Rodents mediate the relationship between seed rain, seed bank, and plant community with increased grazing disturbance.

Seed rain and the soil seed bank represent the dispersal of seeds in space and time, respectively, and can be important sources of recruitment of new individuals during plant community regeneration. However, the temporal dynamics of seed rain and the mechanisms by which the seed rain and soil seed bank may play a role in plant community regeneration with increased grazing disturbance remain unclear. Seed rain, soil seed bank, aboveground vegetation, and rodent density were sampled along a grazing gradient in an alpine marsh on the eastern Tibetan Plateau. We described the temporal dynamics of seed dispersal using Bayesian generalized mixed models, and nonmetric multidimensional scaling and the structural equation model were used to examine the effects of grazing disturbance on the relative role of seed rain and soil seed bank on aboveground plant community regeneration. The temporal dynamics of seed rain changed from a unimodal to a bimodal pattern with increased grazing disturbance. Both species diversity and seed density of the seed rain and seed bank increased significantly with increased grazing disturbance. Increased grazing disturbance indirectly increased the similarity of composition between seed rain, seed bank, and aboveground plant community by directly increasing species diversity and abundance of aboveground plant community. However, increased grazing disturbance also indirectly decreased the similarity of seed rain, soil seed bank, and aboveground plant community by directly increasing rodent density. The similarity between seed rain and aboveground plant community was greater than that of the soil seed bank and aboveground plant community with increased grazing disturbance. Grazing disturbance spreads the risk of seed germination and seedling establishment by changing the temporal dynamics of seed dispersal. Plants (positive) and rodents (negative) mediated the role of seed rain and soil seed bank in plant community regeneration. The role of seed rain in plant community regeneration is higher than the seed bank in disturbed alpine marshes. Our findings increase our understanding of the regeneration process of the plant community, and they provide valuable information for the conservation and restoration of alpine marsh ecosystems.

Diagnostic yield and novel candidate genes by next generation sequencing in 166 children with intrahepatic cholestasis.

BACKGROUND AND AIMS: Cholestatic liver disease is a leading referral to pediatric liver transplant centers. Inherited disorders are the second most frequent cause of cholestasis in the first month of life. METHODS: We retrospectively characterized the genotype and phenotype of 166 participants with intrahepatic cholestasis, and re-analyzed phenotype and whole-exome sequencing (WES) data from patients with previously undetermined genetic etiology for newly published genes and novel candidates. Functional validations of selected variants were conducted in cultured cells. RESULTS: Overall, we identified disease-causing variants in 31% (52/166) of our study participants. Of the 52 individuals, 18 (35%) had metabolic liver diseases, 9 (17%) had syndromic cholestasis, 9 (17%) had progressive familial intrahepatic cholestasis, 3 (6%) had bile acid synthesis defects, 3(6%) had infantile liver failure and 10 (19%) had a phenocopy of intrahepatic cholestasis. By reverse phenotyping, we identified a de novo variant c.1883G > A in FAM111B of a case with high glutamyl transpeptidase (GGT) cholestasis. By re-analyzing WES data, two patients were newly solved, who had compound heterozygous variants in recently published genes KIF12 and USP53, respectively. Our additional search for novel candidates in unsolved WES families revealed four potential novel candidate genes (NCOA6, CCDC88B, USP24 and ATP11C), among which the patients with variants in NCOA6 and ATP11C recapitulate the cholestasis phenotype in mice models. CONCLUSIONS: In a single-center pediatric cohort, we identified monogenic variants in 22 known human intrahepatic cholestasis or phenocopy genes, explaining up to 31% of the intrahepatic cholestasis patients. Our findings suggest that re-evaluating existing WES data from well-phenotyped patients on a regular basis can increase the diagnostic yield for cholestatic liver disease in children.

Warming reduced flowering synchrony and extended community flowering season in an alpine meadow on the Tibetan Plateau.

