Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale.

Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.

Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics.

Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.

Clinical spectrum, over 12-year follow-up and experience of SGLT2 inhibitors treatment on patients with glycogen storage disease type Ib: a single-center retrospective study.

BACKGROUND: Glycogen storage disease type Ib (GSD Ib) is a rare disorder characterized by impaired glucose homeostasis caused by mutations in the SLC37A4 gene. It is a severe inherited metabolic disease associated with hypoglycemia, hyperlipidemia, lactic acidosis, hepatomegaly, and neutropenia. Traditional treatment consists of feeding raw cornstarch which can help to adjust energy metabolism but has no positive effect on neutropenia, which is fatal for these patients. Recently, the pathophysiologic mechanism of the neutrophil dysfunction and neutropenia in GSD Ib has been found, and the treatment with the SGLT2 inhibitor empaglifozin is now well established. In 2020, SGLT2 inhibitor empagliflozin started to be used as a promising efficient remover of 1,5AG6P in neutrophil of GSD Ib patients worldwide. However, it is necessary to consider long-term utility and safety of a novel treatment. RESULTS: In this study, we retrospectively examined the clinical manifestations, biochemical examination results, genotypes, long-term outcomes and follow-up of thirty-five GSD Ib children who visited our department since 2009. Fourteen patients among them underwent empagliflozin treatment since 2020. This study is the largest cohort of pediatric GSD Ib patients in China as well as the largest cohort of pediatric GSD Ib patients treated with empagliflozin in a single center to date. The study also discussed the experience of long-term management on pediatric GSD Ib patients. CONCLUSION: Empagliflozin treatment for pediatric GSD Ib patients is efficient and safe. Increase of urine glucose is a signal for pharmaceutical effect, however attention to urinary infection and hypoglycemia is suggested.

Modified nusinersen intrathecal injection method: inclusion of a septal needle-free closed infusion connector.

Objective: Nusinersen, an extremely expensive biologic drug (around 100,000 US$ per dose) that needs to be administered intrathecally, is approved for the treatment of 5q-spinal muscular atrophy (SMA). Because of the low muscle tone of the back muscles of pediatric SMA patients, especially type 1 SMA patients, the safe, effective, and fast execution of sheath injection is needed. Therefore, a modified intrathecal injection method was developed accordingly. This paper aims to describe the applicability and safety of this modified method. Methods: The modified intrathecal injection method (MIIM) mainly includes a septal needle-free closed infusion connector between the lumbar puncture needle and the syringe, besides the procedures of routine lumbar puncture. Its applicability and safety were evaluated through clinical observation. Results: A total of 92 children with SMA have successfully received nusinersen treatment at our hospital using the modified method since 2019 without obvious adverse events related to the modified injection method. Based on the clinical feedback of operators, the advantages of the modified method include successfully injecting the total dose of nusinersen with constant injection rate and a more stable fixation of the puncture needle, as well as making the operator more relaxed. However, compared with the routine method, the procedure of the modified method has additional steps. Conclusion: The modified intrathecal injection method is an effective and safe method to inject nusinersen when weighing the pros and cons, and it may also be used for administering intrathecal injections of other expensive medicines or for patients with other strict requirements for intrathecal injection.

Clinical characteristics and long-term outcomes of 12 children with vitamin D-dependent rickets type 1A: A retrospective study.

Purpose: Vitamin D-dependent rickets type 1A (VDDR1A) is a rare autosomal recessive disorder caused by deficiency of the CYP27B1 gene. This study aims to investigate the phenotypic and genotypic features of VDDR1A children in southern China and evaluate the long-term therapeutic effects. Methods: Twelve children from southern China with VDDR1A were enrolled in this study. Their clinical, radiological, biochemical, and molecular findings were analyzed retrospectively. The rickets severity score (RSS), biochemical parameters, and height standard deviation score (HtSDS) were used to evaluate clinical outcomes. Results: Six males and six females were included in this VDDR1A cohort. The age of onset was from 6 months to 1.8 years, and the age at diagnosis was 2.1 ± 0.8 years. The most common clinical symptoms at diagnosis were delayed walking (10/12) and severe growth retardation (9/12). HtSDS at diagnosis was negatively associated with age (p < 0.05). All patients presented with hypocalcemia, hypophosphatemia, increased serum alkaline phosphatase and parathyroid hormone, and high RSS at diagnosis. Two allelic variants of the CYP27B1 gene were identified in all patients, including nine different variants, four known and five novel, with c.1319_1325dupCCCACCC(p.Phe443Profs*24) being the most frequent. All patients were treated with calcitriol and calcium after diagnosis, and all patients but one were followed-up from 6 months to 15.6 years. HtSDS, RSS, and biochemical parameters were found to be improved during the first few years of the treatment. However, only five patients had good compliance. Although RSS and biochemical parameters were significantly improved, the HtSDS change was not significant from the time of diagnosis to the last visit, and seven patients remained of a short stature (HtSDS < -2). Conclusion: Our study extends the mutational spectrum of VDDR1A and finds a hotspot variant of the CYP27B1 gene in southern China. The results reconfirm the importance of early diagnosis and treatment compliance and reveal the challenge of height improvement in VDDR1A patients.

