Variable Sites Research Articles

Detection of Hymenoscyphus fraxineus in Leaf Rachises from European Ash (Fraxinus excelsior) in Germany

The ash dieback disease caused by Hymenoscyphus fraxineus is widespread in Germany and is the subject of intensive research efforts. The fungus identification is based on the genomic internal transcribed spacer (ITS) region, which can also be the site of intragenomic variability. In Germany, despite intense research efforts, only a few numbers of H. fraxineus sequence data are recorded. Therefore, this study aims to characterize H. fraxineus isolates obtained from diseased ash leaves in Brandenburg (Germany). Fungal isolates from infected ash leaf tissue were analyzed molecularly using species-specific primers and based on sequencing the ITS region of rDNA. The analysis of the two identified sequences revealed two base substitutionscompared to the reference sequences. Thus, they show an identity of 98.8%–100% to the reference sequences and support the assumption that H. fraxineus has multiple copies of the ITS region. The phylogenetic grouping with reference sequences did not show a distinct cluster for the European, particularly the German, sequences. This indicates that the evolvement of the genetic variability of the ITS region is still an ongoing process.

Common Variants in PLXNA4 and Correlation to Neuroimaging Phenotypes in Healthy, Mild Cognitive Impairment, and Alzheimer's Disease Cohorts.

A comprehensive genome-wide association study (GWAS) has validated the identification of the Plexin-A 4 (PLXNA4) gene as a novel susceptibility factor for Alzheimer's disease (AD). Nonetheless, the precise role of PLXNA4 gene polymorphisms in the pathophysiology of AD remains to be established. Consequently, this study is aimed at exploring the relationship between PLXNA4 gene polymorphisms and neuroimaging phenotypes intimately linked to AD. This study encompassed 812 subjects with PLXNA4 genotype data, procured from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Employing a tagging strategy, we identified five common variant sites within the PLXNA4 gene and assessed their associations with glucose metabolism, atrophy in AD-related brain regions (including the medial temporal lobe, hippocampus, and parahippocampal gyrus), and intracerebral Aβ deposition. We conducted a comprehensive analysis using a multiple linear regression model, with neuroimaging phenotypes as the dependent variable and PLXNA4 gene polymorphisms as the independent variable while incorporating APOE e4 carrier status, education level, age, and gender as covariates. The subjects were stratified into three groups based on their disease status: the Alzheimer's disease (AD) group, the mild cognitive impairment (MCI) group, and the cognitively normal healthy control (CN) group. Within each group, we examined the associations between PLXNA4 gene polymorphisms and various neuroimaging phenotypes. Our study identified significant associations between the rs156676-A and rs78036292-G alleles and the baseline volumes of the anterior cingulate and middle temporal gyrus, respectively, across the entire population. After 1year of follow-up, a significant correlation was observed between the rs6467431-G allele and accelerated volumetric atrophy of the parahippocampal gyrus in the overall population. Additionally, at the 2-year follow-up, significant correlations were observed between three PLXNA4 loci (rs1863015, rs6467431, rs67468325) and volumetric atrophy in the anterior cingulate, middle temporal gyrus, and hippocampus across the entire population. Specifically, the rs1863015-G allele notably accelerated atrophy of the left middle temporal gyrus and bilateral hippocampus, whereas the A alleles of rs6467431 and rs67468325 markedly accelerated atrophy specifically in the bilateral hippocampus. Subgroup analysis further validated these findings. Additionally, in the baseline CN group, the rs78036292 allele showed a significant correlation with intracerebral Aβ deposition, while in the 2-year follow-up CN group, rs67468325 was significantly associated with alterations in glucose metabolism rates in the right cingulate gyrus. Our findings indicate that PLXNA4 genotypes may modulate the development of AD through their regulation of intracerebral Aβ deposition. Additionally, PLXNA4 genotypes are strongly associated with AD-related brain atrophy and glucose metabolism, suggesting that they may alter susceptibility to AD by modulating neurodegenerative biomarkers.

Age-stratified anatomical differences of orbital floor and medial orbital wall blowout fractures.

