Mitochondrial dynamics following global cerebral ischemia.

Global brain ischemia/reperfusion induces neuronal damage in vulnerable brain regions, leading to mitochondrial dysfunction and subsequent neuronal death. Induction of neuronal death is mediated by release of cytochrome c (cyt c) from the mitochondria though a well-characterized increase in outer mitochondrial membrane permeability. However, for cyt c to be released it is first necessary for cyt c to be liberated from the cristae junctions which are gated by Opa1 oligomers. Opa1 has two known functions: maintenance of the cristae junction and mitochondrial fusion. These roles suggest that Opa1 could play a central role in both controlling cyt c release and mitochondrial fusion/fission processes during ischemia/reperfusion. To investigate this concept, we first utilized in vitro real-time imaging to visualize dynamic changes in mitochondria. Oxygen-glucose deprivation (OGD) of neurons grown in culture induced a dual-phase mitochondrial fragmentation profile: (i) fragmentation during OGD with no apoptosis activation, followed by fusion of mitochondrial networks after reoxygenation and a (ii) subsequent extensive fragmentation and apoptosis activation that preceded cell death. We next evaluated changes in mitochondrial dynamic state during reperfusion in a rat model of global brain ischemia. Evaluation of mitochondrial morphology with confocal and electron microscopy revealed a similar induction of fragmentation following global brain ischemia. Mitochondrial fragmentation aligned temporally with specific apoptotic events, including cyt c release, caspase 3/7 activation, and interestingly, release of the fusion protein Opa1. Moreover, we uncovered evidence of loss of Opa1 complexes during the progression of reperfusion, and electron microscopy micrographs revealed a loss of cristae architecture following global brain ischemia. These data provide novel evidence implicating a temporal connection between Opa1 alterations and dysfunctional mitochondrial dynamics following global brain ischemia.

The Protein Complex of Neurodegeneration-related Phosphoinositide Phosphatase Sac3 and ArPIKfyve Binds the Lewy Body-associated Synphilin-1, Preventing Its Aggregation.

The 5-phosphoinositide phosphatase Sac3, in which loss-of-function mutations are linked to neurodegenerative disorders, forms a stable cytosolic complex with the scaffolding protein ArPIKfyve. The ArPIKfyve-Sac3 heterodimer interacts with the phosphoinositide 5-kinase PIKfyve in a ubiquitous ternary complex that couples PtdIns(3,5)P2 synthesis with turnover at endosomal membranes, thereby regulating the housekeeping endocytic transport in eukaryotes. Neuron-specific associations of the ArPIKfyve-Sac3 heterodimer, which may shed light on the neuropathological mechanisms triggered by Sac3 dysfunction, are unknown. Here we conducted mass spectrometry analysis for brain-derived interactors of ArPIKfyve-Sac3 and unraveled the α-synuclein-interacting protein Synphilin-1 (Sph1) as a new component of the ArPIKfyve-Sac3 complex. Sph1, a predominantly neuronal protein that facilitates aggregation of α-synuclein, is a major component of Lewy body inclusions in neurodegenerative α-synucleinopathies. Modulations in ArPIKfyve/Sac3 protein levels by RNA silencing or overexpression in several mammalian cell lines, including human neuronal SH-SY5Y or primary mouse cortical neurons, revealed that the ArPIKfyve-Sac3 complex specifically altered the aggregation properties of Sph1-GFP. This effect required an active Sac3 phosphatase and proceeded through mechanisms that involved increased Sph1-GFP partitioning into the cytosol and removal of Sph1-GFP aggregates by basal autophagy but not by the proteasomal system. If uncoupled from ArPIKfyve elevation, overexpressed Sac3 readily aggregated, markedly enhancing the aggregation potential of Sph1-GFP. These data identify a novel role of the ArPIKfyve-Sac3 complex in the mechanisms controlling aggregate formation of Sph1 and suggest that Sac3 protein deficiency or overproduction may facilitate aggregation of aggregation-prone proteins, thereby precipitating the onset of multiple neuronal disorders.

Release of mitochondrial Opa1 following oxidative stress in HT22 cells.

