In silico analyses of the genomes of three new bacteriocin-producing bacteria isolated from animal’s faeces

Archives of Microbiology - Here, we have analysed and explored the genome sequences of three newly isolated bacteria that were recently characterised for their probiotic activities and ability to...     

High-resolution genome-wide analysis of irradiated (UV and γ-rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events

In diploid eukaryotes, repair of double-stranded DNA breaks by homologous recombination often leads to loss of heterozygosity (LOH). Most previous studies of mitotic recombination in Saccharomyces cerevisiae have focused on a single chromosome or a single region of one chromosome at which LOH events can be selected. In this study, we used two techniques (single-nucleotide polymorphism microarrays and high-throughput DNA sequencing) to examine genome-wide LOH in a diploid yeast strain at a resolution averaging 1 kb. We examined both selected LOH events on chromosome V and unselected events throughout the genome in untreated cells and in cells treated with either γ-radiation or ultraviolet (UV) radiation. Our analysis shows the following: (1) spontaneous and damage-induced mitotic gene conversion tracts are more than three times larger than meiotic conversion tracts, and conversion tracts associated with crossovers are usually longer and more complex than those unassociated with crossovers; (2) most of the crossovers and conversions reflect the repair of two sister chromatids broken at the same position; and (3) both UV and γ-radiation efficiently induce LOH at doses of radiation that cause no significant loss of viability. Using high-throughput DNA sequencing, we also detected new mutations induced by γ-rays and UV. To our knowledge, our study represents the first high-resolution genome-wide analysis of DNA damage-induced LOH events performed in any eukaryote.     

Ichthyofauna of the upper Tom’ affected by thermal pollution (West Siberia)

The paper gives comparative analysis of the species composition of fish in the upper Tom’ from the zone of discharge of warm water of electrical power station and background parts of the riverbed. The areas subjected to thermal pollution feature an increase in the number and biomass of introduced species: the share of invaders makes up 19% of the total ichthyomass, 41% of the total number, and 25% of the species diversity of fish. Fish productivity of the mountain taiga part of the upper Tom’ with the increased water temperature exceeds this value of the main riverbed 2–4 times and correlates with the level of productivity of the plain rivers in the south of West Siberia, which is related to eutrophication.     

Innate Immunity and Non-Hodgkin’s Lymphoma (NHL) Related Genes in a Nested Case-Control Study for Gastric Cancer Risk

Objective

Genetic variants regulating the host immune system may contribute to the susceptibility for the development of gastric cancer. Little is known about the role of the innate immunity- and non-Hodgkin’s lymphoma (NHL)-related genes for gastric cancer risk. This nested case-control study was conducted to identify candidate genes for gastric cancer risk for future studies.

Methods

In the Discovery phase, 3,072 SNPs in 203 innate immunity- and 264 NHL-related genes using the Illumine GoldenGateTM OPA Panel were analyzed in 42 matched case-control sets selected from the Korean Multi-center Cancer Cohort (KMCC). Six significant SNPs in four innate immunity (DEFA6, DEFB1, JAK3, and ACAA1) and 11 SNPs in nine NHL-related genes (INSL3, CHMP7, BCL2L11, TNFRSF8, RAD50, CASP7, CHUK, CD79B, and CLDN9) with a permutated p-value <0.01 were re-genotyped in the Replication phase among 386 cases and 348 controls. Odds ratios (ORs) for gastric cancer risk were estimated adjusting for age, smoking status, and H. pylori and CagA sero-positivity. Summarized ORs in the total study population (428 cases and 390 controls) are presented using pooled- and meta-analyses.

Results

Four SNPs had no heterogeneity across the phases: in the meta-analysis, DEFA6 rs13275170 and DEFB1 rs2738169 had both a 1.3-fold increased odds ratio (OR) for gastric cancer (95% CIs = 1.1–1.6; and 1.1–1.5, respectively). INSL3 rs10421916 and rs11088680 had both a 0.8-fold decreased OR for gastric cancer (95% CIs = 0.7–0.97; and 0.7–0.9, respectively).

Conclusions

Our findings suggest that certain variants in the innate immunity and NHL-related genes affect the gastric cancer risk, perhaps by modulating infection-inflammation-immunity mechanisms that remain to be defined.     