The timing of phenological events is highly sensitive to climate change, and may influence ecosystem structure and function. Although changes in flowering phenology among species under climate change have been reported widely, how species-specific shifts will affect phenological synchrony and community-level phenology patterns remains unclear. We conducted a manipulative experiment of warming and precipitation addition and reduction to explore how climate change affected flowering phenology at the species and community levels in an alpine meadow on the eastern Tibetan Plateau. We found that warming advanced the first and last flowering times differently and with no consistent shifts in flowering duration among species, resulting in the entire flowering period of species emerging earlier in the growing season. Early-flowering species were more sensitive to warming than mid- and late-flowering species, thereby reducing flowering synchrony among species and extending the community-level flowering season. However, precipitation and its interactions with warming had no significant effects on flowering phenology. Our results suggest that temperature regulates flowering phenology from the species to community levels in this alpine meadow community, yet how species shifted their flowering timing and duration in response to warming varied. This species-level divergence may reshape flowering phenology in this alpine plant community. Decreasing flowering synchrony among species and the extension of community-level flowering seasons under warming may alter future trophic interactions, with cascading consequences to community and ecosystem function.

Antisense oligonucleotides rescue an intronic splicing variant in the ABCB11 gene that causes progressive familial intrahepatic cholestasis type 2.

BACKGROUND: Progressive familial intrahepatic cholestasis type 2 (PFIC2) is a rare disorder caused by variants in the ABCB11 gene encoding the bile salt export pump (BSEP). We investigated the molecular defect in a PFIC2 infant and rescued the splicing defect with antisense oligonucleotides (ASOs). METHODS: Whole-exome sequencing (WES) revealed compound heterozygous variants in the ABCB11 gene in a PFIC2 patient. Liver biopsy was immunostained for BSEP. The splicing effect of the candidate variants was investigated by minigene assay. ASOs were designed to rescue aberrant splicing. RESULTS: A Chinese girl of two nonconsanguineous healthy parents suffered from low glutamyl transpeptidase cholestasis and showed no response to the ursodeoxycholic acid. WES revealed that the patient was compound heterozygous for two novel variants in the ABCB11 gene: c.76+29T>G and c.390-2A>G. Liver immunohistochemistry showed the absence of BSEP. The variant c.76+29T>G was confirmed to retain 42 bp in the mature mRNA. The variant c.390-2A>G was confirmed to cause exon 6 skipping. We designed two ASOs and identified one of them that efficiently induced pseudoexon exclusion. CONCLUSION: We reported two novel variants of the ABCB11 gene, c.76+29T>G and c.390-2A>G, in a PFIC2 infant, thereby expanding the genotype of PFIC2. Our findings provide evidence for ASOs as a therapeutic approach for PFIC2 patients carrying intronic variants.

Machine Learning-Based Perihematomal Tissue Features to Predict Clinical Outcome after Spontaneous Intracerebral Hemorrhage.

OBJECTIVES: To explore whether radiomic features of perihematomal tissue can improve the forecasting accuracy for the prognosis of patients with an intracerebral hemorrhage (ICH). MATERIALS AND METHODS: In total, 118 ICH patients were retrospectively studied that had a clinical and radiological diagnosis of spontaneous ICH. The functional outcome 3 months after ictus was measured using the modified Rankin Scale (mRS), which was divided into good (mRS ≤ 2) and poor outcomes (mRS > 2). A total of 2260 radiomics features were obtained from non-contrast computer tomography (NCCT) images, with 1130 features extracted from the hematoma and the hematoma plus perihematoma. The high-dimensional data was modeled by a logistic regression algorithm and the accuracy of the model was verified by five-fold cross-validation. The predictive performance of radiomics models was assessed by the area under the receiver operating characteristic (ROC) curve. RESULTS: In the test set, the mean ROC area under the curve (AUC) of the hematoma set to predict the prognosis of ICH was 0.83, and the specificity and sensitivity were 78% and 81%, respectively. When the hematoma and perihematomal tissue were combined, the mean AUC increased to 0.88, and the specificity and sensitivity reached 85% and 84%, respectively. The hematoma plus perihematoma model showed a significantly higher AUC and specificity. CONCLUSIONS: Analysis of the hematoma and perihematomal tissue NCCT-based radiomics could potentially identify the progression of a hematoma more accurately and could be a valuable clinical target to enhance the prediction of outcomes in patients with ICH.

[Genetic analysis of PYGL gene variants for a child with Glycogen storage disease VI].

