Maple syrup urine disease (MSUD) is a rare autosomal recessive disorder that affects the degradation of branched chain amino acids (BCAAs). Only a few cases of MSUD have been documented in Mainland ...China. In this report, 8 patients (4 females and 4 males) with MSUD from 8 unrelated Chinese Han families were diagnosed at the age of 6 days to 4 months. All the coding regions and exon/intron boundaries of BCKDHA, BCDKHB, DBT and DLD genes were analyzed by targeted NGS in the 8 MSUD pedigrees. Targeted NGS revealed 2 pedigrees with MSUD Ia, 5 pedigrees with Ib, 1 pedigree with MSUD II. Totally, 13 variants were detected, including 2 variants (p.Ala216Val and p.Gly281Arg) in BCKDHA gene, 10 variants (p.Gly95Ala, p.Ser171Pro, p.Phe175Leu, p.Arg183Trp, p.Lys222Thr, p.Arg285Ter, p.Arg111Ter, p.S184Pfs*46, p.Arg170Cys, p.I160Ffs*25) in BCKDHB gene, 1 variant (p.Arg431Ter) in DBT gene. In addition, 4 previously unidentified variants (p.Gly281Arg in BCKDHA gene, p.Ser171Pro, p.Gly95Ala and p.Lys222Thr in BCKDHB gene) were identified. NGS plus Sanger sequencing detection is effective and accurate for gene diagnosis. Computational structural modeling indicated that these novel variations probably affect structural stability and considered as likely pathogenic variants.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
This study aimed to investigate the effect and mechanism of bone marrow mesenchymal stem cell-derived exosomes on osteoblast function.
The expression of KLF3-AS1 and miR-338-3p in serum of fracture ...patients was detected by qRT-PCR. Exosomes from BMSCs were isolated by ultrafast centrifugation. MC3T3-E1 cells were cultured in vitro as experimental cells. Intracellular gene expression was regulated by transfection of si-KLF3-AS1 or miR-338-3p inhibitors. MTT assay, Transwell assay and flow cytometry were used to evaluate cell viability, migration, and apoptosis. The luciferase reporter gene was used to verify the targeting relationship between KLF3-AS1 and miR-338-3p. Bioinformatics analysis was used to identify the basic functions and possible enrichment pathways of miR-338-3p target genes.
The expressions of KLF3-AS1 and miR-338-3p in the serum of fracture patients were down-regulated and up-regulated, respectively. The expression of KLF3-AS1 was increased in MC3T3-E1 cells cultured with BMSCs-Exo, while the viability and migration ability of MC3T3-E1 cells were enhanced, and the apoptosis ability was weakened. Further analysis revealed miR-338-3p was the target gene of KLF3-AS1. The expression of miR-338-3p was downregulated in MC3T3-E1 cells cultured with BMSCs-Exo. Inhibition of miR-338-3p in MC3T3-E1 cells enhanced the viability and migration ability of MC3T3-E1 cells when cultured with BMSCs-Exo, while suppressing apoptosis. Bioinformatics analysis demonstrated that the target genes of miR-338-3p were predominantly localized at the axon's initiation site, involved in biological processes such as development and growth regulation, and mainly enriched in MAPK and ErbB signaling pathways.
In vitro, BMSCs-Exo exhibits the capacity to enhance proliferation and migration while inhibiting apoptosis of MC3T3-E1 cells, potentially achieved through modulation of KLF3-AS1 and miR-338-3p expression in MC3T3-E1 cells.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Background
Spinal muscular atrophy (SMA) is a common and lethal autosomal recessive neurodegenerative disease caused by mutations in the survival motor neuron 1 (SMN1) gene. At present, gene ...therapy medicine for SMA, i.e., Spinraza (Nusinersen), has been approved by the FDA, bringing hope to SMA patients and families. Accurate diagnosis is essential for treatment. Our goal was to detect genetic mutations in SMA patients in China and to show the results of the prenatal diagnosis of SMA.
Methods
In this study, we examined 419 patients in our hospital from January 2010 to September 2019. Multiplex ligation-dependent probe amplification analysis was used to determine the copy numbers of SMN1 and SMN2. Long-range PCR combined with nested PCR was used to detect point mutations in SMN1. In addition to the above detection methods, we also used QF-PCR in prenatal diagnosis to reduce the impact of maternal contamination. We conducted a total of 339 prenatal diagnoses from January 2010 to September 2019.
