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At least 19 recordsLinked to original sources
PubMed2025

Whole-Genome Conservation Analysis for the Specific and Accurate Detection of Influenza A and B Viruses and Respiratory Syncytial Virus by Quadruplex RT-qPCR.

Influenza virus (Flu) and respiratory syncytial virus (RSV) are the primary pathogens responsible for acute respiratory infections. Both viruses are prone to mutations due to the seasonal epidemic, leading to an increasing rate of false-negative results. In this study, comprehensive meta-analyses of the genomes focusing on most conserved fragments have been performed for the four seasonal influenza viruses (two subtypes of Flu A: H1N1 and H3N2; two subtypes of Flu B: Yamagata and Victoria) and the two types of RSV: RSVA and RSVB), respectively. The most conserved sequences of 200 bp were identified as targets of the designed primer/probe sets for RT-qPCR were screened and optimized. Good sensitivities of the optimized primer/probe sets were obtained with the limits of detections of 2.95, 2.82, 1.57, 2.8, 1.19, and 2.12 copies/reaction for H1N1, H3N2, Yamagata, Victoria, RSVA and RSVB, respectively. Eventually, quadruplex qPCR using the four designed primer/probe sets can achieve simultaneous screening of the four viruses at a single tube. Furthermore, the assay's good performance in detecting target viruses from clinical throat swab samples demonstrated its potential for diagnosis of these viruses. The method, based on the identified conserved sequences and primer/probe sets, can effectively reduce false-negative results and rapidly respond to these viruses during respiratory disease outbreaks, or even before their widespread emergence, which aid in preventing outbreaks and guiding clinical treatment.

Humans↗
PubMed2026

Comparative analysis of conserved non-coding elements identifies gene regulatory networks rewired during the water-to-land transition in vertebrates.

The conquest of land by vertebrates has been a pivotal moment in evolutionary history. Adapting to the new habitats necessitated numerous changes in vertebrate anatomy and physiology, creating an enduring imprint on the developmental gene regulatory networks (GRNs) of tetrapods. The increase of high-quality genomic resources over the past decade has made it possible to study the genomic legacy of the water-to-land transition. While much attention has been given to the highly conserved non-coding elements (CNEs) of the genome that share high levels of similarity across evolutionarily diverged clades, recent evidence suggests that perhaps comparable attention should be given to "missing" CNE-s, conserved sequence patches present in extant stem gnathostomes and actinopterygian fishes that have become undetectable in tetrapods during the adaptation to terrestrial life, whether through true sequence loss or divergence beyond alignability. These sequences could help us reveal the relaxation of certain developmental constraints, related to the aquatic lifestyle, that made reaching new adaptive peaks in the developmental landscape possible. In this paper, we search for such CNEs and characterize them in comparison with pan-Gnathostome CNEs, using the zebrafish (Danio rerio) genome as a reference. Our results suggest that the rewiring of developmental networks related to pigmentation and muscle structure formation has left the largest genomic imprint. We also find that components of canonical Wnt and Hedgehog signalling, are enriched among CNEs retained in fish.

cis-regulatory evolution↗
PubMed1977

[Comparative analysis of conservative and surgical treatment of the imminent myocardial infarct].

It is reported on 108 patients with the symptoms of the impending myocardial infarction, of whom 80 patients were treated conservatively. 51 patients developed a fresh definitive myocardial infarction. 28 patients were surgically treated, 5 of them died. Therefore, in patients with instable angina pectoris the possibility of an early coronary-surgical intervention should be taken into consideration to prevent the development of a definitive myocardial infarction.

Acute Disease↗
PubMed1979

A retrospective analysis of conservative versus active management in severe open myelomeningocele.

88 patients with thoraco-lumbar myelomeningocele not operated upon in the 1976-1977 period were compared with 76 patients with the same condition operated upon in the 1964-1971 period. There was no significant difference in sex and hydrocephalus at birth in the two groups. Mortality was less in the surgically treated group only after the age of three months. Ventriculitis appeared to be related to the incidence of hydrocephalus in the surgically treated group. There was a reduced risk of developing progressive hydrocephalus after birth in the untreated group, and the neurological status of the survivors at one year was the same in both groups. Interpreting the results as indicating that early surgery increased the incidence of progressive hydrocephalus and ventriculitis, and might increase survival of more disabled infants, then non-surgical treatment is justified since survivors are no worse as a result of this non-active approach.