Cellular mechanisms involved in multiple neurodegenerative diseases converge on mitochondria to induce overproduction of reactive oxygen species, damage to mitochondria, and subsequent cytochrome c release. Little is currently known regarding the contribution mitochondrial dynamics play in cytochrome c release following oxidative stress in neurodegenerative disease. Here we induced oxidative stress in the HT22 cell line with glutamate and investigated key mediators of mitochondrial dynamics to determine the role this process may play in oxidative stress induced neuronal death. We report that glutamate treatment in HT22 cells induces increase in reactive oxygen species (ROS), release of the mitochondrial fusion protein Opa1 into the cytosol, with concomitant release of cytochrome c. Furthermore, following the glutamate treatment alterations in cell signaling coincide with mitochondrial fragmentation which culminates in significant cell death in HT22 cells. Finally, we report that treatment with the antioxidant tocopherol attenuates glutamate induced-ROS increase, release of mitochondrial Opa1 and cytochrome c, and prevents cell death.

Unfolding the unfolded protein response: unique insights into brain ischemia.

The endoplasmic reticulum (ER) is responsible for processing of proteins that are destined to be secreted, enclosed in a vesicle, or incorporated in the plasma membrane. Nascent peptides that enter the ER undergo a series of highly regulated processing steps to reach maturation as they transit the ER. Alterations in the intracellular environment that induce ER stress are thought to interrupt these processing steps, and result in unfolding of proteins in the ER. Accumulation of unfolded proteins concurrently activates three transmembrane stress sensors, IRE1, ATF6 and PERK, and is referred to as the Unfolded Protein Response (UPR). Our understanding of the mechanisms of UPR induction has been assembled primarily from experiments inducing ER stress with chemical and genetic manipulations. However, physiological stress often induces activation of ER stress sensors in a distinct manner from the canonical UPR. The unique activation profiles in vivo have prompted us to examine the mechanism of UPR activation in neurons following cerebral ischemia.

Exiguobacterium alkaliphilum sp. nov. isolated from alkaline wastewater drained sludge of a beverage factory.

A facultatively anaerobic, alkaliphilic, Gram-stain-positive, rod-shaped bacterium, designated strain 12/1(T), isolated from alkaline wastewater drained sludge of a beverage industry facility located near New Delhi, India, was subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain 12/1(T) belonged to the genus Exiguobacterium and was most closely related to Exiguobacterium aurantiacum DSM 6208(T) (99.46 %), E. aquaticum IMTB-3094(T) (99.18 %), E. mexicanum 8N(T) (99.06 %), E. profundum 10C(T) (98.17 %), E. aestuarii TF-16(T) (98.1 %) and E. marinum TF-80(T) (98.03 %). The DNA G+C content of strain 12/1(T) was 55.6 mol%, major respiratory isoprenoid quinone was MK-7, major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine and the cell-wall peptidoglycan was of the A3α l-Lys-Gly type, characteristics consistent with its affiliation to the genus Exiguobacterium. Strain 12/1(T) showed levels of DNA-DNA hybridization of less than 70 % with the closely related species of the genus Exiguobacterium. Overall, the phenotypic, chemotaxonomic and phylogenetic data presented in this study suggest that strain 12/1(T) represents a novel species of the genus Exiguobacterium, for which the name Exiguobacterium alkaliphilum sp. nov. is proposed. The type strain is 12/1(T) ( = CCM 8459(T) = DSM 21148(T)).

Seasonal variation in heavy metal contamination in water and sediments of river Sabarmati and Kharicut canal at Ahmedabad, Gujarat.

The objective of the study is to reveal the seasonal variations in the river water and sediment quality with respect to heavy metal contamination. To get the extent of trace metals contamination, water and sediment samples were collected from five different sites along the course of Sabarmati River and its tributary Kharicut canal in pre-monsoon, monsoon and post-monsoon seasons. The concentration of trace metals such as chromium, copper, lead, nickel and zinc was determined using inductively coupled plasma spectroscopy. The concentrations of heavy metals were found to be higher in the pre-monsoon season than in the monsoon and post-monsoon seasons in water samples. The pollution load index, contamination factor and degree of contamination (C(d)) in sediments were calculated to know the extent of anthropogenic pressures. The values of C(d) clearly indicated very high degree of contamination at Kharicut canal (S-4: 32.25 and S-5: 54.52) and considerable degree of contamination at three sites of Sabarmati river viz; S-1, S-2 and S-3 with values 14.30, 14.42 and 17.21, respectively. Lead and nickel could not be traced in any of the river water samples.

