected in GWAS. SNPs with a suggestive association level of 1×10 were found near the long intergenic non-protein coding RNA 1824 () and tripartite motif family like 2 () genes in the GWAS using occupational history as a confounder and near the ribosomal protein S2 pseudogene 25 () gene in the GWAS using industrial history as a confounder. No SNPs that met the suggestive association level were observed in the GWAS that did not include occupational and industrial history. Conclusion By adding occupational and industrial history to the confounding factors, there were SNPs detected in the GWAS for prostate cancer development. The consideration of occupational and industrial history may increase the usefulness of GWAS.
PubMed: 38406143
DOI: 10.7759/cureus.52926 -
Biomedicines Feb 2024The molecular explanation about why some pancreatic cancer (PaCa) patients die early and others die later is poorly understood. This study aimed to discover potential...
The molecular explanation about why some pancreatic cancer (PaCa) patients die early and others die later is poorly understood. This study aimed to discover potential novel markers and drug targets that could be useful to stratify and extend expected survival in prospective early-death patients. We deployed a deep learning algorithm and analyzed the gene copy number, gene expression, and protein expression data of death versus alive PaCa patients from the GDC cohort. The genes with higher relative amplification (copy number >4 times in the dead compared with the alive group) were , , , , , and . The most highly up-regulated genes (>8.5-fold change) in the death group were , , , , _, , , -, , and . None of their corresponding proteins were up or down-regulated in the death group. The mRNA of the pseudogene could act as ceRNA sponging the miRNA that was originally directed to the parental gene . We propose mRNA as the most druggable target that can be modulated with small molecules or the RNA technology approach. These markers could be added as criteria to patient stratification in future PaCa drug trials, but further validation in the target populations is encouraged.
PubMed: 38397997
DOI: 10.3390/biomedicines12020395 -
Genes Feb 2024(), a perennial plant renowned for its medicinal roots, provides a unique case for studying the phylogenetic relationships of species based on organelle genomes, as...
(), a perennial plant renowned for its medicinal roots, provides a unique case for studying the phylogenetic relationships of species based on organelle genomes, as well as the transference of DNA across organelle genomes. In order to investigate this matter, we sequenced and characterized the mitochondrial genome (mitogenome) of . Similar to the chloroplast genome (cpgenome), the mitogenome of extends across 181,688 base pairs (bp). Its unique quadripartite structure results from a pair of extensive inverted repeats, each measuring 25,680 bp in length. The annotated mitogenome includes 27 protein-coding genes, 37 tRNAs, 8 rRNAs, and two pseudogenes (, ). Phylogenetic analysis was performed to identify phylogenetic trees consistent with Paeonia species phylogeny in the APG Ⅳ system. Moreover, a total of 12 MTPT events were identified and 32 RNA editing sites were detected during mitogenome analysis of . Our research successfully compiled and annotated the mitogenome of . The study provides valuable insights regarding the taxonomic classification and molecular evolution within the Paeoniaceae family.
Topics: Humans; Phylogeny; Genome, Mitochondrial; Paeonia; Saxifragales; Chloroplasts
PubMed: 38397228
DOI: 10.3390/genes15020239 -
Genes Feb 2024Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger...
Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (, , , , , ) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., , Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman's rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development.
Topics: Humans; Animals; Phylogeny; Whales; Dolphins; Sequence Alignment; Dental Enamel
PubMed: 38397217
DOI: 10.3390/genes15020228 -
International Journal of Molecular... Feb 2024The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged...
The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged in some lineages. In this study, we conducted a comprehensive comparison of the complete plastomes from twenty-two species, covering seventeen genera from three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) of Papaveraceae. Our results revealed a high level of variability in the plastid genome size of Papaveraceae, ranging from 151,864 bp to 219,144 bp in length, which might be triggered by the expansion of the IR region and a large number of repeat sequences. Moreover, we detected numerous large-scale rearrangements, primarily occurring in the plastomes of Fumarioideae and Hypecooideae. Frequent gene loss or pseudogenization were also observed for , , , , , , , , and several tRNA genes, particularly in Fumarioideae and Hypecooideae, which might be associated with the structural variation in their plastomes. Furthermore, we found that the plastomes of Fumarioideae exhibited a higher GC content and more repeat sequences than those of Papaveroideae. Our results showed that Papaveroideae generally displayed a relatively conserved plastome, with the exception of , while Fumarioideae and Hypecooideae typically harbored highly reconfigurable plastomes, showing high variability in the genome size, gene content, and gene order. This study provides insights into the plastome evolution of Papaveraceae and may contribute to the development of effective molecular markers.
Topics: Phylogeny; Papaveraceae; Genome, Plastid; Repetitive Sequences, Nucleic Acid; Gene Rearrangement; Evolution, Molecular
PubMed: 38396955
DOI: 10.3390/ijms25042278