Cerebral Ventricles↗
PubMed2025

MAFin: motif detection in multiple alignment files.

MOTIVATION: Whole Genome and Proteome Alignments, represented by the multiple alignment file format, have become a standard approach in comparative genomics and proteomics. These often require identifying conserved motifs, which is crucial for understanding functional and evolutionary relationships. However, current approaches lack a direct method for motif detection within MAF files. We present MAFin, a novel tool that enables efficient motif detection and conservation analysis in MAF files to address this gap, streamlining genomic and proteomic research. RESULTS: We developed MAFin, the first motif detection tool for Multiple Alignment Format files. MAFin enables the multithreaded search of conserved motifs using three approaches: (i) using user-specified k-mers to search the sequences. (ii) with regular expressions, in which case one or more patterns are searched, and (iii) with predefined Position Weight Matrices. Once the motif has been found, MAFin detects the motif instances and calculates the conservation across the aligned sequences. MAFin also calculates a conservation percentage, which provides information about the conservation levels of each motif across the aligned sequences, based on the number of matches relative to the length of the motif. A set of statistics enables the interpretation of each motif's conservation level, and the detected motifs are exported in JSON and CSV files for downstream analyses. AVAILABILITY AND IMPLEMENTATION: MAFin is offered as a Python package under the GPL license as a multi-platform application and is available at: https://github.com/Georgakopoulos-Soares-lab/MAFin.

Software↗
PubMed2025

Constructing epigenetic regulatory landscapes of plant lncRNAs-an exploration utilizing the novel specialized platform PERlncDB.

Long non-coding RNAs (lncRNAs), once overlooked as transcriptional byproducts, are now recognized for their crucial roles in plant growth, development, and stress responses, with increasing focus on their epigenetic regulation. However, studies investigating epigenomic signals to explore the functions of lncRNAs in plants remain relatively limited. This study collected a comprehensive dataset of over 160 000 high-quality lncRNAs from 19 representative plant species and integrated 6715 ChIP-seq, BS-seq, and RNA-seq datasets to analyze epigenomic patterns at lncRNA loci. Results showed elevated DNA methylation in lncRNA regions. The highest levels occurred in transposable element-associated lncRNAs. Additionally, activating histone modifications at lncRNA loci showed tissue specificity, with epigenetic preferences differed from those at protein-coding gene (PCG) loci. Differential site analysis in epigenetic mutants further highlighted the selective regulation of lncRNA loci by specific epigenetic factors. To facilitate research, we developed PERlncDB, a platform that provides species-specific lncRNA browsing, epigenetic annotation, cross-species conservation analysis, and visualization of epigenomic landscapes. Case studies on MARS and LINC-AP2 emphasized the platform's utility. Conserved epigenetic mechanisms regulating lncRNAs across species, exemplified by a syntenic conserved MET1-regulated lncRNA pair in Arabidopsis and tomato, suggested the stability of regulatory mechanisms underlying lncRNA functions. This work provides critical insights and resources for understanding plant lncRNA epigenetic regulation.

RNA, Long Noncoding↗
PubMed2026

A genetic manipulation tool based on the GP35 recombinase for targeted gene editing in mycoplasmas of ruminants.

Pathogenic ruminant mycoplasmas are major etiological agents in cattle and small ruminants and are responsible for substantial economic losses in the livestock industry. Progress in pathogenesis research and vaccine development has been hampered by a lack of effective genetic tools. The applicability of common genome editing platforms, such as CRISPR, is inherently restricted in these organisms owing to their minimal genomes, the absence of a cell wall, and low homologous recombination efficiency. Although transposon-mediated random mutagenesis and single-base editing are currently used in the editing of bovine mycoplasma, the stochastic nature of transposons, the risk of single-base random deamination, and limitations in editing window selection hinder the genetic manipulation of bovine mycoplasma. Here, we introduce a plasmid-based methodology that employs the GP35 recombinase from bacteriophage SPP1 to mediate long single-stranded DNA (ssDNA) recombineering, thereby enabling precise gene insertions and deletions in Mycoplasma bovis, with a positive-editing rate of 77.78% - 100%. This targeted system eliminates the risk of random deamination. Leveraging this tool, we generated a panel of M. bovis mutants affecting metabolic and virulence genes and obtained key insights into Mb0564, identified as a novel adhesin. The 192 to 287 aa region of GP35 is critical for interaction with SSB. Structural conservation analysis further suggested that this GP35-ssDNA editing system possesses a high potential for translation to other ruminant pathogens. Collectively, our approach expands the existing genetic toolkit for M. bovis, advances synthetic biology and M. bovis pathobiology, facilitates vaccine development, and strengthens the control of high-impact livestock diseases in line with the One Health framework.