Valuation of the loss of plant-related ecosystem services caused by water stress in the wetland of China’s Yellow River Delta

China’s Yellow River Delta is ecologically important because of its role as an eco-tone between terrestrial and aquatic ecosystems. However, water stress caused by drought or flooding creates ecological risks for this important ecosystem. In this study, we assessed community biodiversity, plant biomass, and the plant total nitrogen, total phosphorus, and potassium contents to quantify the potential loss of ecosystem services value arising from water stress. The annual ecosystem services and function value of the wetlands totaled 3.68 × 10⁸ Yuan, of which biomass production and local climate regulation accounted for 39.4% and 49.5% of the total, respectively. The area with the highest value (>2 Yuan m⁻²) lies along both banks of the downstream reaches of the river, whereas areas with the lowest values (<1.5 Yuan m⁻²) were located on the northern bank, near the Bohai Sea coastline. We defined scenarios based on three levels of water stress: drought, sufficient water, and flooding. The potential annual value loss in the drought scenario was 3.60 × 10⁸ Yuan, versus 2.78 × 10⁸ Yuan in the flooding scenario. The minimum loss (with sufficient water) was 2.06 × 10⁸ Yuan. The wetland’s soil water content should therefore be managed to protect the vegetation and minimize the ecological risks (and associated ecosystem service value losses) caused by water stress. Our approach provides a tool for assessing the potential loss of ecosystem services and functions and for calculating ecological compensation payments for wetland damage.     

Lymphotoxin Alpha (LTA) Polymorphism Is Associated with Prognosis of Non-Hodgkin’s Lymphoma in a Chinese Population

Background

Non-Hodgkin’s lymphoma (NHL) has been widely reported to be associated with autoimmune and pro-inflammatory response, and genetic polymorphisms of candidate genes involved in autoimmune and pro-inflammatory response may influence the survival and prognosis of NHL patients. To evaluate the role of such genetic variations in prognosis of NHL, we conducted this study in a Chinese population.

Methods

We used the TaqMan assay to genotype six single nucleotide polymorphisms (SNPs) (TNF rs1799964T>C, LTA rs1800683G>A, IL-10 rs1800872T>G, LEP rs2167270G>A, LEPR rs1327118C>G, TNFAIP8 rs1045241C>T) for 215 NHL cases. Kaplan-Meier analysis was performed to compare progression free survival among two common genotypes. Cox proportional hazard models were used to identify independent risk factors.

Results

We observed that LTA rs1800683G>A was significantly associated with risk of progression or relapse in NHL patients (HR = 1.63, 95%CI = 1.06–2.51; P = 0.028), particularly in Diffuse large B cell lymphoma (DLBCL) cases (HR = 1.50, 95%CI = 1.10–2.04, P = 0.01). Both univariate and multivariate Cox regression analysis showed that in DLBCL patients, Ann Arbor stage III/IV, elevated LDH level before treatment and LTA rs1800683 AA genotype carrier were independent risk factors for progression or relapse. While in NK/T cell lymphoma, Ann Arbor stage III/IV and elevated β₂-MG level before treatment indicated poorer prognosis.

Conclusions

The polymorphism of LTA rs1800683G>A contributes to NHL prognosis in a Chinese population. Further large-scale and well-designed studies are needed to confirm these results.     

The fertility of women Poland in the period of trasformation of the political and economics system (the 80’s and 90’s)

Wielkopolska (western Poland) is a region, with good reason, called the main food base of Poland. All indices of agricultural production have always been there (since 19th century) much higher than elsewhere in the country (Ratajczak 1977/1978, Buszko 1984, Gorzelak 1989, Czyzewski et al. 1992; table 1). Such a situation had a beneficial effect on the amount of the income generated by a family of Wielkopolska and, thus, decided on its better financial status. Additionally, rural inhabitants of this region have always been characterised by a more advantageous educational structure in comparison with people of other Polish villages. Generally, it is easy to detect the relationship between the life standard, the level of education and family planning. The aim of this paper is to assess fertility of women from villages of Wielkopolska in the period of transformation of the political and economic system in Poland.     

Assessment of the Bioaccessibility of Trace Elements in Cat’s Claw Teas by In Vitro Simulated Gastrointestinal Digestion Using FAAS

Beer is a widely consumed drink throughout the world, and because its manufacture involves the use of water, beer can be, in some cases, a source of fluorides. For this reason, the objective of this study was to determine the concentration of fluorides in 50 samples of beers from different sources sold in two different types of container (aluminum can and glass bottle). The possible significant differences between the different types of packaging and the intake of fluoride from the consumption of these beers were evaluated. The concentration of fluoride in beers has been determined using the potentiometric method of fluoride determination by standard addition. The concentration of fluoride ranged between 0.06 and 1.77 mg/L. In general, the concentration was below 1 mg/L, except for three beer samples from Ireland and the USA, whose concentration was over 1.5 mg/L. No significant differences were found between the types of packaging. The contribution of fluoride to the diet from beer consumption is not high (<27%); however, it is necessary to warn consumers whenever they are in areas of high concentrations of fluoride in the water supply.     

