Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes

Glucocorticoids are key regulators of glucose homeostasis and pancreatic islet function, but the gene regulatory programs driving responses to glucocorticoid signaling in islets and the contribution of these programs to diabetes risk are unknown. In this study we used ATAC-seq and RNA-seq to map chromatin accessibility and gene expression from eleven primary human islet samples cultured in vitro with the glucocorticoid dexamethasone at multiple doses and durations. We identified thousands of accessible chromatin sites and genes with significant changes in activity in response to glucocorticoids. Chromatin sites up-regulated in glucocorticoid signaling were prominently enriched for glucocorticoid receptor binding sites and up-regulated genes were enriched for ion transport and lipid metabolism, whereas down-regulated chromatin sites and genes were enriched for inflammatory, stress response and proliferative processes. Genetic variants associated with glucose levels and T2D risk were enriched in glucocorticoid-responsive chromatin sites, including fine-mapped variants at 51 known signals. Among fine-mapped variants in glucocorticoid-responsive chromatin, a likely casual variant at the 2p21 locus had glucocorticoid-dependent allelic effects on beta cell enhancer activity and affected SIX2 and SIX3 expression. Our results provide a comprehensive map of islet regulatory programs in response to glucocorticoids through which we uncover a role for islet glucocorticoid signaling in mediating genetic risk of T2D.     

Zebrafish as a Model to Assess the Teratogenic Potential of Nitrite

High nitrate levels in the environment may result in congenital defects or miscarriages in humans. Presumably, this is due to the conversion of nitrate to nitrite by gut and salivary bacteria. However, in other mammalian studies, high nitrite levels do not cause birth defects, although they can lead to poor reproductive outcomes. Thus, the teratogenic potential of nitrite is not clear. It would be useful to have a vertebrate model system to easily assess teratogenic effects of nitrite or any other chemical of interest. Here, we demonstrate the utility of zebrafish (Danio rerio) to screen compounds for toxicity and embryonic defects. Zebrafish embryos are fertilized externally and have rapid development, making them a good model for teratogenic studies. We show that increasing the time of exposure to nitrite negatively affects survival. Increasing the concentration of nitrite also adversely affects survival, whereas nitrate does not. For embryos that survive nitrite exposure, various defects can occur, including pericardial and yolk sac edema, swim bladder noninflation, and craniofacial malformation. Our results indicate that the zebrafish is a convenient system for studying the teratogenic potential of nitrite. This approach can easily be adapted to test other chemicals for their effects on early vertebrate development.     

Calsyntenins Mediate TGN Exit of APP in a Kinesin-1-Dependent Manner

Kinesin motors are required for the export of membranous cargo from the trans-Golgi network (TGN), yet information about how kinesins are recruited to forming transport intermediates is sparse. Here we show that the Kinesin-1 docking protein calsyntenin-1 localizes to the TGN in vivo and directly and specifically recruits Kinesin-1 to Golgi/TGN membranes as well as to dynamic post-Golgi carriers. Overexpression of various calsyntenin chimeras and kinesin light chain 1 (KLC1) at high levels caused the formation of aberrant membrane stacks at the endoplasmic reticulum (ER) or the Golgi, disrupted overall Golgi structure and blocked exit of calsyntenin from the TGN. Intriguingly, this blockade of calsyntenin exit strongly and selectively impeded TGN exit of amyloid precursor protein (APP). Using live cell microscopy we found that calsyntenins exit the TGN in Kinesin-1-decorated tubular structures which may serve as carriers for calsyntenin-1-mediated post-TGN transport of APP. Abrogation of this pathway via virus-mediated knockdown of calsyntenin-1 expression in primary cultured neurons caused a marked elevation of APP C-terminal fragments. Together, these results indicate a role for calsyntenin-1 in Kinesin-1-dependent TGN exit and post-Golgi transport of APP-containing organelles and further suggest that distinct intracellular routes may exhibit different capacities for proteolytic processing of APP.     

The suicide assessment scale: Psychometric properties of a Norwegian language version

ABSTRACT: BACKGROUND: Rating scales are valuable tools in suicide research and can also be useful supplements to the clinical interview in suicide risk assessments. This study describes the psychometric properties of a Norwegian language version of the Suicide Assessment Scale Self-report version (SUAS-S). METHODS: Participants were fifty-two patients (mean age = 39.3 years, SD = 10.7) with major depression (53.8%), bipolar disorder (25.0%) and/or a personality disorder (63.5%) referred to a psychiatric outpatient clinic. The SUAS-S, the screening section of the Beck Scale for Suicidal Ideation (BSS-5), the Beck Depression Inventory (BDI), Beck's Hopelessness Scale (BHS), the Symptom Check-List-90 R (SCL-90R) and the Clinical Global Impression for Severity of Suicidality (CGI-SS) were administered. One week later, the patients completed the SUAS-S a second time. RESULTS: Cronbach's alpha for SUAS-S was 0.88 and the test-retest reliability was 0.95 (95% CI: 0.93- 0.97). SUAS-S was positively correlated with the BSS-5 (r = 0.66; 95% CI: 0.47-0.85) for the study sample as a whole and for the suicidal (r = 0.52) and non-suicidal groups (r = 0.50) respectively. There was no difference between the SUAS-S and the BSS-5 in the ability to identify suicidality. This ability was more pronounced when the suicide risk was high. There was a substantial intercorrelation between the score on the SUAS-S and the BDI (0.81) and the BHS (0.76). The sensitivity and specificity of the SUAS-S was explored and an appropriate clinical cut-off value was assessed. CONCLUSIONS: The study revealed good internal consistency, test-retest reliability and concurrent validity for the Suicide Assessment Scale Self-report version. The discriminatory ability for suicidality was comparable to that of the BSS-5.     

