Contribution of ADD3 and the HLA Genes to Biliary Atresia Risk in Chinese.

Nonsyndromic biliary atresia (BA) is a rare polygenic disease, with autoimmunity, virus infection and inflammation thought to play roles in its pathogenesis. We conducted a genome-wide association study in 336 nonsyndromic BA infants and 8900 controls. Our results validated the association of rs17095355 in ADD3 with BA risk (odds ratio (OR) = 1.70, 95% confidence interval (95% CI) = 1.49-1.99; p = 4.07 × 10-11). An eQTL analysis revealed that the risk allele of rs17095355 was associated with increased expression of ADD3. Single-cell RNA-sequencing data and immunofluorescence analysis revealed that ADD3 was moderately expressed in cholangiocytes and weakly expressed in hepatocytes. Immuno-fluorescent staining showed abnormal deposition of ADD3 in the cytoplasm of BA hepatocytes. No ADD3 auto-antibody was observed in the plasma of BA infants. In the HLA gene region, no variants achieved genome-wide significance. HLA-DQB1 residue Ala57 is the most significant residue in the MHC region (OR = 1.44, 95% CI = 1.20-1.74; p = 1.23 × 10-4), and HLA-DQB1 was aberrantly expressed in the bile duct cells. GWAS stratified by cytomegalovirus (CMV) IgM status in 87 CMV IgM (+) BA cases versus 141 CMV IgM (-) BA cases did not yield genome-wide significant associations. These findings support the notion that common variants of ADD3 account for BA risk. The HLA genes might have a minimal role in the genetic predisposition of BA due to the weak association signal. CMV IgM (+) BA patients might not have different genetic risk factor profiles compared to CMV IgM (-) subtype.

Distinctive calcium isotopic composition of mice organs and fluids: implications for biological research.

The stable calcium (Ca) isotopes offer a minimally invasive method for assessing Ca balance in the body, providing a new avenue for research and clinical applications. In this study, we measured the Ca isotopic composition of soft tissues (brain, muscle, liver, and kidney), mineralized tissue (bone), and blood (plasma) from 10 mice (5 females and 5 males) with three different genetic backgrounds and same age (3 months old). The results reveal a distinctive Ca isotopic composition in different body compartments of mice, primally controlled by each compartment's unique Ca metabolism and genetic background, independent of sex. The bones are enriched in the lighter Ca isotopes (δ44/40Cabone = - 0.10 ± 0.55 ‰) compared to blood and other soft tissues, reflecting the preferential incorporation of lighter Ca isotopes through bone formation, while heavier Ca isotopes remain preferentially in blood. The brain and muscle are enriched in lighter Ca isotopes (δ44/40Cabrain = - 0.10 ± 0.53 ‰; δ44/40Camuscle = 0.19 ± 0.41 ‰) relative to blood and other soft tissues, making the brain the isotopically lightest soft tissues of the mouse body. In contrast, the kidney is enriched in heavier isotopes (δ44/40Cakidney = 0.86 ± 0.31 ‰) reflecting filtration and reabsorption by the kidney. This study provides important insight into the Ca isotopic composition of various body compartments and fluids.

Stable potassium isotope distribution in mouse organs and red blood cells: implication for biomarker development.

Potassium (K) is an essential electrolyte for cellular functions in living organisms, and disturbances in K+ homeostasis could lead to various chronic diseases (e.g. hypertension, cardiac disease, diabetes, and bone health). However, little is known about the natural distribution of stable K isotopes in mammals and their application to investigate bodily homeostasis and/or as biomarkers for diseases. Here, we measured K isotopic compositions (δ41K, per mil deviation of 41K/39K from the NIST SRM 3141a standard) of brain, liver, kidney, and red blood cells (RBCs) from 10 mice (five females and five males) with three different genetic backgrounds. Our results reveal that different organs and RBCs have distinct K isotopic signatures. Specifically, the RBCs have heavy K isotopes enrichment with δ41K ranging from 0.67 to 0.08‰, while the brains show lighter K isotopic compositions with δ41K ranging from -1.13 to -0.09‰ compared to the livers (δ41K = -0.12 ± 0.58‰) and kidneys (δ41K = -0.24 ± 0.57‰). We found that the K isotopic and concentration variability is mostly controlled by the organs, with a minor effect of the genetic background and sex. Our study suggests that the K isotopic composition could be used as a biomarker for changes in K+ homeostasis and related diseases such as hypertension, cardiovascular, and neurodegenerative diseases.

