A ruminant lncRNA atlas uncovers association with epithelial development and barrier integrity.
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Letter↗
Biomedical subjects
Wen Wang
Publications and source records attributed to Wen Wang.
Uncovering the mechanism of female restitution in sugarcane hybrids.
Variations of meiosis, which normally halve genetic complements prior to fertilization, can have profound consequences. For example, whole-genome duplications (polyploidy) have shaped the evolution and diversification of most angiosperm lineages. The century-long success of sugarcane interspecific hybrids has been attributed to unusual female restitution-an unreduced maternal gamete fusing with a normal haploid paternal gamete1,2. Here we generated haplotype-resolved genomes of octoploid Saccharum officinarum LA Purple and decaploid Saccharum spontaneum US56-14-4. Eight F1 hybrids between these species exhibited 2:1 maternal to paternal genomic ratios, with 2 assemblies revealing canonical haploid sets of approximately 40 paternal and approximately 80 maternal chromosomes. The maternal chromosomes comprise 40 pairs of duplicated, partially recombined sister chromatids that retain around 62.5% of maternal genetic diversity, characteristic of second division restitution. Using single-molecule long-read sequencing and a novel algorithm that is broadly applicable to polyploid genomes, we identified two classes of recombination breakpoints, including a previously unrecognized configuration supported by both recombinant and non-recombinant reads, across all hybrids and diagnostic of second division restitution. These findings resolve a century-old cytological debate, add new insights into meiotic variations, and offer a genomic approach to accelerate genetic gain in this globally critical sugar and bioenergy crop.
Chimera↗
Analyzing salinity tolerance in grass carp (Ctenopharyngodon idella): Insights from genome-wide association study and genomic selection.
Grass carp (Ctenopharyngodon idella) is one of the most widely cultured freshwater fish species globally. However, the expansion of its farming scale faces severe limitation owing to freshwater scarcity; therefore, the development of strains with greater salinity tolerance is key for expanding production using brackish water resources. To investigate the genetic basis of salinity tolerance in grass carp, a genome-wide association study (GWAS) was conducted using 200 individuals representing extreme phenotypes, namely salinity-tolerant and salinity-sensitive groups. In total, 17 single nucleotide polymorphisms (SNPs) related to salinity tolerance were detected, which were distributed across 11 chromosomes. Through gene annotation, 38 candidate genes were obtained from these loci. Enrichment analysis revealed these candidate genes are primarily implicated in key biological processes, including osmotic regulation, energy metabolism, and stress responses. Analyses of different SNP densities revealed that the 5 K SNP density panel can balance prediction accuracy and computational efficiency. The BayesA model achieved the highest prediction accuracy under the GWAS_Evenly selection strategy, with substantial reductions in mean absolute error and mean square error. This study reveals the genetic mechanisms of salinity tolerance in grass carp, which might be optimized through genomic selection, and provides insights for selectively breeding new varieties with greater salinity tolerance.
Animals↗
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.
Emerging spatial multiomics technologies provide an increasingly large amount of information content at multiple scales. However, it remains challenging to efficiently represent and harmonize diverse spatial datasets. Here we present Giotto Suite, a suite of modular packages that provides scalable and extensible end-to-end solutions for multiscale and multiomic data analysis, integration and visualization. At its core, Giotto Suite is centered around an innovative data framework, allowing the representation and integration of spatial omics data in a technology-agnostic manner. Giotto Suite integrates molecular, morphology, spatial and annotated feature information to create a responsive and flexible workflow, as demonstrated by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science in R, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive and multiscale ecosystem for spatial multiomic data analysis.
Genomics↗
A novel variant in the SPTB gene underlying hereditary spherocytosis and a literature review of previous variants.
