Region Of Gene Research Articles

Anthracnose Leaf spot on Hymenocallis littoralis Caused by Colletotrichum endophyticum in Guangxi, China

Hymenocallis littoralis (Jacq.) Salisb. is a secondary protected plant in China with high ornamental value (Nadaf et al. 2018) and widely distributed in Guangxi. In March 2023, 100 % of H. littoralis plants and over 80 % leaves of each plant showed leaf spot in three parks located in Nanning (N22°80′-22°82′, E108°30′-109°33′), Guangxi, China. In the early stages, the edges and central areas of the lesions were yellowish and green, respectively. Later, the lesions became reddish-brown to brown in central areas and yellowish at the edges. A pathogen was isolated from three diseased leaf samples that were collected from the three parks, respectively. Tissues were cut from infected margins, sterilized, and placed on potato dextrose agar (PDA) at 25 °C. After 5 days, twenty-four isolates with similar morphology were retained. Three strains BJB7-1, BJH5-1, and BJH3-1, one from each of three parks, were selected for further studies. On PDA, the isolates exhibited white colonies, with single-celled, hyaline, and cylindrical conidia which measured 12.3 to 14.0×2.0 to 3.8 μm (n = 90). The appressoria were single, brown or black, and irregular in shape, and measured 7.6 to 8.6×6.1 to 6.9 μm (n = 90). These morphological characteristics were similar to Colletotrichum spp. (Damm et al. 2019). The ITS region, and ACT, CAL, CHS-1, GAPDH, and TUB2 genes were sequenced for further identification (Silva et al. 2019). All sequences were deposited in GenBank (ITS: PQ218080 to PQ218082, ACT: PQ219629 to PQ219631, CAL: PQ219632 to PQ219634, CHS-1: PQ219635 to PQ219637, GAPDH: PQ219638 to PQ219640, TUB2: PQ219641 to PQ219643). BLASTn analysis of sequences of three strains exhibited 99% similarity with C. endophyticum (strains LC 0324) NR160814.1 of ITS (over 99%), KF306258.1 of ACT (97-99%), KC832854.1 of GAPDH (over 98%), and MZ673954.1 of TUB2 (over 99%). Based on the concatenated sequence ITS-ACT-CAL-CHS-1-GAPDH-TUB2, a phylogenetic tree was constructed using RAxML version 8.2.10, and the three strains clustered with the type strain C. endophyticum LC 0324. Pathogenicity was performed on healthy, tender, and attached leaves of five-month H. littoralis plants with and without wounds by inoculating the leaves with 20 μL (106 conidia/mL), and blank control was inoculated with 0.05% Tween-20. The plants were kept in a greenhouse at 25°C and covered with plastic bags to maintain humidity. After 9 days, all wounded and inoculated leaves showed symptoms, while the unwounded and control remained asymptomatic. The pathogenicity test was repeated three times with similar results. Koch’s postulates were completed by reisolating from inoculated and non-inoculated tissues. C. endophyticum was only recovered from inoculated tissues, and identity of the fungus was confirmed based on morphology and multigene sequences. C. siamese (Huang et al., 2021) and C. gloeosporioides (Zhao et al., 2019) were reported on H. littoralis in China. C. endophyticum could cause anthracnose leaf spot on Capsicum annuum (Noor et al., 2018), Camellia sinensis (Wang et al., 2016), and coffee plant (Cao et al., 2019). To the best of our knowledge, this is the first report of anthracnose leaf spot caused by C. endophyticum on H. littoralis. The latter is a very important garden plant, but may be susceptible to leaf spots, thus affecting its ornamental value. Therefore, this investigation can contribute to effective management of the disease.

Locuszoomr: an R package for visualising publication-ready regional gene locus plots

Abstract Summary Locuszoomr is an R package for visualising and creating publication-ready regional gene locus plots similar to those produced by the original web interface ‘LocusZoom’, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics or ‘ggplot2’, allowing flexibility and easy customisation. Modular plotting functions enable layering of multiple GWAS plots such as for PheWAS, comparing GWAS with eQTL signals, and aligning multiple locus plots on the same page. Interactive plots can be visualised using ‘plotly’ enabling quick identification of data points for labelling. The ‘LDlink’ API (https://ldlink.nih.gov/) can be programmatically queried to obtain linkage disequilibrium (LD) data from the 1000 Genomes Project which is overlaid on plots. The package allows users to query Ensembl databases from Bioconductor or AnnotationHub for genomic information, so it can be used to show gene track information for any species available in Ensembl. Helper functions enable recombination rate data from UCSC to be overlaid on plots. The package has a detailed vignette and includes embedded example GWAS data to allow users to try out different features. Locuszoomr is also fast: identifying 50 peaks in a GWAS of around 8 million SNPs takes around 0.6 seconds. Exporting 50 locus plots with 1Mbp window with recombination rate takes around 30 seconds on Intel 9th gen CPU or 14 seconds on Apple ARM M3. Availability and implementation The R package locuszoomr is open-source and available from CRAN: https://cran.r-project.org/package=locuszoomr and GitHub: https://github.com/myles-lewis/locuszoomr