Association analysis and functional follow-up identified common variants of JAG1 accounting for risk to biliary atresia.

Background: Biliary atresia (BA) is a destructive, obliterative cholangiopathy characterized by progressive fibro-inflammatory disorder and obliteration of intra- and extrahepatic bile ducts. The Jagged1 (JAG1) gene mutations have been found in some isolated BA cases. We aim to explore the association of common variants in JAG1 with isolated BA risk in the Chinese Han population. Methods: We genotyped 31 tag single nucleotide polymorphisms covering the JAG1 gene region in 333 BA patients and 1,665 healthy controls from the Chinese population, and performed case-control association analysis. The expression patterns of JAG1 homologs were investigated in zebrafish embryos, and the roles of jag1a and jag1b in biliary development were examined by morpholino knockdown in zebrafish. Results: Single nucleotide polymorphisms rs6077861 [P Allelic = 1.74 × 10-4, odds ratio = 1.78, 95% confidence interval: 1.31-2.40] and rs3748478 (P Allelic = 5.77 × 10-4, odds ratio = 1.39, 95% confidence interval: 1.15-1.67) located in the intron region of JAG1 showed significant associations with BA susceptibility. The JAG1 homologs, jag1a and jag1b genes were expressed in the developing hepatobiliary duct of zebrafish, especially at 72 and 96 h postfertilization. Knockdown of both jag1a and jag1b led to poor biliary secretion, sparse intrahepatic bile duct network and smaller or no gallbladders compared with control embryos in the zebrafish model. Conclusion: Common genetic variants of JAG1 were associated with BA susceptibility. Knockdown of JAG1 homologs led to defective intrahepatic and extrahepatic bile ducts in zebrafish. These results suggest that JAG1 might be implicated in the etiology of BA.

ERF4 interacts with and antagonizes TCP15 in regulating endoreduplication and cell growth in Arabidopsis.

Endoreduplication is prevalent during plant growth and development, and is often correlated with large cell and organ size. Despite its prevalence, the transcriptional regulatory mechanisms underlying the transition from mitotic cell division to endoreduplication remain elusive. Here, we characterize ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR 4 (ERF4) as a positive regulator of endoreduplication through its function as a transcriptional repressor. ERF4 was specifically expressed in mature tissues in which the cells were undergoing expansion, but was rarely expressed in young organs. Plants overexpressing ERF4 exhibited much larger cells and organs, while plants that lacked functional ERF4 displayed smaller organs than the wild-type. ERF4 was further shown to regulate cell size by controlling the endopolyploidy level in the nuclei. Moreover, ERF4 physically associates with the class I TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) protein TCP15, a transcription factor that inhibits endoreduplication by activating the expression of a key cell-cycle gene, CYCLIN A2;3 (CYCA2;3). A molecular and genetic analysis revealed that ERF4 promotes endoreduplication by directly suppressing the expression of CYCA2;3. Together, this study demonstrates that ERF4 and TCP15 function as a module to antagonistically regulate each other's activity in regulating downstream genes, thereby controlling the switch from the mitotic cell cycle to endoreduplication during leaf development. These findings expand our understanding of how the control of the cell cycle is fine-tuned by an ERF4-TCP15 transcriptional complex.

Biosensors for the Detection of Bacillus anthracis.

Bacillus anthracis, present in two forms of vegetative cells and spores, is a pathogen that infects humans through contact with infected animals or contaminated animal products and is also maliciously used in terrorist acts. Therefore, a rapid and sensitive test for B. anthracis is necessary but challenging. The challenge comes from the following aspects: an accurate distinction of B. anthracis from other Bacillus species due to their high genomic similarity and the horizontal gene transfer between Bacillus members; direct detection of the B. anthracis spores without damaging them for component extraction to avoid the risk of spore atomization; and the rapid detections of B. anthracis in complex samples, such as soil and suspicious powders, without sample pretreatments and expensive large-scale equipment. Although culturing B. anthracis from samples is the conventional method for the detection of B. anthracis, it is time-consuming and the detection results would not be easy to interpret because many Bacillus species share similar phenotypic features such as a lack of motility and hemolysis, resistance to gamma phages, and so on. Intensive and extensive effort has been expended to develop reliable detection technologies, among which biosensors exhibit comprehensive advantages in terms of sensitivity, specificity, and portability. Here, we briefly review the research progress, providing highlights of the latest achievements and our own practice and experience. The contents can be summarized in three aspects: the discovery of detection targets, including genes, toxins, and other components; the creation of molecular recognition elements, such as monoclonal antibodies, single-chain antibody fragments, specific peptides, and aptamers; and the design and construction of biosensing systems by the integration of appropriate molecular recognition elements and transducer devices. These sensor devices have their own characteristics and different principles. For example, the surface plasmon resonance biosensor and quartz crystal microbalance biosensor are very sensitive, while the multiplex PCR-on-a-chip can detect multitargets. Biosensors for direct spore detection are highly recommended because they are not only fast but also avoid contamination from aerosol-containing spores. The introduction of nanotechnology has significantly improved the performance of biosensors. Superparamagnetic nanoparticles and phage-displayed gold nanoparticle ligand peptides have made the results of spore detection visible to the naked eye. Because of space constraints, many advanced biosensors for B. anthracis are not described in detail but are cited as references. Although biosensors provide a variety of options for various application scenarios, the challenges have not been fully addressed, which leaves room for the development of more advanced and practical B. anthracis detection means.