BACKGROUND: Hereditary spherocytosis (HS, MIM#612641) is one of the most common hereditary hemolytic disorders. This study aimed to confirm a novel variant's pathogenicity and reveal a patient's genetic etiology. METHODS: The clinical data of a patient with HS who underwent genetic sequencing at the Children's Hospital of Chongqing Medical University were reviewed retrospectively. In silico prediction and in vitro minigene splicing reporter system were then conducted on the detected variant to analyze its intramolecular impact. A summary of the literature related to HS due to SPTB gene variants was also presented. RESULTS: A novel variant (c.301-2 A > G) in the SPTB gene (NM_001024858.4) was identified in the proband. Using Sanger sequencing, we conclusively confirmed that the inheritance of the variant could not be traced to the biological parents. The in vitro minigene assay revealed three different transcripts derived from the c.301-2 A > G variant: r.301_474del, r.301_306delCCAAAG, and r.301-1_301-57ins. Through a literature review, patients with HS who had been genotypically validated were summarized and the SPTB gene variant profile was mapped. CONCLUSION: We identified a splicing variant of the SPTB gene, thus confirming its aberrant translation. The novel variant was the probable genetic etiology of the proband with HS. Our findings expanded the variant spectrum of the SPTB gene, thus improving the understanding of the associated hereditary hemolytic disorders from a clinical and molecular perspective and contributing to the foundation of genetic counseling and diagnosis.
Humans↗
Rapid evolution in a pair of recent duplicate segments of rice.
Gene duplication has been considered the most important way of generating genetic novelties. The subsequent evolution right after gene duplication is critical for new function to occur. Here we analyzed the evolutionary pattern for a recently duplicated segment between rice chromosomes 11 and 12. This duplication event was estimated to occur about 6 million years ago, during the divergence of the B- and C-genome rice species. The duplicate segment in chromosome 12 has significantly higher frequency of sequence rearrangement rate than non-duplicated regions. The rearrangement rate is approximately 6.5 breakages/Mb per million years, about six times higher than the fastest rate ever reported in eukaryotes. The genes within both segments experienced accelerated nucleotide substitution rates revealed by synonymous (Ks) and non-synonymous divergence (Ka) between Oryza sativa indica and O. sativa japonica. Analysis using EST data also implicates rapid divergence in expression between these segmental duplicate genes. These overall rapid changes from different perspective for the first time provide evidence that relaxation of selection also occurs in large-scale duplications.
Base Sequence↗
Microsatellite markers within --SEA breakpoints for prenatal diagnosis of HbBarts hydrops fetalis.
BACKGROUND: We sought to develop a rapid prenatal diagnostic test for simultaneous detection of HbBarts hydrops fetalis and exclusion of maternal contamination. METHODS: We developed a multiplex quantitative fluorescent PCR (QF-PCR) test that detects the presence/ absence of 2 microsatellite markers (16PTEL05/16PTEL06) located within breakpoints of the Southeast Asia ((-SEA)) deletion. HbBarts hydrops fetalis ((-SEA/-SEA)) is diagnosed by absence of both markers, and maternal contamination of fetal DNA is excluded by absence of noninherited maternal alleles. Fetal and parental DNA samples from 50 families were analyzed in a blinded clinical validation study, and QF-PCR results were compared with their respective molecular genotypes. RESULTS: The multiplex QF-PCR results included correct diagnoses of HbBarts hydrops fetalis in 11 of the fetuses tested, correct verification as unaffected in 20 fetuses, and correct identification as either carriers (alphaalpha/(-SEA)) or unaffected homozygotes in 18. Misidentification as unaffected occurred for 1 carrier. Sensitivity for diagnosis of HbBarts hydrops fetalis was 100% [lower 95% confidence interval, 76.2%], and specificity was 100% (lower 95% confidence interval, 92.6%). None of the samples tested showed any traces of noninherited maternal alleles; thus false-positives because of maternal contamination were eliminated. CONCLUSIONS: In this QF-PCR method, detection of maternally and paternally inherited fetal alleles allowed diagnosis of the double-deletion syndrome, and the ability to differentiate between these alleles allowed simultaneous exclusion of maternal contamination of the fetal genetic material. This novel strategy using cell-free fetal DNA in maternal plasma could form the basis for noninvasive testing for HbBarts hydrops fetalis.
