Genetic Mechanisms Research Articles

Base editing screens define the genetic landscape of cancer drug resistance mechanisms

Drug resistance is a principal limitation to the long-term efficacy of cancer therapies. Cancer genome sequencing can retrospectively delineate the genetic basis of drug resistance, but this requires large numbers of post-treatment samples to nominate causal variants. Here we prospectively identify genetic mechanisms of resistance to ten oncology drugs from CRISPR base editing mutagenesis screens in four cancer cell lines using a guide RNA library predicted to install 32,476 variants in 11 cancer genes. We identify four functional classes of protein variants modulating drug sensitivity and use single-cell transcriptomics to reveal how these variants operate through distinct mechanisms, including eliciting a drug-addicted cell state. We identify variants that can be targeted with alternative inhibitors to overcome resistance and functionally validate an epidermal growth factor receptor (EGFR) variant that sensitizes lung cancer cells to EGFR inhibitors. Our variant-to-function map has implications for patient stratification, therapy combinations and drug scheduling in cancer treatment.

Impact of Fertilization on Productivity and Nutritional Quality of Napier Varieties in Southern Mindanao, Philippines

Aims: This study investigates the effects of fertilizer application on the growth performance, proximate composition, and chlorophyll content of three Napier grass varieties (King, Pakchong, and Juncao) in Southern Mindanao, Philippines. Study Design: Utilizing a Randomized Complete Block Design with a 3x2 factorial arrangement. Place and Duration of Study: The experiment was performed at the University of Southern Mindanao Animal Production Center facilities from January to March 2023. Methodology: The three Napier grass varieties (King, Pakchong, and Juncao) was the first factor, and fertilizer application (with or without) were the second factor. Four blocks were prepared, each containing six plots, resulting in 24 plots. The fertilized plots received two applications of 150kg N/ha and 75kg N/ha of the recommended NPK fertilizer, respectively, while non-fertilized plots did not receive any fertilizer. Results: Results showed that fertilizer application significantly improved herbage yield, with fertilized plants yielding 20.25 tons per hectare compared to 15.14 tons in non-fertilized plants. Pakchong exhibited the highest yield and crude fiber content, while Juncao grass showed higher crude protein content without fertilizer. Fertilization also increased ether extract content, with Pakchong displaying the greatest response. However, nitrogen-free extract (NFE) was higher in non-fertilized plants across all varieties, indicating a complex interaction between nutrient availability and carbohydrate allocation. Conclusion: These findings underscore the importance of targeted fertilizer management to optimize both growth and nutritional quality, depending on specific production goals. The differential responses among Napier varieties suggest the potential for variety-specific fertilization strategies, which can enhance forage quality and sustainability in livestock farming. Further research is recommended to explore the long-term impacts of continuous fertilization and the underlying genetic mechanisms driving varietal differences.

Association of Ovocalyxin-32 Gene Variants with Egg Quality Traits in Indigenous Chicken Breeds.

This study sought to evaluate the genetic variations of the ovocalyxin-32 gene and its association with egg quality traits in indigenous chicken populations, focusing on exons 1 and 6. Genotype frequencies of SNPs (G/T and A/G) within these exons were assessed for their conformity to the Hardy-Weinberg equilibrium (HWE) across several strains. While most strains exhibited close adherence to HWE expectations, some like light-brown and gray strains indicated substantial discrepancies, particularly for the TT genotype, which points towards the possible effects of genetic drift as well as selection pressures. This study also analyzed the influence of such SNPs on egg quality parameters. A thinner eggshell, reduced shell weight, and decreased breaking strength were associated with the G/T SNP in exon 1, suggesting a likely negative effect on egg quality in T allele carriers. Conversely, the AG genotype displayed better performance in shell thickness, weight and egg weight in the A/G SNP in exon 1, whilst yolk height was best improved by the AA genotype compared to breaking strength. For instance, in exon 6, the A/G SNP enhanced the shell and yolk quality among AG genotypes, while the CC genotype resulted in better eggshell characteristics with enlarged yolks because the C/T SNP was linked. Nonetheless, there were no significant deviations from the HWE despite these associations, which suggested that most breeds had a stable genetic background. Further, considering SNPs' additive and dominant effects in this research, it was indicated that additive effects account for phenotypic expressions given by the G/T SNP located at exon 1. In contrast, significant additive and dominant effects were observed under the A/G SNP situated at the exon. Generally, it therefore could be concluded from this study that specific SNPs within the ovocalyxin-32 gene may act as good markers for marker-assisted selection (MAS) that can improve desired characteristics-such as those of egg quality-in indigenous chicken breeds. This study demonstrated that both additive and dominance effects must be taken into account when performing genetic analyses, thereby emphasizing the complexity of phenotypic variation caused by genetic mechanisms in native chicken races.