To define the anatomical variance between orbital floor and medial orbital wall blowout fractures, and its change with age. This was a retrospective, observational study analyzing data from 557 patients with isolated blowout fractures of the orbital floor or medial orbital wall. Axial and quasi-sagittal CT images were analyzed to compare radiologic data on orbital wall morphology between fracture site groups and among age groups. Patient ages were classified as: 0-9 (childhood), 10-18 (adolescence), 19-44 (early adulthood), 45-64 (middle adulthood), and ≥ 65 years (late adulthood). The orbital floor fracture group demonstrated significantly steeper orbital floors (p < 0.001), while the medial wall fracture group exhibited a tendency for more convex medial orbital walls (p = 0.066). Among age groups, medial wall fracture was predominant in the late adulthood group only (p < 0.001). Patients in the childhood and late adulthood groups had significantly flatter orbital floors (p < 0.001). Patients in the childhood group presented with a concave medial orbital wall (p < 0.001). The anteroposterior length of the medial orbital wall and the number of ethmoid air cells were not different between fracture groups (p = 0.603 and0.753, respectively) and among age groups (p = 0.306 and0.456, respectively). Patients with orbital floor and medial orbital wall fractures had anatomically steeper orbital floors and convex medial orbital walls, respectively. Age-related differences in the shape of the orbital walls may influence variation in orbital blowout fracture sites by age. WHAT IS KNOWN : Fracture sites of the orbital walls differ according to age groups. The floor is morecommonly fractured in children, with a shift to the medial wall in the elderly. Orbital floor and medial orbital wall fractures present with anatomically higher floor and medial walls, respectively, compared to each other. This indicates steeper convexities of the walls which predispose them to fracturing. Children's medial orbital walls are initially concave, then shift to convex structures with facial bone and sinus maturation. This explains why there is a change in blowout fracture site between age groups, as it has been documented that concave structures are more resistant to deformation.

Identification of novel CDH23 heterozygous variants causing autosomal recessive nonsyndromic hearing loss.

Hearing loss adversely impacts language development, acquisition, and the social and cognitive maturation of affected children. The hearing loss etiology mainly includes genetic factors and environmental factors, of which the former account for about 50-60%. This study aimed to investigate the genetic basis of autosomal recessive non-syndromic hearing loss (NSHL) by identifying and characterizing novel variants in the CDH23 gene. Furthermore, it seeks to determine the pathogenic potential of the noncanonical splice site variant c.2398-6G > A. Comprehensive clinical evaluation and whole-exome sequencing (WES) were performed on the girl. The WES analysis revealed two novel variants in the CDH23 gene, associated with nonsyndromic deafness 12 (DFNB12). To further explore the pathogenicity of these variants, functional studies involving in vivo splicing analysis were performed on the novel noncanonical splice site variant, c.2398-6G > A, which was initially classified as a variant of uncertain significance (VUS). Whole-exome sequencing of the patient identified two compound heterozygous variants in CDH23: c.2398-6G > A, a noncanonical splice site variant, and c.6068C > A (p. Ser2023Ter), a nonsense mutation. In vitro splicing assays demonstrated that c.2398-6G > A caused aberrant splicing, leading to a frameshift (p. Val800Alafs*6) and the production of a truncated protein, as confirmed by structural protein analysis. The study revealed novel mutations as likely pathogenic, linking both variants to autosomal recessive NSHL. Our analyses revealed novel compound heterozygous mutations in CDH23 associated with autosomal recessive NSHL, thereby expanding the mutational landscape of CDH23-related hearing loss and increasing knowledge about the CDH23 splice site variants.

Targeting cryptic allosteric sites of G protein-coupled receptors as a novel strategy for biased drug discovery.

G protein-coupled receptors (GPCRs) represent the largest family of membrane receptors and are highly effective targets for therapeutic drugs. GPCRs couple different downstream effectors, including G proteins (such as Gi/o, Gs, G12, and Gq) and β-arrestins (such as β-arrestin 1 and β-arrestin 2) to mediate diverse cellular and physiological responses. Biased signaling allows for the specific activation of certain pathways from the full range of receptors' signaling capabilities. Targeting more variable allosteric sites, which are spatially different from the highly conserved orthosteric sites, represents a novel approach in biased GPCR drug discovery, leading to innovative strategies for targeting GPCRs. Notably, the emergence of cryptic allosteric sites on GPCRs has expanded the repertoire of available drug targets and improved receptor subtype selectivity. Here, we conduct a summary of recent progress in the structural determination of cryptic allosteric sites on GPCRs and elucidate the biased signaling mechanisms induced by allosteric modulators. Additionally, we discuss means to identify cryptic allosteric sites and design biased allosteric modulators based on cryptic allosteric sites through structure-based drug design, which is an advanced pharmacotherapeutic approach for treating GPCR-associated diseases.