Animals↗
PubMed1979

Is ECG monitoring in the operating room cost effective?

ECG monitoring during anesthesia detects many arrhythmias, even in healthy patients. The clinical significance of these arrhythmias is uncertain. However, a conservative analysis of the cost of ECG monitoring in the USA reveals that the prevention of cardiac arrests occurring in 1 of 3,500 cases is quite cost effective. Routine ECG monitoring for all anesthetics in the USA is recommended.

Adolescent↗
PubMed1976

[Urolithiasis and its conservative treatment based on analysis of the calculi].

The exact analysis of urinary calculi is the condition for an aimed conservative therapy of urolithiasis. As standardized method of the analysis of urinary calculi the X-ray diffraction was introduced in the GDR. This investigation method allows a qualitative and quantitative analysis of the concrements. The possibilities of the conservative therapy of urolithiasis were explained. To this conservative treatment belong the treatment of a colic, the removal of a calculus, the litholysis and the prophylaxis of recidivations.

Colic↗
PubMed2026

Analysis of structure and conservation for supporting functional evaluation of PMS2 missense variants.

Germline defects in mismatch repair (MMR) genes are known to significantly increase the risk of developing certain types of cancers, notably colorectal and endometrial cancers. These conditions are characterized under Lynch syndrome. Accurate diagnosis of this predisposition, along with meaningful predictive testing for family members, necessitates the identification of pathogenic variants. However, classifying small coding genetic variants identified in cancer patients is very challenging, specifically in the case of PMS2 variants, since PMS2 pathogenic variants display a lower penetrance and less severe phenotype and therefore a lower tumor burden in affected families. We have assembled clinical data on four PMS2 missense variants of uncertain significance (VUS) identified in 23 patients (p.(Asp286Gly), p.(Asn335Ser), p.(Ile679Thr) and p.(Arg799Trp)). For these variants, functional testing was performed (RNA splicing, protein stability and catalytic activity). Since many protein ortholog sequences and accurate predictive models from AlphaFold2 are available, we also included a systematic analysis of residue conservation and structural role (ConStruct assessment). Overall, our findings indicate that p.(Asp286Gly) and p.(Arg799Trp) behave similarly to wild-type PMS2 and are thus probably neutral. In contrast, p.(Asn335Ser) and p.(Ile679Thr) conferred defects in protein expression or MMR activity. These could be explained by the relevant roles of these amino acids in MLH1-PMS2-N-terminal dimerization (p.Asn335) and C-terminal dimerization (p.Ile679). Our data thus suggest that p.(Asp286Gly) and p.(Arg799Trp) are benign, while the tumor risk in the other two variants remains to be established. Taken together, we suggest roadmaps for the individualized evaluation of difficult uncertain variants by comprising information from all available sources.

Humans↗
PubMed2026

Genome-wide characterization of the bZIP gene family in Rattus norvegicus and expression profiling analysis during brain development.

BACKGROUND: The brown rat (Rattus norvegicus) serves as a cornerstone model organism in biomedical research, particularly for understanding physiological homeostasis and stress responses. The basic leucine zipper (bZIP) transcription factor family is a pivotal regulatory network involved in growth, organogenesis, and neurodevelopment. Despite its importance, a systematic characterization of the bZIP gene family in rats has remained elusive. RESULTS: In this study, we performed a genome-wide identification of 61 RnbZIP genes, which were categorized into 10 distinct subfamilies based on phylogenetic relationships and chromosomal localization. Structural analysis revealed conserved motif arrangements within subfamilies, while collinearity analysis identified significant gene duplication events-predominantly tandem and segmental duplications-that have driven the evolutionary expansion of the RnbZIP family. Quantitative analysis showed that members within the same subfamily shared 45%-92% sequence similarity (calculated using the BLOSUM62 scoring matrix), and all duplicated gene pairs underwent strong purifying selection (Ka/Ks&#x2009;<&#x2009;1). Comparative genomics across seven rodent species further underscored the evolutionary conservation and divergence of these factors. Expression profiling across diverse organs and brain developmental stages indicated that RnbZIP genes exhibit high tissue specificity. Notably, 10 candidate genes, including RnbZIP01, RnbZIP02, and RnbZIP08, demonstrated dynamic expression patterns during brain maturation, suggesting their essential roles in neurodevelopmental processes. CONCLUSIONS: Our findings provide a comprehensive structural and evolutionary framework for the RnbZIP gene family, highlighting their potential regulatory functions in rat organogenesis and brain development. This study establishes a valuable resource for further functional characterization of specific bZIP members in mammalian neurological systems.