Alleles↗
Bistable electrical switching and memory effects in a thin film of copolymer containing electron donor-acceptor moieties and europium complexes.
A nonconjugated methacrylate copolymer (PCzOxEu) containing carbazole moieties (electron donors), 1,3,4-oxadiazole moieties (electron acceptors), and europium complexes in the pendant groups was synthesized via free radical copolymerization of methacrylate monomers containing the respective functional groups. The molecular structure and composition of PCzOxEu was characterized by elemental analysis, FT-IR, 1H NMR, 13C NMR, UV-vis absorption and fluorescence spectroscopies, gel permeation chromatography (GPC), X-ray photoelectron spectroscopy (XPS), and cyclic voltammetry (CyV). The resulting copolymer exhibited a relatively high glass transition temperature (Tg approximately 125 degrees C) and good solubility in common organic solvents. It could be cast into transparent films from solutions. For a thin film of PCzOxEu sandwiched between an indium-tin oxide (ITO) electrode and an Al electrode (ITO/PCzOxEu/Al), the structure behaved as a nonvolatile flash (rewritable) memory with accessible electronic states that could be written, read, and erased. The polymer memory exhibited an ON/OFF current ratio up to 10(5), switching response time of approximately 1.5 micros, more than 10(6) read cycles, retention time of more than 8 h, and write/erase voltages of about 4.4 V/-2.8 V under ambient conditions. The roles of oxadiazole moieties in improving the response time and retention time of the memory device were elucidated from the molecular simulation results.
Journal Article↗
Ultrastructural study on a novel microsporidian, Endoreticulatus eriocheir sp. nov. (Microsporidia, Encephalitozoonidae), parasite of Chinese mitten crab, Eriocheir sinensis (Crustacea, Decapoda).
A microsporidian pathogen, infecting the epithelial cells of the hepatopancreas of Chinese mitten crab, Eriocheir sinensis, was studied by electron microscopy. The detailed ultrastructure of life cycle of the pathogen including proliferative and sporogonic developmental stages are provided. All stages of the parasite are haplokaryotic and develop in a vacuole bounded by a single membrane in contact with host cell cytoplasm. Sporogenesis is synchronous with the same developmental stage in one vacuole. Sporogony shows a characteristic of multinucleate sporogonial plasmodia divided by rosette-like division, producing 4 or 8 sporoblasts. The mature spore is ellipsoidal, length (mean) 1.7 microm, width 1.0 microm, with a uninucleate in the center of the sporoplasm, 7 turns of the polar filament, a bell-like polaroplast of compact membranes and obliquely positioned posterior vacuole. The morphological characteristics of this novel microsporidian pathogen have led us to assign the parasite to a new species of Endoreticulatus, E. eriocheir sp. nov., that has not been reported previously from crab.
Animals↗
Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup.
Comparative genetic analysis between human and chimpanzee may detect genetic divergences responsible for human-specific characteristics. Previous studies have identified a series of genes that potentially underwent Darwinian positive selection during human evolution. However, without a closely related species as outgroup, it is difficult to identify human-lineage-specific changes, which is critical in delineating the biological uniqueness of humans. In this study, we conducted phylogeny-based analyses of 2633 human brain-expressed genes using rhesus macaque as the outgroup. We identified 47 candidate genes showing strong evidence of positive selection in the human lineage. Genes with maximal expression in the brain showed a higher evolutionary rate in human than in chimpanzee. We observed that many immune-defense-related genes were under strong positive selection, and this trend was more prominent in chimpanzee than in human. We also demonstrated that rhesus macaque performed much better than mouse as an outgroup in identifying lineage-specific selection in humans.
Adaptation, Biological↗
High rate of chimeric gene origination by retroposition in plant genomes.
Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, despite abundant retrotransposons in plants and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons, confirming a previously observed role of retroelements in generating plant retrogenes. Substitution analyses revealed that the vast majority are subject to negative selection, suggesting, along with expression data and evidence of age, that they are likely functional retrogenes. In addition, 42% of these retrosequences have recruited new exons from flanking regions, generating a large number of chimerical genes. We also identified young chimerical genes, suggesting that gene origination through retroposition is ongoing, with a rate an order of magnitude higher than the rate in primates. Finally, we observed that retropositions have followed an unexpected spatial pattern in which functional retrogenes avoid centromeric regions, while retropseudogenes are randomly distributed. These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species.
Evolution, Molecular↗
Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian muntjac (Muntiacus muntjak vaginalis).
The karyotype of Indian muntjacs (Muntiacus muntjak vaginalis) has been greatly shaped by chromosomal fusion, which leads to its lowest diploid number among the extant known mammals. We present, here, comparative results based on draft sequences of 37 bacterial artificial clones (BAC) clones selected by chromosome painting for this special muntjac species. Sequence comparison on these BAC clones uncovered sequence syntenic relationships between the muntjac genome and those of other mammals. We found that the muntjac genome has peculiar features with respect to intron size and evolutionary rates of genes. Inspection of more than 80 pairs of orthologous introns from 15 genes reveals a significant reduction in intron size in the Indian muntjac compared to that of human, mouse, and dog. Evolutionary analysis using 19 genes indicates that the muntjac genes have evolved rapidly compared to other mammals. In addition, we identified and characterized sequence composition of the first BAC clone containing a chromosomal fusion site. Our results shed new light on the genome architecture of the Indian muntjac and suggest that chromosomal rearrangements have been accompanied by other salient genomic changes.
Animals↗
Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila.
The formation of chimeric gene structures provides important routes by which novel proteins and functions are introduced into genomes. Signatures of these events have been identified in organisms from wide phylogenic distributions. However, the ability to characterize the early phases of these evolutionary processes has been difficult due to the ancient age of the genes or to the limitations of strictly computational approaches. While examples involving retrotransposition exist, our understanding of chimeric genes originating via illegitimate recombination is limited to speculations based on ancient genes or transfection experiments. Here we report a case of a young chimeric gene that has originated by illegitimate recombination in Drosophila. This gene was created within the last 2-3 million years, prior to the speciation of Drosophila simulans, Drosophila sechellia, and Drosophila mauritiana. The duplication, which involved the Bällchen gene on Chromosome 3R, was partial, removing substantial 3' coding sequence. Subsequent to the duplication onto the X chromosome, intergenic sequence was recruited into the protein-coding region creating a chimeric peptide with approximately 33 new amino acid residues. In addition, a novel intron-containing 5' UTR and novel 3' UTR evolved. We further found that this new X-linked gene has evolved testes-specific expression. Following speciation of the D. simulans complex, this novel gene evolved lineage-specifically with evidence for positive selection acting along the D. simulans branch.
3' Untranslated Regions↗
The effect of the ingestion of Ginkgo biloba extract (EGb 761) on the pharmacokinetics of metformin in non-diabetic and type 2 diabetic subjects--a double blind placebo-controlled, crossover study.