A new highly polymorphic DNA restriction site marker in the 5′ region of the human tyrosine hydroxylase gene (TH) detecting loss of heterozygosity in human embryonal rhabdomyosarcoma

We have isolated a new marker (cos11-5TH) that detects an MspI restriction fragment length polymorphism in the 5 region of the human tyrosine hydroxylase gene (TH) on chromosome band 11p15.5. This region of human chromosome 11 contains several important loci for disease phenotypes including Beckwith-Wiedemann syndrome (BWS), Wilms' tumor, and embryonal rhabdomyosarcoma. Thus, identification of new polymorphic markers in this region are important for future gene mapping and linkage analyses. To better define the region of 11p15.5 deleted in embryonal rhabdomyosarcoma, this new marker was used to investigate allelic losses in embryonal rhabdomyosarcoma tumors.     

Validation of the Chinese Version of the Children’s ChronoType Questionnaire (CCTQ) in school-aged children

ABSTRACT

The Children’s ChronoType Questionnaire (CCTQ) is a valid and reliable measure for assessing prepubertal children aged 4–11 years. The CCTQ is a parent-reported, 27-item questionnaire consisting of sleep-wake parameters for scheduled and free days (16 items), a morningness/eveningness scale (M/E, 10 items), and a five-point, single-item, chronotype score. The CCTQ has been translated into different languages, but a Chinese version is not available. In the present study, we aimed to produce a Chinese version of the CCTQ and test its validity and reliability on school-aged children. A total of 555 children aged 7–11 years were recruited from five primary schools. The parents were told to complete the CCTQ and record their child’s sleep pattern in a 7-day sleep diary. Sixty-six children and their parents were invited to participate in determining the test-retest reliability of the CCTQ over a 2-week interval, and their sleep patterns were assessed using a sleep diary. The internal consistency of the Chinese CCTQ M/E score as measured by Cronbach’s alpha was acceptable (0.74). Regarding the test-retest reliability of the instrument, moderate to strong Spearman’s correlation coefficients were found for most of the CCTQ – sleep-wake items (ρ = 0.52–0.86) and for the CCTQ-M/E total score (ρ = 0.78). For the concurrent validity, Spearman’s correlations between the sleep-wake parameters of the CCTQ and the sleep diary were moderate to high on both the scheduled days (ρ = 0.54 to 0.87) and free days (ρ = 0.36 to 0.60). For the correlations measured with actigraphs, significant correlations were found in the CCTQ sleep-wake parameters, including bedtime, get-up time, sleep latency, sleep period, time in bed, and mid-sleep point on both the scheduled (ρ = 0.31 to 0.76) and free days (ρ = 0.27 to 0.52), but not in sleep latency and sleep period on free days. The results of the present study suggest that the Chinese version of the CCTQ is a reliable and valid tool for assessing chronotypes in Chinese school-aged children in Hong Kong.     

Differences in levels of heterozygosity in populations of the common gudgeon (Gobio gobio,Cyprinidae) among adjacent drainages in Central Europe: an effect of postglacial range dynamics?

Twenty-nine allozyme loci analyzed in 295 common gudgeons (Gobio gobio) from the Rhine, the upper Danube and the Elbe river systems revealed variability measures of P = 0.590, H(e) = 0.066, and G(ST) = 0.1415. Gene flow was estimated at N(e)m = 1.88 over 223 river km in the Danube basin, and at N(e)m = 1.96 over 300 river km in the Rhine system. Isolation-by-distance was not observed. Danubian gudgeons proved significantly more heterozygous (H(e) = 0.106) than those from the Rhine (H(e) = 0.057) or the Elbe drainages (H(e) = 0.029). Nine polymorphic enzymes contributed to this difference, which probably indicates dispersal bottlenecking of the postglacial immigrants into the Atlantic drainages of the study area. Refugial bottlenecking of gudgeons from Atlantic drainages in a Pleistocene refuge located in oceanic northwest Europe also seems possible. Slightly deeper genetic lineages in the Danube (G(ST) = 0.0859) than in the Rhine (G(ST) = 0.0793) agree with this explanation, as does the greater mean genetic distance among pairs of population samples from the Danube (D = 0.0138) than from the Rhine (D = 0.0054). A genetic distance of D = 0.0085 separated Rhenish and Danubian gudgeons.     

