Protein homeostasis,regulation of energy production and activation of DNA damage-repair pathways are involved in the heat stress response of Pseudogymnoascus spp.

Proteome changes can be used as an instrument to measure the effects of climate change, predict the possible future state of an ecosystem and the direction in which is headed. In this study, proteomic and gene ontology functional enrichment analysis of six Pseudogymnoascus spp. isolated from various global biogeographical regions were carried out to determine their response to heat stress. In total, 2122 proteins were identified with high confidence. Comparative quantitative analysis showed that changes in proteome profiles varied greatly between isolates from different biogeographical regions. Although the identities of the proteins that changed varied between the different regions, the functions they governed were similar. Gene ontology analysis showed enrichment of proteins involved in multiple protective mechanisms, including the modulation of protein homeostasis, regulation of energy production and activation of DNA damage and repair pathways. Our proteomic analysis did not show any clear relationship between protein changes and the strains' biogeographical origins.     

Geochemical Speciation and Risk Assessment of Heavy Metals in Sediments of a River in Bangladesh

The surface sediment of a downstream river (Paira) connected to the marine ecosystems of the Bay of Bengal was assessed by sequential extraction technique. The objectives of this study were to evaluate the mobility and dynamics of heavy metals and their probable ecological risks. The results revealed high environmental risk of Cd due to higher availability in the exchangeable fraction (21%) and a considerable portion in the carbonate bound fraction due to the special affinity towards carbonate and co-precipitation with its minerals. Toxic metals like Cr, Ni, and Cd are of concern, and can occasionally be associated with adverse biological effects. The risk assessment code (RAC) suggests that the highest mobility of Cd poses a higher environmental risk and threat to the aquatic biota, as well.     

Proteomic Analysis of ABCA1-Null Macrophages Reveals a Role for Stomatin-Like Protein-2 in Raft Composition and Toll-Like Receptor Signaling

Lipid raft membrane microdomains organize signaling by many prototypical receptors, including the Toll-like receptors (TLRs) of the innate immune system. Raft-localization of proteins is widely thought to be regulated by raft cholesterol levels, but this is largely on the basis of studies that have manipulated cell cholesterol using crude and poorly specific chemical tools, such as β-cyclodextrins. To date, there has been no proteome-scale investigation of whether endogenous regulators of intracellular cholesterol trafficking, such as the ATP binding cassette (ABC)A1 lipid efflux transporter, regulate targeting of proteins to rafts. Abca1^−/− macrophages have cholesterol-laden rafts that have been reported to contain increased levels of select proteins, including TLR4, the lipopolysaccharide receptor. Here, using quantitative proteomic profiling, we identified 383 proteins in raft isolates from Abca1^+/+ and Abca1^−/− macrophages. ABCA1 deletion induced wide-ranging changes to the raft proteome. Remarkably, many of these changes were similar to those seen in Abca1^+/+ macrophages after lipopolysaccharide exposure. Stomatin-like protein (SLP)-2, a member of the stomatin-prohibitin-flotillin-HflK/C family of membrane scaffolding proteins, was robustly and specifically increased in Abca1^−/− rafts. Pursuing SLP-2 function, we found that rafts of SLP-2-silenced macrophages had markedly abnormal composition. SLP-2 silencing did not compromise ABCA1-dependent cholesterol efflux but reduced macrophage responsiveness to multiple TLR ligands. This was associated with reduced raft levels of the TLR co-receptor, CD14, and defective lipopolysaccharide-induced recruitment of the common TLR adaptor, MyD88, to rafts. Taken together, we show that the lipid transporter ABCA1 regulates the protein repertoire of rafts and identify SLP-2 as an ABCA1-dependent regulator of raft composition and of the innate immune response.Lipid rafts are cholesterol-enriched membrane microdomains, thought to be present in all cells, that concentrate and organize cell-surface signal transduction events in several signaling cascades, including those of the Toll-like receptors (TLRs) (1). The selectivity of rafts for particular proteins, and, consequently, the signal strength of pathways initiating from ligated raft-resident receptors, are thought to derive in large part from the high cholesterol content of raft microdomains (2–4). In vitro, altering raft cholesterol of living cells downward or upward with chemical tools (e.g. cyclodextrins) leads to parallel changes in raft protein abundance (3, 4). The relevance of cholesterol-driven alterations in the raft proteome to disease is suggested by reports that hypercholesterolemia cholesterol-loads macrophage rafts and amplifies their responsiveness to lipopolysaccharide (LPS) (3, 4). Proteomic strategies have recently been applied to raft isolates from a variety of cell types, aiming to better understand the identity of proteins tonically present in rafts, as well as proteins dynamically recruited to rafts upon cell stimulation (2, 5–8). To date, however, most reports have used cell lines of uncertain physiological relevance. In addition, although raft cholesterol levels are regulated in vivo by intracellular cholesterol trafficking (1), no reports to date have sought to define how the raft proteome is physiologically regulated by cholesterol trafficking proteins.ATP binding cassette (ABC) A1, a member of the ABC transporter superfamily, plays a key role in regulating levels of cholesterol in macrophages and other cells via promoting efflux of cellular cholesterol to extracellular acceptors, in particular lipid-free apolipoprotein (apo) A-I (9). The importance of ABCA1¹ to human health is clearly illustrated by Tangier disease, a rare ABCA1 mutation syndrome typified by severe HDL deficiency, widespread macrophage foam cells, and premature atherosclerosis (10). In addition, the large number of common ABCA1 polymorphisms that have been associated with human cardiovascular disease (10) suggest a broad-spanning impact of ABCA1 on human health. It remains somewhat controversial whether ABCA1-effluxed cholesterol derives from raft or extra-raft membranes (11). Nonetheless, both human Tangier disease cells and ABCA1-null murine macrophages have been shown to have greatly expanded lipid rafts that contain increased cholesterol and increased TLR4 (12, 13). These changes are associated with enhanced responsiveness to LPS that can be reversed by cholesterol depletion (13–15). Collectively, these findings indicate that ABCA1 may regulate the raft proteome and innate immune response through control of raft cholesterol. However, no proteomic analysis of rafts from ABCA1-deficient cells has been reported to date.Herein, we report a proteomic analysis of raft isolates from naive and LPS-stimulated Abca1^+/+ and Abca1^−/− primary murine macrophages. Unexpectedly, we found that ABCA1 deletion and LPS stimulation induced many similar changes in the raft proteome. Stomatin-like protein 2 (SLP-2), a lesser known member of the stomatin-prohibitin-flotillin-HflK/C (SPFH) family of membrane scaffolding proteins, was unique among SPFH proteins in being robustly up-regulated in rafts of unstimulated Abca1^−/− cells compared with Abca1^+/+ counterparts. We found that rafts of SLP-2 knockdown cells were abnormal, displaying increased binding of cholera toxin subunit B—a probe for the raft-specific ganglioside GM1—but markedly decreased protein, including flotillins-1 and -2, and CD14. Whereas SLP-2 silencing did not compromise ABCA1-dependent cholesterol efflux, it reduced macrophage responsiveness to LPS and multiple additional TLR ligands. Taken together, we report that ABCA1 regulates the macrophage raft proteome and identify SLP-2 as a novel ABCA1-dependent regulator of raft composition that controls the innate immune response.     

