Identification of Six Pathogenic Genes for Tibetan Familial Ventricular Septal Defect by Whole Exome Sequencing

INTRODUCTION

Ventricular septal defect (VSD) is the most common congenital heart malformation in children. This study aimed to investigate potential pathogenic genes associated with Tibetan familial VSD.

METHODS

Whole genomic DNA was extracted from eight Tibetan children with VSD and their healthy parents (a total of 16 individuals). Whole-exome sequencing was performed using the Illumina HiSeq platform. After filtration, detection, and annotation, single nucleotide variations and insertion-deletion markers were examined. Comparative evaluations using the Sorting Intolerant from Tolerant, PolyPhen V2, Mutation Taster, and Combined Annotation Dependent Depletion databases were conducted to predict harmful mutant genes associated with the etiology of Tibetan familial VSD.

RESULTS

A total of six missense mutations in genetic disease-causing genes associated with the development of Tibetan familial VSD were identified: activin A receptor type II-like 1 (c.652 C > T: p.R218 W), ATPase cation transporting 13A2 (c.1363 C > T: p.R455 W), endoplasmic reticulum aminopeptidase 1 (c.481 G > A: p.G161 R), MRI1 (c.629 G > A: p.R210Q), tumor necrosis factor receptor-associated protein 1 (c.224 G > A: p.R75H), and FBN2 (c.2260 G > A: p.G754S). The Human Gene Mutation Database confirmed activin A receptor type II-like 1, MRI1, and tumor necrosis factor receptor-associated protein 1 as pathogenic mutations, while FBN2 was classified as a probable pathogenic mutation.

CONCLUSIONS

This novel study directly screens genetic variations associated with Tibetan familial VSD using whole-exome sequencing, providing new insights into the pathogenesis of VSD.

Enterobacter sp. E1 increased arsenic uptake in Pteris vittata by promoting plant growth and dissolving Fe-bound arsenic

Microbes affect arsenic accumulation in the arsenic-hyperaccumulator Pteris vittata, but the associated molecular mechanism remains uncertain. Here, we investigated the effect of Enterobacter sp. E1 on arsenic accumulation by P. vittata. Strain E1 presented capacities of arsenate [As(V)] and Fe(III) reduction during cultivation. In the pot experiment with P. vittata, the biomass, arsenic content, and chlorophyll content of P. vittata significantly increased by 30.03%, 74.9%, and 112.1%, respectively. Strikingly, the water-soluble plus exchangeable arsenic (WE-As) significantly increased by 52.05%, while Fe-bound arsenic (Fe-As) decreased by 29.64% in the potted soil treated with strain E1. The possible role of activation of arsenic by strain E1 was subsequently investigated by exposing As(V)-absorbed ferrihydrite to the bacterial culture. Speciation analyses of As showed that strain E1 significantly increased soluble levels of As and Fe and that more As(V) was reduced to arsenite. Additionally, increased microbial diversity and soil enzymatic activities in soils indicated that strain E1 posed few ecological risks. These results indicate that strain E1 effectively increased As accumulation in P. vittata mainly by promoting plant growth and dissolving soil arsenic. Our findings suggest that As(V) and Fe(III)-reducer E1 could be used to enhance the phytoremediation of P. vittata in arsenic-contaminated soils.

[Depressive symptoms are not associated with risks of rapid renal function decline or chronic kidney disease in middle-aged and elderly with normal kidney function: a longitudinal investigation]

OBJECTIVE

To explore the association between depressive symptoms and the risks of rapid decline in renal function and chronic kidney disease (CKD) in middle-aged and elderly with normal kidney function.