Unraveling the Genetic Puzzle: Could MAP3K7 Be a Candidate Gene for RASopathies? Case Presentation.

Noonan Syndrome (NS) diagnosis is challenging due to diverse clinical manifestations. Here, our case report highlights MAP3K7's novel role in NS. A 10.4-year-old female patient presented with short stature and suggestive clinical findings of RASopathy. Despite atypical facial features, the patient met two major diagnostic criteria of Van der Burgt.Initial genetic testing for known NS-associated genes did not find any variants. Later, whole exome sequencing (WES) discovered a unique de novo heterozygous variant (c.65C>A, p.(P22H)) in the MAP3K7. This variant, categorized as a variant of uncertain significance (VUS) by the American College of Medical Genetics and Genomics (ACMG) criteria, raised questions about its potential role in NS. The patient's clinical presentation deviated from classical manifestations of MAP3K7-associated syndromes, underscoring the genetic and molecular mechanisms' complexity. Notably, this is the first case reported to associate MAP3K7 variants with NS, advancing knowledge of the condition's genetic causes. Despite challenges in NS diagnosis, proper management, including recombinant growth hormone therapy, is crucial for optimizing growth potential. The case underscores MAP3K7 as a potential candidate gene for NS, and more functional genetic investigations are required to clarify the delicate interaction between genetic abnormalities, the RAS/MAPK pathway, and clinical manifestations observed in NS cases.

Extreme-Phenotype Genome-Wide Association Analysis for Growth Traits in Spotted Sea Bass (Lateolabrax maculatus) Using Whole-Genome Resequencing.

Spotted sea bass (Lateolabrax maculatus) is an important marine economic fish in China, ranking third in annual production among marine fish. However, a declined growth rate caused by germplasm degradation has severely increased production costs and reduced economic benefits. There is an urgent need to develop the fast-growing varieties of L. maculatus and elucidate the genetic mechanisms underlying growth traits. Here, whole-genome resequencing technology combined with extreme phenotype genome-wide association analysis (XP-GWAS) was used to identify candidate markers and genes associated with growth traits in L. maculatus. Two groups of L. maculatus, consisting of 100 fast-growing and 100 slow-growing individuals with significant differences in body weight, body length, and carcass weight, underwent whole-genome resequencing. A total of 4,528,936 high-quality single nucleotide polymorphisms (SNPs) were used for XP-GWAS. These SNPs were evenly distributed across all chromosomes without large gaps, and the average distance between SNPs was only 175.8 bp. XP-GWAS based on the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (Blink) and Fixed and random model Circulating Probability Unification (FarmCPU) identified 50 growth-related markers, of which 17 were related to body length, 19 to body weight, and 23 to carcass weight. The highest phenotypic variance explained (PVE) reached 15.82%. Furthermore, significant differences were observed in body weight, body length, and carcass weight among individuals with different genotypes. For example, there were highly significant differences in body weight among individuals with different genotypes for four SNPs located on chromosome 16: chr16:13133726, chr16:13209537, chr16:14468078, and chr16:18537358. Additionally, 47 growth-associated genes were annotated. These genes are mainly related to the metabolism of energy, glucose, and lipids and the development of musculoskeletal and nervous systems, which may regulate the growth of L. maculatus. Our study identified growth-related markers and candidate genes, which will help to develop the fast-growing varieties of L. maculatus through marker-assisted breeding and elucidate the genetic mechanisms underlying the growth traits.

