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Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern.

Noroviruses are the major cause of acute gastroenteritis worldwide, and recombination is recognized as the important mechanism for its continuous emergence. In this study, for the common GII.P12 and GII.3 recombinants, phylogenetic relationships based on different proteins in three ORFs were comparatively analyzed, focusing on the influence of intergenic recombination. By using newly designed primers, genomes of two GII.P12/GII.3 Guangzhou recombinants were firstly amplified. Combined with other reported sequences of GII.P12_ORF1 (n = 20), GII.3_ORF2 (n = 131), GII.3_ORF3 (n = 36), all GII.P12

LOH, LST, and TAI Profiles in Solid Tumors Harboring Pathogenic or Likely Pathogenic BRCA1/2 Variants: An Exploratory Study.

Homologous recombination deficiency (HRD) is a critical indicator of genomic instability; however, the composite HRD score may not reflect the distribution of distinct genomic scar components underlying this phenotype. In this exploratory study, we compared the absolute and relative contributions of loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) among solid tumors harboring pathogenic or likely pathogenic (P/LP) variants in BRCA1 or BRCA2. This retrospective study included 76 patients with solid tumors who underwent HRD testing between …

Effect of Repair Gene Polymorphism on the Risk of Malignant Neoplasm Development after Chronic Radiation Exposure.

UNLABELLED: The efficiency of DNA integrity repair processes after radiation exposure may depend on hereditary variations of repair genes caused by single nucleotide polymorphisms. Disturbances or even failure of repair processes trigger a chain of reactions leading to genome instability and oncogenic transformation of the cell. OBJECTIVE: : To investigate the association of single nucleotide polymorphism in genes of nucleotide excision repair (ERCC2 rs13 181, XPC rs2 228 001), AP site repair (APEX rs1 130 409), homologous recombination (XRCC3 rs861 539), single-strand DNA break repair (XRCC1…

Establishment of the auxin inducible degron system for Babesia duncani: a conditional knockdown tool to study precise protein regulation in Babesia spp.

BACKGROUND: Babesia duncani is a pathogen within the phylum Apicomplexa that causes human babesiosis. It poses a significant threat to publi … n TIR1 from Oryza sativa (OsTIR1) was achieved by constructing a transgenic parasite strain using a homologous recombination strategy. Polymerase chain reaction (PCR), western blot, and indirect immunofluorescence assay (IFA) were used to confirm the correct monoclonal parasite strain. The degradation of enhanced green fluorescent protein (eGFP) tagged with an AID degron …

Recombined sequences between the non-coding control regions of JC and BK viruses found in the urine of a renal transplantation patient.

Kidney cells are the common host for JC virus (JCV) and BK virus (BKV). Reactivation of JCV and/or BKV in patients after organ transplantation, such as renal transplantation, may cause hemorrhagic cystitis and polyomavirus-associated nephropathy. Furthermore, JCV and BKV may be shed in the urine after reactivation in the kidney. Rearranged as well as archetypal non-coding control regions (NCCRs) of JCV and BKV have been frequently identified in human samples. In this study, three JC/BK recombined NCCR sequences were identified in the urine of a patient who had undergone renal transplantation.

Characterization of a recombinant Onchocerca volvulus antigen (Ov33) produced in yeast.

A yeast (Saccharomyces cerevisiae) expression system has been adapted to produce reagent quantities of a major Onchocerca antigen, Ov33. Using a pool of monoclonal antibodies produced against third-stage larvae, a cDNA library constructed from adult O. volvulus worms was screened. Twenty-seven cDNAs were isolated, two of which had sequence homology to Ov33, a putative aspartyl protease inhibitor, which is the immunodominant antigen of O. volvulus. These cDNAs were expressed at high levels intracellularly or through the secretory pathway of S. cerevisiae. Localization studies using antisera pro

R-loops and D-loops: a delicate balance in genomic stability and instability.

R-loops and D-loops are three-stranded nucleic acid structures that have emerged as central regulators of genome stability, gene expression, … rising through context-dependent mechanisms that include RAD51- or DMC1-mediated strand invasion in homologous recombination, shelterin-assisted invasion at telomeres, and replication-coupled strand displacement at the mitochondrial DNA origin. They serve as indispensable intermediates in double-strand break repair, telomere maintenance, and mitochondrial DNA replication. …

Genomic Characterization of an Emergent Cross-Border Recombinant Duck Plague Virus With High Pathogenicity and Reduced Vaccine Efficacy in Guangxi, China.

