Isolation and Characterization of Thermophilic Bacteria from Gavmesh Goli Hot Spring in Sabalan Geothermal Field,Iran: Thermomonas hydrothermalis and Bacillus altitudinis Isolates as a Potential Source of Thermostable Protease

Abstract

Thermophilic bacteria have attracted great attention due to their ability to produce thermostable enzymes. The aim of this study was the isolation and characterization of thermophilic bacteria from Gavmesh Goli hot spring in Sareyn, North West of Iran. Of 10 water samples collected, 36 thermophilic bacteria were obtained. The thermophilic bacteria were tested for their ability to produce hydrolase enzymes. All the isolates were potentially protease producers. Lipase, DNase, and amylase activities were confirmed in 34 (94.4%), 8 (22.2%), and 3 (8.3%) isolates, respectively. Five isolates with higher levels of enzyme activity were selected for further studies. Morphological, biochemical, and molecular analysis by 16S rRNA gene sequencing revealed that four isolates (DH15, DH16, DH20, and DH29) could be identified as Thermomonas hydrothermalis and one (PA10) Bacillus altitudinis. The protease produced by these isolates was optimally active at 50–55?°C, pH 8–8.5, and 0–0.5?M NaCl. In this first time study, we isolated T. hydrothermalis and B. altitudinis from Iranian hot springs and demonstrated the characteristics of T. hydrothermalis protease. Accordingly, due to the valuable potential of these bacteria such as the production of protease with high temperature and pH stability, these isolates can be introduced as promising candidates for industrial applications.     

Sensitivity Analysis of U.S. EPA's Estimates of Skin Cancer Risk from Inorganic Arsenic in Drinking Water

The current U.S. Environmental Protection Agency's (USEPA's) risk analysis on the Integrated Risk Information System (IRIS) for arsenic in drinking water is based on an epidemiological study of skin cancer in Taiwan. Assumptions used in the USEPA application of the multistage-Weibull model for risk estimation were varied to assess the effect on predicted risk of skin cancer to the U.S. population at arsenic concentrations of 1 to 50?µg/L in drinking water. Among the assumptions tested, the only notable change in risk estimates was a reduction when the arsenic concentration used as representative for Taiwan villages in the low range (<300?µg/L) was increased to the 75th percentile (245?µg/L) in place of the mean used in the USEPA analysis (170?µg/L), but the representative value for Taiwan villages in the high range (≥600?µg/L) was not increased simultaneously to the 75th percentile. Additionally, a simulation study was conducted using records of arsenic measurements in wells from the same period and region of Taiwan as the original study. The exposure-response curve estimated from 60 villages (60 data points) differed only marginally from the outcome when data were summarized into four data points (as in the USEPA skin cancer analysis). Briefly discussed are differences between the study area of Taiwan and the U.S. in nutritional status and consumption of inorganic arsenic in food that might bias predicted U.S. skin cancer risks.     

Comparison of Metagenomic DNA Extraction Methods for Soil Sediments of High Elevation Puga Hot Spring in Ladakh,India to Explore Bacterial Diversity

Extraction of good-quality metagenomic DNA from extreme environments is quite challenging, particularly from high elevation hot spring sediments. Low microbial load, high humic acid content and other contaminants complicate the process of extraction of metagenomic DNA from hot spring sediments. In the present study, efficacy of five manual DNA extraction protocols with modifications has been evaluated for metagenomic DNA extraction from boron–sulfur rich high elevation Puga hot spring sediments. Best suited protocol was identified based on the cell lysis efficiency, DNA yield, humic acid content, PCR reproducibility and representation of bacterial diversity. Quantity as well as quality of crude metagenomic DNA differed remarkably between various protocols used and were not pure enough to give PCR amplification using 16S rRNA bacterial and archaeal primers. Crude metagenomic DNA extracted using five different DNA extraction protocols was purified using spin column based purification method. Even after purification, only three protocols C, D and E yielded metagenomic DNA that could be amplified using both archaeal and bacterial primers. To evaluate the degree of microbial diversity represented by protocols C, D and E, phylogenetic genes amplified were subjected to amplified ribosomal DNA restriction analysis (ARDRA) and denaturing gradient gel electrophoresis analysis (DGGE) analysis. ARDRA banding pattern of amplicons generated for all the three extraction protocols, i.e., C, D and E were found to be similar. DGGE of protocol E derived amplicons resulted in the similar number of dominant bands but a greater number of non-dominant bands, i.e., the highest microbial diversity in comparison to protocols C and D, respectively. In the present study, protocol E developed from Yeates et al. protocol has been found to be best in terms of DNA yield, DNA purity and bacterial diversity depiction associated with boron–sulfur rich sediment of high elevation hot springs.     