Age-related Variation in Sleep-dependent Obstruction in Surgically Naive Children.

Little is known about age-related variations in sites and grade of sleep-dependent airway obstruction in children with obstructive sleep apnea (OSA) or obstructive sleep-disordered breathing (oSDB). The objective was to compare sites and grade of obstruction on drug-induced sleep endoscopy (DISE) across different age groups of surgically naïve children with OSA or oSDB. A retrospective chart review was performed for surgically naïve children aged 0-18 years with OSA/oSDB who underwent DISE from July 2021 to August 2023. Participants were categorized into: infants (aged 0-1 years), younger toddlers (aged 1-2 years), older toddlers (aged 2-3 years), preschool (aged 3-5 years), younger school-aged (aged 5-10 years), and older school-aged (aged 10-18 years). On DISE, obstruction was rated 0 = none/mild, 1 = moderate, 2 = severe for inferior turbinates, adenoid, velum, palatine tonsils/lateral pharyngeal wall, lingual tonsils, tongue base, epiglottis, and supra-arytenoid tissue. A series of multiple regression analyses were used to identify age differences in the grade of obstruction across all sites combined and at each individual site separately. The sample consisted of 252 children aged 1 month to 17 years with 57.9% males. Older patients had greater total obstruction scores (B = 0.42, SE = 0.10, p < 0.01) and greater number of sites that were severely obstructed (B = 0.11, SE = 0.05, p = 0.03). Older age groups had more obstruction at inferior turbinates (p = 0.02), adenoid (p < 0.01), palatine tonsils/lateral pharyngeal wall (p < 0.01), lingual tonsil (p < 0.01), and base of tongue (p < 0.01). Younger age groups had more obstruction at the supra-arytenoid tissue (p < 0.01). Varying patterns of sleep-dependent airway obstruction should be expected across different age groups in children with OSA or oSDB. 3 Laryngoscope, 135:463-468, 2025.

New insights on health benefits, interactions with food components and potential application of marine-derived sulfated polysaccharides: A review.

Sulfated polysaccharides refer to polysaccharides containing sulfate groups on sugar units. In nature, sulfated polysaccharides are widely distributed in marine organisms, and the variation in sulfation sites, monosaccharide composition, and branched chain distribution among different species results in differences in the physicochemical properties and biological activities. From the latest perspective, this review summarized the types, structural characteristics, and potential health benefits of sulfated polysaccharides in marine foods. In recent years, marine-derived sulfated polysaccharides have been widely used as stabilizers and antimicrobial agents applied in nutraceutical delivery systems and food packaging, which depend on their interactions with food components. Hence, we outlined the non-covalent/covalent interactions of marine-derived sulfated polysaccharides with food components (e.g., proteins, polysaccharides, and polyphenols) as well as the application in food industry. Additionally, the prospects and potential development for sulfated polysaccharides are concluded, aiming to provide a deep understanding of marine-derived sulfated polysaccharides to promote the industrial application in food health.

Novel KCNQ2 Variants Related to a Variable Phenotypic Spectrum Ranging from Epilepsy with Auditory Features to Severe Developmental and Epileptic Encephalopathies.

Pathogenic KCNQ2 variants are associated with neonatal epilepsies, ranging from self-limited neonatal epilepsy to KCNQ2-developmental and epileptic encephalopathy (DEE). In this study, next-generation sequencing was performed, applying a panel of 142 epilepsy genes on three unrelated individuals and affected family members, showing a wide variability in the epileptic spectrum. The genetic analysis revealed two likely pathogenic missense variants (c.1378G>A and c.2251T>G) and the already-reported pathogenic splice site (c.1631+1G>A) in KCNQ2 (HGNC:6296). The phenotypes observed in the affected members of family 1, which shared the c.2251T>G variant, were epilepsy with auditory features (EAFs), focal epilepsy, and generalized epilepsy, and none of them suffered from neonatal seizures. The gene panel contained further genes related to EAFs (LGI1, RELN, SCN1A, and DEPDC5), which were tested with negative results. The phenotypes observed in family 2 members, sharing the splice site variant, were neonatal seizures and focal epilepsy in childhood. The last unrelated proband, harboring the de novo missense c.1378G>A, presented a clinical phenotype consistent with DEE. In conclusion, we identified two unreported KCNQ2 variants, and report a proband with EAFs and individuals without typical KCNQ2 neonatal seizures. Our study underscores the extreme variability in the phenotypic spectrum of KCNQ2-related epilepsies and unveils the prospect of its inclusion in screening panels for EAFs.