Biodegradation of sewage wastewater using autochthonous bacteria.

The performance of isolated designed consortia comprising Bacillus pumilus, Brevibacterium sp, and Pseudomonas aeruginosa for the treatment of sewage wastewater in terms of reduction in COD (chemical oxygen demand), BOD (biochemical oxygen demand) MLSS (mixed liquor suspended solids), and TSS (total suspended solids) was studied. Different parameters were optimized (inoculum size, agitation, and temperature) to achieve effective results in less period of time. The results obtained indicated that consortium in the ratio of 1 : 2 (effluent : biomass) at 200 rpm, 35°C is capable of effectively reducing the pollutional load of the sewage wastewaters, in terms of COD, BOD, TSS, and MLSS within the desired discharge limits, that is, 32 mg/L, 8 mg/L, 162 mg/L, and 190 mg/L. The use of such specific consortia can overcome the inefficiencies of the conventional biological treatment facilities currently operational in sewage treatment plants.

Usefulness of organic acid produced by Exiguobacterium sp. 12/1 on neutralization of alkaline wastewater.

The aim of this study was to investigate the role of organic acids produced by Exiguobacterium sp. strain 12/1 (DSM 21148) in neutralization of alkaline wastewater emanated from beverage industry. This bacterium is known to be able to grow in medium of pH as high as pH 12.0 and to neutralize alkaline industrial wastewater from pH 12.0 to pH 7.5. The initial investigation on the type of functional groups present in medium, carried out using FT-IR spectroscopy, revealed the presence of peaks corresponding to carbonyl group and hydroxyl group, suggesting the release of carboxylic acid or related metabolic product(s). The identification of specific carboxylic group, carried out using RP-HPLC, revealed the presence of a single peak in the culture supernatant with retention time most similar to formic acid. The concentration of acid produced on different carbon sources was studied as a function of time. Although acid was present in same final concentration, the rate of acid production was highest in case of medium supplemented with sucrose followed by fructose and glucose. The knowledge of metabolic products of the bacterium can be considered as a first step towards realization of its potential for large-scale bioremediation of alkaline wastewater from beverage industry.

Bioremediation of agro-based pulp mill effluent by microbial consortium comprising autochthonous bacteria.

Small-scale agro-based pulp and paper mills are characterized as highly polluting industries. These mills use Kraft pulping process for paper manufacturing due to which toxic lignified chemicals are released into the environment. Lack of infrastructure, technical manpower, and research and development facilities restricts these mills to recover these chemicals. Therefore, the chemical oxygen demand (COD) of the emanating stream is quite high. For solving the above problem, four bacteria were isolated from the premises of agro-based pulp and paper mill which were identified as species of Pseudomonas, Bacillus, Pannonibacter, and Ochrobacterum. These bacteria were found capable of reducing COD up to 85%-86.5% in case of back water and 65-66% in case of back water : black liquor (60:40), respectively, after acclimatization under optimized conditions (pH 6.8, temperature 35°C, and shaking 200 rpm) when the wastewater was supplemented with nitrogen and phosphorus as trace elements.

Restructuring BOD : COD ratio of dairy milk industrial wastewaters in BOD analysis by formulating a specific microbial seed.

BOD (Biochemical oxygen demand) is the pollution index of any water sample. One of the main factors influencing the estimation of BOD is the nature of microorganisms used as seeding material. In order to meet the variation in wastewater characteristics, one has to be specific in choosing the biological component that is the seeding material. The present study deals with the estimation of BOD of dairy wastewater using a specific microbial consortium and compares of the results with seeding material (BODSEED). Bacterial strains were isolated from 5 different sources and were screened by the conventional BOD method. The selected microbial seed comprises of Enterobacter sp., Pseudomonas sp. BOD : COD (Chemical oxygen demand) ratio using the formulated seed comes in the range of 0.7-0.8 whereas that using BODSEED comes in the ratio of 0.5-0.6. The ultimate BOD (UBOD) was also performed by exceeding the 3-day dilution BOD test. After 90 days, it has been observed that the ratio of BOD : COD increased in case of selected consortium 7 up to 0.91 in comparison to 0.74 by BODSEED. The results were analyzed statistically by t-test and it was observed that selected consortium was more significant than the BODSEED.