OBJECTIVE: To explore the clinical features and genetic basis of a patient with glycogen storage disease type VI (GSD-VI). METHODS: Clinical data of the patient was collected. Genomic DNA was extracted from peripheral blood samples of the proband and his parents. Genetic variants were detected by using whole exome sequencing. Candidate variants were verified by Sanger sequencing followed by bioinformatics analysis. RESULTS: The proband presented fasting hypoglycemia, hepatomegaly, growth retardation, transaminitis, metabolic acidosis and hyperlactatemia. Liver biopsy indicated GSD. Novel compound heterozygous PYGL gene variants (c.2089A>G/c.158_160delACT) were detected in the proband. Compound heterozygosity was confirmed by Sanger sequencing of the patient's genomic DNA. Provean and MutationTaster predicted the two variants as deleterious and the variant sites are highly conserved. CONCLUSION: The compound heterozygous variants (c.2089A>G/c.158_160delACT) of PYGL gene probably underlay the GSD in the patient. The two novel variants have expanded the spectrum of PYGL gene variants and provided the basis for genetic counseling of the family.

A Synonymous Variant c.579A>G in the ETFDH Gene Caused Exon Skipping in a Patient With Late-Onset Multiple Acyl-CoA Dehydrogenase Deficiency: A Case Report.

Background: Multiple acyl-CoA dehydrogenase deficiency (MADD) is an autosomal recessive disorder characterized by a wide range of clinical features, including muscle weakness, hypoglycemia, metabolic acidosis, and multisystem dysfunctions. Loss-of-function mutations in the electron transfer flavoprotein dehydrogenase (ETFDH) gene are associated with MADD. Disease-causing synonymous variants in the ETFDH gene have not been reported so far. Methods: We reported the clinical course of a Chinese girl who was diagnosed with late-onset MADD by the whole exome sequencing. The effects of variants on mRNA splicing were analyzed through transcript analysis in vivo and minigene splice assay in vitro. Results: The 6-month-old girl initially showed muscle weakness, muscular hypotonia, mild myogenic damage, and fatty liver. The blood and urine metabolic screening by tandem mass spectrometry suggested MADD. Molecular analysis of ETFDH gene revealed two novel heterozygous variants, a frameshift mutation c.1812delG (p.V605Yfs*34) in exon 13 and a synonymous variant c.579A>G (p.E193E) in exon 5. The transcript analysis in vivo exhibited that the synonymous variant c.579A>G caused exon 5 skipping. The minigene splice assay in vitro confirmed the alteration of ETFDH mRNA splicing which could lead to the production of a truncated protein. Supplementation of riboflavin, carnitine and low-fat diet improved the clinical symptoms. Conclusion: We firstly report a rare case of MADD with a pathogenic synonymous variant in the ETFDH gene which highlights the importance and necessity of bioinformatic analysis and functional testing for synonymous variants when searching for causative gene mutations. The results expand the spectrum of pathogenic variants in MADD.

Eosinophilic colitis in a boy with a novel XIAP mutation: a case report.

BACKGROUND: X-linked inhibitor of apoptosis (XIAP) deficiency is a rare primary immunodeficiency disease characterized by haemophagocytic lymphohistiocytosis, recurrent splenomegaly and inflammatory bowel disease (IBD). The only curative treatment is haematopoietic stem cell transplant (HSCT). CASE PRESENTATION: Here, we report the case of a 22-month-old male with a long history of abdominal distension and anaemia. Clinical and laboratory findings were consistent with eosinophilic colitis. To identify the underlying disease, we performed exome sequencing, which showed an unreported frameshift mutation in the XIAP gene. CONCLUSION: We present eosinophilic colitis as the initial manifestation of XIAP deficiency for the first time in this article, which expands the mutation spectrum and phenotype of this disease.

De Novo ARID1B mutations cause growth delay associated with aberrant Wnt/ß-catenin signaling.