Depression symptom-specific genetic associations in clinically diagnosed and proxy case Alzheimer’s disease

Abstract Depression is a risk factor for the later development of Alzheimer’s disease (AD), but evidence for the genetic relationship is mixed. Assessing depression symptom-specific genetic associations may better clarify this relationship. To address this, we conducted genome-wide meta-analysis (a genome-wide association study, GWAS) of the nine depression symptom items, plus their sum score, on the Patient Health Questionnaire (PHQ-9) (GWAS-equivalent N: 224,535–308,421) using data from UK Biobank, the GLAD study and PROTECT, identifying 37 genomic risk loci. Using six AD GWASs with varying proportions of clinical and proxy (family history) case ascertainment, we identified 20 significant genetic correlations with depression/depression symptoms. However, only one of these was identified with a clinical AD GWAS. Local genetic correlations were detected in 14 regions. No statistical colocalization was identified in these regions. However, the region of the transmembrane protein 106B gene (TMEM106B) showed colocalization between multiple depression phenotypes and both clinical-only and clinical + proxy AD. Mendelian randomization and polygenic risk score analyses did not yield significant results after multiple testing correction in either direction. Our findings do not demonstrate a causal role of depression/depression symptoms on AD and suggest that previous evidence of genetic overlap between depression and AD may be driven by the inclusion of family history-based proxy cases/controls. However, colocalization at TMEM106B warrants further investigation.

Identification and Analysis of Melon (Cucumis melo L.) SHMT Gene Family Members and Their Functional Studies on Tolerance to Low-Temperature Stress

Melon (Cucumis melo L.) is a significant cash crop globally and is cherished for its sweet and flavorful fruits, as well as its high nutritional values. However, its yield and quality are limited by various factors, including drought, salinity, and low temperatures. Low temperatures are one of the primary factors influencing the growth and development of melons, diminishing the viability, germination, and growth rate of melon seeds. Concurrently, low temperatures also reduce light absorption efficiency and fruit yields, thereby affecting melon growth and development. Serine hydroxymethyltransferase (SHMT), a conserved phosphopyridoxal-dependent enzyme, plays a crucial role in plant resistance to abiotic stressors. In this study, eight CmSHMT family genes were identified from the melon genome. We predicted their chromosomal locations, physicochemical properties, gene structures, evolutionary relationships, conserved motifs, cis-acting elements of promoters, and tissue-specific expression patterns. The expression levels of CmSHMT family genes in response to low-temperature stress was then analyzd using qRT-PCR. The phylogenetic results indicated that these CmSHMT genes were classified into four subfamilies and were unevenly distributed across five chromosomes, with relatively high conservation among them. Furthermore, our investigation revealed that the promoter regions of the CmSHMT family genes contain many cis-acting elements related to phytohormones, growth, and various stress responses. The relative expression levels of CmSHMT3, CmSHMT4, CmSHMT6, and CmSHMT7 were higher under low-temperature stress compared to the control group. Notably, the promoter region of CmSHMT3 contains cis-acting elements associated with low-temperature response (LTR) and abscisic acid response (ABRE). It is suggested that the mechanism through which CmSHMT3 responds to low-temperature stress treatments may be associated with hormonal regulation. These findings provide a foundation for the further exploration of CmSHMT family genes in melon and their functional roles in response to low-temperature stress, and they provide a theoretical basis for the targeted breeding of superior melon varieties with enhanced tolerance to low temperatures.

Environmental gradients shape genetic variation in the desert moss, Syntrichia caninervis Mitt. (Pottiaceae)

The moss Syntrichia caninervis Mitt. is distributed throughout drylands globally, and often anchors ecologically significant communities known as biological soil crusts (biocrusts). The species occupies a variety of dryland habitats with varying levels of drought and temperature stress, suggesting the potential for ecological specialization within S. caninervis. Here, we sampled S. caninervis from sites along two elevation gradients and used restriction site associated DNA sequencing to compare the relative impacts of environmental factors and geospatial distances on genetic differentiation in S. caninervis populations. While we found no evidence of isolation by distance in our data, one environmental variable, mean annual precipitation (MAP), was found to be a positive predictor of FST. An ecological association analysis identified 32 SNP alleles that covary significantly with MAP, 15 of which fall within the exonic regions of genes with annotations suggesting diverse roles in response to dehydration stress. Understanding the degree to which genetic variation in S. caninervis is associated with environmental factors is key to predicting its potential for persistence in the face of global climate change, which is predicted to be especially detrimental to desert organisms already living at their physiological limits.