Association Analysis of Variants of DSCAM and BACE2 With Hirschsprung Disease Susceptibility in Han Chinese and Functional Evaluation in Zebrafish.

Hirschsprung disease (HSCR) has a higher incidence in children with Down syndrome (DS), which makes trisomy 21 a predisposing factor to HSCR. DSCAM and BACE2 are close together on the HSCR-associated critical region of chromosome 21. Common variants of DSCAM and rare variants of BACE2 were implicated to be associated with sporadic HSCR. However, the submucosal neuron defect of DS mouse model could not be rescued by normalization of Dscam. We aimed to explore the contribution of DSCAM and BACE2 to the development of the enteric nervous system (ENS) and HSCR susceptibility. We genotyped 133 tag single-nucleotide polymorphisms (SNPs) in DSCAM and BACE2 gene region in 420 HSCR patients and 1,665 controls of Han Chinese. Expression of DSCAM and BACE2 homologs was investigated in the developing gut of zebrafish. Overexpression and knockdown of the homologs were performed in zebrafish to investigate their roles in the development of ENS. Two DSCAM SNPs, rs430255 (P Addtive = 0.0052, OR = 1.36, 95% CI: 1.10-1.68) and rs2837756 (P Addtive = 0.0091, OR = 1.23, 95% CI: 1.05-1.43), showed suggestive association with HSCR risk. Common variants in BACE2 were not associated with HSCR risk. We observed dscama, dscamb, and bace2 expression in the developing gut of zebrafish. Knockdown of dscama, dscamb, and bace2 caused a reduction of enteric neurons in the hindgut of zebrafish. Overexpression of DSCAM and bace2 had no effects on neuron number in the hindgut of zebrafish. Our results suggested that common variation of DSCAM contributed to HSCR risk in Han Chinese. The dysfunction of both dscams and bace2 caused defects in enteric neuron, indicating that DSCAM and BACE2 might play functional roles in the occurrence of HSCR. These novel findings might shed new light on the pathogenesis of HSCR.

Pore scale investigation on scaling-up micro-macro capillary number and wettability on trapping and mobilization of residual fluid.

The mobilization mechanism of the trapped phases controlled by the viscous force and capillary force in porous media is crucial to various engineering applications. In this paper, pore scale water flooding process in rock models with nonuniform wettability is simulated by computational fluid dynamics (CFD) using the volume of fluid (VOF) model. Four types of rock are imaged by micro-CT (µ-CT) and adopted as inputs to generate the structured mesh models. The simulations of two-phase flow are carried out to study the immiscible displacement process in the development of oil fields. The scaling-up critical capillary number at micro-macro scale are acquired and validated, the effects of which on relative permeability, residual oil recovery and immiscible displacement efficiency are analyzed. The simulation results indicate that the critical capillary number at microscopic scale ranges from 10-6 to 10-5 for water-wetted and oil-wetted rock respectively, and approaches to 1 at the macro scale. The effect of wettability on oil recovery is positive for intermediate-wetted or weak water-wetted rock, while negative for strong wettability.

[Adsorption Characteristics of Phosphorus Wastewater on the Synthetic Ferrihydrite].

