Molecular communication: An acid tale of prion formation

Some bacteria use lactic acid to communicate with yeast cells

Quantitative Proteomics Reveals Differences in the Response of Neutrophils Isolated from Healthy or Diabetic Subjects to Infection with Capsule-Variant Burkholderia thailandensis

In Thailand, diabetes mellitus is the most significant risk factor for melioidosis, a severe disease caused by Burkholderia pseudomallei. In this study, neutrophils isolated from healthy or diabetic subjects were infected with B. thailandensis E555, a variant strain with a B. pseudomallei-like capsular polysaccharide used here as a surrogate micro-organism for B. pseudomallei. At 2 h post-infection, neutrophil proteins were subjected to 4-plex iTRAQ-based comparative proteomic analysis. A total of 341 proteins were identified in two or more samples, of which several proteins involved in oxidative stress and inflammation were enriched in infected diabetic neutrophils. We validated this finding by demonstrating that infected diabetic neutrophils generated significantly elevated levels of pro-inflammatory cytokines TNFα, IL-6, IL-1β, and IL-17 compared to healthy neutrophils. Our data also revealed that infected neutrophils from healthy or diabetic individuals undergo apoptotic cell death at distinctly different rates, with infected diabetic neutrophils showing a diminished ability to delay apoptosis and an increased likelihood of undergoing a lytic form of cell death, compared to infected neutrophils from healthy individuals. Increased expression of inflammatory proteins by infected neutrophils could contribute to the increased susceptibility to infection and inflammation in diabetic patients in melioidosis-endemic areas.</p

Novel Adiponectin Variants Identified in Type 2 Diabetic Patients Reveal Multimerization and Secretion Defects

ADIPOQ, encoding adiponectin, is a candidate gene for type 2 diabetes (T2D) identified by genome-wide linkage analyses with supporting evidence showing the protein function in sensitizing insulin actions. In an endeavor to characterize candidate genes causing T2D in Thai patients, we identified 10 novel ADIPOQ variations, several of which were non-synonymous variations observed only in the patients. To examine the impact of these non-synonymous variations on adiponectin structure and biochemical characteristics, we conducted a structural analysis of the wild-type and variant proteins by in silico modeling and further characterized biochemical properties of the variants with predicted structural abnormalities from the modeling by molecular and biochemical studies. The recombinant plasmids containing wild-type and variant ADIPOQ cDNAs derived from the variations identified by our study (R55H, R112H, and R131H) and previous work (G90S and R112C) were constructed and transiently expressed and co-expressed in cultured HEK293T cells to investigate their oligomerization, interaction, and secretion. We found that the novel R55H variant impaired protein multimerization but it did not exert the effect over the co-expressed wild-type protein while novel R131H variant impaired protein secretion and also affected the co-expressed wild-type protein in a dominant negative fashion. The R131H variant could traffic from the endoplasmic reticulum to the Golgi, trans-Golgi network, and early endosome but could not be secreted. The R131H variant was likely to be degraded through the lysosomal system and inhibition of its degradation rescued the variant protein from secretion defect. We have shown the possibility of using in silico modeling for predicting the effect of amino acid substitution on adiponectin oligomerization. This is also the first report that demonstrates a dominant negative effect of the R131H variant on protein secretion and the possibility of using protein degradation inhibitors as therapeutic agents in the patients carrying adiponectin variants with secretion defect

Microbial Ecology of Watery Kimchi

© 2015 Institute of Food Technologists®. This article has been contributed by US Government employees and their work is in the public domain in the USA. The biochemistry and microbial ecology of 2 similar types of watery (mul) kimchi, containing sliced and unsliced radish and vegetables (nabak and dongchimi, respectively), were investigated. Samples from kimchi were fermented at 4, 10, and 20 °C were analyzed by plating on differential and selective media, high-performance liquid chromatography, and high-throughput DNA sequencing of 16S rDNA. Nabak kimchi showed similar trends as dongchimi, with increasing lactic and acetic acids and decreasing pH for each temperature, but differences in microbiota were apparent. Interestingly, bacteria from the Proteobacterium phylum, including Enterobacteriaceae, decreased more rapidly during fermentation at 4 °C in nabak cabbage fermentations compared with dongchimi. Although changes for Proteobacterium and Enterobacteriaceae populations were similar during fermentation at 10 and 20 °C, the homolactic stage of fermentation did not develop for the 4 and 10 °C samples of both nabak and dongchimi during the experiment. These data show the differences in biochemistry and microbial ecology that can result from preparation method and fermentation conditions of the kimchi, which may impact safety (Enterobacteriaceae populations may include pathogenic bacteria) and quality (homolactic fermentation can be undesirable, if too much acid is produced) of the product. In addition, the data also illustrate the need for improved methods for identifying and differentiating closely related lactic acid bacteria species using high-throughput sequencing methods.This work was carried out as part of the international collaborative R&D program funded by the Agency for Korea Natl. Food Cluster (2013), and supported in part by a grant from Pickle Packers Intl. Inc., Washington, D.C., U.S.A. The authors thank the Spanish Government (MECD) for the postdoctoral fellowship support for Dr. E. Medina-Pradas.Peer Reviewe

The combined impact of sauerkraut with Leuconostoc mesenteroides to enhance immunomodulatory activity in Escherichia coli-infected mice