Animals↗
PubMed2026

Genome-wide characterization of BraABCB transporters reveals their potential roles in hormone responses in Brassica rapa var. parachinensis.

Thirty-six BraABCB genes were identified in Brassica rapa var. parachinensis; expression and interaction analyses suggest BraABCB27 and BraABCB28 as hormone-responsive candidates associated with BRI1-related proteins. ABCB transporters are ATP-dependent membrane proteins that mediate the transport of diverse substrates, including phytohormones, and play important roles in plant development and environmental adaptation. Previous studies in Arabidopsis have shown that several ABCB proteins participate in phytohormone transport, including auxin and brassinosteroid transport, whereas the functions of their homologs in Brassica rapa var. parachinensis remain poorly understood. In this study, 36 BraABCB genes were identified and classified into four phylogenetic groups. Conserved domain analysis showed that BraABCB proteins contain typical nucleotide-binding domains and transmembrane domains. Chromosomal distribution, collinearity, and Ka/Ks analyses suggested that the BraABCB family is evolutionarily conserved and mainly subject to purifying constraints. Promoter analysis and RT-qPCR assays of selected Group IV BraABCB genes revealed diverse expression patterns and responses to drought, high temperature, brassinolide, and indole-3-acetic acid treatments. Subcellular localization assays showed that selected Group IV BraABCB proteins exhibited predominant plasma membrane localization. Notably, BraABCB27 and BraABCB28, two close AtABCB1/AtABCB19-related homologs, showed detectable physical associations with BRI1-related proteins in BiFC and split-ubiquitin yeast two-hybrid assays. Together, these results provide a genome-wide characterization of the BraABCB gene family and identify BraABCB27 and BraABCB28 as candidate genes for future studies of their possible associations with BR-related membrane processes and hormone-regulated growth responses in B. rapa var. parachinensis.

Plant Growth Regulators↗
PubMed2026

Genome-wide characterization of NOD-like receptor genes links NLR repertoire evolution to spleen immune responses after Aeromonas hydrophila challenge in the Chinese spiny frog (Quasipaa spinosa).

NOD-like receptors (NLRs) are cytosolic pattern-recognition receptors that detect pathogen-associated and damage-associated molecular patterns and mediate innate immune signaling in vertebrates. However, the genomic repertoire, evolutionary diversification, and infection-associated expression of NLR genes remain poorly defined in non-model amphibians. In this study, 66 NLR genes were identified from the Chinese spiny frog (Quasipaa spinosa) genome and designated as QsNLR1-QsNLR66. These genes were unevenly distributed across chromosomes and were classified into three phylogenetic groups, with most members exhibiting conserved motif architectures. Gene duplication analysis indicated that dispersed duplication was the main contributor to QsNLR expansion. Synteny analysis detected five conserved orthologous gene pairs between Q. spinosa and Pelophylax nigromaculatus, suggesting partial conservation of NLR genomic organization between the two amphibians. Ka/Ks analysis showed that several duplicated gene pairs, including NLRC3-like/QsNLR36 and NLRC3-like/QsNLR50, exhibited Ka/Ks ratios greater than one, suggesting potential sequence divergence after duplication. Spleen RNA sequencing (RNA-seq) after Aeromonas hydrophila challenge revealed enrichment of immune-related Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Weighted gene co-expression network analysis linked several QsNLRs to infection-associated modules, among which QsNLR57 was co-expressed with CYBB, ADAM17, SPI1, and HK2. RT-qPCR using time-matched phosphate-buffered saline (PBS) controls showed distinct temporal patterns, with stronger induction of QsNLR29, QsNLR57, and QsNLR66 and weaker or delayed responses of QsNLR50 and QsNLR56. These results characterize the NLR repertoire of Q. spinosa and identify infection-associated QsNLR candidates for future studies of antibacterial immunity in amphibians.