BACKGROUND & AIMS: Ginkgo biloba extract (EGb 761) has been shown to ameliorate some defects associated with the insulin resistance syndrome and so patients with Type 2 diabetes mellitus (T2DM) may be inclined to co-ingest the herb with their medications, such as metformin. This study was designed to determine if the co-ingestion of EGb 761 and metformin would alter the pharmacokinetic properties of metformin in T2DM patients and persons without diabetes, who may ingest it for other purposes. METHOD: Normal glucose tolerance (NGT) subjects (n=10; age, 39.2+/-14.0 years; fasting plasma glucose (FPG), 90+/-7 mg/dl; body mass index (BMI), 24.1+/-3.7 kg/m(2)) and 10 T2DM patients (n=10; age, 51.7+/-8.9 years; FPG, 150+/-7 mg/dl; BMI, 33.7+/-5.7 kg/m(2)) completed a randomized, double-blind, placebo-controlled crossover study. They ingested either EGb 761 (12 0mg/day as a single dose) or a vegetable-based placebo during each arm for 3 months. At the end of each arm, the NGT subject ingested a single 500 mg dose of metformin (non-diabetics) and the T2DM subject took his/her prescribed metformin dose (250-850 mg) with 120 mg EGb 761. Blood and urine samples were collected over an 8-h period, and in the case of T2DM subjects, additionally over the first 2h of the subsequent 3 days. RESULTS: Ingestion of EGb 761 produced no significant changes in diagnostic laboratory tests in either group, except reducing glycosylated hemoglobin A(1c) levels (from 7.7+/-1.2 to 7.2+/-0.9%, P<0.05) in T2DM the subjects. The pharmacokinetic parameters of metformin were all significantly different (P<0.05) between the NGT (500 mg) and 8 out of 10 of the T2DM subjects who were prescribed 500 mg of metformin during the placebo cycles. During the EGb 761 cycles, only the elimination half-life in the T2DM subjects was significantly increased (0.117+/-0.085 to 0.141+/-0.100, P<0.05). CONCLUSION: The co-ingestion of 120 mg of EGb 761 and 500 mg of metformin did not significantly affect the pharmacokinetic properties of metformin. Further studies are required to verify this observation for smaller and larger dose of metformin with other doses of EGb 761, since T2DM patients on medication constitute a very heterogeneous group.
Adult↗
Indices of electromyographic activity and the "slow" component of oxygen uptake kinetics during high-intensity knee-extension exercise in humans.
The control of pulmonary oxygen uptake (VO2) kinetics above the lactate threshold (LT) is complex and controversial. Above LT, VO2 for square-wave exercise is greater than predicted from the sub-LT VO2-WR relationship, reflecting the contribution of an additional "slow" component (VO2(sc)). Investigators have argued for a contribution to this slow component from the recruitment of fast-twitch muscle fibres, which are less aerobically efficient than slow-twitch fibres. Six healthy subjects performed a rapid-incremental bilateral knee-extension exercise test to the limit of tolerance for the estimation of VO2(peak), ventilatory threshold (VT), and the difference between VO2(peak) and VO2 at VT (Delta). Subjects then completed three repetitions of square-wave exercise at 30% of VT for 10 min (moderate intensity), and at VT + 25%Delta (heavy intensity) for 20 min. Pulmonary gas exchange was measured breath-by-breath. Surface EMG was recorded from m. rectus femoris; integrated EMG (IEMG) and mean power frequency (MPF) were derived for successive contractions. In comparison to moderate-intensity exercise, the phase 2 VO2 kinetics in heavy exercise were marginally slower than for moderate-intensity exercise (time constant (+/- SD) 25 +/- 9 and 22 +/- 10 s, respectively; NS), with a discernible VO2(sc) (VO2 difference between minutes 6 and 3 of exercise: 74 +/- 21 and 0 +/- 20 ml min(-1), respectively). However, there was no significant change in IEMG or MPF, either in the moderate domain or in the heavy domain over the period when the slow component was manifest. These observations argue against an appreciable preferential recruitment of fast-twitch units with high force-generating characteristics and fast sarcolemmal conduction velocities in concert with the development of the VO2 slow component during heavy-intensity knee-extensor exercise. The underlying mechanism(s) remains to be resolved.
Adult↗
Origination and evolution of a human-specific transmembrane protein gene, c1orf37-dup.