Archaeal Community Revealed by 16s rRNA and Fluorescence in situ Hybridization in a Sulphuric Hydrothermal Hot Spring, Northern Taiwan

Summary The archaeal community composition of Yangmingshan National Park in northern Taiwan was investigated by 16S rRNA and fluorescence in situ hybridization (FISH). Optimization of tetrameric restriction enzyme (TRE) was performed to achieve efficient digestion and differentiation in the restriction fragment length polymorphism (RFLP) fragments, and AciI, BstUI and RsaI were shown to be the optimal TREs for TRE-RFLP. Nine clones were obtained in the studies, with clones M70 and M6 being found to be phylogenetically affiliated to Sulfolobus and Caldisphaera in domain Crenarchaeota, respectively, whereas seven other clones were found to be affiliated to an uncultured and unidentified archaeon isolated from thermoacidic environments. In FISH, soil and water region cells were hybridized with DAPI (4′, 6-diamidino-2-phenylindole) and specific fluorescently labelled probes. 15.69 and 7.16% of the DAPI-stained cells hybridized with universal archaeal probe ARC915 and sulphate-reducing bacterial probe SRB385, respectively.     

Neighborhood Deprivation and Risk of Cancer Incidence,Mortality and Survival: Results from a Population-Based Cohort Study in Japan

Background

In many developed countries, socioeconomic status is associated with cancer incidence and survival. However, research in Japan is sparse. We examined the association between neighborhood deprivation based on the Japanese Deprivation Index and the risk of incidence, mortality and survival from total and major cancers in the Japan Public Health Center-based Prospective Study.

Methods

86,112 participants were followed through the end of 2009. A total of 10,416 incident cases and 5,510 deaths from cancer were identified among 1,348,437 person-years of follow-up (mean follow-up: 15.7 years). The Japanese deprivation index was used to access neighborhood deprivation. Hazard ratios and 95% confidence intervals were calculated by Cox regression analysis.

Results

We found no associations between neighborhood deprivation index and the incidence of total and major cancers. In some cancer risks or deaths, however, we found positive or inverse associations with a higher deprivation index, such as a decreased risk of colorectal cancer incidence and an increased risk of liver cancer incidence and deaths in women.

Conclusion

Although some positive or inverse associations were detected for specific sites, the neighborhood deprivation index has no substantial overall association with the risk of incidence, mortality and survival from cancer in the Japanese population.     

Life in Hot Spring Microbial Mats Located in the Trans-Mexican Volcanic Belt: A 16S/18S rRNA Gene and Metagenomic Analysis

The geothermal system of the Araró region, located in the Trans-Mexican Volcanic Belt of México, hosts various hot springs with unique physicochemical characteristics, including temperatures ranging from 45°C to 78°C. The microbial diversity in these hot springs has been explored only by culture-dependent surveys. In this study, we performed metagenomic Illumina MiSeq, and 16S and 18S rRNA pyrosequencing analysis of the microbial life are residing in the microbial mats of the springs called “Tina–Bonita”. Our results show the presence of 186 operational taxonomic units, 99.7% of which belong to bacteria, 0.27% to eukaryotes, and 0.03% to archaea. The most abundant bacterial divisions are the Proteobacteria, Chloroflexi, and Cyanobacteria, which include 105 genera. The ecological indexes indicate that the microbial mats have moderate microbial diversity. An abundant group of genes that participate in photosynthesis, including photosynthetic electron transport, as well as photosystems I and II, were detected. Another cluster of genes was found that participates in sulfur, nitrogen, and methane metabolism. Finally, this phylogenetic and metagenomic analysis revealed an unexpected taxonomic and genetic diversity, expanding our knowledge of microbial life under specific extreme conditions.     