METHODS

The residents aged 40- 75 years with eGFR≥60 mL·min^-1·1.73 m^-2 without proteinuria in Lanzhou region, who participated in the "REACTION" study carried out in 2011, were selected and followed up in 2014. A total of 4961 individuals with complete and qualified data from the two surveys were included in the subsequent analysis. Based on PHQ-9 questionnaire scores, the baseline population was divided into two groups with and without depressive symptoms. Cox proportional hazard analysis was used to compare the incidences of rapid renal function decline and CKD between the two groups and study the association of depressive symptoms with the risk of these renal conditions.

RESULTS

PHQ-9 questionnaire scores were not found to correlate with baseline SCr, ALB, UACR or eGFR levels among the participarts (P>0.05). After a mean follow-up time of 3.4±0.6 years, 33.9% of the participants with depressive symptoms at baseline experienced a rapid decline in renal function and 3.6% progressed to CKD. During the follow-up, the incidence of rapid decline in renal function and the risk of developing CKD were not found to correlate with depressive symptoms in these participants (P>0.05) regardless of the type of the depressive syndromes.

CONCLUSION

Depressive symptoms are not associated with the risks of rapid renal function decline or progression to CKD in middle-aged and elderly with normal kidney function.

NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing

Background

Ventricular septal defect (VSD) is the most common congenital cardiac abnormality in children and the second most common in adults. This study aimed to explore the potentially causative genes in VSD patients in the Chinese Tibetan population, and to provide a theoretical basis for the genetic mechanism of VSD.

Methods

Peripheral venous blood was collected from 20 VSD subjects, and whole-genome DNA was extracted. High-throughput sequencing was performed on qualified DNA samples using whole-exome sequencing (WES) technology. After filtering, detecting, and annotating qualified data, single nucleotide variations (SNVs) and insertion-deletion (InDel) markers were analyzed, and data processing software such as GATK, SIFT, Polyphen, and MutationTaster were used for comparative evaluation and prediction of pathogenic deleterious variants associated with VSD.

Results

A total of 4793 variant loci, including 4168 SNVs, 557 InDels and 68 unknown loci and 2566 variant genes were obtained from 20 VSD subjects through bioinformatics analysis. According to the screening of the prediction software and database, the occurrence of VSD was predicted to be associated with five inherited pathogenic gene mutations, all of which were missense mutations, including NOTCH2 (c.1396C >A:p.Gln466Lys), ATIC (c.235C >T:p.Arg79Cys), MRI1 (c.629G >A:p.Arg210Gln), SLC6A13 (c.1138G >A:p.Gly380Arg), ATP13A2 (c.1363C >T:p.Arg455Trp).

Conclusion

This study demonstrated that NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 gene variants were potentially associated with VSD in Chinese Tibetan population.

[Correlation of baseline serum 25-hydroxyvitamin D level with the risk of type 2 diabetes mellitus: a prospective cohort study]

OBJECTIVE

To investigate the correlation of baseline serum 25(OH) D level with the risk of type 2 diabetes mellitus (T2DM) and blood glucose control in diabetic patients among the middle-aged and elderly individuals in Chengguan District of Lanzhou, Gansu Province.

OBJECTIVE

Residents aged 40 to 75 years in Lanzhou were selected from the "REACTION" study conducted in 2011 and had been followed up since 2014. A total of 5044 subjects with complete data from the two surveys were analyzed. Participants were divided into Q1, Q2, Q3, and Q4 subgroups based on quartiles of serum 25(OH)D level for comparison of the incidence of T2DM and blood glucose control.

OBJECTIVE

Baseline 25(OH)D level was not found to correlate with FPG, 2h-PG or HbA1c levels among the residents (P>0.05). The participants were followed up for a mean of 3.4±0.6 years, and compared with those in Q1 group, the participants in Q2, Q3 and Q4 groups did not show significantly lowered risk of prediabetes or diabetes regardless of glucose tolerance status. Among the patients with T2DM, the compliance rate of glycemic control after the follow-up was significantly higher than that before the follow-up (63.4% vs 60.6%), and the levels of HbA1c, FPG, and 2h-PG decreased obviously after the follow-up. But compared with Q1 group, Q2, Q3 and Q4 groups showed no significant changes in glycemic control compliance rate or levels of HbA1c, FPG and 2h-PG after the follow-up (P>0.05).