Molecular specializations underlying phenotypic differences in inner ear hair cells of zebrafish and mice.

Hair cells (HCs) are the sensory receptors of the auditory and vestibular systems in the inner ears of vertebrates that selectively transduce mechanical stimuli into electrical activity. Although all HCs have the hallmark stereocilia bundle for mechanotransduction, HCs in non-mammals and mammals differ in their molecular specialization in the apical, basolateral, and synaptic membranes. HCs of non-mammals, such as zebrafish (zHCs), are electrically tuned to specific frequencies and possess an active process in the stereocilia bundle to amplify sound signals. Mammalian HCs, in contrast, are not electrically tuned and achieve amplification by somatic motility of outer HCs (OHCs). To understand the genetic mechanisms underlying differences between adult zebrafish and mammalian HCs, we compared their RNA-seq-characterized transcriptomes, focusing on protein-coding orthologous genes related to HC specialization. There was considerable shared expression of gene orthologs among the HCs, including those genes associated with mechanotransduction, ion transport/channels, and synaptic signaling. However, there were some notable differences in expression among zHCs, OHCs, and inner HCs (IHCs), which likely underlie the distinctive physiological properties of each cell type. For example, OHCs highly express Slc26a5 which encodes the motor protein prestin that contributes to OHC electromotility. However, zHCs have only weak expression of slc26a5, and subsequently showed no voltage-dependent electromotility when measured. Notably, the zHCs expressed more paralogous genes including those associated with HC-specific functions and transcriptional activity, though it is unknown whether they have functions similar to their mammalian counterparts. There was overlap in the expressed genes associated with a known hearing phenotype. Our analyses unveil substantial differences in gene expression patterns that may explain phenotypic specialization of zebrafish and mouse HCs. This dataset also includes several protein-coding genes to further the functional characterization of HCs and study of HC evolution from non-mammals to mammals.

Genetic analysis of drug resistance mechanisms and phylogenetic clustering in Candida auris isolates from Western India

Objectives: Candida auris is an emerging multidrug-resistant fungal pathogen that poses a significant threat to global health. Limited information is available from the Indian subcontinent regarding mutations associated with drug resistance and genetic variability among the isolates. In this study, we employed whole-genome sequencing (WGS) to investigate the genetic variations and drug resistance mechanisms within C. auris isolates from the western region of India. Materials and Methods: A total of twenty archived isolates were subjected to WGS on the Illumina NextSeq 2000 platform. A set of 18 genes was analyzed to check for the presence of drug-resistant mutations. Phylogenetic analysis was done using MEGA v6.06 software to identify the C. auris subgroup or clade and to check genetic relatedness among species. Statistical Analysis: The data related to drug resistance were presented in numbers and percentages. Results: Through manual analysis, drug-resistant mutations were detected in ERG11, CDR1, and TAC1b genes, which are known to be associated with reduced susceptibility to antifungal agents. Phylogenetic analysis revealed that all the isolates clustered within Clade I, indicating a high degree of genetic similarity among isolates. The absence of comprehensive antifungal mutation databases and automated tools for drug resistance detection necessitated the utilization of specialized computational skills of bioinformaticians for data analysis. Conclusions: The study provides valuable insights into the genetic diversity and drug resistance mechanisms of C. auris isolates in the western region of India and emphasizes the need for continued research and surveillance to combat this emerging pathogen. Our findings underscore the need for the development of user-friendly automated tools and comprehensive databases to facilitate rapid and accurate identification of drug resistance in C. auris.

