Reconstitution of 5'-directed human mismatch repair in a purified system

This paper reports reconstitution of 5'-nick-directed mismatch repair using purified human proteins. The reconstituted system includes MutSalpha or MutSbeta, MutLalpha, RPA, EXO1, HMGB1, PCNA, RFC, polymerase delta, and ligase I. In this system, MutSbeta plays a limited role in repair of base-base mismatches, but it processes insertion/deletion mispairs much more efficiently than MutSalpha, which efficiently corrects both types of heteroduplexes. MutLalpha reduces the processivity of EXO1 and terminates EXO1-catalyzed excision upon mismatch removal. In the absence of MutLalpha, mismatch-provoked excision by EXO1 occurs extensively. RPA and HMGB1 play similar but complementary roles in stimulating MutSalpha-activated, EXO1-catalyzed excision in the presence of a mismatch, but RPA has a distinct role in facilitating MutLalpha-mediated excision termination past mismatch. Evidence is provided that efficient repair of a single mismatch requires multiple molecules of MutSalpha-MutLalpha complex. These data suggest a model for human mismatch repair involving coordinated initiation and termination of mismatch-provoked excision.     

Probabilistic Identification of Spin Systems and their Assignments including Coil–Helix Inference as Output (PISTACHIO)

We present a novel automated strategy (PISTACHIO) for the probabilistic assignment of backbone and sidechain chemical shifts in proteins. The algorithm uses peak lists derived from various NMR experiments as input and provides as output ranked lists of assignments for all signals recognized in the input data as constituting spin systems. PISTACHIO was evaluate00000000d by comparing its performance with raw peak-picked data from 15 proteins ranging from 54 to 300 residues; the results were compared with those achieved by experts analyzing the same datasets by hand. As scored against the best available independent assignments for these proteins, the first-ranked PISTACHIO assignments were 80–100% correct for backbone signals and 75–95% correct for sidechain signals. The independent assignments benefited, in a number of cases, from structural data (e.g. from NOESY spectra) that were unavailable to PISTACHIO. Any number of datasets in any combination can serve as input. Thus PISTACHIO can be used as datasets are collected to ascertain the current extent of secure assignments, to identify residues with low assignment probability, and to suggest the types of additional data needed to remove ambiguities. The current implementation of PISTACHIO, which is available from a server on the Internet, supports input data from 15 standard double- and triple-resonance experiments. The software can readily accommodate additional types of experiments, including data from selectively labeled samples. The assignment probabilities can be carried forward and refined in subsequent steps leading to a structure. The performance of PISTACHIO showed no direct dependence on protein size, but correlated instead with data quality (completeness and signal-to-noise). PISTACHIO represents one component of a comprehensive probabilistic approach we are developing for the collection and analysis of protein NMR data.Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users.     

hMRE11 deficiency leads to microsatellite instability and defective DNA mismatch repair

DNA mismatch repair (MMR) is essential in the surveillance of accurate transmission of genetic information, and defects in this pathway lead to microsatellite instability and hereditary nonpolyposis colorectal cancer (HNPCC). Our previous study raised the possibility that hMRE11 might be involved in MMR through physical interaction with hMLH1. Here, we show that hMRE11 deficiency leads to significant increase in MSI for both mono- and dinucleotide sequences. Furthermore, RNA-interference-mediated hMRE11-knockdown in HeLa cells results in MMR deficiency. Analysis of seven HNPCC-associated hMLH1 missense mutations located within the hMRE11-interacting domain shows that four mutations (L574P, K618T, R659P and A681T) cause near-complete disruption of the interaction between hMRE11 and hMLH1, and two mutations (Q542L and L582V) cause a 30% reduction of protein interaction. These findings indicate that hMRE11 represents a functional component of the MMR pathway and the disruption of hMLH1-hMRE11 interaction could be an alternative molecular explanation for hMLH1 mutations in a subset of HNPCC tumours.     