Elucidation of intragenomic variation of ribosomal DNA sequences in the enigmatic fungal genus Ceraceosorus, including a newly described species Ceraceosorus americanus

AbstractMulticopy nuclear ribosomal DNA (rDNA) genes have been used as markers for fungal identification for three decades. The rDNA sequences in a genome are thought to be homogeneous due to concerted evolution. However, intragenomic variation of rDNA sequences has recently been observed in many fungi, which may make fungal identification and species abundance estimation based on these loci problematic. Ceraceosorus is an enigmatic genus in the smut lineage Ustilaginomycotina for which very limited distribution data exist. Our previous research demonstrated intragenomic variation in the internal transcribed spacer (ITS1-5.8S-ITS2) region of two Ceraceosorus species. In this study, we described the fourth known species of Ceraceosorus, C. americanus, isolated from an asymptomatic rosemary leaf collected in Louisiana, USA. This is the first report of this genus in the Americas. We then selected all four known Ceraceosorus species, plus exemplar smut fungi representing all major lineages of subphylum Ustilaginomycotina, to examine sequence heterogeneity in three regions of the rDNA repeat (partial 18S, ITS, and partial 28S regions). Three methods were used: PCR-cloning-Sanger sequencing, targeted amplicon high-throughput sequencing, and whole-genome shotgun high-throughput sequencing. Our results show that Ceraceosorus is the only sampled fungal genus in Ustilaginomycotina with significant intragenomic variation at the ITS, with up to 25 nucleotide variant sites in the ITS1–5.8S–ITS2 region and 2.6% divergence among analyzed ITS haplotypes. We found many conflicting patterns across the three detection methods, with up to 27 conflicting variant sites recorded from a single individual. At least 40% of the conflicting patterns are possibly due to PCR-cloning-sequencing errors, as the corresponding variant sites were not observed in the other detection methods. Based on our data and the literature, we evaluated the characteristics and advantages/disadvantages of each detection method. Finally, a model for how intragenomic variation in the rDNA copies within a genome may arise is presented.

Prediction of Synthetic Seismograms and Accelerograms for Two-Layer Basis Beddings

A method has been developed for predicting strong ground motion displacements and accelerations, assuming that an earthquake is an instantaneous mechanical rupture of the Earth’s crust. The method uses derived theoretical formulas to calculate all three parameters of the ground motion: displacements, velocities, and accelerations during strong (with a magnitude of M 6.0) earthquakes for any non-homogeneous (multilayer) ground beddings with various physical and mechanical characteristics – thicknesses, densities, and shear moduli – and at a certain distance from the expected earthquake’s rupture. The example provided involves the results obtained for a number of two-layer heterogeneous site variants in seismic categories I-IV at the magnitude of M=7.0 and distance of 15 km from the expected earthquake’s rupture. A comparison of the results obtained for actual heterogeneous foundation beddings with the equivalent homogeneous beddings showed divergences by 1.3-1.6 times, depending on the number of higher mode oscillations considered. Recommendations are provided for simplified calculation of seismograms and accelerograms for heterogeneous foundation beddings, with a certain correction of calculation results for equivalent homogeneous beddings.

Further evidence of biallelic NAV3 variants associated with recessive neurodevelopmental disorder with dysmorphism, developmental delay, intellectual disability, and behavioral abnormalities.

Neuron navigators (NAVs) are cytoskeleton-associated proteins well known for their role in axonal guidance, neuronal migration, and neurite growth necessary for neurodevelopment. Neuron navigator 3 (NAV3) is one of the three NAV proteins highly expressed in the embryonic and adult brain. However, the role of the NAV3 gene in human disease is not well-studied. Recently, five bi-allelic and three mono-allelic variants in NAV3 were reported in 12 individuals from eight unrelated families with neurodevelopmental disorder (NDD). Here, we report five patients from three unrelated consanguineous families segregating autosomal recessive NDD. Patients have symptoms of dysmorphism, intellectual disability, developmental delay, and behavioral abnormalities. Exome sequencing (ES) was performed on two affected individuals from one large family, and one affected individual from each of the other two families. ES revealed two homozygous nonsense c.6325C > T; p.(Gln2109Ter) and c.6577C > T; p.(Arg2193Ter) and a homozygous splice site (c.243 + 1G > T) variants in the NAV3 (NM_001024383.2). Analysis of single-cell sequencing datasets from embryonic and young adult human brains revealed that NAV3 is highly expressed in the excitatory neurons, inhibitory neurons, and microglia, consistent with its role in neurodevelopment. In conclusion, in this study, we further validate biallelic protein truncating variants in NAV3 as a cause of NDD, expanding the spectrum of pathogenic variants in this newly discovered NDD gene.