Results
Homozygous deletion of SMN1 exon 7 was detected in 96.40% (404/419) of patients. Homozygous deletion of SMN1 exon 7 alone was detected in 15 patients (3.60%). In total, 10 point mutations were detected in the 15 pedigrees. Most patients with SMA Type I have 1 ~ 2 copies of the SMN2 gene. Patients with SMA Type II have 2 or 3 copies of the SMN2 gene. The results of prenatal diagnoses showed that 118 fetuses were normal, 149 fetuses were carriers of heterozygous variants, and the remaining 72 fetuses harbored compound heterozygous variants or homozygous variants.
Conclusions
Our study found that the most common mutation in SMA was homozygous deletion of SMN1 exon 7 in our study. We suggest that detecting only the deletion of exon 7 of SMN1 can meet most of the screening needs. We also believe that SMN2 copy numbers can help infer the disease classification and provide some reference for future treatment options.
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Soil organic carbon (SOC) decomposition, a key process controlling the carbon (C) loss from terrestrial soils to the atmosphere, varies with soil aggregate size and is influenced by increasing ...nitrogen (N) and phosphorus (P) inputs from anthropogenic activities. However, how increasing N and P affects SOC decomposition and its temperature sensitivity (Q10) in soil aggregates remains unclear. Thus, we collected soils from a subtropical Cunninghamia lanceolata forest receiving N and P addition for 8 years to explore the interactive effects of N and P fertilization on SOC decomposition and its Q10 in mega-aggregates (>2 mm, MeA), macroaggregates (0.25–2.0 mm, MaA), and microaggregates (<0.25 mm, MiA). Results showed that aggregate size has a huge influence on SOC decomposition and its Q10. Specifically, SOC decomposition in MiA is 49.2% and 26.0% higher than MeA and MaA, respectively. Moreover, the averaged Q10 values were 2.29, 2.26 and 1.83 in MeA, MaA and MiA. SOC decomposition significantly increased by 39.4% in MaA and 23.7% in MiA with N fertilization, but P fertilization had less impact. However, P fertilization increased Q10 by 46.7% in MeA and 46.6% in MaA. Furthermore, we found P fertilization changed the influences of N fertilization on SOC decomposition in MaA and MiA but had no effect on responses of Q10 to N fertilization. Overall, our findings suggested that there were differences in SOC decomposition and Q10 among aggregates, and fertilization treatment had an impact on them. Our results highlighted the significance of considering differences in SOC decomposition and its response to climate warming and nutrient input among different aggregates in the prediction of SOC dynamics and its feedback to environmental changes in terrestrial ecosystems under climate warming scenarios.
To analyze the dynamic variant and clinical subtype of a pedigree affected with spinocerebellar ataxia (SCA) by using fluorescent-labeled primer combined with capillary electrophoresis.
Genomic DNA ...was extracted from 8 members including 6 patients and 2 healthy individuals from the pedigree. Six pairs of fluorescent-labeled primers were designed to screen pathological variants in association with common subtypes of SCA including SCA1, SCA2, SCA3, SCA6, SCA12 and SCA17.The PCR products were detected by capillary electrophoresis.
The number of CAG repeats in the SCA3 gene of the proband were determined as 8 and 70, exceeded the normal range(12 to 40), which suggested a diagnosis of SCA3. The other five patients were all detected with abnormal CAG repeats in the SCA3 gene, while the two healthy individuals were determined to be within the normal range.
The abnormal expansion of CAG repeats in the SCA3 gene probably underlay the pathogenesis of the disease in this pedigree. Combined fluorescent-labeled primers PC
Primary periodic paralysis (PPP) is an inherited disorders of ion channel dysfunction characterized by recurrent episodes of flaccid muscle weakness, which can classified as hypokalemic (HypoPP), ...normokalemic (NormoPP), or hyperkalemic (HyperPP) according to the potassium level during the paralytic attacks. However, PPP is charactered by remarkable clinical and genetic heterogeneity, and the diagnosis of suspected patients is based on the characteristic clinical presentation then confirmed by genetic testing. At present, there are only limited cohort studies on PPP in the Chinese population.