H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle

Recent investigations into ferredoxin-dependent transhydrogenases, a class of enzymes responsible for electron transport, have highlighted the biological importance of flavin-based electron bifurcation (FBEB). FBEB generates biomolecules with very low reduction potential by coupling the oxidation of an electron donor with intermediate potential to the reduction of high and low potential molecules. Bifurcating systems can generate biomolecules with very low reduction potentials, such as reduced ferredoxin (Fd), from species such as NADPH. Metabolic systems that use bifurcation are more efficient and confer a competitive advantage for the organisms that harbor them. Structural models are now available for two NADH-dependent ferredoxin-NADP⁺ oxidoreductase (Nfn) complexes. These models, together with spectroscopic studies, have provided considerable insight into the catalytic process of FBEB. However, much about the mechanism and regulation of these multi-subunit proteins remains unclear. Using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and statistical coupling analysis (SCA), we identified specific pathways of communication within the model FBEB system, Nfn from Pyrococus furiosus, under conditions at each step of the catalytic cycle. HDX-MS revealed evidence for allosteric coupling across protein subunits upon nucleotide and ferredoxin binding. SCA uncovered a network of co-evolving residues that can provide connectivity across the complex. Together, the HDX-MS and SCA data show that protein allostery occurs across the ensemble of iron?sulfur cofactors and ligand binding sites using specific pathways that connect domains allowing them to function as dynamically coordinated units.     

Sensitivity to the two‐peptide bacteriocin lactococcin G is dependent on UppP,an enzyme involved in cell‐wall synthesis

Most bacterially produced antimicrobial peptides (bacteriocins) are thought to kill target cells by a receptor‐mediated mechanism. However, for most bacteriocins the receptor is unknown. For instance, no target receptor has been identified for the two‐peptide bacteriocins (class IIb), whose activity requires the combined action of two individual peptides. To identify the receptor for the class IIb bacteriocin lactococcin G, which targets strains of Lactococcus lactis, we generated 12 lactococcin G‐resistant mutants and performed whole‐genome sequencing to identify mutations causing the resistant phenotype. Remarkably, all had a mutation in or near the gene uppP (bacA), encoding an undecaprenyl pyrophosphate phosphatase; a membrane protein involved in peptidoglycan synthesis. Nine mutants had stop codons or frameshifts in the uppP gene, two had point mutations in putative regulatory regions and one caused an amino acid substitution in UppP. To verify the receptor function of UppP, it was shown that growth of non‐sensitive Streptococcus pneumoniae could be inhibited by lactococcin G when L. lactis uppP was expressed in this bacterium. Furthermore, we show that the related class IIb bacteriocin enterocin 1071 also uses UppP as receptor. The approach used here should be broadly applicable to identify receptors for other bacteriocins as well.     

Chemical Composition,Antimicrobial, Nitric Oxide Inhibition and Cytotoxic Activity of Essential Oils from Zanthoxylum acanthopodium DC. Leaves and Stems from Vietnam

This study was aimed to investigate the chemical composition and biological activities of leaf and stem essential oils of Zanthoxylum acanthopodium DC. from Vietnam. Their chemical composition was analyzed by GC/MS. Antimicrobial activities were evaluated by microdilution broth assay. Anti-inflammatory activity was evaluated by the ability to inhibit nitric oxide production in macrophage cells. Cytotoxic activity was evaluated using the sulforhodamine B assay on three human cancer cell lines. Forty-four compounds were identified in the leaf oil, among which dehydroaromadendrane (23.4 %), (E)-carpacin (17.6 %), 2-tridecanone (12.2 %), and 9-methyl-2-decanone (11.8 %) were the most abundant. The stem oil contained fifty-five identified constituents, mainly γ-gurjunene (51.1 %) and butyl acetate (11.8 %). Both oils exhibited inhibitory effects on three bacterial strains, namely S. aureus, E. coli, P. aeruginosa and a fungal strain C. albican, while showed insignificant effects on B. subtilis, L. fermentum, and S. enterica. Both oils showed weak NO production inhibition in LPS-induced RAW264.7 cells, but exhibited potent cytotoxic activity against all three tested cell lines SK-LU-1, MCF-7, and HepG2 with the IC₅₀ values ranging from 16.03±0.77 to 35.60±1.62 μg/mL. This is the first report on the antimicrobial, anti-inflammatory and cytotoxic activities of essential oils from the leaves and stems of Z. acanthopodium.     

Methods for rapid prototyping novel labware: using CAD and desktop 3D printing in the microbiology laboratory

Although the microbiology laboratory paradigm has increasingly changed from manual to automated procedures, and from functional to molecular methods, traditional culture methods remain vital. Using inexpensive desktop fused filament fabrication 3D printing, we designed, produced and tested rapid prototypes of customised labware for microbial culture namely frames to make dip slides, inoculation loops, multi-pin replicators, and multi-well culture plates for solid medium. These customised components were used to plate out samples onto solid media in various formats, and we illustrate how they can be suitable for many microbiological methods such as minimum inhibitory concentration tests, or for directly detecting pathogens from mastitis samples, illustrating the flexibility of rapid-prototyped culture consumable parts for streamlining microbiological methods. We describe the methodology needed for microbiologists to develop their own novel and unique tools, or to fabricate and customise existing consumables. A workflow is presented for designing and 3D printing labware and quickly producing easy-to-sterilise and re-useable plastic parts of great utility in the microbiology laboratory.