Processes Forming Daily Lamination in a Microbe-Rich Travertine Under Low Flow Condition at the Nagano-yu Hot Spring,Southwestern Japan

A daily rhythm of microbial processes, in terms of sub-mm order lamination, was identified for a microbe-rich aragonite travertine formed at a low-flow site of the Nagano-yu Hot Spring in Southwestern Japan. Continuous observation and sampling clearly showed that the lamination consisted of diurnal microbe-rich layers (M-layers) and nocturnal crystalline layers (C-layers). The M-layers originated from biofilm formed by growth and upward migration of filamentous cyanobacteria related to Microcoleus sp., which can rapidly glide and secrete extracellular polymeric substances (EPS). During the daytime, cyanobacterial biofilm development inhibited aragonite precipitation on the travertine surface due to the calcium-binding ability of EPS. After sunset, aragonite precipitation started on the surface where aerobic heterotrophic bacteria decomposed EPS, which induced precipitation of micritic crystals. This early stage of C-layer formation was followed by abiotic precipitation of fan-shaped aragonite aggregates. Despite their major role in lamina formation, the cyanobacteria were readily degraded within 6–10 days after embedding, and the remaining open spaces in the M-layers were sparsely filled with crystal clots. These lamina-forming processes were different from those observed in a high-flow site where the travertine has a dense texture of aragonite crystals. The microbial travertine at Nagano-yu is similar to some Precambrian stromatolites in terms of in situ mineral precipitation, regular sub-mm order lamination, and arrangement of filamentous microbes; therefore, the lamination of these stromatolites possibly occur with a daily rhythm. The microbial processes demonstrated in this study may revise the interpretation of ancient stromatolite formation.     

Interaction Biases in Two-Period Crossover Studies: A Modified Analysis to Test with More Sensitivity

The two-period crossover trial is considered the most powerful means of determining the efficacy of new drugs. However, this study design is frequently invalidated by treatment-by-period interaction. If, for example, the effect of the first treatment period carries on into the next one, then it influences the response to the latter period (carryover effect). A second problem is, that the standard approach (Hills-Armitage analysis) for interaction bias has a low statistical sensitivity. The author recently described an alternative method entitled the clinical approach because it looks at the clinical performance of the separate treatment groups and not, as the standard approach, at the means of the groups. It may be hypothesized that this alternative approach is statistically more sensitive than the standard in situations where there is interaction in just one of the treatment groups. The present study uses two examples and a mathematical model. It shows that in case of single-group interaction the clinical approach can, indeed, detect carryover effect at a 30% lower level than the standard. On the other hand, however, the standard approach does so even at a 40% lower level than the clinical in case of two-group interaction. I conclude that one approach supplements the other and that they be used in future studies simultaneously.     

Mitochondrial Common Deletion,a Potential Biomarker for Cancer Occurrence,Is Selected against in Cancer Background: A Meta-Analysis of 38 Studies