Presence of the Anopheles culicifacies complex species A in southeast Iran

BackgroundThe Anopheles culicifacies complex is one of the most important malaria vectors in Southeast Asia and Southeastern Iran. Although the sibling species within this complex are morphologically indistinguishable, they differ significantly in their disease transmission potential, blood-feeding behaviour, and other biological traits. Cytogenetic and chromosomal studies have identified five sibling species within this complex: A, B, C, D, and E. Understanding the species composition and distribution of this complex is crucial for malaria control strategies.ObjectivesThis study aimed to identify the sibling species of the An. culicifacies complex in Qaleh Ganj County, Kerman Province, Southeastern Iran. Specifically, the study sought to determine the presence of species A, which is known to be a primary vector of malaria in the region.MethodsWe employed allele-specific PCR and sequencing PCR techniques to identify the sibling species. DNA was extracted from mosquito specimens, and the D3 region of the 28S rDNA gene and a segment of the COII gene from the mitochondrial genome (mtDNA) were targeted for amplification and sequencing.ResultsData analysis revealed a positive correlation between An. culicifacies s.l. specimens and altitude, with most specimens collected from mountainous areas. Both allele-specific PCR and sequencing PCR confirmed the presence of species A in the study areas of Kerman Province.ConclusionsGiven that species A is a primary malaria vector, the findings of this study provide valuable insights for guiding malaria control strategies in Southeastern Iran. Further studies are recommended to assess the vector competence and ecological dynamics of other species within the An. culicifacies complex in the region.

Changes in RNA Splicing: A New Paradigm of Transcriptional Responses to Probiotic Action in the Mammalian Brain

Elucidating the gene regulatory mechanisms underlying the gut–brain axis is critical for uncovering novel gut–brain interaction pathways and developing therapeutic strategies for gut bacteria-associated neurological disorders. Most studies have primarily investigated how gut bacteria modulate host epigenetics and gene expression; their impact on host alternative splicing, particularly in the brain, remains largely unexplored. Here, we investigated the effects of the gut-associated probiotic Lacidofil® on alternative splicing across 10 regions of the rat brain using published RNA-sequencing data. The Lacidofil® altogether altered 2941 differential splicing events, predominantly, skipped exon (SE) and mutually exclusive exon (MXE) events. Protein–protein interactions and a KEGG analysis of differentially spliced genes (DSGs) revealed consistent enrichment in the spliceosome and vesicle transport complexes, as well as in pathways related to neurodegenerative diseases, synaptic function and plasticity, and substance addiction across brain regions. Using the PsyGeNET platform, we found that DSGs from the locus coeruleus (LConly), medial preoptic area (mPOA), and ventral dentate gyrus (venDG) were enriched in depression-associated or schizophrenia-associated genes. Notably, we highlight the App gene, where Lacidofil® precisely regulated the splicing of two exons causally involved in amyloid β protein-based neurodegenerative diseases. Although the splicing factors exhibited both splicing plasticity and expression plasticity in response to Lacidofil®, the overlap between DSGs and differentially expressed genes (DEGs) in most brain regions was rather low. Our study provides novel mechanistic insight into how gut probiotics might influence brain function through the modulation of RNA splicing.

First Report of Anthracnoseon on Annona squamosa L. Caused by Colletotrichum fructicola in China.