OBJECTIVE

There is no evidence that baseline 25(OH)D levels are associated with the risk of diabetes and blood glucose control in patients with T2DM.

Research on the application of liquid-liquid extraction-gas chromatography-mass spectrometry (LLE-GC-MS) and headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) in distinguishing the Baiyunbian aged liquors

The purpose of the study was to reveal the differences of the flavor compounds among five Baiyunbian aged liquors by liquid-liquid extraction-gas chromatography-mass spectrometry (LLE-GC-MS) and headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS). In optimizing the LLE parameters, an extractant, methyl tert-butyl ether, was found which has a good extract effect and has never been used for the extraction of liquor flavor substances. Then the optimized LLE method has been applied to comprehensively analyze flavor compounds in 3-year-storage liquors (3Y), 5Y, 12Y, 15Y, and 20Y of Baiyunbian liquors combined with GC-MS. The results showed that the number and concentration of total flavor compounds also enhanced with the increase of cellaring ages. The total concentration of flavor compounds in 20Y was the highest (4543.23 mg/L), and the 3Y was the lowest (3984.96 mg/L). Among them, the significant differences among five samples were esters, alcohols, acids and nitrogen-containing compounds. Cluster analysis was used to analyze the aromas profiles by LLE-GC-MS, which revealed relationship among five samples. The results showed that the similarity of the samples was highest between 15Y and 20Y, followed by 3Y and 5Y. The characteristic flavors fingerprints of five kinds of Baiyunbian aged liquors were established by HS-GC-IMS. The results showed that the characteristic peaks in GC-IMS 3D spectra corresponding to flavor compounds can effectively characterize the sample information areas. The sectional intensities of 60 characteristic peaks in the corresponding three-dimensional spectra were selected as variables. After the principal components analysis (PCA) was used to reduce information dimensionality, it was further distinguished by HS-GC-IMS that 3Y and 5Y can be completely separated, but 15Y and 20Y were very similar and cannot be completely distinguished. The obtained results are valuable for the in-depth understanding and further study of flavors of Baiyunbian liquors.

Plasmid-mediated degradation of 4-chloronitrobenzene by newly isolated Pseudomonas putida strain ZWL73

A strain of Pseudomonas putida ZWL73 was isolated from soil contaminated with chloronitrobenzenes and identified by 16S rDNA sequencing. This bacterium released chloride and ammonia into the medium when grown on 4-chloronitrobenzene (4CNB) as the sole source of carbon, nitrogen and energy. A plasmid designated pZWL73 of approximately 100 kb in this strain was found to be responsible for 4CNB degradation. This was based on the fact that the plasmid-cured strains showed 4CNB- phenotype and the 4CNB+ phenotype could be conjugally transferred. The cell-free extracts of strain ZWL73 exhibited chloronitrobenzene nitroreductase and 2-amino-5-chlorophenol 1, 6-dioxygenase (2A5CPDO) activities, but neither activity was found from that of the plasmid-cured strain. We have also cloned a 4.9-kb EcoRI fragment exhibiting 2A5CPDO activity. Sequencing results revealed beta-subunit (cnbCa) and alpha subunit (cnbCb) of a meta-cleavage dioxygenase, which were subsequently expressed in E. coli with 2A5CPDO activity. The phylogenetic analysis suggested that 2A5CPDO may form a new subgroup in class III meta-cleavage dioxygenase with its close homologs.