EHMT2 as a Candidate Gene for an Autosomal Recessive Neurodevelopmental Syndrome.

Neurodevelopmental disorders (NDD) comprise clinical conditions with high genetic heterogeneity and a notable enrichment of genes involved in regulating chromatin structure and function. The EHMT1/2 epigenetic complex plays a crucial role in repression of gene transcription in a highly tissue- and temporal-specific manner. Mutations resulting in heterozygous loss-of-function (LoF) of EHMT1 are implicated in Kleefstra syndrome 1 (KS1). EHMT2 is a gene acting inepigenetic regulation; however, the involvement of mutations in this gene in the etiology of NDDs has not been established thus far. A homozygous EHMT2 LoF variant [(NM_006709.5):c.328 + 2T > G] was identified by exome sequencing in an adult female patient with a phenotype resembling KS1, presenting with intellectual disability, aggressive behavior, facial dysmorphisms, fused C2-C3 vertebrae, ventricular septal defect, supernumerary nipple, umbilical hernia, and fingers and toes abnormalities. The absence of homozygous LoF EHMT2 variants in population databases underscores the significant negative selection pressure exerted on these variants. In silico evaluation of the effect of the EHMT2(NM_006709.5):c.328 + 2T > G variant predicted the abolishment of intron 3 splice donor site. However, manual inspection revealed potential cryptic donor splice sites at this EHMT2 region. To directly access the impact of this splice site variant, RNAseq analysis was employed and disclosed the usage of two cryptic donor sites within exon 3 in the patient's blood, which are predicted to result in either an out-of-frame or in-frame effect on the protein. Methylation analysis was conducted on DNA from blood samples using the clinically validated EpiSign assay, which revealed that the patient with the homozygous EHMT2(NM_006709.5):c.328 + 2T > G splice site variant is conclusively positive for the KS1 episignature. Taken together, clinical, genetic, and epigenetic data pointed to a LoF mechanism for the EHMT2 splice variant and support this gene as a novel candidate for an autosomal recessive Kleefstra-like syndrome. The identification of additional cases with deleterious EHMT2 variants, alongside further functional validation studies, is required to substantiate EHMT2 as a novel NDD gene.

Prevalence and molecular characterization of human bocavirus-1 in children and adults with influenza-like illness from Kunming, Southwest China.

Human bocavirus-1 (HBoV-1) has been associated with respiratory infections in both children and adults, often presenting symptoms similar to those of influenza. Understanding the prevalence and molecular characteristics of HBoV-1 in individuals with influenza-like illness (ILI) is essential for enhancing the diagnosis and treatment of respiratory infections in Kunming, Southwest China. Between December 2017 and December 2023, demographic and clinical data, along with respiratory tract specimens from individuals aged 0 to 97 years with ILI, were collected at three sentinel hospitals in Kunming. Each specimen was tested for 18 respiratory viruses, and the positive rates of HBoV-1 across different age groups were analyzed. Amplification of the near-complete HBoV genome was achieved through three overlapping fragments, followed by next-generation sequencing (NGS) and phylogenetic analysis. A total of 20,181 respiratory samples were collected from patients aged 1 month to 97 years presenting with ILI symptoms between December 2017 and December 2023, with HBoV detected in 0.8% of the samples. The prevalence was 1.0% (165/16,406) in children and 0.1% (3/3,775) in adults, with a significantly higher detection rate in pediatric patients (<18 years old) compared to adults (≥18 years old) (P < 0.001). Among the 168 HBoV-positive participants, 165 (98.2%) were children under 18 years, while 3 (1.8%) were adults. Genome-wide phylogenetic analyses indicated that HBoV-1 was the predominant genotype, showing that the HBoV-1 strains circulating in Kunming are closely related to strains from other regions of China and globally. Our findings confirm the prevalence of HBoV-1 in individuals with ILI in Kunming and provide valuable insights into the molecular characteristics of HBoV-1 in this region. Further studies are necessary to explore the clinical implications of HBoV-1 infection and its role in respiratory illnesses.IMPORTANCEViral respiratory infections are a leading cause of morbidity- and mortality-associated influenza-like illness (ILI) cases. It is estimated that there are several billion cases of ILI globally each year. Monitoring data from China in 2023 indicate that there are approximately 17 million cases of ILI nationwide. In the United States, the annual incidence of ILI ranges from 9 to 49 million cases. Human bocavirus-1 (HBoV-1) has been identified as a causative agent of ILI. The global prevalence of HBoV-1 respiratory infections varies from 1% to 56.8%, with the majority of studies focusing on pediatric populations; however, research including a broader age range is limited. Currently, the prevalence of HBoV-1 in the Kunming area is not well characterized, and its molecular features remain inadequately described. This study aims to analyze the prevalence of HBoV-1 among ILI cases in Kunming, encompassing both pediatric and adult patients. We present 107 complete genomic sequences of HBoV-1 strains obtained from three ILI sentinel hospitals in the region. Furthermore, we conducted phylogenetic analysis, homology comparisons, and assessments of nucleotide and amino acid substitution site variations. These findings provide important insights for further investigations into HBoV-1 and its epidemiological significance.