Features of chinese patients with sitosterolemia.

BACKGROUND: Sitosterolemia is a lipid disorder characterized by the accumulation of phytosterols in plasma and organs, caused by mutations in the ABCG5 and/or ABCG8 genes. The disease is frequently misdiagnosed and mistreated as familial hypercholesterolemia (FH). To gain a better understanding of the disease, the current status of diagnosis and treatment of Chinese patients with sitosterolemia was reviewed and summarized. METHOD: Literature search was performed. The clinical features and molecular characteristics of Chinese patients with sitosterolemia were analysed. Four children with sitosterolemia and the treatment experience were described. RESULTS: Fifty-five patients with sitosterolemia have been reported in China. These patients were aged from 3 months to 67 years at diagnosis, and the median was 8 years of age. Several complications, such as xanthomas in 47 patients (85%), thrombocytopenia in 17 patients (31%), anemia in 14 patients (25%), and cardiovascular damage in 12 patients (22%), were observed. Thirty-nine patients (71%) exhibited mutations in the ABCG5 gene, 15 patients (27%) showed mutations in ABCG8, and variations in both genes occurred in one patient (2%). A patient with two clinically rare diseases, namely, sitosterolemia and glycogen storage disease type VI (GSD VI)), is reported here for the first time. The four reported patients were treated with low cholesterol and phytosterol-limited diet alone or combined with cholestyramine. Even though decreases were observed for total plasma cholesterol (TC) and low-density-lipoprotein cholesterol (LDL-C), and these levels were as low as normal in some patients, the levels of plant sterols remained above the normal range. However, TC, LDL-C and plant sterol levels remained at high levels in patients treated with a control diet control only. CONCLUSIONS: The analysis reveals that different from Caucasians carrying mainly variations in ABCG8, most Chinese patients have mutations in the ABCG5 gene, and Arg446Ter, Gln251Ter, anArg389His might be hot-spot mutations in Chinese patients. The current survey provides clinical data to enable the development of a standardized protocol for the diagnosis and treatment of sitosterolemia in China.

Direct infusion-tandem mass spectrometry combining with data mining strategies enables rapid chemome characterization of medicinal plants: A case study of Polygala tenuifolia.

Data-independent MS2 spectrum acquisition after fragmenting the precursor ion cohort with 1 Da bin, termed as MS/MSALL ®, offers an opportunity to achieve rapid chemome characterization when being coupled with direct infusion (DI). Some post-acquisition data processing strategies, such as mass defect filtering (MDF), diagnostic fragment ion filtering (DFIF), and neutral loss filtering (NLF), facilitate data extraction from massive dataset, and moreover, molecular weight (MW) imprinting allows rapid capturing those reported components. Here, DI-MS/MSALL ® was employed to acquire cubic spectral dataset, and the strategies such as MW imprinting, MDF, DFIF, and NLF, were subsequently applied to filter the structural information. The integrated pipeline was utilized for the chemome characterization of Polygala tenuifolia, a famous edible medicinal plant. To aid information filtering, an in-house chemical library was built by comprehensively collecting structural information from some available databases. A single analytical run was completed within 5 min. For MS1 spectrum processing, MW imprinting was firstly applied to capture the compounds in the chemical library, and "five-point" MDF frames were employed to pursue saponins, oligosaccharide esters, and xanthones. Regarding MS2 spectral plot, DFIF and NLF were deployed to search information-of-interest. Structural identification was accomplished by carefully correlating precursor ions and MS2 spectra, applying the well-defined mass cracking rules, and referring to literature information as well as available databases. A total of 109 compounds, mainly saponins (40 ones), oligosaccharide esters (29 ones), and xanthones (19 ones), were captured and structurally annotated. MS1 spectra were also implemented for chemome comparison between Polygala tenuifolia and several similar plants belonging to Polygala genus, resulting in the observation of significant inter- and intra-species differences. Above all, DI-MS/MSALL ® is a promising choice for high-throughput chemome profiling of, but not limited to, medicinal plants, in particular when being integrated with post-acquisition data processing strategies.

Serial hyphenation of dried spot, reversed phase liquid chromatography, hydrophilic interaction liquid chromatography, and tandem mass spectrometry towards direct chemical profiling of herbal medicine-derived liquid matrices, an application in Cistanche sinensis.