Bradyrhizobium iriomotense sp. nov., isolated from a tumor-like root of the legume Entada koshunensis from Iriomote Island in Japan

A polyphasic study was performed to determine the taxonomic position of strain EK05(T) isolated from a root-outgrowth of Entada koshunensis, a legume available in Okinawa, Japan. Phylogenetic analysis of the 16S rRNA gene showed that the strain belongs to the genus Bradyrhizobium. Subsequent multilocus sequence analysis with ITS, glnII, recA, gyrB, and atpD sequences revealed that the isolate represents a distinct evolutionary lineage within the genus Bradyrhizobium. DNA-DNA hybridization indicated that strain EK05(T) shares <61% DNA relatedness with the type strains of all six recognized species of Bradyrhizobium, confirming that this strain is a novel species within the genus. Phylogenetic trees based on symbiotic loci, nifH and nodC, also placed strain EK05(T) clearly in a novel branch. On the basis of its phylogenetic distinctiveness, we propose Bradyrhizobium iriomotense sp. nov. for strain EK05(T). The type strain is EK05(T) (= NBRC 102520(T) = LMG 24129(T)).     

Optimization of culture conditions for glucose oxidase production by a Penicillium chrysogenum SRT 19 strain

The enzyme glucose oxidase (GOD) has been used for a variety of biotechnological applications in food and pharmaceutical industries. In this study, the optimization of extracellular GOD production was carried out in a Penicillium chrysogenum SRT 19 strain isolated from contaminated and decaying cheese samples. Maximum GOD production was attained at pH 6 and 20°C in fermentation broth after 72 h of incubation. The effects of metal ions and sugars were screened for the induction of higher GOD production. The results revealed that glucose and lactose give the highest production of enzyme (0.670 and 0.552 U/mL, respectively) as compared with other sugars (sucrose, cellulose, mannitol and fructose). Out of the seven metal ions studied, CaCO₃ (1.123 U/mL) and FeSO₄ (0.822 U/mL) act as modulators, while MgSO₄ (0.535 U/mL), CuSO₄ (0.498 U/mL), HgCl₂ (0.476 U/mL), ZnSO₄ (0.457 U/mL) and BaSO₄ (0.422 U/mL) yield lower production. The study therefore suggests that a strain of P. chrysogenum SRT 19 can be used as a new strain for GOD production.     