Haploinsufficiency of ARID1B (AT-rich interaction domain 1B) has been involved in autism spectrum disorder, nonsyndromic and syndromic intellectual disability, and corpus callosum agenesis. Growth impairment is a major clinical feature caused by ARID1B mutations; however, the mechanistic link has not been elucidated. Here, we confirm that growth delay is a common characteristic of patients with ARID1B mutations, which may be associated with dysregulation of the Wnt/ß-catenin signaling pathway. An analysis of patients harboring pathogenic variants of ARID1B revealed that nearly half had short stature and nearly all had below-average height. Moreover, the percentage of patients with short stature increased with age. Knockdown of arid1b in zebrafish embryos markedly reduced body length and perturbed the expression of both chondrogenic and osteogenic genes including sox9a, col2a1a, runx2b, and col10a1. Knockout of Arid1b in chondrogenic ATDC5 cells inhibited chondrocyte proliferation and differentiation. Finally, Wnt/ß-catenin signaling was perturbed in Arid1b-depleted zebrafish embryos and Arid1b knockout ATDC5 cells. These data indicate that ARID1B modulates bone growth possibly via regulation of the Wnt/ß-catenin pathway, and may be an appropriate target for gene therapy in disorders of growth and development.

Genetic Evaluation of 114 Chinese Short Stature Children in the Next Generation Era: a Single Center Study.

BACKGROUND/AIMS: The genetics of human height is a frequently studied and complex issue. However, there is limited genetic research of short stature. To uncover the subgroup of patients to have higher yield and to propose a simplified diagnostic algorithm in the next generation era. METHODS: This study included 114 Chinese children with height SDS ≤ -2.5 and unknown etiology from 2014 to 2015. Target/whole exome sequencing (referred as NGS) and chromosomal microarray analysis (CMA) were performed on the enrolled patients sequentially to identify potential genetic etiologies. The samples solved by NGS and CMA were retrospectively studied to evaluate the clinical pathway of the patients following a standard diagnostic algorithm. RESULTS: In total, a potential genetic etiology was identified in 41 (36%) patients: 38 by NGS (33.3%), two by CMA (1.8%), and an additional one by both (0.9%). There were 46 different variants in 29 genes and 2 pathogenic CNVs identified. The diagnostic yield was significantly higher in patients with facial dysmorphism or skeletal abnormalities than those without the corresponding phenotype (P=0.006 and P=0.009, respectively, Pearson's χ2 test). Retrospectively study the cohort indicate 83.3% patients eventually would be evaluated by NGS/CMA. CONCLUSION: This study confirms the utility of high-throughput molecular detection techniques for the etiological diagnosis of undiagnosed short stature and suggests that NGS could be used as a primary diagnostic strategy. Patients with facial dysmorphism and/or skeletal abnormalities are more likely to have a known genetic etiology. Moving NGS forward would simplified the diagnostic algorithm.

Mutations in methionyl-tRNA synthetase gene in a Chinese family with interstitial lung and liver disease, postnatal growth failure and anemia.

Methionyl-tRNA synthetase (MARS) catalyzes the ligation of methionine to tRNA. Heterozygous MARS mutations have been reported to cause Charcot-Marie-Tooth disease, axonal, type 2U (CMT2U). Homozygous or compound heterozygous mutations in MARS gene would cause interstitial lung and liver disease (ILLD), a severe disease onset in infancy or early childhood. Here we report a Chinese ILLD family with two affected boys diagnosed by exome sequencing. They carry novel compound heterozygous MARS mutations (p.Asp145Asn and p.Phe802Ser). Their phenotype is concordant with ILLD description. As ILLD patients were only reported by two studies, we summarized all the reported patients and characterized the principle clinical features as interstitial lung disease, developmental delay, postnatal growth failure, non-life-threatening liver dysfunction and anemia. Genotype-phenotype correlation analysis suggests most of the ILLD mutations locate in the catalytic domain of MARS. ILLD and CMT2U might have different disease mechanism.

Further delineation of the phenotype of truncating KMT2A mutations: The extended Wiedemann-Steiner syndrome.