Preimplantation genetic testing for a Chinese pedigree affected with Primary carnitine deficiency

To investigate the results of preimplantation genetic testing for monogenic diseases (PGT-M) in a Chinese pedigree affected with Primary carnitine deficiency (PCD). A pedigree affected with PCD who visited Hainan Women and Children's Medical Center in April 2023 due to "SLC22A5 gene mutation found in offspring genetic testing and preparing for a second child" was selected as the study subject. Pathogenicity of the proband's variant sites was determined by referring to the Standards and Guidelines for the Interpretation of Sequence Variants established by the American College of Medical Genetics and Genomics (ACMG). Sanger sequencing was used to verify the variant sites of SLC22A5 gene in the proband and her parents, and the single nucleotide polymorphism (SNP) haplotype of the family was constructed by SNP microarray (SNP array) method to determine the carrier status of pathogenic genes. After fertilization via assisted reproductive technology, whole genome amplification (WGA) was performed on the biopsied trophoblastic cells. Sanger sequencing, next-generation sequencing (NGS), and SNP array techniques were then used to detect the variants in the SLC22A5 gene and chromosome copy number variation (CNV) in the embryos. Embryos without the variants were selected for transferring. After the successful pregnancy of the proband's mother, amniocentesis was not performed for prenatal diagnosis due to repeated vaginal bleeding. After delivery, neonatal peripheral blood sample was collected to verify the results of PGT-M, and follow-up was conducted. This study was reviewed and approved by the Medical Ethics Committee of Hainan Women and Children's Medical Center (Ethics No. HNWCMC-2022-178). In this study, the c.338G>A and c.760C>T variants in SLC22A5 gene were evaluated as pathogenic variants. Sanger sequencing results of this family showed that the c.338G>A and c.760C>T variants of the proband were inherited from his father and mother, respectively. Haplotypes of c.338G>A and c.760C>T variants of SLC22A5 gene were successfully constructed. PGT-M results showed that 2 of the 8 blastulas biopsied failed WGA, and the CNV detection results of the remaining 6 blastocysts were all euploid: 2 had no mutations in the SLC22A5 gene, 3 were single heterozygous carriers of paternal or maternal origin, and 1 was compound heterozygous carriers of paternal and maternal origin. Combined with the embryo morphology score, an intrauterine singleton pregnancy was achieved after the successful transfer of an optimal embryo with no CNV abnormalities and no paternal or maternal SLC22A5 gene mutations, resulting in the birth of a healthy female baby at 38+3 weeks of gestation. The results of peripheral blood chromosomal karyotyping analysis, CNV detection and SLC22A5 gene c.338G>A and c.760C>T site variant detection of the infant were consistent with those of PGT-M, and no abnormality was found. PGT-M had helped the couple carrying SLC22A5 gene variant to have a healthy offspring and effectively blocked the transmission of PCD in this family.