Annona squamosa L. is a tropical fruit, cultivated in various provinces of China, such as Guangxi, Taiwan, and Yunnan. This fruit has good edible and medicinal value. In November 2021, anthracnose on A. squamosa L. fruits was observed in a plantation in Longzhou (22°11´N, 106°51´E), Guangxi, China. The incidence rate of the plantation was 13.6%. The symptoms included gray-black to black spots, initially small and blackish brown, which expanded into large irregular spots(Fig.1A-B). To isolate the pathogen, symptomatic fruits were collected and small pieces (5 mm2) were cut from the lesions, surface sterilized in 75% ethanol for 15 seconds, followed by 2% AI sodium hypochlorite solution for 3 minutes, rinsed three times with sterile water, and incubated on PDA at 28°C. A total of 23 isolates with identical morphology were obtained and 3 representative isolates (FLZ-1 to FLZ-3) were selected for further characterization. The fungal colonies presented concentric rings on PDA plates, initially white, later turning gray green and producing light orange conidia(Fig.1C). The mature conidia were cylindrical, unicellular, with dimensions of 11.09-20.02 μm × 4.06-6.54 μm, usually containing 2 oil droplets with a size of 3.21-8.36 μm × 2.50-4.55 μm, and L/W ratio of 1.11-2.09(n=100) (Fig.1D). These morphological features were aligned with those of Colletotrichum spp. (Weir et al. 2012). To confirm the identity of the isolates, DNA was extracted and specific gene regions were amplified and sequenced using the following primer sets: ITS (ITS1 and ITS4), GAPDH (GPD1 and GPD2), ACT (ACT-512F and ACT-783R), TUB (T1 and Bt2b), CHS-1 (CHS-79F and CHS-354R), and ApMat (AM-F and AM-R) (Wang et al. 2024). Sequences were submitted to GenBank (Accession nos. PP968176 to PP968178 for ITS, PQ122814 to PQ122816 for GAPDH, PQ122808 to PQ122810 for ACT, PQ169643 to PQ169645 for TUB2, PQ122811 to PQ122813 for CHS-1, and PQ152017 to PQ152019 for ApMat). Maximum likelihood phylogenetic analysis using combined sequences of ITS, GAPDH, ACT, TUB2, CHS-1 and ApMat in MEGA X confirmed the isolates as Colletotrichum fructicola (Fig.2), marking the first report of this pathogen on A. squamosa L. in China. Pathogenicity tests were conducted on wound and nonwound healthy A. squamosa L. fruits to confirm the pathogenicity of the isolated C. fructicola. The fruits were wounded using a sterile needle. Each wounded and nonwounded fruit was inoculated with a 10 µL conidial suspension (1×106 conidia/mL) drop at corresponding sites. Control fruits were inoculated with sterile water. Five fruits per treatment were used and the experiment repeated three times. The fruits were placed in an incubator at 28°C and 85% RH. Anthracnose symptoms developed on the inoculated fruits within 5 days (Fig.1E-F), while control fruits remained symptom-free (Fig.1G-H). C. fructicola was successfully reisolated from the symptomatic fruits, fulfilling Koch's postulates and confirming its role as the causal agent of the disease. According to previous reports, C. fructicola also causes anthracnose on Psidium guajava (William R. O et al. 2024), leaf spots on apple (Moreira Rafaele R et al. 2019), and Kadsura coccinea (Jiang et al.2021). This study identifies C. fructicola as the pathogen causing anthracnose on A. squamosa L. and no cases have yet been discovered in the field in China. This report will raise awareness among growers about the anthracnose disease of A. squamosa L. and develop effective disease control strategies.

Genetic Diversity of Tobacco mosaic virus (TMV) isolates from tobacco growing fields of Western Anatolia, Türkiye

Tobacco mosaic virus (TMV) is an important plant virus that is common in agriculture. It is the first evidence of the existence of viruses in history. Studies on the genetic diversity of the CP gene of TMV, which plays a leading role in host interaction, are limited both in our country and around the world. Genetic diversity analyses were conducted on ten isolates of the full CP gene region of TMV obtained from the most intensive tobacco cultivation areas in our country, and compared with global isolates. TMV infection was detected in 32 out of 300 plants collected from the Aegean and Marmara regions (Çanakkale, Balıkesir, İzmir, Manisa, Uşak, Aydın and Denizli) between 2019 and 2020 using conventional molecular techniques. To genetically characterize the virus, 10 samples were selected from each region, and the complete CP gene region sequences were determined. The aligned CP gene region sequences of TMV from Türkiye and its global isolates exhibited nucleotide homology ratios ranging from 87.7% to100%, with amino acid ratios ranging from 88.7% to 100%. The Türkiye isolates displayed similarity rates of 98.5% to 100% at the nucleotide level and 98.7% and 100% at the amino acid level. In phylogenetic analysis, the 196 known isolates of TMV registered in GenBank, belong to the CP gene region, were divided into two main clades (I and II) and two subclades (Ia and Ib). Turkish isolates were clustered in the major branch with the main clade I and subclade Ia isolates. Therefore, genetic analyses were performed on the CP gene region isolates obtained from different parts of the world and a wide range of hosts, including the isolates obtained from Türkiye. The results showed high genetic stability, similar to many tobamoviruses.

