Functional analysis and application of the cryptic plasmid pBSG3 harboring the RapQ-PhrQ system in Bacillus amyloliquefaciens B3

This work sequenced and characterized a cryptic plasmid called pBSG3 from wild-type Bacillus amyloliquefaciens B3--a powerful agent for suppression of plant pathogenic organisms. It is an 8439 bp circular molecule, with G+C content of 40.3%. We provide evidence that pBSG3 replicates via the rolling-circle (RC) mechanism and, sequence comparisons place it in the pC194 family of rolling-circle-replicons. The plasmid contains seven putative open reading frames (ORFs), including genes repB3, mobB3, rapQ, phrQ, pgsR, and two unknown ORFs (orf1c and orf2). Our observations reveal that the RapQ-PhrQ (response regulator aspartate phosphatase-phosphatase regulator) system is involved in sporulation and RapQ can delay the onset of sporulation. Two Escherichia coli and Bacillus potential shuttle vectors, pTRD (containing the minimal replicon) and pTRDS (containing the minimal replicon and the single-strand origin) were developed from pBSG3 and tested the stability. Moreover, HpaG(xooc) protein, which can induce disease and insect resistance in plants, was tried to express with the stable vector pTRDS in Bacillus subtilis. In summary, the pBSG3 plasmid containing various genes is not only a candidate tool for vector development in Bacillus genus research but also a potential vehicle for the exchange of genetic elements among Bacillus populations that contributes to the survival of bacilli in natural environments.     

The anticancer flavonoid chrysin induces the unfolded protein response in hepatoma cells

Chrysin is a natural and biologically active flavonoid with anticancer effects. However, little is known about the adaptive response of cancer cells to chrysin. Chrysin reportedly has proteasome inhibitor activity. Previous studies demonstrated that proteasome inhibitors might induce endoplasmic reticulum (ER) stress response. In this study, we aimed to determine the effects of chrysin on hepatoma cells and roles of the ER-resident protein GRP78 (glucose-regulated protein 78) in its action. Also, we investigated the effects of green tea polyphenol (-)-epigallocatechin-3-gallate (EGCG), a natural GRP78 inhibitor, on the sensitivity of hepatoma cells to chrysin. Here, we report that chrysin inhibits hepatoma cells growth and induces apoptosis in a dose-dependent manner. Chrysin induces GRP78 overexpression, X-box binding protein-1 splicing and eukaryotic initiation factor 2α phosphorylation, hallmarks of the unfolded protein response. GRP78 knockdown potentiates chrysin-induced caspase-7 cleavage in hepatoma cells and enhances chrysin-induced apoptosis. EGCG overcomes chrysin-induced GRP78 expression. Combination of EGCG potentiates chrysin-induced caspase-7 and poly (ADP-ribose) polymerase (PARP) cleavage. Finally, EGCG sensitizes hepatoma cells to chrysin through caspase-mediated apoptosis. These data suggest that chrysin triggers the unfolded protein response. Abrogation of GRP78 induction may improve the anticancer effects of chrysin. Combination of EGCG and chrysin represents a new regimen for cancer chemoprevention and therapeutics.     

Derivation of human embryonic stem cells with NEMO deficiency

Deficiency of the nuclear factor-kappa-B essential modulator (NEMO) is a rare X-linked disorder that presents in boys as hypohydrotic ectodermal dysplasia with immunodeficiency due to defective nuclear factor-κB activation. Here we report on the generation of 2 human embryonic stem cell lines from discarded in vitro fertilization (IVF) embryos ascertained via preimplantation genetic diagnosis. We have derived two human embryonic stem cell lines that carry a T458G hypomorphic mutation in exon 4 of the NEMO (or IKBKG) gene. One of the lines is diploid male; the other is diploid female but has clonally inactivated the X-chromosome that harbors the wild-type IKBKG gene. We show that both lines are pluripotent, have the capacity to differentiate into hematopoietic progenitors, and have defective inhibitor of nuclear factor kappa-B kinase activity. These NEMO deficiency hES cell lines provide an unlimited source for differentiated cell types and may serve as a unique tool to study NEMO deficiency and potentially lead to the development of new therapies for this disease.     

Genome Sequence of Borrelia afzelii Strain HLJ01, Isolated from a Patient in China

We report here the genome sequence of Borrelia afzelii strain HLJ01, isolated from a patient with Lyme disease in China. It is the first report of the whole genome of a B. burgdorferi sensu lato isolate from a human in China.     

Human protein-disulfide isomerase is a redox-regulated chaperone activated by oxidation of domain a'

Protein-disulfide isomerase (PDI), with domains arranged as abb'xa'c, is a key enzyme and chaperone localized in the endoplasmic reticulum (ER) catalyzing oxidative folding and preventing misfolding/aggregation of proteins. It has been controversial whether the chaperone activity of PDI is redox-regulated, and the molecular basis is unclear. Here, we show that both the chaperone activity and the overall conformation of human PDI are redox-regulated. We further demonstrate that the conformational changes are triggered by the active site of domain a', and the minimum redox-regulated cassette is located in b'xa'. The structure of the reduced bb'xa' reveals for the first time that domain a' packs tightly with both domain b' and linker x to form one compact structural module. Oxidation of domain a' releases the compact conformation and exposes the shielded hydrophobic areas to facilitate its high chaperone activity. Thus, the study unequivocally provides mechanistic insights into the redox-regulated chaperone activity of human PDI.     