Genome-wide identification and characterization of BASIC PENTACYSTEINE transcription factors and their binding motifs in coconut palm

IntroductionBASIC PENTACYSTEINE (BPC) is a small transcription factor family known for its role in various developmental processes in plants, particularly in binding GA motifs and regulating flower and seed development. However, research on the functional characteristics and target genes of BPCs in coconut (Cocos nucifera) is limited.MethodsIn this study, we systematically characterized the gene structure, conserved protein domains, gene expansion, and target genes of CnBPCs in the coconut genome. We conducted yeast one-hybrid (Y1H) and dual-luciferase assay to explore gene interactions. We identified genes with the GA motif in their promoter regions and combined this information with a weighted gene co-expression network to identify the target genes of CnBPCs.ResultsEight CnBPCs were identified, including three Class I CnBPCs from triplication, four Class II CnBPCs (with CnBPC6A and CnBPC6B resulting from segmental duplication), and one Class III CnBPC (CnBPC7). Three conserved DNA-binding motifs were detected, exhibiting variation in certain sites. Widespread BPC gene expansion was detected in coconut and other plant species, while only three BPCs were found in the most basal extant flowering plant. Notably, 92% of protein-coding genes contained at least one GA motif, with the (GA)3 motif being most prevalent. Genes containing the GA motif that exhibit a high expression correlation with CnBPCs, tend to interact strongly with the corresponding CnBPCs. Additionally, promoters rich in the GA motif tend to interact with all members of CnBPC. The dual-luciferase assay showed that CnBPCs could activate or repress the transcriptional activities of promoters containing either (GA)3 or (GA)11 motif but with a bias toward certain genes. Furthermore, we constructed co-expressed networks identifying 426 genes with GA motifs as potential CnBPC targets.DiscussionOur findings suggest that CnBPCs may play significant roles in seed germination, flower development, and mesocarp development by interacting with genes such as CnAG1, CnAG2, CnSTK, CnMFT, and CnCS. This study characterized CnBPCs’ binding motif and possible target genes, laying a theoretical foundation to reveal CnBPCs’ function in flower and seed development.

Search for germline gene variants in colorectal cancer families presenting with multiple primary colorectal cancers.

A double primary colorectal cancer (CRC) in a familial setting signals a high risk of CRC. In order to identify novel CRC susceptibility genes, we whole-exome sequenced germline DNA from nine persons with a double primary CRC and a family history of CRC. The detected variants were processed by bioinformatics filtering and prioritization, including STRING protein-protein interaction and pathway analysis. A total of 150 missense, 19 stop-gain, 22 frameshift and 13 canonical splice site variants fulfilled our filtering criteria. The STRING analysis identified 20 DNA repair/cell cycle proteins as the main cluster, related to genes CHEK2, EXO1, FAAP24, FANCI, MCPH1, POLL, PRC1, RECQL, RECQL5, RRM2, SHCBP1, SMC2, XRCC1, in addition to CDK18, ENDOV, ZW10 and the known mismatch repair genes. Another STRING network included extracellular matrix genes and TGFβ signaling genes. In the nine whole-exome sequenced patients, eight harbored at least two candidate DNA repair/cell cycle/TGFβ signaling gene variants. The number of families is too small to provide evidence for individual variants but, considering the known role of DNA repair/cell cycle genes in CRC, the clustering of multiple deleterious variants in the present families suggests that these, perhaps jointly, contributed to CRC development in these families.

The first mitogenome of the genus Amphalius (Siphonaptera: Ceratophyllidae) and its phylogenetic implications.

Amphalius spirataenius belongs to Arthropoda, Insecta, Siphonaptera, Ceratophylloidea, Ceratophyllinae, Amphalius. Only 2 species from the subfamily Ceratophyllinae have been sequenced for mitogenomes to date. The genus Amphalius mitogenome research was still blank. The A. spirataenius mitogenome was determined, annotated and analysed for the first time in this study. The 14 825 bp long genome has the typical metazoan of 37 genes with insect ancestral genome arrangement pattern. There was no significant difference in codon usage of 13 protein-coding genes: UUA, UCU, GUU, ACU and GCU were the most frequently used codons. It was found that the reason for codon preference mainly contributed to natural selection base on PR2, ENC-plot and neutrality curve analysis. Evolutionary rate, conserved sites, variable sites and nucleotide diversity analysis indicated that nad6 of A. spirataenius had the fastest evolutionary rate, while cox1 had the slowest evolutionary rate. Phylogenetic trees were reconstructed based on 13 protein-coding genes and 2 rRNA genes datasets using Bayesian inference and maximum likelihood method. The phylogenetic tree supported that both Siphonaptera and Mecoptera were monophyletic, and were sister groups to each other. This study filled gap of the genus Amphalius mitogenome sequences and was of great significance for understanding evolution of the order Siphonaptera.

Complete chloroplast genome characterization of three Plagiomnium species and the phylogeny of family Mniaceae.