Selective utilization of glucose metabolism guides mammalian gastrulation

The prevailing dogma for morphological patterning in developing organisms argues that the combined inputs of transcription factor networks and signalling morphogens alone generate spatially and temporally distinct expression patterns. However, metabolism has also emerged as a critical developmental regulator1–10, independent of its functions in energy production and growth. The mechanistic role of nutrient utilization in instructing cellular programmes to shape the in vivo developing mammalian embryo remains unknown. Here we reveal two spatially resolved, cell-type- and stage-specific waves of glucose metabolism during mammalian gastrulation by using single-cell-resolution quantitative imaging of developing mouse embryos, stem cell models and embryo-derived tissue explants. We identify that the first spatiotemporal wave of glucose metabolism occurs through the hexosamine biosynthetic pathway to drive fate acquisition in the epiblast, and the second wave uses glycolysis to guide mesoderm migration and lateral expansion. Furthermore, we demonstrate that glucose exerts its influence on these developmental processes through cellular signalling pathways, with distinct mechanisms connecting glucose with the ERK activity in each wave. Our findings underscore that—in synergy with genetic mechanisms and morphogenic gradients—compartmentalized cellular metabolism is integral in guiding cell fate and specialized functions during development. This study challenges the view of the generic and housekeeping nature of cellular metabolism, offering valuable insights into its roles in various developmental contexts.

Pathogenesis of multiple sclerosis: genetic, environmental and random mechanisms

BackgroundThe pathogenesis of multiple sclerosis (MS) requires both genetic factors and environmental events. The question remains, however, whether these factors and events completely describe the MS disease process. This question...

Cellulose synthase-like OsCSLD4: a key regulator of agronomic traits, disease resistance, and metabolic indices in rice.

Cellulose synthase-like OsCSLD4 plays a pivotal role in regulating diverse agronomic traits, enhancing resistance against bacterial leaf blight, and modulating metabolite indices based on the multi-omics analysis in rice. To delve deeper into this complex network between agronomic traits and metabolites in rice, we have compiled a dataset encompassing genome, phenome, and metabolome, including 524 diverse accessions, 11 agronomic traits, and 841 metabolites, enabling us to pinpoint eight hotspots through GWAS. We later discovered four distinct metabolite categories, encompassing 15 metabolites that are concurrently present on the QTL qC12.1, associated with leaf angle of flag and spikelet length, and finally focused the cellulose synthase-like OsCSLD4, which was pinpointed through a rigorous process encompassing sequence variation, haplotype, ATAC, and differential expression across diverse tissues. Compared to the wild type, csld4 exhibited significant reductions in the plant height, flag leaf length, leaf width, spikelet length, 1000-grain weight, grain width, grain thickness, fertility, yield per plant, and bacterial blight resistance. However, there were significant increase in tiller numbers, degree of leaf rolling, flowering period, growth period, grain length, and empty kernel rate. Furthermore, the content of four polyphenol metabolites, excluding metabolite N-feruloyltyramine (mr1268), notably rose, whereas the levels of the other three polyphenol metabolites, smiglaside C (mr1498), 4-coumaric acid (mr1622), and smiglaside A (mr1925) decreased significantly in mutant csld4. The content of amino acid L-tyramine (mr1446) exhibited a notable increase, whereas the alkaloid trigonelline (mr1188) displayed a substantial decrease among the mutants. This study offered a comprehensive multi-omics perspective to analyze the genetic mechanism of OsCSLD4, and breeders can potentially enhance rice's yield, bacterial leaf blight resistance, and metabolite content, leading to more sustainable and profitable rice production.

Genetic Characterization of the Glucose-PTS in Streptococcus sanguinis, examining competitive fitness.

Ecological shifts in dental microbiome from homeostasis to dysbiosis have been hypothesized to underlie several oral diseases including dental caries. Streptococcus sanguinis, a commensal bacterium, is pivotal in maintaining oral health through its metabolic activities, including the production of ammonia and hydrogen peroxide (H2O2). This study aims to elucidate the genetic underpinnings of the glucose::phosphotransferase system (PTS) in the physiology and competitive fitness of S. sanguinis within the oral microbiome, by examining single nucleotide polymorphisms (SNPs) in the EIIABMan (manL) and HPr of PTS in S. sanguinis strain SK36. Employing genetic engineering, bioinformatic analysis, growth and metabolic assays, recreating and characterizing several unique ManL SNPs in SK36 that were identified among clinical strains of S. sanguinis. Mutations in ManL and HPr correlated with altered growth dynamics, H2O2 production, acid production, and pH homeostasis in a manner uncoupled from canonical regulators such as CcpA and Rex. These genetic variations likely contributed to S. sanguinis's competitiveness, although their ecological impact remains to be further elucidated. This research is part of the ongoing effort to understand the genetic mechanisms that contribute to microbial ecology in relation to health, knowledge from which may allow for enhanced diagnostics, pro-health formulations, and other microbial interventions.