Expression of the whey acidic protein (Wap) is necessary for adequate nourishment of the offspring but not functional differentiation of mammary epithelial cells

Whey acidic protein (WAP) is the principal whey protein found in rodent milk, which contains a cysteine-rich motif identified in some protease inhibitors and proteins involved in tissue modeling. The expression of the Wap gene, which is principally restricted to the mammary gland, increases more than 1,000-fold around mid-pregnancy. To determine whether the expression of this major milk protein gene is a prerequisite for functional differentiation of mammary epithelial cells, we generated conventional knockout mice lacking two alleles of the Wap gene. Wap-deficient females gave birth to normal litter sizes and, initially, produced enough milk to sustain the offspring. The histological analysis of postpartum mammary glands from knockout dams does not reveal striking phenotypic abnormalities. This suggests that the expression of the Wap gene is not required for alveolar specification and functional differentiation. In addition, we found that Wap is dispensable as a protease inhibitor to maintain the stability of secretory proteins in the milk. Nevertheless, a significant number of litters thrived poorly on Wap-deficient dams, in particular during the second half of lactation. This observation suggests that Wap may be essential for the adequate nourishment of the growing young, which triple in size within the first 10 days of lactation. Important implications of these findings for the use of Wap as a marker for advanced differentiation of mammary epithelial cells and the biology of pluripotent progenitors are discussed in the final section.     

Efficient Gene Knockdown in Mouse Oocytes through Peptide Nanoparticle-Mediated SiRNA Transfection

The use of mouse oocytes as a model for studying female meiosis is very important in reproductive medicine. Gene knockdown by specific small interfering RNA (siRNA) is usually the first step in the study of the function of a target gene in mouse oocytes during in vitro maturation. Traditionally, the only way to introduce siRNA into mouse oocytes is through microinjection, which is certainly less efficient and strenuous than siRNA transfection in somatic cells. Recently, in research using somatic cells, peptide nanoparticle-mediated siRNA transfection has been gaining popularity over liposome nanoparticle-mediated methods because of its high efficiency, low toxicity, good stability, and strong serum compatibility. However, no researchers have yet tried transfecting siRNA into mouse oocytes because of the existence of the protective zona pellucida surrounding the oocyte membrane (vitelline membrane). We therefore tested whether peptide nanoparticles can introduce siRNA into mouse oocytes. In the present study, we showed for the first time that our optimized program can efficiently knock down a target gene with high specificity. Furthermore, we achieved the expected meiotic phenotypes after we knocked down a test unknown target gene TRIM75. We propose that peptide nanoparticles may be superior for preliminary functional studies of unknown genes in mouse oocytes.     

Obesity and Cardio-Metabolic Risk Factors in an Urban and Rural Population in the Ashanti Region-Ghana: A Comparative Cross-Sectional Study

There is a surge in chronic diseases in the developing world, driven by a high prevalence of cardio-metabolic risk factors. This study described differences in prevalence of obesity and cardio-metabolic risk factors between urban and rural settlements in the Ashanti Region of Ghana. This comparative cross-sectional study included 672 participants (median age 50 years), of which 312 were from Kumasi (urban) and 360 from Jachie-Pramso (rural). Demographic, anthropometric and other cardio-metabolic risk factors were gathered and venous blood samples were drawn for biochemical assays. Results suggested significant differences in diastolic blood pressure (80.0 mmHg vs 79.5 mmHg; p = 0.0078), and fasting blood sugar (5.0 mmo/l vs 4.5 mmol/l; p < 0.0001) between the two groups. Further differences in anthropometric measures suggested greater adiposity amongst participants in the urban area. Participants in the urban area were more likely than rural participants, to have high total cholesterol and LDL-c (p < 0.0001 respectively). Risk factors including BMI ≥ 25 (p < 0.0001), BMI ≥ 30 (p < 0.0001), high waist circumference (p < 0.0001), high waist-to-height ratio (p < 0.0001) and alcohol consumption (p = 0.0186) were more prevalent amongst participants in the urban area. Markers of adiposity were higher amongst females than males in both areas (p < 0.05). In the urban area, hypertension, diabetes and lifestyle risk factors were more prevalent amongst males than females. Differences in risk factors by urban / rural residence remained significant after adjusting for gender and age. Obesity and cardio-metabolic risk factors are more prevalent amongst urban settlers, highlighting an urgent need to avert the rise of diet and lifestyle-related chronic diseases.     

Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data

Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR) markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3%) could be classified into gene ontology categories, 25,451 (64.4%) into Swiss-Prot categories and 21,982 (55.6%) into KOG database categories (E-value < 1.0E-5). A total of 9,301 (23.5%) were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%), AAG/CTT (8.1%) and AGAA/TTCT (20.0%) are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.     

New Derivatives of Nonactic and Homononactic Acids from Bacillus pumilus Derived from Breynia fruticosa

Six new nonactic and homononactic acid derivatives, ethyl homononactate ( 1 ), ethyl nonactate ( 2 ), homononactyl homononactate ( 6 ), ethyl homononactyl nonactate ( 7 ), ethyl homononactyl homononactate ( 8 ), and ethyl nonactyl nonactate ( 9 ), as well as four known compounds, homononactic acid ( 3 ), nonactic acid ( 4 ), homononactyl nonactate ( 5 ), and bishomononactic acid ( 10 ), were isolated from culture broth of Bacillus pumilus derived from Breynia fruticosa. The structures of new compounds were elucidated by spectroscopic analysis and chemical methods. The optical purities of 1 – 6 were determined by HPLC/MS after treatment with L ‐phenylalanine methyl ester. The dimeric compounds 5 – 9 showed weak cytotoxic activities against five human cancer cell lines (IC₅₀ 19–100 μg/ml).     

Biocontrol of Aspergillus Species on Peanut Kernels by Antifungal Diketopiperazine Producing Bacillus cereus Associated with Entomopathogenic Nematode

The rhabditid entomopathogenic nematode associated Bacillus cereus and the antifungal compounds produced by this bacterium were evaluated for their activity in reducing postharvest decay of peanut kernels caused by Aspergillus species in in vitro and in vivo tests. The results showed that B. cereus had a significant effect on biocontrol effectiveness in in vitro and in vivo conditions. The antifungal compounds produced by the B. cereus were purified using silica gel column chromatography and their structure was elucidated using extensive spectral analyses. The compounds were identified as diketopiperazines (DKPs) [cyclo-(L-Pro-Gly), cyclo(L-Tyr-L-Tyr), cyclo-(L-Phe-Gly) and cyclo(4-hydroxy-L-Pro-L-Trp)]. The antifungal activities of diketopiperazines were studied against five Aspergillus species and best MIC of 2 µg/ml was recorded against A. flavus by cyclo(4-hydroxy-L-Pro-L-Trp). To investigate the potential application of cyclo(4-hydroxy-L-Pro-L-Trp) to eliminate fungal spoilage in food and feed, peanut kernels was used as a food model system. White mycelia and dark/pale green spores of Aspergillus species were observed in the control peanut kernels after 2 days incubation. However the fungal growth was not observed in peanut kernels treated with cyclo(4-hydroxy-L-Pro-L-Trp). The cyclo(4-hydroxy-L-Pro-L-Trp) was nontoxic to two normal cell lines [fore skin (FS) normal fibroblast and African green monkey kidney (VERO)] up to 200 µg/ml in MTT assay. Thus the cyclo(4-hydroxy-L-Pro-L-Trp) identified in this study may be a promising alternative to chemical preservatives as a potential biopreservative agent which prevent fungal growth in food and feed. To the best of our knowledge, this is the first report demonstrating that the entomopathogenic nematode associated B. cereus and cyclo(4-hydroxy-L-Pro-L-Trp) could be used as a biocontrol agents against postharvest fungal disease caused by Aspergillus species.