KMT2A mutations cause Wiedemann-Steiner syndrome (WDSTS), which is characterized by hypertrichosis cubiti, short stature, and distinct facial features in general. Here, we report two Chinese boys with novel nonsense KMT2A mutations. Most of their phenotypes are concordant with WDSTS. They, however, lack the key WDSTS feature-hypertrichosis cubiti. Additionally, their transverse palmar creases are absent. We further summarized the genotypes and phenotypes of the KMT2A mutation carriers. The consensus phenotypes include postnatal growth retardation, developmental delay, short stature, and intellectual disability. The common facial features include thick eyebrows, long eyelashes, downslanting, and narrow palpebral fissures, wide nasal bridge, and broad nasal tip. They have generalized hypertrichosis. A hairy back can be observed as frequently as hairy elbows in patients with KMT2A mutations. Absent palmar proximal transverse creases are only observed in these two Chinese boys. This might be due to the difference in ethnic background. Thus far, all mutations in KMT2A are located before the FYRC domain. They would truncate KMT2A mRNA transcripts. Haploinsufficiency of the histone methyltransferase activity would therefore influence transcriptional regulation. © 2016 Wiley Periodicals, Inc.

Copy number variations in 119 Chinese children with idiopathic short stature identified by the custom genome-wide microarray.

BACKGROUND: Idiopathic short stature (ISS) refers to short stature with no evident etiologies. The custom genome-wide microarray specifically designed to cover height-related genes may be helpful to detect copy number variations (CNVs) in ISS patients, which may be missed by the general microarray. The aim of the study was to validate the applicability of the custom microarray and to analyze CNVs in Chinese ISS children. RESULTS: Sixty non-polymorphic CNVs were identified in 119 ISS patients. There were 13 small CNVs with a size below 50 kb, accounting for 21.7 % of all the CNVs (13/60). Five pathogenic or possibly pathogenic CNVs were detected in five patients, including deletions at 22q11.21, duplications at 4q11-q13.1, 4q12 and Yp11.32-p11.2. Taking only the pathogenic variants into account, the diagnostic yield was 2.5 % (3/119). The TMEM165, POLR2B and PDGFRA genes were analyzed as candidate genes. A 15 kb deletion in the RASA2 gene was of interest for further investigation. CONCLUSIONS: This study showed that the custom microarray is applicable to detect CNVs in patients with short stature. Candidate genes and CNVs detected in ISS patients may be helpful for CNV analysis of short stature, especially in East Asian population.

Curcumin-induced histone acetylation inhibition improves stress-induced gastric ulcer disease in rats.

Curcumin is known to possess anti­inflammatory properties. Despite the fact that curcumin is known to be a strong inhibitor of H+, K+­ATPase activity, the mechanism underlying the curcumin­induced inhibition of the transcription of the H+, K+­ATPase α subunit in gastric mucosal parietal cells remains unclear. The present study investigated the possible mechanism by which curcumin inhibits stomach H+, K+­ATPase activity during the acute phase of gastric ulcer disease. A rat model of stress­induced gastric ulcers was produced, in which the anti­ulcer effects of curcumin were examined. Curcumin­induced inhibition of the H+, K+­ATPase promoter via histone acetylation, was verified using a chromatin immunoprecipitation assay. The results showed that curcumin improved stress­induced gastric ulcer disease in rats, as demonstrated by increased pH values and reduced gastric mucosal hemorrhage and ulcer index. These effects were accompanied by a significant reduction in the level of histone H3 acetylation at the site of the H+, K+­ATPase promoter and in the expression of the gastric H+,K+­ATPase α subunit gene and protein. In conclusion, curcumin downregulated the acetylation of histone H3 at the site of the H+, K+­ATPase promoter gene, thereby inhibiting the transcription and expression of the H+, K+­ATPase gene. Curcumin was shown to have a preventive and therapeutic effect in gastric ulcer disease.

Crigler-Najjar syndrome type II in a Chinese boy resulting from three mutations in the bilirubin uridine 5'-diphosphate-glucuronosyltransferase (UGT1A1) gene and a family genetic analysis.

BACKGROUND: The UGT1A1 gene encodes a responsible enzyme, UDP-glucuronosyltransferase1A1 (UGT1A1), for bilirubin metabolism. Many mutations have already been identified in patients with inherited disorders with unconjugated hyperbilirubinemia, such as Crigler-Najjar syndromes and Gilbert's syndrome. CASE PRESENTATION: In this report, we presented a boy with intermittent unconjugated hyperbilirubinemia, whose genetic analysis showed a new compound heterozygote determined by three mutations, c.211G > A (p.G71R), c.508_510delTTC (p.F170-) and c.1456 T > G (p.Y486D) in the hotspot regions of the UGT1A1 gene (exons 1 and 5) in Asian populations, presenting a genotype compatible with clinical picture of CNS-II. The family genetic analysis confirmed the origin of these mutations. CONCLUSION: UGT1A1 gene analysis should be performed in all cases with unexplained unconjugated hyperbilirubinemia. The description of patients with peculiar genotypes especially including family analysis could help explain the relationship between the genotype and phenotype,it is helpful for clinicians to predict the outcome of the patients.