Cisplatin Impact on Kasumi-1 Leukemia: Gene Expression and DNA Damage

Purpose: Leukemia is a type of cancer caused by the uncontrolled proliferation of blood cells. The purpose of this study was to investigate the effects of cisplatin (CIS), a chemotherapeutic agent used in the treatment of leukemia, on the Kasumi-1 leukemia cell line. Materials and methods: The study measured the effect of CIS on Kasumi-1 cells by calculating IC50 values for cell viability. The mRNA expression levels of apoptosis and cell cycle-related genes were then assessed using Real-Time PCR. In addition, the effects of CIS on DNA damage were investigated using the comet assay. Results: Significant changes in apoptosis and cell cycle-related genes were observed in CIS-treated groups. These included alterations in the mRNA levels of p53, BCL-2, CHECK 1, CDC25C, CDK 6, URG4/URGCP, GADD45A, CCND1, GADD45G, and ATM genes. Comet analysis confirmed CIS's effects on DNA damage. Conclusion: This study aimed to better understand how CIS affects genetic mechanisms in leukemia cells and provide new insights into leukemia treatment. The findings will help us better understand the role of CIS in leukemia treatment and will serve as a valuable reference for future research.

Phylogenetic Relations and High-Altitude Adaptation in Wild Boar (Sus scrofa), Identified Using Genome-Wide Data.

The Qinghai-Tibet Plateau (QTP) wild boar is an excellent model for investigating high-altitude adaptation. In this study, we analyzed genome-wide data from 93 wild boars compiled from various studies worldwide, including the QTP, southern and northern regions of China, Europe, Northeast Asia, and Southeast Asia, to explore their phylogenetic patterns and high-altitude adaptation based on genome-wide selection signal analysis and run of homozygosity (ROH) estimation. The findings demonstrate the alignment between the phylogenetic associations among wild boars and their geographical location. An ADMIXTURE analysis indicated a relatively close genetic relationship between QTP and southern Chinese wild boars. Analyses of the fixation index and cross-population extended haplotype homozygosity between populations revealed 295 candidate genes (CDGs) associated with high-altitude adaptation, such as TSC2, TELO2, SLC5A1, and SLC5A4. These CDGs were significantly overrepresented in pathways such as the mammalian target of rapamycin signaling and Fanconi anemia pathways. In addition, 39 ROH islands and numerous selective CDGs (e.g., SLC5A1, SLC5A4, and VCP), which are implicated in glucose metabolism and mitochondrial function, were discovered in QTP wild boars. This study not only assessed the phylogenetic history of QTP wild boars but also advanced our comprehension of the genetic mechanisms underlying the adaptation of wild boars to high altitudes.

Epilepsy in Angelman syndrome and the most common electroencephalographic findings

Angelman syndrome is a genetic disorder characterised by severe mental retardation, subtle dysmorphic facial features, a characteristic behavioural phenotype, seizures and abnormalities in video electroencephalograms (video EEG). Angelman syndrome may be associated with genetic mechanisms involving the region of chromosome 15q11-13. Up to 90% of cases have epileptic seizures, usually in the early years of life. Videoelectroencephalography patterns with some typical characteristics associated with Angelman syndrome have been reported, although these are not specific to it, and as such it is also useful for early diagnosis, especially in the first months or years of life. To characterise the videoelectroencephalography findings of 17 patients diagnosed with Angelman syndrome, and compare them with previously published studies. We conducted a retrospective observational study of 34 video EEGs performed on 17 patients diagnosed with Angelman syndrome at the clinical neurophysiology service of the Puerta de Hierro University Hospital in Madrid between 2019 and 2022. The primary objective was to characterise the videoelectroencephalographic findings and compare them with previously published studies. As secondary objectives, we analysed the patterns proposed by Dan and Boyd, and other demographic, genetic and clinical data. Video EEG supported the clinical suspicion in our study, as baseline brain activity was altered in all the patients. We identified a pattern similar to those defined by Dan and Boyd in 88% of the cases, and the type III pattern was the most common in our series. These findings confirm that video EEG is highly sensitive for the diagnosis of Angelman syndrome, and very useful as a diagnostic biomarker in the early stages of life.