Mitochondrial dysfunction has been long proposed to play a major role in tumorigenesis. Mitochondrial DNA (mtDNA) mutations, especially the mtDNA 4,977 bp deletion has been found in patients of various types of cancer. In order to comprehend the mtDNA 4,977 bp deletion status in various cancer types, we performed a meta-analysis composed of 33 publications, in which a total of 1613 cancer cases, 1516 adjacent normals and 638 healthy controls were included. When all studies were pooled, we found that cancerous tissue carried a lower mtDNA 4,977 bp deletion frequency than adjacent non-cancerous tissue (OR = 0.43, 95% CI = 0.20–0.92, P = 0.03 for heterogeneity test, I² = 91.5%) among various types of cancer. In the stratified analysis by cancer type the deletion frequency was even lower in tumor tissue than in adjacent normal tissue of breast cancer (OR = 0.19, 95% CI = 0.06–0.61, P = 0.005 for heterogeneity test, I² = 82.7%). Interestingly, this observation became more significant in the stratified studies with larger sample sizes (OR = 0.70, 95% CI = 0.58–0.86, P = 0.0005 for heterogeneity test, I² = 95.1%). Furthermore, when compared with the normal tissue from the matched healthy controls, increased deletion frequencies were observed in both adjacent non-cancerous tissue (OR = 3.02, 95% CI = 2.13–4.28, P<0.00001 for heterogeneity test, I² = 53.7%), and cancerous tissue (OR = 1.36, 95% CI = 1.04–1.77, P = 0.02 for heterogeneity test, I² = 83.5%). This meta-analysis suggests that the mtDNA 4,977 bp deletion is often found in cancerous tissue and thus has the potential to be a biomarker for cancer occurrence in the tissue, but at the same time being selected against in various types of carcinoma tissues. Larger and better-designed studies are still warranted to confirm these findings.     

Focus: A Multifaceted Battle Against Cancer: Approaches to Identifying Synthetic Lethal Interactions in Cancer

Targeting synthetic lethal interactions is a promising new therapeutic approach to exploit specific changes that occur within cancer cells. Multiple approaches to investigate these interactions have been developed and successfully implemented, including chemical, siRNA, shRNA, and CRISPR library screens. Genome-wide computational approaches, such as DAISY, also have been successful in predicting synthetic lethal interactions from both cancer cell lines and patient samples. Each approach has its advantages and disadvantages that need to be considered depending on the cancer type and its molecular alterations. This review discusses these approaches and examines case studies that highlight their use.     

Natural CO2 springs in Italy: a resource for examining long-term response of vegetation to rising atmospheric CO2 concentrations

It is estimated that more than 100 geothermal CO₂ springs exist in central-western Italy. Eight springs were selected in which the atmospheric CO₂ concentrations were consistently observed to be above the current atmospheric average of 354μmol mol^-1. CO₂ concentration measurements at some of the springs are reported. The springs are described, and their major topographic and vegetational features are reported. Preliminary observations made on natural vegetation growing around the gas vents are then illustrated. An azonal pattern of vegetation distribution occurs around every CO₂ spring regardless of soil type and phytoclimatic areas. This is composed of pioneer populations of a Northern Eurasiatic species (Agrostis canina L.) which is often associated with Scirpus lacustris L. The potential of these sites for studying the long-term response of vegetation to rising atmospheric CO₂ concentrations is discussed.     

Cancer and Non-Cancer Risk Assessment from Exposure to Arsenic,Copper, and Cadmium in Borehole,Tap, and Surface Water in the Obuasi Municipality,Ghana

Cancer and non-cancer risk assessment from exposure to As, Cd, and Cu by resident adults and children from different water sources in Obuasi Municipality, Ghana, were measured in this study in accordance with the U.S. Environmental Protection Agency's (USEPA's) Human Health Risk Assessment guidelines. The results of cancer health risk for resident adults in Obuasi exposed to As in their tap water for both Central Tendency Exposure (CTE) and Reasonable Maximum Exposure (RME) parameters, respectively, are 6.6 × 10^?4 and 5.5 × 10^?6. For resident children in Odumasi, we obtained 4.7 × 10^?1 (CTE) and 6.7 × 10^?1 (RME). The results of the study obtained in most cases were found to exceed the USEPA's acceptable cancer risk range of 1 × 10^?6 to 1 × 10^?4 (i.e., 1 case of cancer out of 1,000,000 people to 1 case of cancer out of 10,000 people). Similarly, the results of the non-cancer human health risk for both resident adults and children were also found in most cases to be greater than the USEPA's acceptable non-cancer human health hazard index of 1.     