Diagnosis of ABCB11 gene mutations in children with intrahepatic cholestasis using high resolution melting analysis and direct sequencing.

Intrahepatic cholestasis represents a heterogeneous group of disorders that begin during childhood, most commonly manifesting as neonatal cholestasis, and lead to ongoing liver dysfunction in children and adults. For children, inherited pathogenic factors of cholestasis have gained increasing attention owing to the rapid development of molecular biology technology. However, these methods have their advantages and disadvantages in terms of simplicity, sensitivity, specificity, time required and expense. In the present study, an effective, sensitive and economical method is recommended, termed high-resolution melting (HRM) analysis and direct sequencing, based on general polymerase chain reaction, to detect mutations in disease­causing genes. As one type of inherited intrahepatic cholestasis, progressive familial intrahepatic cholestasis type 2 (PFIC2) is caused by pathogenic mutations in the ABCB11 gene, HRM was used to detect mutations in the ABCB11 gene in the present study, and the diagnosis for PFIC2 was made by comprehensive analysis of genetic findings and clinical features. Furthermore, the characteristics of mutations and single nucleotide polymorphisms (SNPs) in the ABCB11 gene were elucidated. A total of 14 types of mutations/polymorphisms were identified in 20 patients from mainland China, including six missense mutations (p.Y337H, p.Y472C, p.R696W, p.Q931P, p.D1131V and p.H1198R), one nonsense mutation (p.R928X) and seven SNPs (p.D36D/rs3815675, p.F90F/rs4148777, p.Y269Y/rs2287616, p.I416I/rs183390670, p.V444A/rs2287622, p.A865V/rs118109635 and p.A1028A/rs497692). Five mutations were novel. The majority of the mutations were different from those detected in other population groups. A total of 4/20 patients (1/5) were diagnosed to be PFIC2 by combining genetic findings with the clinical features. Polymorphisms V444A and A1028A, with an allele frequency of 74.5 and 67.2%, respectively, were highly prevalent in the mainland Chinese subjects. No differences were found between the patients with cholestasis and the control subjects. Efficient genetic screening facilitates the clinical diagnosis of genetic disorders. The present study demonstrated that HRM analysis was efficient and effective in detecting mutations and expanded the known spectrum of ABCB11 gene mutations.

Association between TGFB1 915G/C polymorphism and susceptibility to chronic hepatitis C virus infection: A meta-analysis.

The human transforming growth factor-ß1 (TGF-ß1) gene, namely TGFB1, contains several single-nucleotide polymorphisms (SNPs) and some of the polymorphic variants were shown to affect the TGF-ß1 protein levels. A number of studies reported the association between 915G/C polymorphism and susceptibility to chronic hepatitis C virus (HCV) infection. However, the results were inconsistent. This meta-analysis was conducted to assess the association of TGFB1 915G/C polymorphism with susceptibility to chronic HCV infection. PubMed, ISI Web of Knowledge, ScienceDirect and Google Scholar databases were systematically searched up to August, 2013 to identify relevant studies. The pooled odds ratios (ORs) with their corresponding 95% confidence intervals (95% CIs) were calculated in 5 genetic comparison models (C vs. G, CC vs. GG, GC vs. GG, CC vs. GG+GC and CC+GC vs. GG). The Galbraith plot and subgroup analyses based on ethnicity, genotyping methods, sample size and fibrosis were performed to investigate possible sources of heterogeneity. A sensitivity analysis and assessment of publication bias were also conducted. Finally, 8 eligible case-control studies on TGFB1 915G/C polymorphism, including a total of 910 cases and 632 controls, were included in this meta-analysis. Overall, there was no evidence of any gene-disease association obtained from the subgroup analyses. Therefore, this meta-analysis demonstrated that there is no association between TGFB1 915G/C polymorphisms and susceptibility to chronic HCV infection.