Genome-Wide Functional Profiling Identifies Genes and Processes Important for Zinc-Limited Growth of Saccharomyces cerevisiae

Zinc is an essential nutrient because it is a required cofactor for many enzymes and transcription factors. To discover genes and processes in yeast that are required for growth when zinc is limiting, we used genome-wide functional profiling. Mixed pools of ∼4,600 deletion mutants were inoculated into zinc-replete and zinc-limiting media. These cells were grown for several generations, and the prevalence of each mutant in the pool was then determined by microarray analysis. As a result, we identified more than 400 different genes required for optimal growth under zinc-limiting conditions. Among these were several targets of the Zap1 zinc-responsive transcription factor. Their importance is consistent with their up-regulation by Zap1 in low zinc. We also identified genes that implicate Zap1-independent processes as important. These include endoplasmic reticulum function, oxidative stress resistance, vesicular trafficking, peroxisome biogenesis, and chromatin modification. Our studies also indicated the critical role of macroautophagy in low zinc growth. Finally, as a result of our analysis, we discovered a previously unknown role for the ICE2 gene in maintaining ER zinc homeostasis. Thus, functional profiling has provided many new insights into genes and processes that are needed for cells to thrive under the stress of zinc deficiency

Direct gene delivery to synovium. An evaluation of potential vectors in vitro and in vivo.

OBJECTIVE: To assess the abilities of various vectors to transfer genes to the synovial lining of joints. METHODS: Vectors derived from retrovirus, adenovirus, and herpes simplex virus as well as cationic liposomes and naked plasmid DNA were evaluated. Each construct contained the lac Z marker gene; and one retroviral construct, and one plasmid also contained a gene encoding human interleukin-1 receptor antagonist. Gene expression was under the control of the human cytomegalovirus promoter in all vectors except the retrovirus, where the endogenous 5' long terminal repeat was retained as the promoter. Cultures of rabbit synovial fibroblasts were exposed to these vectors and stained with X-gal to identify lac Z+ cells. Vectors were then injected directly into rabbits' knee joints, and gene transfer and expression were assessed by X-gal staining and polymerase chain reaction (PCR). RESULTS: Adenovirus was a highly effective vector both in vitro and in vivo, with lac Z gene expression persisting for at least 28 days. However, an inflammatory response was noted in vivo. Cells infected in vitro and in vivo with herpes simplex virus also expressed the lac Z gene at high levels, but expression was limited by cytotoxicity. Retroviruses, in contrast, were effective only under in vitro conditions, permitting cell division. Liposomes gave variable in vitro results; when injected into joints in vivo, gene expression was low and was detectable for only a few days, even though a PCR signal persisted for at least 28 days. Unexpectedly, plasmid DNA was captured by the synoviocytes and expressed transiently following intraarticular injection. CONCLUSION: None of the vectors was ideal for in vivo gene delivery to synovium, although adenovirus was clearly the most effective of those tested. Retroviruses, although poor vectors for in vivo gene delivery, are well suited for ex vivo gene transfer to the synovial lining of joints

The role of probiotic bacteria in managing periodontal disease: a systematic review

The frequent recolonization of treated sites by periodontopathogens and the emergence of antibiotic resistance have led to a call for new therapeutic approaches for managing periodontal diseases. As probiotics are considered a new tool for combating infectious diseases, we systematically reviewed the evidences for their effectiveness in the management of periodontitis.An electronic search was performed in the MEDLINE, SCOPUS and Cochrane Library databases up to March 2016 using the terms 'periodontitis', 'chronic periodontitis', 'probiotic(s)', 'prebiotic(s)', 'symbiotic(s)', 'Bifidobacterium and 'Lactobacillus'. Only randomized controlled trials (RCTs) were included in the present study. Analysis of 12 RCTs revealed that in general, oral administration of probiotics improved the recognized clinical signs of chronic and aggressive periodontitis such as probing pocket depth, bleeding on probing, and attachment loss, with a concomitant reduction in the levels of major periodontal pathogens. Continuous probiotic administration, laced mainly with Lactobacillus species, was necessary to maintain these benefits. Expert commentary: Oral administration of probiotics is a safe and effective adjunct to conventional mechanical treatment (scaling) in the management of periodontitis, specially the chronic disease entity. Their adjunctive use is likely to improve disease indices and reduce the need for antibiotics

Elevated levels of whole blood nickel in a group of Sri Lankan women with endometriosis: a case control study

<p>Abstract</p> <p>Background</p> <p>Endometriosis is characterized by the persistence of endometrial tissue in ectopic sites outside the uterine cavity. Presence of nickel, cadmium and lead in ectopic endometrial tissue has been reported previously. While any association between blood levels of nickel and endometriosis is yet to be described in literature, conflicting reports are available with regards to cadmium and lead levels in blood and urine.</p> <p>Findings</p> <p>In fifty patients with endometriosis and fifty age-matched controls confirmed by laparoscopy or laparotomy, whole blood samples were collected and digested using supra pure 65% HNO₃. Whole blood levels of nickel and lead were measured using Total Reflection X-ray Fluorescence (TXRF) while cadmium levels were evaluated using graphite furnace atomic absorption spectroscopy (GFASS). Women with endometriosis had significantly higher (<it>P</it>=0^.016) geometric mean (95% CI) whole blood nickel levels [2.6(1.9-3.3) μg/L] as compared to women without endometriosis [0.8 (0.7-0.9) μg/L]. Whole blood levels of cadmium and lead were similar between the two groups.</p> <p>Conclusions</p> <p>Although women with endometriosis in this study population had higher levels of nickel in whole blood compared to controls, whether nickel could be considered as an aetiological factor in endometriosis remains inconclusive in view of the smaller sample that was evaluated.</p

Dynamic Coupling of Near-Field and Far-Field Models

Deepwater spills pose a unique challenge for reliable predictions of oil transport and fate, since live oil spewing under very high hydrostatic pressure has characteristics remarkably distinct from oil spilling in shallow water. It is thus important to describe in detail the complex thermodynamic processes occurring in the near-field, meters above the wellhead, and the hydrodynamic processes in the far-field, up to kilometers away. However, these processes are typically modeled separately since they occur at different scales. Here we directly couple two oil prediction applications developed during the Deepwater Horizon blowout operating at different scales: the near-field Texas A&M Oilspill Calculator (TAMOC) and the far-field oil application of the Connectivity Modeling System (oil-CMS). To achieve this coupling, new oil-CMS modules were developed to read TAMOC output, which consists of the description of distinct oil droplet “types,” each of specific size and pseudo-component mixture that enters at a given mass flow rate, time, and position into the far field. These variables are transformed for use in the individual-based framework of CMS, where each droplet type fits into a droplet size distribution (DSD). Here we used 19 pseudo-components representing a large range of hydrocarbon compounds and their respective thermodynamic properties. Simulation results show that the dispersion pathway of the different droplet types varies significantly. Indeed, some droplet types remain suspended in the subsea over months, while others accumulate in the surface layers. In addition, the decay rate of oil pseudo-components significantly alters the dispersion, denoting the importance of more biodegradation and dissolution studies of chemically and naturally dispersed live oil at high pressure. This new modeling tool shows the potential for improved accuracy in predictions of oil partition in the water column and of advancing impact assessment and response during a deepwater spill