The synthetic ferrihydrite, FerrorMox (FM), was used as adsorbent for removing phosphorus from wastewater. SEM, EDS, XRD, FTIR and Raman were used to characterize FM, and the results indicated that FM was amorphous 2 L ferrihydrite and was composed of Fe, O, Ca and Si, etc. Afterwards, FM was applied to adsorb phosphorus from wastewater, and the adsorption performance, influence factors and adsorption mechanism were investigated. The phosphorus removal rate reached 99.14% under the condition of adsorption time of 60 min, initial pH phosphate solution of 2, relative dosing quantity of 7 g·L-1, reaction temperature of 25℃, initial concentration of 10 mg·L-1, and solution volume of 50 mL. Adsorption isotherms were well fitted with the Langmuir isothermal adsorption model at different temperature with the correlation coefficient reaching above 0.95. The thermodynamic parameters showed that the phosphorus adsorption by FM was a spontaneous endothermic reaction. The phosphate removal kinetics well followed both pseudo-first-order model and pseudo-second-order model. About 99% of phosphate adsorbed on FM could be desorbed in 0.1 mol·L-1 NaOH solution. Therefore, FM was a promising absorbent material for the removal of phosphate from waste water.

Relationship between haze and acute cardiovascular, cerebrovascular, and respiratory diseases in Beijing.

Haze is an atmospheric phenomenon in which dry particulate pollutants obscure the sky. Haze has been associated with chronic diseases, but its relationship with acute diseases is less clear. We aimed to determine the association between haze and acute cardiovascular, cerebrovascular, and respiratory diseases, in order to determine the influence of haze on human health. We compared the number of cases of acute cardiovascular, cerebrovascular, and respiratory diseases in Beijing Emergency Center between 2006 and 2013, with haze data from Beijing Observatory. The relationship between the number of hazy days and the number of cases of the above types of diseases was analyzed using univariate analyses. Both the number of cases and the number of hazy days showed a rising trend. The average number of cases per day for all three diseases was higher on hazy days than on non-hazy days. There was a positive correlation between the number of hazy days and the number of cases, and this correlation showed a hysteretic quality. Haze has an influence on acute cardiovascular (CVDs), cerebrovascular (CBDs), and respiratory system (RSDs) diseases. Haze seems to have an additive effect, since the associations between haze and number of cases were stronger in the following month than in the preceding month. The increasing trend in the number of hazy days might worsen the problem of haze-related diseases.

[Bioconversion of cellulose to methane by a consortium consisting of four microbial strains].

Cellulose was usually degraded by microbial communities in natural habitats. Construction of a simple cellulolytic consortium is necessary to understand the underlying interaction within microorganisms involved in cellulose conversion. A screening approach was developed to obtain a simple microbial community with the ability of cellulose degradation to methane. This technique was based on the method of enrichment culture accompanying with denaturing gel gradient electrophoresis (DGGE) fingerprint detection technology and roll-tube method. Moreover, a four-strain mixed culture capable of degrading cellulose to methane was isolated from Zoige alpine wetland of the Tibetan Plateau. The results showed that the microbial consortia consisted of three functional groups: the cellulolytic bacterium Clostridium glycolicum, the non-celluloytic bacteria group of Trichococcus flocculiformis and Parabacteroides merdae, and the methanogenic bacterium Methanobacterium subterraneum. This four-strain co-culture can convert cellulose to methane. In the future, the isolated cellulolytic consortia could provide a platform for controlling metabolic pathways and genetic modification involved in methane production from cellulose.

[Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)].

MicroRNAs (miRNAs), a recently discovered class of small (-21nt), non-coding, endogenous, single-stranded RNAs in eukaryotes, regulate gene expression negatively at the post-transcriptional levels depending on the extent of complementation between miRNA and mRNA. To date, a large number of miRNAs have been reported in many species, but none for eggplant (Solanum melongena L.). In this paper, a computational homology search approach based on the conservation of miRNA sequences and the stem-loop hairpin secondary structures of miRNAs was adopted. The search was started with the known plant miRNAs compared to eggplant expressed sequence tags (EST) databases to find potential miRNAs. Following a range of filtering criteria, a total of 16 potential miRNAs belonging to 12 families were identified. Three pairs of sense and antisense strand eggplant miRNAs belonging to three different miRNA families were also found. Furthermore, miR390 and miR399 sense/antisense pairs are identified for the first time in plants. Using online software psRNATarget, we further predicted the target genes of these 16 miRNAs and got 71 potential targets genes on base of 15 eggplant miRNAs. Most of these target genes were predicted to encode proteins that play key role in eggplant growth, development, metabolism, and stress responses.