Identification of fetal nucleated red cells in co-cultures from fetal and adult peripheral blood: differential effects of serum on fetal and adult erythropoiesis

Seeking to optimize a novel method of isolating rare fetal erythroid cells in cultures from maternal blood, we have explored the effects of serum supplement on fetal and adult erythropoiesis. We used flow cytometry and sorting after labelling with antibodies to fetal haemoglobin (HbF) and adult haemoglobin (HbA). In adult blood-derived cultures, most nucleated red cells accumulated either only adult haemoglobin (F-A+) or a combination of fetal and adult haemoglobin (F+A+). Only a few were F+A-. Serum affected the proportions of adult cells expressing fetal haemoglobin (both F+A- and F+A+), which were minimized, but not eliminated altogether, with the use of charcoal-treated sera at low concentrations. In contrast, the expansion of fetal red cells, which made only fetal haemoglobin (F+A-) during at least one week of culture, was strongly increased with the use of charcoal treated sera, due to the removal of a charcoal-absorbable inhibitor. In co-cultures of fetal and adult erythroid cells, fetal cells could be enriched in the order of 200-fold by flow sorting with the F+A- criterion. However, since adult F+A- cells could not be suppressed completely, the purity of sorted fetal cells still depended on the relative numbers of fetal and maternal erythroid clonogenic cells in the blood sample. Thus, we demonstrate a method by which fetal nucleated red cells potentially present in maternal blood cultures can be identified and isolated from the vast majority of maternal erythroid cells, based on their correlated contents of fetal and adult haemoglobin.

Differential development of fetal and adult haemoglobin profiles in colony culture: isolation of fetal nucleated red cells by two-colour fluorescence labelling

Fetal cells in maternal peripheral blood are a source of fetal DNA for prenatal genetic diagnosis, but their numbers are so small and variable that a reliable isolation procedure has yet to be demonstrated. The problem of scarcity may be overcome by amplification of fetal progenitor cells in cultures from maternal blood samples. One challenge is to identify post-culture fetal cells and colonies. We have found that the progeny of fetal and adult erythroid progenitors developed differential haemoglobin profiles in co-culture. Fetus-derived cells initially made only fetal haemoglobin (HbF) and began to express adult haemoglobin (HbA) only after intracellular HbF had reached maximum levels, which occurred after c 7 d in culture. By this time the large majority of adult-derived erythroid cells contained already high levels of HbA alone or combined with HbE Using the HbF+ HbA- criterion, we were able to flow-sort fetal cells with up to nearly 50% purity from some post-termination blood cultures, and with >90% purity in cultures from maternal blood spiked with 1% blood from the fetus. Fetal cell purity depended on culture time and serum supplement. After 7-10 d, purity was higher in low concentrations of human cord serum (1-3%) than in the standard 30% fetal calf serum. This was reversed at later times. Thus, if fetal clonogenic erythroid cells were present in maternal blood. their progeny could be isolated from most adult erythoid cells based on haemoglobin profiles. Cultures using CD34+ cells could be performed complementary to other methods targeting more mature fetal cells in the same maternal blood samples, thus increasing the overall chances of finding fetal cells and potentially providing clonal isolation of such cells.

The assessment of malnutrition in children under 3 years of age in Sichuan areas of China using two different growth standards

6,666 children under 3 years of age were selected from 231 villages in 25 townships of the Sichuan Province using a stratified random sampling design. The subjects consisted of 3,356 boys (50.3%) and 3,310 girls (49.7%); 2,510 from plain areas (37.8%),1,857 from hill areas (27.9%), and 2,299 from mountain areas (34.4%). All the children in this study had four anthropometric variables measured: body weight, length, head circumference (HC), upper-arm circumference (UAC). Three anthropometric indicators were used to measure the prevalence of malnutrition: weight-for-age (underweight), length-for-age (stunting) and weight-for-length (wasting). The prevalence of malnutrition and Z scores were calculated for male and female, respectively, by age to compare the Chinese rural children with the Chinese standard (1985) and NCHS Standard. The prevalence of moderate plus severe underweight, stunting and wasting were 20.8%,40.7% and 1.78% in boys and 19.5%, 38.3% and 2.26% in girls. The prevalence of malnutrition also varied with age. The group with the highest prevalence of malnutrition was in the first year of life, with weaning time proving to be a critical period influencing child growth and development. Z score indicated that the growth and development of Chinese rural children was behind the Chinese Urban and NCHS populations, especially after 6 months of age. Furthermore, the mean head circumference and upper arm circumference was lower in mildly malnourished children in each age gr 1000 oup than in normal children, and much lower still in moderately and severely malnourished children. The influences of malnutrition were also manifested on bone and muscle development.