Fatal Outbreak from Consuming Xanthium strumarium Seedlings during Time of Food Scarcity in Northeastern Bangladesh

Background

An outbreak characterized by vomiting and rapid progression to unconsciousness and death was reported in Sylhet Distrct in northeastern Bangladesh following destructive monsoon floods in November 2007.

Methods and Findings

We identified cases presenting to local hospitals and described their clinical signs and symptoms. We interviewed patients and their families to collect illness histories and generate hypotheses about exposures associated with disease. An epidemiological study was conducted in two outbreak villages to investigate risk factors for developing illness. 76 patients were identified from 9 villages; 25% (19/76) died. Common presenting symptoms included vomiting, elevated liver enzymes, and altered mental status. In-depth interviews with 33 cases revealed that 31 (94%) had consumed ghagra shak, an uncultivated plant, in the hours before illness onset. Ghagra shak was consumed as a main meal by villagers due to inaccessibility of other foods following destructive monsoon flooding and rises in global food prices. Persons who ate this plant were 34.2 times more likely (95% CI 10.2 to 115.8, p-value<0.000) than others to develop vomiting and unconsciousness during the outbreak in our multivariate model. Ghagra shak is the local name for Xanthium strumarium, or common cocklebur.

Conclusions

The consumption of Xanthium strumarium seedlings in large quantities, due to inaccessibility of other foods, caused this outbreak. The toxic chemical in the plant, carboxyatratyloside, has been previously described and eating X. strumarium seeds and seedlings has been associated with fatalities in humans and livestock. Unless people are able to meet their nutritional requirements with safe foods, they will continue to be at risk for poor health outcomes beyond undernutrition.     

Detection of Methicillin-Resistant Staphylococcus aureus Using mecA/nuc Genes and Antibiotic Susceptibility Profile of Malaysian Clinical Isolates

The aim of this study is to compare methicillin-resistant Staphylococcus aureus (MRSA) detection methods and to generate antibiogram profile of S. aureus clinical isolates from two teaching hospitals in Malaysia including three reference isolates from American Type Culture Collection (ATCC). The mecA/nuc gene PCR amplification, spot inoculation test and oxacillin disc diffusion test were applied to compare its MRSA detection abilities. No disagreement between the three methods was observed. From 29 bacterial isolates (including the ATCC strains) tested, 19 isolates were confirmed as S. aureus with 14 isolates exhibiting multidrug-resistance. All isolates are still susceptible to vancomycin as indicated by the E-test result. Current biochemical tests are comparable with the molecular detection method for MRSA used in this study while multidrug-resistance traits are present in both MRSA and MSSA clinical isolates. Presently, mupirocin seems to be the best alternative for vancomycin against multidrug-resistant S. aureus infections in Malaysia. Susceptibility profile of 19 S. aureus isolates acquired from two teaching hospitals and ATCC towards 16 selected antibiotics was analyzed and an antibiogram was generated. Findings also indicated resistance against many of the available antibiotics and thus an urgent need to search for alternative antibiotics.     

Effect of codon-optimized E. coli signal peptides on recombinant Bacillus stearothermophilus maltogenic amylase periplasmic localization,yield and activity

Recombinant proteins can be targeted to the Escherichia coli periplasm by fusing them to signal peptides. The popular pET vectors facilitate fusion of target proteins to the PelB signal. A systematic comparison of the PelB signal with native E. coli signal peptides for recombinant protein expression and periplasmic localization is not reported. We chose the Bacillus stearothermophilus maltogenic amylase (MA), an industrial enzyme widely used in the baking and brewing industry, as a model protein and analyzed the competence of seven, codon-optimized, E. coli signal sequences to translocate MA to the E. coli periplasm compared to PelB. MA fusions to three of the signals facilitated enhanced periplasmic localization of MA compared to the PelB fusion. Interestingly, these three fusions showed greatly improved MA yields and between 18- and 50-fold improved amylase activities compared to the PelB fusion. Previously, non-optimal codon usage in native E. coli signal peptide sequences has been reported to be important for protein stability and activity. Our results suggest that E. coli signal peptides with optimal codon usage could also be beneficial for heterologous protein secretion to the periplasm. Moreover, such fusions could even enhance activity rather than diminish it. This effect, to our knowledge has not been previously documented. In addition, the seven vector platform reported here could also be used as a screen to identify the best signal peptide partner for other recombinant targets of interest.