Sex differences in genotype frequency and the risk of polycythemia associated with rs13419896 and rs2790859 among Tibetan highlanders living in Tsarang, Mustang, Nepal

BackgroundTibetan highlanders have adapted to hypoxic environments through genetic mechanisms that avoid hemoglobin concentration increases and prevent polycythemia. Recently, sex differences in hemoglobin dynamics with age have been reported among Tibetan highlanders living in Tsarang. Additionally, concerns have been raised that dietary changes associated with modernization may increase the risk of polycythemia and lifestyle-related diseases among Tibetan highlanders. However, the relationship between genetic polymorphisms and the risk of lifestyle-related diseases in Tibetan highlanders has been investigated in only a few regions. This study aims to elucidate whether polymorphisms in genes related to hypoxic adaptation are associated with the incidence of lifestyle-related diseases and polycythemia and whether these polymorphisms affect hemoglobin dynamics in the residents of Tsarang, Mustang, Nepal.MethodsHealth checkup data from individuals living in Tsarang in Mustang District, Nepal, collected in 2017, were used to determine the prevalence of obesity, hypertension, diabetes, hypoxemia, and polycythemia. DNA was extracted from whole-blood samples, and data for the single-nucleotide polymorphisms (SNPs) rs13419896 (EPAS1), rs12619696 (EPAS1), and rs2790859 (EGLN1) were obtained using real-time PCR. The health checkup data were statistically analyzed to determine the associations of these diseases with polymorphisms in genes related to hypoxic adaptation.ResultsA total of 168 participants, comprising 78 males and 90 females, were included in the final analysis. In terms of the prevalence of each disease, only the prevalence of polycythemia significantly differed between sexes (p < 0.01). Additionally, among the three analyzed SNPs, significant sex differences in genotype frequency were observed for rs13419896 and rs2790859. For rs2790859 in females, Tibetan highlanders with the adaptive genotype had a significantly lower incidence of polycythemia (p < 0.01) and significantly lower hemoglobin concentrations (p < 0.01).ConclusionsThis study revealed that there are sex differences in the genotype frequency of gene-related hypoxic adaptations among the residents of Tsarang. The findings also suggested that the rs2790859 polymorphism might be involved in the recent incidence of polycythemia among Tsarang residents. If the frequency of non-Tibetan genotypes increases due to intermixing with other populations in the Mustang District, polycythemia may emerge as a modern disease. It is essential to continue investigating the health status of Mustang residents to elucidate various aspects of hypoxic adaptation and disease susceptibility.

Discovery of key volatile compound and regulatory gene governing the ‘taro-like’ aroma in wax gourd (Benincasa hispida)