Interaction studies of novel cell selective antimicrobial peptides with model membranes and E. coli ATCC 11775.

Cationic antimicrobial peptides (CAMPs) are novel candidates for drug development. Here we describe design of six short and potent CAMPs (SA-1 to SA-6) based on a minimalist template of 12 residues H+HHG+HH+HH+NH2 (where H: hydrophobic amino acid and +: charged hydrophilic amino acid). Designed peptides exhibit good antibacterial activity in micro molar concentration range (1-32 mug/ml) and rapid clearance of Gram-positive and Gram-negative bacterial strains at concentrations higher than MIC. For elucidating mode of action of designed peptides various biophysical studies including CD and Trp fluorescence were performed using model membranes. Further based on activity, selectivity and membrane bound structure; modes of action of Trp rich peptide SA-3 and template based peptide SA-4 were compared. Calcein dye leakage and transmission electron microscopic studies with model membranes exhibited selective membrane active mode of action for peptide SA-3 and SA-4. Extending our work from model membranes to intact E. coli ATCC 11775 in scanning electron micrographs we could visualize different patterns of surface perturbation caused by peptide SA-3 and SA-4. Further at low concentration rapid translocation of FITC-tagged peptide SA-3 into the cytoplasm of E. coli cells without concomitant membrane perturbation indicates involvement of intracellular targeting mechanism as an alternate mode of action as was also evidenced in DNA retardation assay. For peptide SA-4 concentration dependent translocation into the bacterial cytoplasm along with membrane perturbation was observed. Establishment of a non specific membrane lytic mode of action of these peptides makes them suitable candidates for drug development.

Mini-medical school programs decrease perceived barriers of pursuing medical careers among underrepresented minority high school students.

CONTEXT: The percent of underrepresented minority (URM) students who apply to medical school has changed minimally in the past 40 years. Due to the lack of URM applicants, the consequent matriculation of URMs is grossly disproportionate from their percent representation of the US population. Increasing diversity among medical students and physicians has previously been identified as essential to decreasing healthcare disparities among US minorities. OBJECTIVES: The objective of our study was to recognize the barriers of applying to medical school among URMs in high school. METHODS: To identify and assess the prevalence of barriers, surveys were distributed to participants of Med-Achieve, a mini-medical school program of diverse high school students in New York City during the 2019-2020 academic year. RESULTS: Among students who will be first in their immediate family to attend college, 80.0% perceived a barrier to pursuing medical school. Specified barriers indicated include the cost of medical school (77%), a lack of guidance/role models (53.9%), and the predicted inability to do well in medical school classes (53.9%). At the end of the program, a statistically significant reduction in the barrier of lack of guidance/role models was seen. CONCLUSIONS: This study highlights the benefit of mini-medical school programs, especially programs with a mentoring component, to decrease the perceived barriers of applying to medical school among URMs. It also suggests the potential role of similar programs to increase diversity in medicine and to decrease healthcare disparities among minorities in the United States.

Three dimensional model for N-terminal A domain of DmpR (2-dimethylphenol) protein based on secondary structure prediction and fold recognition.

DmpR (dimethylphenol regulatory protein) is a member of the NtrC family of transcriptional activators and controls the transcription of the dmp operons in response to aromatic effector compounds. Secondary structure and fold recognition prediction of N-terminal A domain of this protein (210 amino acid) was performed in Genesilico Metaserver and 3DJury. The consensus result from these servers suggested MJ_1460 as a template. Three dimensional structures were generated from the sequence structure alignments of the template and target protein with MODELLER. The results suggested that the N-terminal A domain of DmpR belongs to Muramoyl pentapeptide carboxypeptidase domain family. The binding interaction sites of the known effectors were predicted using protein-ligand docking. The proposed active site of N-terminal A domain of DmpR comprises of key residues such as Phe93, Glu127, Phe132, Ser160, Phe163, Met164, Arg166 and Pro189. The findings provide some direction to the experimental studies that aim to broaden the range of phenolic derivative which can be sensed by N-DmpR in order to improve the biodegradation potential.