Genetic mapping of the Lablab purpureus genome suggests the presence of ’cuckoo’ gene(s) in this species

A linkage map of Lablab purpureus consisting of 127 RFLP and 91 RAPD loci was constructed in an F₂ population of 119 individuals. This population was derived from a cross between ’Rongai’ (an annual cultivar) and CPI 24973 (a perennial wild accession). The map comprises 17 linkage groups and covers 1610 centiMorgans (cM) with an average distance of 7 cM between markers. Severe segregation distortions were observed, with the very extreme situation where no paternal type was recovered from the mapping population. These results strongly suggest the presence of a gene conferring preferential transmission from the maternal parent ’Rongai’. It was also clear that, while the majority of RAPD markers are valuable when used together with RFLP or other stringent marker systems, they could be problematic when used solely in mapping exercises. Received: 20 April 1999 / Accepted: 23 August 1999     

Rationale and design of the Measuring Athlete’s Risk of Cardiovascular events (MARC) study: The role of coronary CT in the cardiovascular evaluation of middle-aged sportsmen

BackgroundMore than 90 % of exercise-related cardiac arrests occur in men, predominantly those aged 45 years and older with coronary artery disease (CAD) as the main cause. The current sports medical evaluation (SME) of middle-aged recreational athletes consists of a medical history, physical examination, and resting and exercise electrocardiography. Coronary CT (CCT) provides a minimally invasive low radiation dose opportunity to image the coronary arteries. We present the study protocol of the Measuring Athlete’s Risk of Cardiovascular events (MARC) study. MARC aims to assess the additional value of CCT to a routine SME in asymptomatic sportsmen ≥45 years without known CAD.DesignMARC is a prospective study of 300 asymptomatic sportsmen ≥45 years who will undergo CCT if the SME does not reveal any cardiac abnormalities. The prevalence and determinants of CAD (coronary artery calcium score ≥100 Agatston Units (AU) or ≥50 % luminal stenosis) will be reported. The number needed to screen to prevent the occurrence of one cardiovascular event in the next 5 years, conditional to adequate treatment, will be estimated.DiscussionWe aim to determine the prevalence and severity of CAD and the additional value of CCT in asymptomatic middle-aged (≥45 years) sportsmen whose routine SME revealed no cardiac abnormalities.

Electronic supplementary material

The online version of this article (doi:10.1007/s12471-014-0630-0) contains supplementary material, which is available to authorized users.     

Effects of microwave exposure and Gemcitabine treatment on apoptotic activity in Burkitt’s lymphoma (Raji) cells

Abstract

We investigated the effects of 1.8?MHz Global System for Mobile Communications (GSM)-modulated microwave (MW) radiation on apoptotic level and cell viability of Burkitt’s lymphoma (Raji) cells with or without Gemcitabine, which exhibits cell phase specificity, primarily killing cells undergoing DNA synthesis (S-phase). Raji cells were exposed to 1.8?GHz GSM-modulated MW radiation at a specific absorption rate (SAR) of 0.350?W/kg in a CO₂ incubator. The duration of the exposure was 24?h. The amount of apoptotic cells was analyzed using Annexin V-FITC and propidium iodide (PI) staining with flow cytometer. The apoptotic activity of MW exposed Raji cells was increased significantly. In addition, cell viability of exposed samples was significantly decreased. Combined exposure of MW and Gemcitabine increased the amount of apoptotic cells than MW radiation alone. Moreover, viability of MW?+?Gemcitabine exposed cells was lower than that of cells exposed only to MW. These results demonstrated that MW radiation exposure and Gemcitabine treatment have a synergistic effect on apoptotic activity of Raji cells.     

Genetic variation at storage protein-coding loci of common wheat (cv ‘Chinese Spring’) induced by nitrosoethylurea and by the cultivation of immature embryos in vitro