Duck plague virus (DPV) is a major pathogen causing recurrent outbreaks in waterfowl. This study reports the comprehensive characterization … RFs). Comparative genomic analysis identified 40 amino acid deletions and mutations across 26 ORFs. Homologous recombination analysis confirmed that GXGG240520 originated from cross-border recombination between the Chinese virulent strain CHv (major parent) and the Bangladeshi strain YLBRDP 11 (minor parent). Furthermore, structure prediction of the UL47 protein revealed …

Genome data cross-contamination versus interdomain recombination: Equus caballus and Mus musculus genetic loci in the insertion sequence-rich genomes of two clonally related methicillin-resistant Staphylococcus aureus strains from China.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) represents a significant global health threat, responsible for infections in both humans and animals. Determining genetic patterns associated with the genome plasticity of MRSA is critical for predicting the evolutionary trajectories of its emerging pathogenic clones. RESULTS: The specific genetic loci of the MRSA strains WH3018 and WH9628 from Wuhan, China, ranging in size from 399 to 3,622 base pairs, were determined to be highly homologous (DNA identity: 90.95-100%) to corresponding chromosomal regions from Equus caballus and M

Beginning at the ends: telomere and telomere-based cancer therapeutics.

Telomeres, which are situated at the terminal ends of chromosomes, undergo a reduction in length with each cellular division, ultimately reaching a critical threshold that triggers cellular senescence. Cancer cells circumvent this senescence by utilizing telomere maintenance mechanisms (TMMs) that grant them a form of immortality. These mechanisms can be categorized into two primary processes: the reactivation of telomerase reverse transcriptase and the alternative lengthening of telomeres (ALT) pathway, which is dependent on homologous recombination (HR). Various strategies have been develope…

The genes from the pseudoautosomal region 1 (PAR1) of the mammalian sex chromosomes: Synteny, phylogeny and selection.

Sex chromosomes recombine restrictly in their homologous area, the pseudoautosomal region (PAR), represented by PAR1 and PAR2, which behave like an autosome in both pairing and recombination. The PAR1, common to most of the eutherian mammals, is located at the terminus of the sex chromosomes short arm and exhibit recombination rates ~20 times higher than the autosomes. Here, we assessed the interspecific evolutionary genomic dynamics of 15 genes of the PAR1 across 41 mammalian genera (representing six orders). The strong negative selection detected in most of the assessed groups reinforces the

Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots.

Genomic structural variants (SVs) are distributed nonrandomly across the human genome. The "hotspots" of SVs have been implicated in evolutionary innovations, as well as medical conditions. However, the evolutionary and biomedical features of these hotspots remain incompletely understood. Here, we analyzed data from 2,504 genomes to construct a refined map of 1,148 SV hotspots in human genomes. We confirmed that segmental duplication-related nonallelic homologous recombination is an important mechanistic driver of SV hotspot formation. However, to our surprise, we also found that a majority of…

Inducible transgenic expression of tripeptidyl peptidase 1 in a mouse model of late-infantile neuronal ceroid lipofuscinosis.

Late-infantile neuronal ceroid lipofuscinosis is a fatal neurodegenerative disease of children caused by mutations resulting in loss of acti … er and a sequence encoding murine TPP1 (TgLSL-TPP1) was integrated into the ROSA26 locus in mice by homologous recombination. Tested in both transfected CHO cells and in transgenic mice, the TgLSL-TPP1 did not express TPP1 until cre-mediated removal of the LSL cassette, which resulted in supraphysiological levels of TPP1 activity. We tested four cre/ERT2 transgenes to all …

Three novel, multiple recombinant types of species of human mastadenovirus D (HAdV-D 73, 74 & 75) isolated from diarrhoeal faeces of immunocompromised patients.

Species D is the largest of the seven species of human mastadenoviruses (HAdV), but few of its multiple types are associated with asevere di … ulation of opportunistic HAdV-D types facilitated co- and super-infections, which are essential for homologous recombination, and thus resulted in the evolution of novel genotypes by lateral gene transfer.

Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3.

Alu repetitive elements are known to be major contributors to genome instability by generating Alu-mediated copy-number variants (CNVs). Most of the reported Alu-mediated CNVs are simple deletions and duplications, and the mechanism underlying Alu-Alu-mediated rearrangement has been attributed to non-allelic homologous recombination (NAHR). Chromosome 17 at the p13.3 genomic region lacks extensive low-copy repeat architecture; however, it is highly enriched for Alu repetitive elements, with a fraction of 30% of total sequence annotated in the human reference genome, compared with the 10% genom…

Hlamidiaceae Genomics Reveals Inspeices Admixture и недавняя эволюция хламидийного аборта заражает нижние виды млекопитающих и людей.

Хламидиацеаи обязывают к внутриклеточным бактериям, которые вызывают разнообразие серьезных инфекций среди людей и скота в глобальном масштабе. Выявление новых видов с 1989 года и появление зоонотических инфекций, включая аборты среди женщин, подчеркивают необходимость последовательности генома множественных штаммов каждого вида для углубления наших знаний о эволюционной динамике на хламидиацее. Здесь мы секвенировали геном изолировали его от птичьего, низшего млекопитающего и человека. На основе фундаментальной генной филогении пять изолирующих веществ, ранее отнесенных к категории хламидийны

Совпадение в аннотации оригинала
Chlamydiaceae are obligate intracellular bacteria that cause a diversity of severe infections among humans and livestock on a global scale. … ies to acquire multiple species in their intestinal tract. This could facilitate transformation and homologous recombination with the potential for new species emergence. Our findings indicate that incubator hosts such as birds-of-prey likely promote Chlamydiaceae evolution resulting in novel pathogenic lineages.

Genomic basis of aromatase excess syndrome: recombination- and replication-mediated rearrangements leading to CYP19A1 overexpression.

CONTEXT: Genomic rearrangements at 15q21 have been shown to cause overexpression of CYP19A1 and resultant aromatase excess syndrome (AEXS). … 9A1 and the property of the fused promoters. Sequences at the fusion junctions suggested nonallelic homologous recombination, nonhomologous end-joining, and replication-based errors as the underlying mechanisms. The breakpoint-flanking regions were not enriched with GC content, palindromes, noncanonical DNA structures, or known rearrangement-associated motifs. The rearran …

Full-length characterization of A1/D intersubtype recombinant genomes from a therapy-induced HIV type 1 controller during acute infection and his noncontrolling partner.

To increase the understanding of mechanisms of HIV control we have genetically and immunologically characterized a full-length HIV-1 isolated from an acute infection in a rare case of undetectable viremia. The subject, a 43-year-old Danish white male (DK1), was diagnosed with acute HIV-1 infection after 1 year in Uganda. Following transient antiretroviral therapy DK1 maintained undetectable viral load for more than 10 years. His Ugandan wife (UG1) developed high viral load. HIV-1 sequences from both individuals were compared by bootscanning for recombination break points. Diversity plots and p

A new perspective on Listeria monocytogenes evolution.

Listeria monocytogenes is a model organism for cellular microbiology and host-pathogen interaction studies and an important food-borne patho … e 7, and 1/2c for clone 9), with no association of clones with clinical forms of human listeriosis. Homologous recombination was extremely limited (r/m<1 for nucleotides), implying long-term genetic stability of multilocus genotypes over time. Bayesian analysis based on 438 SNPs recovered the three previously defined lineages, plus one unclassified isolate of mixed ancest …

Evidence for emergence of diverse polioviruses from C-cluster coxsackie A viruses and implications for global poliovirus eradication.

The poliovirus (PV) eradication campaign is conducted on the premise that this virus, because of the lack of a zoonotic reservoir, will not … provide experimental evidence for C-CAVs being partners to PVs in generating diverse PV progeny by homologous recombination. They support speciation of a novel human pathogen (PV) from a pool of different human pathogens (C-CAVs). In a PV-free world without PV neutralizing antibodies, contemporary C-CAV, like their ancestor(s), could be fertile ground for a PV-like agent …