Insulin blocks cytochrome c release in the reperfused brain through PI3-K signaling and by promoting Bax/Bcl-XL binding.

The critical event of the intrinsic pathway of apoptosis following transient global brain ischemia is the release of cytochrome c from the mitochondria. In vitro studies have shown that insulin can signal specifically via phosphatidylinositol-3-OH-kinase (PI3-K) and Akt to prevent cytochrome c release. Therefore, insulin may exert its neuroprotective effects during brain reperfusion by blocking cytochrome c release. We hypothesized that insulin acts through PI3-K, Akt, and Bcl-2 family proteins to inhibit cytochrome c release following transient global brain ischemia. We found that a single bolus of insulin given immediately upon reperfusion inhibited cytochrome c release for at least 24 h, and produced a fivefold improvement in neuronal survival at 14 days. Moreover, insulin's ability to inhibit cytochrome c release was completely dependent on PI3-K signaling and insulin induces phosphorylation of Akt through PI3-K. In untreated animals, there was an increase in mitochondrial Bax at 6 h of reperfusion, and Bax binding to Bcl-X(L) was disrupted at the mitochondria. Insulin prevented both these events in a PI3-K-dependent manner. In summary, insulin regulates cytochrome c release through PI3-K likely by activating Akt, promoting the binding between Bax and Bcl-X(L), and by preventing Bax translocation to the mitochondria.

An in silico [correction of insilico] approach to bioremediation: laccase as a case study.

Laccase (E.C. 1.10.3.2) is one of the well-studied enzymes used for bioremediation of xenobiotics such as phenols, anilines, etc. Its broad substrate specificity offers a wide opportunity for screening pollutants in order to predict potential targets for degradation. Present study utilizes protein-ligand docking as a tool to achieve the said. For virtual screening, a set of pollutants were selected from five different industries from EPA. X-ray crystal structures of laccase enzymes were taken from the Brookhaven Protein Data Bank (PDB). Two-dimensional structures of pollutants were downloaded from the NCBI Pubchem, which were further converted into three-dimensional structures using CORINA. Protein-ligand docking was carried out using GOLD. Nearly 30 and 17% of the selected datasets showed the best average GOLD fitness score for fungal and bacterial laccase enzyme respectively, suggesting thereby that laccase might be able to oxidize these pollutants. Moreover, in few cases like anthracene, phenanthrene, etc., there is experimental data to support this hypothesis. Similar kind of work would be helpful to find putative pollutants for other biodegradative enzymes.

Alignment of emergency medicine research efforts with Clinical and Translational Science Awards.

The Clinical and Translational Science Awards (CTSA) represent a major new funding pathway for health science investigators seeking National Institutes of Health (NIH) funds. This new pathway provides institutional-level support for clinical and translational research and is not tied to one organ system or disease process, fitting well with emergency medicine (EM) research needs. These awards open unique opportunities for advancing EM research. The CTSA mechanism provides institutional support from the NIH to promote both clinical and translational science. Of the 60 expected awards, 38 sites are currently funded. EM investigators can benefit the institutions applying for these awards and simultaneously gain from involvement. Some opportunities for participation provided by the CTSA include research training programs, joining multidisciplinary research teams, seed grant funding, and use of the CTSA-developed research infrastructure. Involvement of EM can benefit institutions by enhancing acute care research collaboration both within and among institutions. Emergency medicine researchers at institutions either planning to submit a CTSA application or with funded CTSA grants are encouraged to become actively involved in CTSA-related research programs.

Correction: ExtremeDB: A Unified Web Repository of Extremophilic Archaea and Bacteria.

[This corrects the article DOI: 10.1371/journal.pone.0063083.].

Gene expression analysis of the development of congenital hydrocephalus in the H-Tx rat.