Localization and Molecular Cloning of the ASMT Gene for Melatonin Synthesis in Pigs

Melatonin is synthesized in multiple tissues and organs of pigs, and existing studies have shown the presence of the melatonin-synthesizing enzyme ASMT protein. However, the genomic information for the ASMT gene has been lacking. The aim of this study was to locate the genomic information of the ASMT gene in pigs using comparative genomics analysis and then obtain the coding region information through molecular cloning. First, using the NCBI Genome Data Viewer, we found that in most animals, the AKAP17A gene is often located next to the ASMT gene, with both genes arranged in the same direction. Similarly, the P2RY8 gene is commonly adjacent to the ASMTL gene, also in the same orientation. We also discovered that the ASMTL gene is frequently adjacent to the ASMT gene and arranged in the opposite direction. Using the “three-point localization” principle, we inferred the position of the ASMT gene based on the coordinates of AKAP17A and ASMTL in pigs. Our results revealed that on the pig X chromosome, a gene called LOC110258194 is located next to the AKAP17A and ASMTL genes, and its arrangement aligns with the ASMT gene in other species. Additionally, Ensembl contains a gene, ENSSSCG00000032659, at the same position, with completely overlapping exons, though it is not annotated as ASMT. Further analysis using the TreeFam tool from EMBL-EBI and the CDD tool from NCBI revealed that LOC110258194 and ENSSSCG00000032659 do not contain the typical Maf domain of ASMTL and, thus, should not be annotated as ASMTL, but rather as the ASMT gene. Using a slow-down PCR method for high-GC content genes, we successfully cloned the full CDS region of the pig ASMT gene and identified a new transcript missing Exon 6 and Exon 7. This transcript was submitted to NCBI and assigned the GenBank accession number MW847601. Our results represent the first successful localization of the ASMT gene in pigs, the first cloning of the ASMT gene’s coding region, and the first discovery of a new transcript of the pig ASMT gene.

Genome-Wide Analysis and Expression Profiling of Watermelon VQ Motif-Containing Genes Under Abiotic and Biotic Stresses

Valine-glutamine (VQ) motif-containing proteins play important roles in diverse plant developmental processes and signal transduction in response to biotic and abiotic stresses. However, no systematic investigation has been conducted on VQ genes in watermelon. In this study, we identified 31 watermelon VQ genes, which were classified into six subfamilies (I–VI). All of the deduced proteins contained a conserved FxxxVQxL/F/VTG motif. Eleven ClVQs were involved in segment duplication, which was the main factor in the expansion of the VQ family in watermelon. Numerous stress- and hormone-responsive cis-elements were detected in the putative promoter region of the ClVQ genes. Green fluorescent protein fusion proteins for ten selected ClVQs were localized in the nucleus, but three ClVQs also showed signals in cell membranes and the cell wall, thus confirming their predicted divergent functionality. Quantitative real-time PCR (qRT-PCR) analysis indicated that the majority of ClVQ genes were specifically or preferentially expressed in certain tissues or organs, especially in the male flower. Analyses of RNA-sequencing data under osmotic, cold, and drought stresses and Cucumber green mottle mosaic virus (CGMMV) infection revealed that the majority of ClVQ genes, especially those from subfamily IV, were responsive to these stresses. The results provide useful information for the functional characterization of watermelon ClVQ genes to unravel their biological roles.

Loss of Myostatin Affects m6A Modification but Not Semen Characteristics in Bull Spermatozoa

N6-methyladenosine (m6A) modification is a key methylation modification involved in reproductive processes. Myostatin gene editing (MT) in cattle is known to enhance muscle mass and productivity. However, the changes in m6A modification in MT bull sperm remain poorly understood. In the MT and wild-type (WT) groups, we identified 25,542 and 22,253 m6A peaks, respectively, mainly concentrated in the coding sequence (CDS) and 3′ untranslated region (UTR) of genes. The MT group showed an increase in gene transcription, but there was no significant difference in the overall m6A peaks pattern. There was also no significant difference in m6A motif and chromosome distribution between MT and WT groups. Most genes had less m6A modification sites. A total of 1120 m6A peaks were significantly different, corresponding to 1053 differentially m6A-methylated genes (DMMGs). These DMMGs are mainly associated with G protein-coupled receptor signaling pathways and the overall composition of the cell membrane. Furthermore, an MCL clustering analysis of 111 differentially m6A-methylated and expressed genes identified seven key genes (RHOA, DAAM1, EXOC4, GNA12, PRICKLE1, SCN1A, and STXBP5L), with the cytoskeleton and migration-related gene, RHOA, being the most important gene located at the center of the gene network. However, the analysis of sperm morphology and motility indicated no significant changes in semen volume, sperm count, sperm viability, plasma membrane integrity, acrosome membrane integrity, or mitochondrial membrane integrity. This study provides a map of m6A methylation in spermatozoa from MT and WT bulls, identifies key differential m6A genes that are affected by the myostatin gene but do not affect sperm morphology and viability in MT bulls, and provides a theoretical basis for the breeding quality of MT bulls.