Improved fetal nucleated erythrocyte sorting purity using intracellular antifetal hemoglobin and Hoechst 33342

Fetal nucleated erythrocytes (FNRBC) flow sorted from maternal peripheral blood, using monoclonal antibodies (mAb) that bind fetal cell surface antigens, are a noninvasive source of fetal DNA for prenatal diagnosis. These mAbs, however, also bind antigens shared by maternal cells. In sorted populations, this results in maternal cell contamination and low fetal cell purities, which complicates genetic analysis by fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR). Fetal hemoglobin, (alpha 2 gamma 2), has been proposed as a useful fetal marker. To improve fetal cell enrichment from maternal blood, we developed an intracellular staining protocol that combines anti-gamma mAb with Hoechst 33342 to identify and flow sort FNRBC. Artificial mixtures of male umbilical cord cells (as a source of fetal hemoglobin) and female adult, non-pregnant peripheral blood mononuclear cells were stained and flow sorted using this protocol. FISH analysis was performed using chromosome X and Y specific probes. Fetal cell purities were calculated by microscope confirmation of anti-gamma staining and counting the number of X and Y signals present after FISH. Results from microscope analyses showed a fetal cell yield of 39-100% and fetal cell purities of 59-73%. These purities are significantly higher than the .001-4.8% previously reported by us in maternal samples using cell surface staining protocols. FISH results demonstrated that 83-100% (mean = 98%) of anti-gamma positive cells were male, whereas 82-100% (mean = 92.5%) of anti-gamma negative cells were female. These results confirmed that the anti-gamma mAb is highly fetal specific. When applied to maternal blood samples, this protocol should lead to increased sensitivity for prenatal diagnosis.

Flow sorting of fetal erythroblasts using intracytoplasmic anti-fetal haemoglobin: preliminary observations on maternal samples

Monoclonal antibody to fetal haemoglobin (alpha 2 gamma 2) has been proposed as a fetal-specific reagent. We developed an intracellular staining protocol that combines fluorescein isothiocyanate or phycoerythrin conjugated anti-gamma with the DNA binding dye Hoechst 33342 to identify and flow sort fetal erythroblasts from maternal blood. Our preliminary observations on anti-gamma-positive cells sorted from four different pregnant women are described here, using fluorescence in situ hybridization (FISH) with chromosome-specific probes to identify fetal cells. Our data demonstrate that far fewer candidate fetal cells are sorted with this protocol than by current cell surface staining methods that employ the monoclonal antibody CD71. This results in increased fetal cell sorting purities. With this protocol, standard FISH techniques require modification due to the rigorous fixation with 4 per cent paraformaldehyde. Our initial data indicate the promise of this approach.

Photochemical studies on the anti-inflammatory drug diclofenac

Irradiation with UVA light of the anti-inflammatory drug diclofenac [2-(2,6-dichloroanilino)phenylacetic acid] in aqueous buffer or methanol solution leads to sequential loss of both chlorine substituents and ring closure to carbazole-1-acetic acid as the major product. Minor products result from substitution by the solvent. The photosensitizing properties of diclofenac and its major photoproduct were tested with singlet oxygen substrates and in the free radical polymerization of acrylamide. Although the major carbazole product is a weakly phototoxic agent, able to generate singlet oxygen more efficiently than diclofenac, the free radical photodechlorination process is postulated as the probable initiation step of in vivo photosensitivity responses.