Inspired by dried blood spots (DBS), "dried spots of herbal medicines" (DSHM) concept was proposed here. In response to this superior sampling means, a new platform integrating dried spot, serially coupled reversed phase liquid chromatography and hydrophilic interaction liquid chromatography (RPLC-HILIC), and tandem mass spectrometry (MS/MS), was configured for directly, comprehensively chemical profiling of HM-derived liquid matrices. As an important original source of Cistanches Herba (Chinese name: Roucongrong) that is a well-known tonic HM, Cistanche sinensis (Csi) was employed to illustrate and validate the applicability. Dried spots (I.D.  3.0 mm) were prepared by loading 2 µL aliquots of Csi extract onto filter paper. Each dried spot was packed into an in-line filter holder (I.D. 3.0 mm × 4.0 mm) and then inserted behind the auto-sampler of a well-defined instrumentation named RPLC-HILIC-MS/MS. Hybrid ion trap-time of flight MS and hybrid triple quadrupole-linear ion trap MS were deployed in combination for the in-depth MS/MS data acquisition of diverse chemical families, such as phenylethanoid glycosides, lignans, iridoids, amino acids, and so forth. To assist chemical profiling, an in-house chemical library was built by collecting as much prior knowledge as possible. A total of 88 components were detected and tentatively annotated in Csi by matching their multi-stage MS spectra with those of authentic standards and literature data. Collectively, DSHM carried all merits of DBS, and the integrative dried spot-RPLC-HILIC-MS/MS platform was a promising analytical tool for direct chemical analysis and rapid quality evaluation of HMs, in particular those traditional Chinese medicine injections.

Clinical features and mutational analysis in 114 young children with Wilson disease from South China.

Wilson disease (WD) is a rare autosomal recessive disorder caused by mutations in the ATP7B gene. Clinical features and mutational analysis of Chinese children with WD at early age were rarely described. Herein, we retrospectively examined 114 children with WD at the mean of 5.9 years old age at diagnosis. Eight patients developed acute liver failure at mean age of 9.7 years old, 4 of whom died. Among the 114 patients, 86.0% were presymptomatic with isolated elevation of transaminases at diagnosis, 99.1% had decreased ceruloplasmin, and 68.4% had urinary copper excretion over 100 µg/24 hr. Bi-allele pathogenic ATP7B mutations were identified in all patients. Among the 60 mutations detected, 10 were novel, including 7 missense mutations (p.I566N, p.T704I, p.C980F, p.G1030 V, p.A1096Q, p.L1327P, and p.L1373F), 1 nonsense mutation (p.K866X), 1 small insertion (p.Y44LfsX2), and 1 small deletion (p.R1118PfsX10). The most frequent mutations were p.R778L, p.P992L, and p.I1148T, which affected 27.2, 25.4, and 20.2% of the 114 WD children, respectively. The patients carrying p.R778L presented a higher rate of acute liver failure than the patients without p.R778L (9.7% vs. 4.8%). These results will be helpful in establishing early diagnosis of WD at the gene level, offering beneficial information for genetic counseling and providing clues to genotype/phenotype correlation of ATP7B mutations.

Dopa-responsive dystonia in Chinese patients: Including a novel heterozygous mutation in the GCH1 gene with an intermediate phenotype and one case of prenatal diagnosis.

Dopa-responsive dystonia (DRD) is a rare inherited disorder characterized by childhood-onset dystonia with diurnal fluctuation and dramatic response to levodopa. DRD is caused by the mutations in the genes encoding the enzymes involved in the dopamine and tetrahydrobiopterin (BH4) biosynthesis, including the GTP cyclohydrolase 1 (GCH1) gene and the tyrosine hydroxylase (TH) gene. In order to improve the diagnosis and expand the knowledge of the disease, we collected and analyzed relevant data of clinical diagnosis and molecular mutational analysis in five Chinese patients with DRD. The patients presented with heterogenous symptoms of neurologic disorders. One novel mutation p.Leu117Arg was identified in GCH1 gene with an intermediate phenotype which was predicted in sillico to have a deleterious effect on the GCH1 protein function. Seven different mutations were identified in TH gene including four known mutations: p.Arg233His, p.Gly315Ser, p.Gly247Ser, p.Arg153X, and three novel mutations: p.Arg476Ser, IVS6-34G > C, p.Arg328Gln. The mutation p.Arg233His was predicted to link to the second type of TH deficiency (dopa-responsive infantile parkinsonism with delayed motor development). The mutation p.Arg153X may link to the first type of TH deficiency (typical DRD). The three novel mutations were predicted to be damaging in sillico. A prenatal diagnosis was made in the fourth pregnancy of the parents of patient 2 and proved to be a carrier of a heterozygous mutation. Our study expands the spectrum of genotype of DRD in China, provides new insights into the molecular mechanism of DRD and help to the diagnosis and treatment of this disease.