Comprehensive Analysis of TSPAN32 Regulatory Networks and Their Role in Immune Cell Biology

Tetraspanin 32 (TSPAN32), a member of the tetraspanin superfamily, is one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of chromosome 11p15.5, a critical tumor-suppressor gene region. Although the biology of TSPAN32 remains largely unexplored, accumulating evidence suggests its involvement in hematopoietic functions. In this study, we performed a comprehensive analysis of the expression patterns and regulatory roles of TSPAN32. Notably, TSPAN32 is highly expressed in immune cells, particularly in natural killer (NK) cells and CD8+ T cells. The observed downregulation of TSPAN32 during immune cell activation highlights its potential role as a regulator of immune cell activation and metabolic adaptations, which are crucial for effective immune responses against pathogens and tumors. Moreover, the modulation of biological processes following TSPAN32 knockout further supports its critical role in regulating immune cell physiology and responses. These findings not only shed light on the biology of TSPAN32 but also provide the basis for exploring its diagnostic, prognostic, and therapeutic potential in autoimmune and inflammatory disorders, as well as in hematopoietic cancers.

A leucine responsive small RNA AbcR200 regulates expression of the lactate utilization (lut) operon in Acinetobacter baumannii DS002.

Noncoding small RNAs are essential for modulating bacterial gene expression, especially under carbon and nutrient-limited conditions. In this study, by employing both in silico and molecular hybridization tools, we identified a carbon source responsive small RNA in A. baumannii DS002. Expression of corresponding gene, abcR200, located at the intergenic region of omt (O-methyltransferase) and orf72 genes, is under the transcriptional control of a global transcriptional factor, Leucine Responsive Regulatory Protein (Lrp). A sequence motif that serves as a target for Lrp was found overlapping the abcR200 promoter (PabcR200). Chromatin immunoprecipitation (ChIP) demonstrated that Lrp oligomers, formed under low leucine conditions, strongly interacted to the PabcR200. However, the observed interactions were disrupted in the presence of leucine, as leucine promoted dissociation of Lrp to monomers and dimers, the conformation unfavourable to interact with PabcR200. The abcR200 promoter activity increased with increase of exogenous leucine concentrations, and at 2 mM maximum promoter activity was observed. The AbcR200 target mRNAs were identified by analysing the transcriptome of abcR200 negative strain of A. baumannii. Intriguingly, in abcR200 negative background, expression of lut (lactate utilization) mRNA has increased, suggesting that lut mRNA as one of the mRNA targets for AbcR200. Consistent of this observation, there existed extensive sequence complementarity between AbcR200 and lut mRNA, especially in the regions coding LutP, LutE and LutR. In support of the observed sequence complementarity, the levels of lut mRNA encoded proteins got elevated in abcR200 negative HS002 strains suggesting a role for AbcR200 in translational inhibition of lut mRNA.

Tandem mass spectrometry screening and genetic analysis of neonates with Urea cycle disorders

To explore the results of four types of Urea cycle disorders (UCDs) in newborns from the Xuzhou region, assess the efficacy of newborn screening by tandem mass spectrometry (MS/MS), and analyze their genetic characteristics. A retrospective analysis was performed using tandem mass spectrometry to screen for inherited metabolic disorders in 691 712 newborns at the Maternal and Child Health Care Hospital of Xuzhou from November 2015 to December 2023. Ten children (cases 1-10) were diagnosed with Ornithine transcarbamylase deficiency (OTCD), Carbamoylphosphate synthase 1 deficiency (CPS1D), Arginase deficiency (ARGD), and Argininosuccinate synthase deficiency (ASSD) based on MS/MS and genetic testing. This study was approved by the Medical Ethics Committee of Xuzhou Maternity and Child Health Care Hospital (Ethics No.XZFY2024-051K-01J). A total of 691 712 neonates were screened for UCDs using MS/MS, which identified 1 237, 1 237, 510, and 1 009 initial positive cases for OTCD, CPS1D, ASSD, and ARGD, respectively. After genetic testing, 1 case of OTCD, 1 case of CPS1D, 1 case of ASSD, and 7 cases of ARGD were confirmed. The overall positive predictive value for these four UCDs was 0.362%. Among the 10 diagnosed UCD cases, four novel variants were identified, which included OTC: c.1024C>A (p.L342M) and ASS1: c.826A>G (p.M276V), c.695C>T (p.P232L) and c.694C>T (p.P232S). Bioinformatic analysis has rated these as variants of uncertain clinical significance or likely pathogenic based on guidelines from the American College of Medical Genetics and Genomics (ACMG). The incidence of four UCDs in neonates from the Xuzhou area is relatively low, and there is a correlation between genetic variants and clinical phenotypes. For novel variants with uncertain clinical significance or suspected pathogenicity, their pathogenicity should be clarified in conjunction with clinical and biochemical indicators. The four novel pathogenic variants of UCDs identified in this study have enriched the mutational spectrum of UCDs-associated genes in the Xuzhou region.