To discover candidate genes in the pathogenesis of congenital hydrocephalus, gene arrays were utilized to analyze transcripts from the midbrain region of 5-day-old H-Tx rats; these animals develop hydrocephalus due to closure of their cerebral aqueduct between embryonic day 18 and post-natal day 5. Of the 15,924 transcripts assayed, we detected 47 differentially expressed transcripts representing 23 genes and 24 expressed sequence tags (ESTs); 17 transcripts (7 genes and 10 ESTs) were upregulated and 30 (16 genes and 14 ESTs) were downregulated in the hydrocephalic animals relative to control non-hydrocephalic animals. Seven of these genes, Cck, Nfix, Lgals3, Gsta1, Xdh, Tnf, and Tfpi-2, can be linked to hydrocephalus. In addition, 17 genes that displayed altered expression in our study are not currently known to be associated with the presence or development of hydrocephalus. These results indicate that a relatively few number of transcripts were found to be altered in the development of hydrocephalus in this model. This is the first experiment of its kind to identify changes in gene expression in a congenital model of rodent hydrocephalus that are occurring locally in the area surrounding the cerebral aqueduct. Studies are now needed to examine these candidate genes and their cognate proteins to delineate their role in hydrocephalus.

Molecular Characterization and Functional Analysis of Annulate Lamellae Pore Complexes in Nuclear Transport in Mammalian Cells.

Annulate lamellae are cytoplasmic organelles containing stacked sheets of membranes embedded with pore complexes. These cytoplasmic pore complexes at annulate lamellae are morphologically similar to nuclear pore complexes at the nuclear envelope. Although annulate lamellae has been observed in nearly all types of cells, their biological functions are still largely unknown. Here we show that SUMO1-modification of the Ran GTPase-activating protein RanGAP1 not only target RanGAP1 to its known sites at nuclear pore complexes but also to annulate lamellae pore complexes through interactions with the Ran-binding protein RanBP2 and the SUMO-conjugating enzyme Ubc9 in mammalian cells. Furthermore, upregulation of annulate lamellae, which decreases the number of nuclear pore complexes and concurrently increases that of annulate lamellae pore complexes, causes a redistribution of nuclear transport receptors including importin α/ß and the exportin CRM1 from nuclear pore complexes to annulate lamellae pore complexes and also reduces the rates of nuclear import and export. Moreover, our results reveal that importin α/ß-mediated import complexes initially accumulate at annulate lamellae pore complexes upon the activation of nuclear import and subsequently disassociate for nuclear import through nuclear pore complexes in cells with upregulation of annulate lamellae. Lastly, CRM1-mediated export complexes are concentrated at both nuclear pore complexes and annulate lamellae pore complexes when the disassembly of these export complexes is inhibited by transient expression of a Ran GTPase mutant arrested in its GTP-bound form, suggesting that RanGAP1/RanBP2-activated RanGTP hydrolysis at these pore complexes is required for the dissociation of the export complexes. Hence, our findings provide a foundation for further investigation of how upregulation of annulate lamellae decreases the rates of nuclear transport and also for elucidation of the biological significance of the interaction between annulate lamellae pore complexes and nuclear transport complexes in mammalian cells.

Biodegradation of kerosene: Study of growth optimization and metabolic fate of P. janthinellum SDX7.

Penicillum janthinellum SDX7 was isolated from aged petroleum hydrocarbon-affected soil at the site of Anand, Gujarat, India, and was tested for different pH, temperature, agitation and concentrations for optimal growth of the isolate that was capable of degrading upto 95%, 63% and 58% of 1%, 3% and 5% kerosene, respectively, after a period of 16 days, at optimal growth conditions of pH 6.0, 30 °C and 180 rpm agitation. The GC/MS chromatograms revealed that then-alkane fractions are easily degraded; however, the rate might be lower for branched alkanes, n-alkylaromatics, cyclic alkanes and polynuclear aromatics. The test doses caused a concentration-dependent depletion of carbohydrates of P. janthinellum SDX7 by 3% to 80%, proteins by 4% to 81% and amino acids by 8% to 95% upto 16 days of treatment. The optimal concentration of 3% kerosene resulted in the least reduction of the metabolites of P. janthinellum such as carbohydrates, proteins and amino acids with optimal growth compared to 5% and 1% (v/v) kerosene doses on the 12(th) and 16(th) day of exposure. Phenols were found to be mounted by 43% to 66% at lower and higher concentrations during the experimental period. Fungal isolate P. janthinellum SDX7 was also tested for growth on various xenobiotic compounds.