Arsenic in drinking water: sources,occurrence and health effects (a review)

Because dramatic cases of arsenic contamination of water resources, soils, vegetables, humans and animals increase, this review has focussed on the fate and behaviour of this element and what kind of health impacts are related with its release in surface or ground waters. In a first part, we point out how the primary minerals can lead to As mobilization and exportation by surface waters and suspended matter. We also emphasize the particular key role for As retention through both adsorption onto natural Fe(III) (hydr)oxides, Mn oxides and/or precipitation as Fe(III) arsenates. Nowadays, numerous and efficient systems for arsenic removal from any natural resources are available to produce good quality drinking water (with <10 μg/l As); however it is not within the scope of the present review. In a second part we focus on recent knowledge about the human toxicity of the various arsenic species. Chronic exposure to As in drinking water lead to many health diseases and, although the mechanisms of toxification/detoxification are not well identified, the role of methylated species is discussed. Some epidemiologic studies are cited, but the exact relationship between past chronic As exposure and present health diseases has been questioned.     

"Kissing a Baby Is Not at All Good for Him": Infant Mortality, Medicine, and Colonial Modernity in the U.S.-Occupied Philippines

Feminist scholars have begun to consider the ways indigenous practices of child rearing were and are challenged in (post)colonial discourse and practice, and how these practices have become a terrain on which definitions of nation, state, and economy are contested. In this article, I adopt a historical anthropological approach to consider how Filipino child-rearing strategies were described and stigmatized in educational, public health, and public welfare discourses in the U.S.-occupied Philippines in the early 20th century. I demonstrate how public health practices and discourses that were generated as part of a "benevolent" campaign against high rates of infant mortality were strategically used as a weapon against Filipino arguments for independence. I also consider how discourses constructing Filipino caregivers as overly indulgent were linked to metropolitan concerns about production of the "new industrial man" and were used to develop a racialized critique of the cultural practices of Filipinos.     

A close call: the role of screening mammography in the fight against breast cancer: health and medicine for women: a multidisciplinary, evidence-based review of mid-life health concerns

A multidisciplinary panel debated the role of screening mammography in fighting breast cancer during the Health and Medicine for Women continuing medical education (CME) conference at Yale Medical School in September 2010. Different guidelines from professional societies have presented conflicting recommendations for patients regarding both the benefits of mammography and the appropriate age and frequency of screening. In addition, a recent longitudinal study argues that screening mammography may only offer a modest benefit in terms of reducing cancer mortality. In light of these considerations, the panel debated whether mammography should be an informed decision that must be discussed and individualized for each patient based on the context of risk factors such as family history, age, and genetic dispositions.     

A practical protocol to assess impacts of unplanned disturbance: a case study in Tuggerah Lakes Estuary,NSW

Summary Environmental managers are often confronted with unplanned or accidental disturbances that may lead to environmental impacts. Procedures for detecting or measuring the size of such impacts are complicated because of the lack of data available before the disturbance and because of the intrinsic variability of most natural measures. Here, a protocol for detecting impacts is illustrated for single‐measure variables (numbers of individual species) and multivariate measures (relative abundances of invertebrates in assemblages). The present paper describes a case concerning drainage of acidified water into an estuary due to construction of a drainage channel in an area of wetland for which there had been no prior investigations (i.e. no ‘before’ data). The spatial extent of any impact was also unknowable. Sampling was, therefore, designed to allow for impacts of only a few tens of metres (using control sites 50 m from the mouth of the channel) and impacts covering much larger areas (500 m and 1 km from the mouth of the channel). Invertebrates in the mud around the channel and in control sites were sampled in replicated cores and the amount of seagrass in each core was weighed. Average abundances of invertebrate animals and weights of seagrass were compared, as was variation among samples in potentially impacted and control sites (using univariate analyses of variance). Sets of species were compared using multivariate methods to test the hypothesis that there was an impact at one of the scales examined. In fact, there was no evidence for any sort of impact on the fauna or seagrasses; the disturbance was a short‐term pulse without any obvious or sustained ecological response. One consequence of the study was that the local council was able to demonstrate no impact requiring remediation and no penalties were imposed for the unapproved construction of the channel. The implications of this type of study after an environmental disturbance are discussed. The present study identifies the need for clear definition of relevant hypotheses, coupled with rigorous planning of sampling and analyses, so that reliable answers are available to regulators and managers.