First Report of Agroathelia delphinii Causing Rhizome Rot of Polygonatum cyrtonema Hua (Duohua Huangjing) in China.

Polygonatum cyrtonema Hua (Duohua Huangjing, Asparagaceae in angiosperms) is a traditional medicinal and edible plant in China. Its rhizomes can potentially enhance immunity, reduce tumor growth and the effects of aging, improve memory, and even reduce blood sugar levels (Zhao et al. 2020). Many Polygonatum-derived health-care products have been developed, and annual demand in China for processed Polygonatum is up to 4000 tons (Su et al. 2018). However, in May 2024 there was an outbreak of rhizome rot in the P. cyrtonema Hua planting fields (N31°01'50″, E121°26'31″) located on the Shanghai Jiao Tong University campus, China. Approximately 40 % of the plants were affected. The surfaces of the rhizomes appeared rotten and were covered with white and turquoise hyphae. We also observed brown, basal stem necrosis, as well as leaf yellowing and wilting. To isolate the causal organism, affected rhizome tissues were disinfected with 75% ethanol for 1 min, rinsed 5 times with sterile water, placed on potato dextrose agar (PDA) medium containing 50 µg/ml of Chlortetracycline, and then incubated at 28 ℃. Hyphal tips of the resulting fungal colonies were sub-cultured after 3 days of incubation. The suspect pathogen had white, fluffy aerial mycelium, and grew radially at an average rate of 13.75 ± 0.55 mm/day. White sclerotia werebserved after 5 days of incubation, which subsequently turned yellow-brown, and ultimately reddish brown after 2 weeks. Mature sclerotia were of the globular or ellipsoidal type (0.6-2.1 mm in diameter with a mean of 1.23 mm; n = 100). Septal hyphae and clamp connections were observed with the Olympus microscope. These morphological features were similar to the description of Agroathelia delphinii (anamorph Sclerotium delphinii), a known pathogen of delphinium (Punja and Damiani 1996). Our isolated strain was denoted as HYW-1. For molecular identification, HYW-1 genomic DNA was extracted using the CTAB method (Mahadevakumar et al. 2018). The internal transcribed spacer region (ITS) and large subunit rRNA (LSU) gene were subsequently PCR-amplified with the primer pairs ITS1/ITS4 and LR5/LROR (White et al. 1990) and then sequenced at Sangon Biotech (Shanghai, China). The resulting HYW-1 ITS and LSU sequences were submitted to the NCBI nr database for BlastN analysis (GenBank accessions PP976559 and PP907792, respectively), and they were 99.69%, and 99.46% identical to the corresponding to the type strain of Agroathelia delphinii (Welch) Redhead (Amylocorticiaceae, Agaricomycotina) sequences (GenBank accessions JN241576 and MH866785, respectively). Based on the ITS and LSU sequences, a phylogenetic tree was generated using the the maximum likelihood method of MEGA 7.0. Strains HYW-1 and CBS 305.32 were members of the same clade. To complete Koch's Postulates, two HYW-1 hyphal discs (5 mm in diameter) were placed on each of the rhizomes of six healthy P. cyrtonema Hua seedlings. As a control, two uncolonized agar discs were placed on the rhizomes of six additional healthy seedlings. All seedlings were moved to a greenhouse with conditions of 90% RH and 28 °C. White hyphae were observed on the surface of inoculated plants after 3 days, and leaf wilt was observed after 10 days. The control seedlings showed no symptomatology. Infected tissues were collected for pathogen re-isolation, and subsequent ITS sequence analysis revealed that the causal agent was consistent with the original isolate HYW-1. To the best of our knowledge, this is the first report of A. delphinii causing rhizome rot on P. cyrtonema Hua in China.

Characteristics and Clinical Significance of Gut Microbiota in Patients With Epstein-Barr Virus-Associated Liver Dysfunction.