Animals↗
PubMed2026

Proteomic Analysis of Biomineralization Proteins in the Shell Plates and Spicules of Chiton Acanthochitona rubrolineata.

Chitons, ancient polyplacophoran mollusks, are ideal models for studying biomineralization evolution due to their conserved morphology since the Cambrian. This study investigates the matrix proteins in shell plates and spicules of Acanthochitona rubrolineata using liquid chromatography-tandem mass spectrometry. By extracting proteins from 30 individuals and using proteomic method, we identified 26 soluble proteins and 22 insoluble proteins in the shell plates and 25 insoluble proteins, and found domains such as von Willebrand factor type A, chitin-binding, ferritin, and cadherin. These domains, prevalent in molluscan biominerals, suggest conserved roles in organic matrix formation. Despite genomic dynamism, the conservation of key domains across species highlights a core biomineralization mechanism. Notably, eight of the shell proteins and eight of the spicule proteins were homologous between A. rubrolineata and chiton Acanthopleura loochooana, indicating functional conservation. Phylogenetic analysis further supported the evolutionary significance of these domains in chitons. The study advances understanding of biomineralization in Polyplacophora, emphasizing the interplay between morphological stasis and molecular evolution.

matrix proteins↗
PubMed1979

Developmental relations between notational counting and number conservation.

The 2 studies of this report sought to determine the developmental relationship between the child's use of counting as a notational symbol system to extract, compare, and reproduce numerical information and the development of number conservation. In study 1, children between 4 and 6 years of age were administered notational-counting and number-conservation tasks. Analysis of children's profiles across tasks indicated that children develop quantitative counting strategies (but do not necessarily count accurately) before they develop number-conservation concepts. In study 2, the generality of this sequence was tested. A population of 7- to 9-year-old "learning-disabled" children who reportedly were developing atypical counting skills were administered notational-counting and number-conservation tasks. All of these children who conserved number also used quantitative counting strategies, although some of these children frequently counted arrays inaccurately. The significance of these findings is discussed with respect to existing models of counting/number-conservation relations, and an alternative formulation is suggested based upon the new findings.

Child↗
PubMed2026

Endemic Circulation and Genetic Characterization of Foot-and-Mouth Disease Virus in Buffalo Populations of Bangladesh.

Foot-and-mouth disease (FMD) virus (FMDV) is endemic in Bangladesh, causing severe economic losses in the livestock sector. While it primarily affects cattle, buffaloes (Bubalus bubalis) remain highly susceptible. Therefore, this study aimed to determine the prevalence and molecular characteristics of FMDV in buffaloes across three districts (Sylhet, Rajshahi, and Noakhali) of Bangladesh from January to June 2024. In a cross-sectional study, a total of 622 nasal swabs from 67 herds were collected and tested for FMDV RNA using reverse transcription polymerase chain reaction (RT-PCR). Overall, 255 samples were positive, resulting in an individual-level prevalence of 41.0%(255/622), while 88.1% (59/67) of herds were FMDV-positive. Animal-level prevalence was highest in Sylhet (47.1%), followed by Noakhali (38.9%) and Rajshahi (37.1%). To further characterize circulating strains, eight representative RT-PCR-positive samples were sequenced, revealing the co-circulation of serotypes O (n&#x2009;=&#x2009;5) and Asia-1 (n&#x2009;=&#x2009;3). Phylogenetic analysis showed that the isolates belonged to the ME-SA/Ind2001e lineage of the serotype O and the Asia-1 Group V lineage, clustering with contemporary strains from Bangladesh and neighboring countries, suggesting possible intra- and transboundary transmission. Pairwise genetic distance evaluation revealed high regional similarity, while Mantel tests indicated significant associations between genetic, geographic, and temporal distances. Comparative genomic analysis revealed largely conserved genomic regions, whereas VP1 analysis indicated that purifying selection predominated across both serotypes, with serotype O exhibiting greater genetic diversity (&#x3c0;&#x2009;=&#x2009;0.11642) than Asia-1 (&#x3c0;&#x2009;=&#x2009;0.05258), suggesting localized antigenic variability and possible immune-mediated viral evolution. These findings highlight the need for strengthened surveillance, improved biosecurity, and integrated vaccination strategies to enhance FMD control and reduce economic losses in Bangladesh.

Animals↗