This study investigated the combined impact of sauerkraut and Leuconostoc mesenteroides culture on immunomodulatory activity in experimental animal. The in vivo immunomodulatory activity of Escherichia coli-infected Balb-C mice was ascertained in fermented sauerkrauts [test vs. control]. Both sauerkrauts enhanced the adaptive immune response [evidenced by an increase in CD4+ CD8+ IFN-γ, TNFα] and innate immune response [represented by a decrease of CD68-IL-6]. Nev- ertheless, the in vivo immunomodulatory activity of sauerkraut combined with L. mesenteroides was higher than that shown in sauerkraut control solely

Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi

Transcriptional regulation by transcriptional regulatory factors (TRFs) of their target TRF genes is central to the control of gene expression. To study a static multi-tiered inter-TRF regulatory network in the human hepatoma cells, we have applied a Matrix RNAi approach in which siRNA knockdown and quantitative RT-PCR are used in combination on the same set of TRFs to determine their interdependencies. This approach focusing on several liver-enriched TRF families, each of which consists of structurally homologous members, revealed many significant regulatory relationships. These include the cross-talks between hepatocyte nuclear factors (HNFs) and the other TRF groups such as CCAAT/enhancer-binding proteins (CEBPs), retinoic acid receptors (RARs), retinoid receptors (RXRs) and RAR-related orphan receptors (RORs), which play key regulatory functions in human hepatocytes and liver. In addition, various multi-component regulatory motifs, which make up the complex inter-TRF regulatory network, were identified. A large part of the regulatory edges identified by the Matrix RNAi approach could be confirmed by chromatin immunoprecipitation. The resultant significant edges enabled us to depict the inter-TRF TRN forming an apparent regulatory hierarchy of (FOXA1, RXRA) → TCF1 → (HNF4A, ONECUT1) → (RORC, CEBPA) as the main streamline

Intracellular Serotonin Modulates Insulin Secretion from Pancreatic β-Cells by Protein Serotonylation

Non-neuronal, peripheral serotonin deficiency causes diabetes mellitus and identifies an intracellular role for serotonin in the regulation of insulin secretion

Microbial Ecology of Sauerkraut Fermentation and Genome Analysis of Lactic Acid Bacterium Leuconostoc Mesenteroides ATCC 8293.

Previous studies using traditional biochemical methods to study the ecology of commercial sauerkraut fermentations revealed that four major lactic acid bacteria species, namely, Leuconostoc mesenteroides, Lactobacillus plantarum, Pediococcus pentosaceus, and Lactobacillus brevis were involved. Brine samples from commercial fermentation tanks were sampled several times, over a period of 14 days. The samples were plated on MRS agar and selected numbers of isolates for each time point were recovered. A total of six hundred eighty-six isolates were collected for analysis. A database of PCR fragment patterns has been generated by amplifying the intergenic transcribed spacer regions between the 16S and 23S rDNA genes. The 16S rDNA gene has been sequenced to further identify selected isolates. The use of molecular techniques to complement biochemical identification methods has revealed the presence of species not previously reported to be present in sauerkraut fermentations, namely Leuconostoc citreum, Leuconostoc argentinum, Lactobacillus paraplantarum, Lactobacillus coryniformis, and Weissella sp..The ecology of these commercial fermentations has been shown to be more complex than previously reported. Realizing L. mesenteroidesc practical significance in fermentation, bioprocesssing, agriculture, food, and medicine, the whole genome sequence of L. mesenteroides ATCC 8293 originally isolated from olive fermentation has been determined. The chromosome has 2,038,395 bp and contains predicted 1,924 protein-encoding genes. Putative biological functions could be assigned to 54% of the predicted proteins. Consistent with the classification of L. mesenteroides as heterofermentative lactic acid bacterium, the genome encoded all enzymes required for the 6-phosphogluconate/phosphoketolase pathway. Furthermore, L. mesenteroides encodes a number of pyruvate dissipating enzymes that are predicted to catalyze the production of many metabolites leading to various end products of fermentation. A large proportion of the genes are encoded for carbohydrate transport and utilization. The chromosome also contains genes belonging to phage remnants and mobile genetic elements. The genomic sequence also indicated a potential horizontal transfer of genetic information between L. mesenteroides and gram-negative bacteria.The data presented here can help facilitate evaluation of L. mesenteroides as a model organism for studies of heterofermentative LAB metabolism, physiology, and regulation

Use of RAPD-PCR as a method to follow the progress of starter cultures in sauerkraut fermentations

Abstract DNA fingerprinting methods were used to follow the progress of unmarked starter cultures in laboratory sauerkraut fermentations (1.2 and 13 l). Random prime PCR (RAPD-PCR) was used for strain-specific identification of Leuconostoc mesenteroides cultures. A comparative analysis of RAPD banding patterns for fermentation isolates and starter cultures was carried out using both genetically marked and unmarked cultures. While some variation in the RAPD patterns was observed, the results showed that the starter cultures dominated the fermentation during early heterofermentative stage for up to 5 days after the start of fermentation. Results from marked and unmarked starter cultures were confirmed by intergenic transcribed spacer (ITS)-PCR, and strain identify was confirmed by pulse field gel electrophoresis (PFGE) patterns. The results demonstrate the utility of RAPD to follow the progression of unmarked starter cultures of L. mesenteroides in sauerkraut fermentations.