Infectious mononucleosis (IM) is mainly triggered by Epstein-Barr virus (EBV) infection. There are few studies on the role of the gut microbiota in IM and EBV-associated liver dysfunction. The aim of this study was to investigate the characteristics of the gut microbiota in the EBV-associated liver dysfunction and to evaluate the relationship between the severity of gut microbiota dysbiosis and cytokine levels. A case-control study was performed. Individuals meeting the inclusion and exclusion criteria for EBV-induced IM were enrolled and their fecal and blood samples were collected. The V3-V4 region of the 16s rDNA gene of fecal microbiota was sequenced; bioinformatics analysis including α-diversity, β-diversity, and linear discriminant analysis (LDA) effect size (LEfSe) was performed; and the correlation between bacteria and clinical indices was analysed. A total of 48 participants completed fecal and blood tests, including 18 IM, 11 EBV-associated liver dysfunction, 12 healthy children and 7 EBV-negative liver dysfunction. The α-diversity and β-diversity of the gut microbiota in the EBV-associated liver dysfunction was more than that in IM. The abundance of Granulicatella, Enterococcus, Atopobium and Acinetobacter increased, while the abundance of Prevotella, Sutterella, Collinsella, Desulfovibrio decreased in the EBV-associated liver dysfunction compared with the IM. The abundance of Enterococcus, Atopobium and Acinetobacter correlated positively with the levels of IL-1β, IL-6, TNF-α and CD8+ cytotoxic T lymphocytes%. Gut microbiota of EBV-associated liver dysfunction was significantly disturbed and associated with systemic immune response.

A new pipeline SPICE identifies novel JUN-IKZF1 composite elements.

Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements. One such novel interaction was identified at CNS9, an upstream conserved noncoding region in the human IL10 gene, which harbors a non-canonical IKZF1 binding site. We confirmed the cooperative binding of JUN and IKZF1 and showed that the activity of an IL10-luciferase reporter construct in primary B and T cells depended on both this site and the AP1 binding site within this composite element. Overall, our findings reveal an unappreciated global association of IKZF1 and AP1 and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.

Genetic Basis and Identification of Candidate Genes for Alkalinity Tolerance Trait in Spotted Sea Bass (Lateolabrax maculatus) by Genome-Wide Association Study (GWAS).

Given the challenges of overcrowded coastal aquaculture spaces and insufficient production, utilizing saline-alkaline water areas represents a vital strategy to alleviate these bottlenecks. Spotted sea bass (Lateolabrax maculatus), with its formidable osmoregulatory capabilities, is an ideal candidate to develop a saline-alkaline tolerant strain. In our study, genotypic and phenotypic data from 287 L. maculatus individuals exposed to carbonate alkaline conditions were collected, and a genome-wide association study (GWAS) conducted to elucidate genetic basis related to carbonate alkalinity tolerance trait. Results showed that 14 SNPs and 8 InDels were markedly related to carbonate alkalinity tolerance trait, and 404 candidate genes were pinpointed within a ± 300-kb region surrounding these variants. Notably, the most significant SNP (SNP_05_17240108), along with two adjacent SNPs (SNP_05_17240102 and SNP_05_17240340) and two InDels (InDel_05_17240228 and InDel_05_17240231), was situated in the intron region of trio gene that could play vital roles in cell remodeling, and cell junction and activity of aquaporins to deal with carbonate alkalinity stress. Furthermore, candidate genes were significantly involved in pathways associated with carbohydrate metabolism, cell remodeling, ion transport, and RNA degradation, which were consistent with RNA-Seq analysis results of gills and kidneys in response to alkalinity stress. Our study will contribute to elucidate the genetic basis of alkalinity tolerance and the identified SNPs and InDels could be used for marker-assisted selection (MAS) and genomic selection (GS) for alkalinity tolerance trait in the breeding programs of spotted sea bass.

Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data

Genomic variants causing abnormal splicing play important roles in genetic disorders and cancer development. Among them, variants that cause the formation of novel splice-sites (splice-site creating variants, SSCVs) are particularly difficult to identify and often overlooked in genomic studies. Additionally, these SSCVs are frequently considered promising candidates for treatment with splice-switching antisense oligonucleotides (ASOs). To leverage massive transcriptome sequence data such as those available from the Sequence Read Archive, we develop a novel framework to screen for SSCVs solely using transcriptome data. We apply it to 322,072 publicly available transcriptomes and identify 30,130 SSCVs. Among them, 5121 SSCVs affect disease-causing variants. By utilizing this extensive collection of SSCVs, we reveal the characteristics of Alu exonization via SSCVs, especially the hotspots of SSCVs within Alu sequences and their evolutionary relationships. We discover novel gain-of-function SSCVs in the deep intronic region of the NOTCH1 gene and demonstrate that their activation can be suppressed using splice-switching ASOs. Collectively, we provide a systematic approach for automatically acquiring a registry of SSCVs, which facilitates the elucidation of novel biological mechanisms underlying splicing and serves as a valuable resource for drug discovery. The catalogs of SSCVs identified in this study are accessible on the SSCV DB (https://sscvdb.io).