The taxonomic concepts and phylogenetic relations among genera of the family Mniaceae have given rise to much controversy in recent years, including Mnium, Plagiomnium, and Pohlia. Chloroplast genome study of these genera will be helpful to reflect the fact of this relationship. In this study, we sequenced three species in the Plagiomnium genus using an Illumina HiSeq 4000 platform. The complete chloroplast genomes of P. rostratum, P. succulentum and P. vesicatum were 125,196bp, 124,689bp, and 124,663bp in length, which all contained a quadripartite structure including two copies of the invert repeats (IR, 10,120bp, 9,818bp, and 9,665bp), one large single copy region (LSC, 86,395bp, 86,299bp, and 86,532bp), and one single copy region (SSC, 18,561bp, 18,754bp, and 18,801bp). The overall GC contents were 29.8%, 30.5%, and 30.5% respectively. The simple sequence repeats (SSRs) were detected in conjunction with Plagiomnium acutum, with variable sites genes observed: rpoC2, ycf1, and ycf2. Combined with the other three sequences published in Mniaceae, analyses of codon usage, repeats sequences, GC contents, and gene features revealed similarities among the seven species in Mniaceae. The trend of nucleotide diversity (Pi) in the seven complete chloroplast genomes showed Pi > 0.056: trnI-rpl23, petG-petL-psbE, trnK-chlB, trnG-trnR-atpA, rpoB-trnC-ycf66, ndhB, trnN-ndhF, and rps15-ycf1. We confirmed the phylogenetic relationships that Plagiomnium genus is a sister group with Mnium, while the Pohlia genus is not a monophyletic group. Phylogenetic analyses corroborated the monophyly of Mniaceae and supported the transfer of the Pohlia genus into Mniaceae.

Patient-derived induced pluripotent stem cells to study non-canonical splicing variants associated with Hypertrophic Cardiomyopathy

Hypertrophic cardiomyopathy (HCM) is the most prevalent inherited cardiomyopathy and a leading cause of sudden death. Genetic testing and familial cascade screening play a pivotal role in the clinical management of HCM patients. However, conventional genetic tests primarily focus on the detection of exonic and canonical splice site variation. Oversighting intronic non-canonical splicing variants potentially contributes to a proportion of HCM patients remaining genetically undiagnosed. Here, using a non-integrative reprogramming strategy, we generated induced pluripotent stem cell (iPSC) lines from four individuals carrying one of two variants within intronic regions of MYBPC3: c.1224-52G > A and c.1898-23A > G. Upon differentiation to iPSC-derived cardiomyocytes (iPSC-CMs), mis-spliced mRNAs were identified in cells harbouring these variants. Both abnormal mRNAs contained a premature termination codon (PTC), fitting the criteria for activation of nonsense mediated decay (NMD). However, the c.1898-23A > G transcripts escaped this mRNA quality control mechanism, while the c.1224-52G > A transcripts were degraded. The newly generated iPSC lines represent valuable tools for studying the functional consequences of intronic variation and for translational research aimed at reversing splicing abnormalities to prevent disease progression.

Site-Invariant Meta-Modulation Learning for Multisite Autism Spectrum Disorders Diagnosis.

Large amounts of fMRI data are essential to building generalized predictive models for brain disease diagnosis. In order to conduct extensive data analysis, it is often necessary to gather data from multiple organizations. However, the site variation inherent in multisite resting-state functional magnetic resonance imaging (rs-fMRI) leads to unfavorable heterogeneity in data distribution, negatively impacting the identification of biomarkers and the diagnostic decision. Several existing methods have alleviated this shift of domain distribution (i.e., multisite problem). Statistical tuning schemes directly regress out site disparity factors from the data prior to model training. Such methods have a limitation in processing data each time through variance estimation according to the added site. In the model adjustment approaches, domain adaptation (DA) methods adjust the features or models of the source domain according to the target domain during model training. Thus, it is inevitable that it needs updating model parameters according to the samples of a target site, causing great limitations in practical applicability. Meanwhile, the approach of domain generalization (DG) aims to create a universal model that can be quickly adapted to multiple domains. In this study, we propose a novel framework for disease diagnosis that alleviates the multisite problem by adaptively calibrating site-specific features into site-invariant features. Specifically, it applies directly to samples from unseen sites without the need for fine-tuning. With a learning-to-learn strategy that learns how to calibrate the features under the various domain shift environments, our novel modulation mechanism extracts site-invariant features. In our experiments over the Autism Brain Imaging Data Exchange (ABIDE I and II) dataset, we validated the generalization ability of the proposed network by improving diagnostic accuracy in both seen and unseen multisite samples.