We included 37 patients with a clinical diagnosis of PPP. Eleven (29.7%) patients were tested using a specific gene panel and 26 (70.3%) by the whole-exome sequencing (WES). Twenty-two cases had a genetic variant identified, representing a diagnostic rate of 59.5% (22/37). All the identified mutations were either in the SCN4A or the CACNA1S gene. The overall detection rate was comparable between the panel (54.5%: 6/11) and WES (61.5%: 16/26). The remaining patients unresolved through panel sequencing were further analyzed by WES, without the detection of any mutation. The novel atypical splicing variant c.2020-5G > A affects the normal splicing of the SCN4A mRNA, which was confirmed by minigene splicing assay. Among 21 patients with HypoPP, 15 patients were classified as HypoPP-2 with SCN4A variants, and 6 HypoPP-1 patients had CACNA1S variants.
Our results suggest that SCN4A alleles are the main cause in our cohort, with the remainder caused by CACNA1S alleles, which are the predominant cause in Europe and the United States. Additionally, this study identified 3 novel SCN4A and 2 novel CACNA1S variants, broadening the mutation spectrum of genes associated with PPP.
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Abstract
The response of soil carbon release to global warming is largely determined by the temperature sensitivity of soil respiration, yet how this relationship will be affected by increasing ...atmospheric nitrogen deposition is unclear. Here, we present a global synthesis of 686 observations from 168 field studies to investigate the relationship between nitrogen enrichment and the temperature sensitivity of soil respiration. We find that the temperature sensitivity of total and heterotrophic soil respiration increased with latitude. In addition, for total and autotrophic respiration, the temperature sensitivity responded more strongly to nitrogen enrichment with increasing latitude. Temperature and precipitation during the Last Glacial Maximum were better predictors of how the temperature sensitivity of soil respiration responds to nitrogen enrichment than contemporary climate variables. The tentative legacy effects of paleoclimate variables regulate the response through shaping soil organic carbon and nitrogen content. We suggest that careful consideration of past climate conditions is necessary when projecting soil carbon dynamics under future global change.
The genome topology network (GTN) is a new approach for studying the phylogenetics of bacterial genomes by analysing their gene order. The previous GTN tool gives a phylogenetic tree and calculate ...the different degrees (DD) of various adjacent gene families with complete genome data, but it is limited to the gene family level.
In this study, we collected 51 published complete and draft group B Streptococcus (GBS) genomes from the NCBI database as the case study data. The phylogenetic tree obtained from the GTN method assigned the genomes into six main clades. Compared with single nucleotide polymorphism (SNP)-based method, the GTN method exhibited a higher resolution in two clades. The gene families located at unique node connections in these clades were associated with the clusters of orthologous groups (COG) functional categories of "G Carbohydrate transport and metabolism,", "L Replication, recombination, and repair" and "J translation, ribosomal structure and biogenesis". Thus, these genes were the major factors affecting the differentiation of these six clades in the phylogenetic tree obtained from the GTN.
The modified GTN analyzes draft genomic data and exhibits greater functionality than the previous version. The gene family clustering algorithm embedded in the GTN tool is optimized by introducing the Markov cluster algorithm (MCL) tool to assign genes to functional gene families. A bootstrap test is performed to verify the credibility of the clades when allowing users to adjust the relationships of the clades accordingly. The GTN tool gives additional evolutionary information that is a useful complement to the SNP-based method. Information on the differences in the connections between a gene and its adjacent genes in species or clades is easily obtained. The modified GTN tool can be downloaded from https://github.com/0232/Genome_topology_network.
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BackgroundThe reactor period will dramatically decrease at the beginning of reactivity insertion in the nuclear reactor, which may trigger the protection system of the reactor period and lead to ...unnecessary shutdown. The instantaneous short reactor period is influenced greatly by the inserting rate of reactivity, but also related with the present delayed neutron precursors, which is difficult to quantify.PurposeThis study aims to explore the relationship between the instantaneous short reactor period and the inserting rate of reactivity from a theoretical perspective.MethodsA point reactor model was used to deduce the inserting rate of the reactivity function using the variable factors of reactivity, reactor period, and reactor dynamic parameters, with some conservative assumptions to omit the effect of delayed neutron precursors. The relationship between reactivity insertion rate and transient period of reactor was derived after analysis on the short period phenomenon. Then, the formula of relationship was v
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