A transmembrane protein gene, c1orf37-dup, was identified as a young gene specific to humans. It was derived from the conserved c1orf37 gene through retroposition after the divergence of human and chimpanzee. This gene has evolved rapidly driven by positive Darwinian selection as evident from a significantly high ratio of non-synonymous substitution rate to synonymous substitution rate (K(a)/K(s)=2.08) between the new c1orf37-dup and the parental c1orf37 genes. Population genetics analysis disclosed a very low level of polymorphism in the c1orf37-dup gene and its neighboring regions, thus providing support for the occurrence of a recent selective sweep. The GFP experiments revealed that it encodes a transmembrane protein associated with cell membranes. Non-random distribution of amino acid changes indicates the C1ORF37-DUP protein may have evolved diverged functions in the presumably functionally important N-terminal region in the cytoplasm and the extracellular loop. These lines of evidence support that the functional adaptation of c1orf37-dup has occurred in humans. Unlike its ubiquitously expressed parental gene, c1orf37-dup expresses selectively in several human tissues including brain. It is suggested that c1orf37-dup encodes a novel transmembrane protein in humans which potentially endows new properties to cell surface interactions.
Animals↗
[Bone density of calcaneus of 2769 healthy persons in Zhejiang province].
OBJECTIVE: To provide a scientific basis for the diagnosis and prevention of osteoporosis in Chinese populations. METHODS: The stiffness index (STI) of the calcaneus was measured with the Achilles Express ultrasound apparatus made in USA among 2769 healthy persons, 1262 males and 1507 females, aged 10 to over 60, in Zhejiang province. The relationships between the STI and sex and age were analyzed. RESULTS: The peak STI appeared in the age 20 - 24 among the males, and appeared in the age 15 - 19 among the females. Beyond these age periods the STI decreased along with the age. The STI values of the males aged over 54 were significantly higher than those of the females the same age. The speed of STI decrease of the females aged over 55 was higher than the males of the same age (P < 0.01). The prevalence of osteoporosis was higher in the females than in the males. The STI was negatively correlated with age, and positively correlated with height and body weight in both sexes. The practically measured T values were mostly significantly lower than the instrument' T values (with young adult Japanese as reference population). CONCLUSION: There are significant relationships between STI and age, height, and body weight in both males and females. The distribution of bone mineral density of the reference population for the imported instrument does not completely accord with that of Chinese. It is necessary to establish a standard adaptable to the specific condition of Chinese.
Adolescent↗
Gene expression analysis of distinct populations of cells isolated from mouse and human inner ear FFPE tissue using laser capture microdissection--a technical report based on preliminary findings.
Laser Capture Microdissection (LCM) allows microscopic procurement of specific cell types from tissue sections that can then be used for gene expression analysis. We first tested this method with sections of adult mouse inner ears and subsequently applied it to human inner ear sections. The morphology of the various cell types within the inner ear is well preserved in formalin fixed paraffin embedded (FFPE) sections, making it easier to identify cell types and their boundaries. Recovery of good quality RNA from FFPE sections can be challenging, however, recent studies in cancer research demonstrated that it is possible to carry out gene expression analysis of FFPE material. Thus, a method developed using mouse FFPE tissue can be applied to human archival temporal bones. This is important because the majority of human temporal bone banks have specimens preserved in formalin and a technique for retrospective analysis of human archival ear tissue is needed. We used mouse FFPE inner ear sections to procure distinct populations of cells from the various functional domains (organ of Corti, spiral ganglion, etc.) by LCM. RNA was extracted from captured cells, amplified, and assessed for quality. Expression of selected genes was tested by RT-PCR. In addition to housekeeping genes, we were able to detect cell type specific markers, such as Myosin 7a, p27(kip1) and neurofilament gene transcripts that confirmed the likely composition of cells in the sample. We also tested the method described above on FFPE sections from human crista ampullaris. These sections were approximately a year old. Populations of cells from the epithelium and stroma were collected and analyzed independently for gene expression. The method described here has potential use in many areas of hearing research. For example, following exposure to noise, ototoxic drugs or age, it would be highly desirable to analyze gene expression profiles of selected populations of cells within the organ of Corti or spiral ganglion cells rather than a mixed population of cells from whole inner ear tissue. Also, this method can be applied for analysis of human archival ear tissue.
Animals↗