Ultrasensitive and selective non-enzymatic glucose detection using copper nanowires

In the pursuit of more economical electrocatalysts for non-enzymatic glucose sensors, one-dimensional Cu nanowires (Cu NWs) with uniform size distribution and a large aspect ratio (>200) were synthesized by a facile, scalable, wet-chemistry approach. The morphology, crystallinity, and surface property of the as-prepared Cu NWs were examined by SEM, XRD, and XPS, respectively. The electrochemical property of Cu NWs for glucose electrooxidation was thoroughly investigated by cyclic voltammetry. In the amperometric detection of glucose, the Cu NWs modified glassy carbon electrode exhibited an extraordinary limit of detection as low as 35 nM and a wide dynamic range with excellent sensitivity of 420.3 μA cm(-2) mM(-1), which was more than 10,000 times higher than that of the control electrode without Cu NWs. The performance of the developed glucose sensor was also independent to oxygen concentration and free from chloride poisoning. Furthermore, the interference from uric acid, ascorbic acid, acetaminophen, fructose, and sucrose at the level of their physiological concentration were insignificant, indicating excellent selectivity. Finally, good accuracy and high precision for the quantification of glucose concentration in human serum samples implicate the applicability of Cu NWs in sensitive and selective non-enzymatic glucose detection.     

Toward nitrogen neutral biofuel production

Environmental concerns and an increasing global energy demand have spurred scientific research and political action to deliver large-scale production of liquid biofuels. Current biofuel processes and developing approaches have focused on closing the carbon cycle by biological fixation of atmospheric carbon dioxide and conversion of biomass to fuels. To date, these processes have relied on fertilizer produced by the energy-intensive Haber-Bosch process, and have not addressed the global nitrogen cycle and its environmental implications. Recent developments to convert protein to fuel and ammonia may begin to address these problems. In this scheme, recycling ammonia to either plant or algal feedstocks reduces the demand for synthetic fertilizer supplementation. Further development of this technology will realize its advantages of high carbon fixation rates, inexpensive and simple feedstock processing, in addition to reduced fertilizer requirements.     

Association of assisted reproductive technology,germline de novo mutations and congenital heart defects in a prospective birth cohort study

Emerging evidence suggests that children conceived through assisted reproductive technology (ART) have a higher risk of congenital heart defects (CHDs) even when there is no family history. De novo mutation (DNM) is a well-known cause of sporadic congenital diseases; however, whether ART procedures increase the number of germline DNM (gDNM) has not yet been well studied. Here, we performed whole-genome sequencing of 1137 individuals from 160 families conceived through ART and 205 families conceived spontaneously. Children conceived via ART carried 4.59 more gDNMs than children conceived spontaneously, including 3.32 paternal and 1.26 maternal DNMs, after correcting for parental age at conception, cigarette smoking, alcohol drinking, and exercise behaviors. Paternal DNMs in offspring conceived via ART are characterized by C>T substitutions at CpG sites, which potentially affect protein-coding genes and are significantly associated with the increased risk of CHD. In addition, the accumulation of non-coding functional mutations was independently associated with CHD and 87.9% of the mutations were originated from the father. Among ART offspring, infertility of the father was associated with elevated paternal DNMs; usage of both recombinant and urinary follicle-stimulating hormone and high-dosage human chorionic gonadotropin trigger was associated with an increase of maternal DNMs. In sum, the increased gDNMs in offspring conceived by ART were primarily originated from fathers, indicating that ART itself may not be a major reason for the accumulation of gDNMs. Our findings emphasize the importance of evaluating the germline status of the fathers in families with the use of ART.Subject terms: Genomic analysis, Developmental biology     

IVUS Validation of Patient Coronary Artery Lumen Area Obtained from CT Images

Aims

Accurate computed tomography (CT)-based reconstruction of coronary morphometry (diameters, length, bifurcation angles) is important for construction of patient-specific models to aid diagnosis and therapy. The objective of this study is to validate the accuracy of patient coronary artery lumen area obtained from CT images based on intravascular ultrasound (IVUS).

Methods and Results

Morphometric data of 5 patient CT scans with 11 arteries from IVUS were reconstructed including the lumen cross sectional area (CSA), diameter and length. The volumetric data from CT images were analyzed at sub-pixel accuracy to obtain accurate vessel center lines and CSA. A new center line extraction approach was used where an initial estimated skeleton in discrete value was obtained using a traditional thinning algorithm. The CSA was determined directly without any circular shape assumptions to provide accurate reconstruction of stenosis. The root-mean-square error (RMSE) for CSA and diameter were 16.2% and 9.5% respectively.

Conclusions

The image segmentation and CSA extraction algorithm for reconstruction of coronary arteries proved to be accurate for determination of vessel lumen area. This approach provides fundamental morphometric data for patient-specific models to diagnose and treat coronary artery disease.