Electrophoretic patterns of seed storage proteins, the high-molecular-weight glutenins and gliadins, were studied in 468 plants of the common wheat cultivar Chinese Spring regenerated from callus culture of immature embryos, in 115 plants grown from seeds treated with nitrosoethylurea and in 260 control plants. From 5 to 21 single grains were analysed from each plant. In these three groups, the frequency of inherited mutations causing the loss of all proteins controlled by a locus (null-mutations, probably caused by a chromosomal deficiency) was 0.69%, 2.07%, and 0.05% per locus (the differences were statistically significant), respectively, while that of mutations causing the loss of a single protein band was 0.11%, 0.33%, and 0.05%, respectively. The loss of all of the gliadins controlled by Gli-B1 or GH-B2 (mutations were probably caused by a deletion of satellites of the corresponding chromosomes), was significantly higher than the loss of gliadins controlled by genomes A and D. Gene mutations altering the electrophoretic mobility of a single protein band in the pattern were found only in the second group of plants (0.44%). Therefore, chemical mutagenesis which produced not only more mutations than cultivation of immature wheat embryos in vitro, but also a higher ratio of mutations that altered DNA sequences, can be considered as an easier and comparatively more promising way for obtaining new improved variants of loci controlling biochemical characteristics in wheat. Somaclonal variation, on the other hand, was probably mainly caused by chromosomal abnormalities and could therefore hardly be considered as a useful tool in wheat breeding.     

Significance of the potential role of pharmacological MRI (phMRI) in diagnosis of Parkinson’s disease

The initial diagnosis of Parkinson's disease (PD) is currently based on a clinical assessment.Many patients who receive an initial diagnosis of PD have parkinsonian features related to other diseases s...     

Seasonal variations in the energy budget of Elliot’s pheasant (Syrmaticus ellioti) in cage

This study aimed to discuss the energy budget of Elliot’s pheasant Syrmaticus ellioti in different seasons, with life and health, good growth and normal digestion of Elliot’s pheasant as the tested objects, The energy budget of Elliot’s pheasant was measured by daily collection of the trial pheasants’ excrement in the biological garden of Guangxi Normal University from March 2011 to February 2012. The results showed that the gross energy consumption, metabolic energy and excrement energy varied by season, increasing as temperature decreased. There was significant difference in gross energy consumption, metabolic energy, excrement energy between adults and nonages. There was also a trend that food digestibility of pheasants increases as temperature increases. In the same season, the food digestibility of adults was better than that of nonages. Throughout spring, summer, autumn and winter, the metabolic energy of 4-year adults were 305.77±13.40 kJ/d, 263.67±11.89 kJ/d, 357.23±25.49 kJ/d and 403.12±24.91 kJ/d, respectively, and the nonages were 284.86±17.22 kJ/d, 284. 66±15.16 kJ/d, 402. 26±31.46 kJ/d and 420. 30±31.98 kJ/d, respectively. The minimum metabolic energies were 247.65±21.81 g, 265.86±26.53 g, respectively for each group, detected between 4-year adults and 1-year nonages. Further study is needed to determine whether 29.6 C is the optimal temperature for the Elliot’s pheasant.     

Homology of the muscles within the uropatagium membrane in Leschenault’s rousette (Rousettus leschenaultii)

Pteropodidae possess unique muscles in the uropatagium called Musculus uropatagialis and M. depressor ossis styliformis. The homology of these muscles is important for the phylogenetic analysis of bats because the wing membrane is a characteristic feature for them. Here, I discuss the homology of M. uropatagialis and M. depressor ossis styliformis in Rousettus leschenaultii by tracing their innervations. I found that the dominant nerve for the M. uropatagialis contains the components of the sciatic nerve associated with the dominant nerve of the flexor muscles of the thigh. This result shows that M. uropatagialis is homologous to the flexor muscles of the thigh. The dominant nerve of M. depressor ossis styliformis is the lateral plantar nerve derived from the tibial nerve. Thus, this innervation pattern proposes the hypothesis that M. depressor ossis styliformis is homologous to one of the muscles of the foot sole.     

Microsatellite Evolution in the Mitochondrial Genome of Bechstein’s Bat (Myotis bechsteinii)

Being highly polymorphic, microsatellites are widely used genetic markers. They are abundant throughout the nuclear genomes of eukaryotes but rare in the mitochondrial genomes (mtDNA) of animals. We describe a short but highly polymorphic AT microsatellite in the mtDNA control region of Bechstein’s bat and discuss the role of mutation, genetic drift, and selection in maintaining its variability. As heteroplasmy and hence mutation rate were positively correlated with repeat number, a simple mutation model cannot explain the observed frequency distribution of AT copy numbers. Because of the unimodal distribution of repeat numbers found in heteroplasmic individuals, single step mutations are likely to be the predominant mechanism of copy number alternations. Above a certain copy number (seven repeats), deletions of single dinucleotide repeats seem to be more common than additions, which results in a decrease in frequency of long alleles. Heteroplasmy was inherited from mothers to their offspring and no evidence of paternal inheritance of mitochondria was found. Genetic differences accumulated with more distant ancestry, which suggests that microsatellites can be useful genetic markers in population genetics.[Reviewing Editor: Dr. Rafael Zardoya]