The distinctive ‘taro-like’ aroma in wax gourd has become a crucial flavor characteristic, significantly enhancing its market value. Despite its importance, the volatile compounds responsible for this aroma and their genetic regulatory mechanisms have not been sufficiently studied. Utilizing headspace-gas chromatography-quadrupole time of flight-mass spectrometry (HS-GC-QTOF-MS), this research examined the volatile compounds in wax gourd germplasms with and without the ‘taro-like’ aroma, identifying 2-acetyl-1-pyrroline (2-AP) as the primary volatile responsible for this aroma. To uncover the genetic basis of this trait, segregating populations and recombinant inbred lines (RILs) were developed from MY-1 x GX-71 germplasms, which exhibit significant differences in aroma expression. Genetic analysis revealed that a single recessive gene governs the ‘taro-like’ aroma trait in wax gourd. Through bulked segregant analysis sequencing (BSA-seq) and quantitative trait loci (QTL) mapping, the candidate region for this aroma gene was localized to a 285.29 kb interval on Chromosome 2. Further examination of candidate gene expression and sequence variations highlighted the BhBADH gene's critical role in the formation of the ‘taro-like’ aroma. Additionally, RNA-seq analysis revealed significant enrichment of differentially expressed genes (DEGs) associated with metabolic pathways involved in environmental information processing, which contribute to 2-AP synthesis in wax gourd with a ‘taro-like’ aroma. Our research provides a theoretical foundation for the molecular breeding to enhance the aroma quality of wax gourd.

Genomic Analysis and Virulence Assessment of Hypervirulent Klebsiella pneumoniae K16-ST660 in Severe Cervical Necrotizing Fasciitis

ObjectiveTo investigate the source of infection in a patient with recurrent severe neck infections caused by Klebsiella pneumoniae and to analyze the virulence of isolates obtained from different sites of the patient. MethodsWe collected preoperative neck abscess puncture fluid, intraoperative neck drainage fluid, sputum, intestinal fecal specimens, and blood samples from a patient who visited Wuxi Second People's Hospital twice between 2017 and 2018. We conducted isolation, identification, drug sensitivity tests, and string tests on the isolates. Capsule serotyping and virulence gene analysis were performed using PCR. The genetic relationship of different isolates was assessed by Multilocus Sequence Typing and virulence was evaluated using the Galleria mellonella infection model. Additionally, whole-genome sequencing was used to analyze the chromosomal and plasmid genes of one isolate. ResultsKlebsiella pneumoniae was detected in the sputum and fecal specimens from both hospitalizations, as well as the preoperative ultrasound-guided puncture fluid and intraoperative drainage fluid from the first hospitalization, resulting in six isolates. These isolates were all K16 serotype, positive in the string test, and identified as ST660 by Multilocus Sequence Typing, indicating they belonged to the same clone. Virulence gene analysis showed that wcaG, iucB, iroNB, rmpA, rmpA2, Aer, kfuBC, ureA, fimH, mrkD, uge, and peg344 were positive, while allS, cf29a, and Wzy_K1 were negative. In the Galleria mellonella virulence assay, the lethality of different isolates was dose-dependent. The K16 group showed significantly higher larval mortality compared to other control groups (including K1, K2, K5, K20, and K57 groups). Genome sequencing revealed that plasmid p17388 carried numerous virulence genes and insertion sequences, particularly ISKPN74, and showed high homology with other Klebsiella plasmids. ConclusionThis study is the first to report severe cervical necrotizing fasciitis caused by the K16-ST660 Klebsiella pneumoniae Isolate. The high virulence of these isolates was confirmed by the Galleria mellonella virulence assay and the detection of numerous virulence genes. In-depth analysis of plasmid p17388 suggests that ISKPN74 may enhance stable integration of the plasmid into the bacterial chromosome through recombinases and transposases, thereby reducing the likelihood of plasmid loss and increasing bacterial virulence. Additionally, IS5 family insertion sequences may carry extra promoters or enhancers that, when inserted upstream of mucoviscosity-associated genes such as rmpA, may increase the transcription levels of downstream genes. This ISKPN74-mediated integration or insertion reveals a complex genetic mechanism that may contribute to the severity of infections caused by ST660 isolates. Our findings offer new insights into the virulence and structure of ST660-K16 Klebsiella pneumoniae, suggesting that further investigation into the specific mechanisms by which these insertion sequences enhance virulence could aid in developing novel infection management strategies.

Genome of Russian Snow-White Chicken Reveals Genetic Features Associated with Adaptations to Cold and Diseases.