[Clinical and molecular analysis of two Chinese siblings with Cockayne syndrome].

OBJECTIVE: Cockayne syndrome is a rare disease and difficult to be recognized. This study aimed to expand the knowledge of the clinical and molecular characteristics of the children with Cockayne syndrome (CS). METHOD: Clinical data of two siblings with classic CS of Guangzhou Women and Children's Medical Center from July 2013 to November 2014 were obtained and analyzed. The whole DNA of peripheral blood was collected from two CS siblings and their parents. Amplification of all exons and adjacent introns for ERCC6 gene was conducted using PCR, and measurement of reaction product was performed to find mutation sites by two-way sequencing. RESULT: Two affected siblings were males, and came from unconsanguineous parents, 7 years and 5 months old and 4 years and 8 months old, respectively. They were in treatment because of developmental and mental retardation for years. When they were younger than one year of age, their heights and weight were within normal limits. However, poor growth of height and weight and psychomotor retardation appeared after one and a half years of age, as well as skin and eye sensitivity to sunshine, hearing impairment, optic nerve atrophy, microcephaly, and deep-set eyes. The proband's height was 90.8 cm, and weight 9.1 kg, head circumference 41 cm, and chest circumference 44 cm when he was taken to hospital. The elder brother of the proband had a height of 92 cm, weight 11.2 kg, head circumference 41 cm, and chest circumference 44 cm when he was taken to hospital. When the proband was four and a half years old, ventricular enlargement, hypomyelination, and brain atrophy were detected for his elder brother at 7 years of age by cranial MRI. MRS imaging indicated that damages occurred at the left and right sides of dorsal thalamus, lobus insularis, along with the left half circle of central neurons. Symmetrical calcification on bilateral basal ganglia was found on the brain CT scan. Pathogenic compound heterozygous c. 1357C > T (p.Arg453Ter) and c. 1607T > G (p.Leu536Trp) mutations of ERCC6 gene were identified in the two siblings which were separately inherited from their unaffected parents. CONCLUSION: CS children are usually normal at birth, however, they have severe clinical characteristics such as poor growth, psychomotor retardation, cerebral injury, microcephalus, deep-set eyes, and skin sensitivity to sunshine. ERCC6 gene mutation usually occurs, and it is easy to misdiagnose CS as cerebral palsy, primary microcephaly, and so on.

[Kniest dysplasia due to mutation of COL2A1 gene].

OBJECTIVE: To detect potential mutation of COL2A1 gene in two children suspected for Kniest dysplasia. METHODS: The 54 exons and splicing regions of the COL2A1 gene were amplified with PCR and the product was subjected to direct sequencing. RESULTS: A missense mutation (c.905C>T, p.Ala302Val) was found in the coding region of the COL2A1 gene, which has been previously reported in abroad. The patients appeared to have short trunk dwarfism, enlarged joints and midface hypoplasia. CONCLUSION: The probands are the first cases of Kniest dysplasia described in China, and so was the p.Ala302Val mutation.

[Clinical features of pyruvate dehydrogenase complex deficiency and gene testing in one case].

OBJECTIVE: To analyze the clinical characteristics and genetype of one children who had been diagnosed with pyruvate dehydrogenase complex deficiency. METHOD: Comprehensive analyses of this case were performed, including clinical symptoms, signs, biochemical examinations and therapeutic effects. The eleven exons and splicing areas of PDHA1 were amplified with genomic DNA from whole blood. And variations were investigated by sequencing the PCR product. The patient was diagnosed with pyruvate dehydrogenase complex deficiency by sequence analysis of PDHA1 gene. RESULT: The patient was a 2 years and 4 monthes old boy. He presented with muscle hypotonia and weakness for one year, and experienced recurrent episodes of unstable head control, unable to sit by himself or stand without support, with persistently hyperlactacidemia. Metabolic testing revealed blood lactate 5.37 mmol/L, pyruvate 0.44 mmol/L, and lactate/pyruvate ratio was 12.23. MRI of the brain showed hyperintense signals on the T2 and T2 Flair weighted images in the basal ganglia bilaterally. Sequence analysis of PDHA1 gene showed a G>A point mutation at nucleotide 778, resulting in a substitution of glutarnine for arginine at position 263 (R263Q). And the diagnosis of pyruvate dehydrogenase complex deficiency was identified. By giving the therapy with ketogenic diet, vitamin B(1), coenzyme Q(10) and L-carnitine , the boy was in a stable condition. CONCLUSION: The severity and the clinical phenotypes of pyruvate dehydrogenase complex deficiency varied. Sequence analysis of PDHA1 gene revealed a 788G>A (R263Q) mutation. Patients who presented with unexplained muscle hypotonia, weakness and hyperlactacidemia could be diveded by gene analysis. And appropriate treatment can improve the quality of life.