Russian Snow White (RSW) chickens are characterized by high egg production, extreme resistance to low temperatures, disease resistance, and by the snow-white color of the day-old chicks. Studying the genome of this unique chicken breed will reveal its evolutionary history and help to understand the molecular genetic mechanisms underlying the unique characteristics of this breed, which will open new breeding opportunities and support future studies. We have sequenced and made a de novo assembly of the whole RSW genome using deep sequencing (250×) by the short reads. The genome consists of 40 chromosomes with a total length of 1.1 billion nucleotide pairs. Phylogenetic analysis placed the RSW near the White Leghorn, Fayoumi, and Houdan breeds. Comparison with other chicken breeds revealed a wide pool of mutations unique to the RSW. The functional annotation of these mutations showed the adaptation of genes associated with the development of the nervous system, thermoreceptors, purine receptors, and the TGF-beta pathway, probably caused by selection for low temperatures. We also found adaptation of the immune system genes, likely driven by selection for resistance to viral diseases. Integration with previous genome-wide association studies (GWAS) suggested several causal single nucleotide polymorphisms (SNPs). Specifically, we identified an RSW-specific missense mutation in the RALYL gene, presumably causing the snow-white color of the day-old chicks, and an RSW-specific missense mutation in the TLL1 gene, presumably affecting the egg weight.

Expression of CLDN1 and EGFR in PTC

Papillary thyroid carcinoma (PTC) involves complex genetic mechanisms, notably involving CLDN1 and EGFR. This study investigates the expression and variations of these genes and their effects on tumor behavior and patient outcomes. Meta-analysis of CLDN1 and EGFR expression in TCGA–PTC patients and GEO datasets was conducted. cBioPortal was used for clinical analysis. GSEA, GO, KEGG, Hallmark pathways, and cibersort analysis were applied. Cell proliferation, migration, invasion, and apoptosis were assessed in vitro. Co-culturing with CD8+ T cells, MTT assay, ELISA, subcutaneous tumor models, and immunohistochemistry were performed. TGF-β pathway-related proteins were analyzed via Western blot. CLDN1 and EGFR were overexpressed in PTC tumors, correlating with higher-risk patients and reduced CD8+ T cell infiltration. Silencing these genes inhibited tumor cell functions and enhanced CD8+ T cell activity, both in vitro and in vivo. CLDN1 and EGFR are crucial in PTC, linked to tumor invasiveness, EMT, and immune suppression, presenting them as potential therapeutic targets.

Activity History of the Gangga Graben in the Southern Segment of Kung Co Rift in Southern Tibet Constrained by ESR and U‐Series Dating

ABSTRACTCharacterising the spatial and temporal distribution of the S‐N‐trending rift in southern Tibet is crucial for elucidating the dynamics of E‐W extension within the Tibetan Plateau since the Miocene. The Kung Co–Tangra Yumco rift, located in the central part of the rift system, was initiated at the peak of rifting development. While the initiation of rifting has been ascertained through low‐temperature thermochronology, direct timing constraints remain absent for the Gangga Graben in the southernmost region. Utilising the quartz electron spin resonance (ESR) dating technique, we ascertained the onset age of the eastern boundary fault of the Gangga Graben to be 12.00 ± 1.80 Ma, with an accelerated activity phase at 9.17 ± 1.19 Ma, and an activity age for the western boundary fault at 2.22 ± 0.24 Ma. U‐series dating conducted on the western boundary disclosed a time span of 20–13 ka for hot spring fissure activity. Seismic evidence, inclusive of those from the Gongdapu Horst, indicates persistent activity of the Gangga Graben since the Pleistocene. Comparative analysis of age data from the Kung Co–Tangra Yumco rift suggests that it commenced almost synchronously along its strike at ~14.5–12 Ma. Considering the rifts trending from west to east in southern Tibet and the genetic mechanism of leucogranite, we propose an E‐W extension mechanism in southern Tibet. At ~26–14 Ma, the lithosphere experienced weakened delamination and asthenosphere upwelling, leading to a series of magmatic activities and onset of E‐W extension in southern Tibet. At ~17–7 Ma, as the basal shearing of the underthrusting Indian Plate increased, it marked the peak phase of rifting in southern Tibet.