Robust identification of interactions between heat-stress responsive genes in the chicken brain using Bayesian networks and augmented expression data.

Bayesian networks represent a useful tool to explore interactions within biological systems. The aims of this study were to identify a reduced number of genes associated with a stress condition in chickens (Gallus gallus) and to unravel their interactions by implementing a Bayesian network approach. Initially, one publicly available dataset (3 control vs. 3 heat-stressed chickens) was used to identify the stress signal, represented by 25 differentially expressed genes (DEGs). The dataset was augmented by looking for the 25 DEGs in other four publicly available databases. Bayesian network algorithms were used to discover the informative relationships between the DEGs. Only ten out of the 25 DEGs displayed interactions. Four of them were Heat Shock Proteins that could be playing a key role, especially under stress conditions, where maintaining the correct functioning of the cell machinery might be crucial. One of the DEGs is an open reading frame whose function is yet unknown, highlighting the power of Bayesian networks in knowledge discovery. Identifying an initial stress signal, augmenting it by combining other databases, and finally learning the structure of Bayesian networks allowed us to find genes closely related to stress, with the possibility of further exploring the system in future studies.

A Bayesian network structure learning approach to identify genes associated with stress in spleens of chickens.

Differences in the expression patterns of genes have been used to measure the effects of non-stress or stress conditions in poultry species. However, the list of genes identified can be extensive and they might be related to several biological systems. Therefore, the aim of this study was to identify a small set of genes closely associated with stress in a poultry animal model, the chicken (Gallus gallus), by reusing and combining data previously published together with bioinformatic analysis and Bayesian networks in a multi-step approach. Two datasets were collected from publicly available repositories and pre-processed. Bioinformatics analyses were performed to identify genes common to both datasets that showed differential expression patterns between non-stress and stress conditions. Bayesian networks were learnt using a Simulated Annealing algorithm implemented in the software Banjo. The structure of the Bayesian network consisted of 16 out of 19 genes together with the stress condition. Network structure showed CARD19 directly connected to the stress condition plus highlighted CYGB, BRAT1, and EPN3 as relevant, suggesting these genes could play a role in stress. The biological functionality of these genes is related to damage, apoptosis, and oxygen provision, and they could potentially be further explored as biomarkers of stress.

High frequency of gram-negative bacilli harboring blaKPC-2 in the different stages of wastewater treatment plant: A successful mechanism of resistance to carbapenems outside the hospital settings.

Wastewater treatment plants (WWTPs) are considered to be a reservoir and a source of bacterial resistance. Worryingly, the presence of carbapenem-resistant Gram-negative bacilli (CRGNB) in WWTPs has recently been reported, but there are still many research gaps regarding its emergence and impact. The distribution of CRGNB in the different stages of a WWTP in Colombia and the relationship between the physicochemical factors involved with their presence are described in this paper. Additionally, given the impact on public health, the CRGNB detected were compared with isolates previously found in hospital patients. Residual water samples were taken from five different stages of a WWTP between January and July 2017. A total of 390 GNB were isolated, and a significant frequency of CRGNB harboring blaKPC-2 (38.2%, n = 149/390) was detected, of which 57% were Enterobacteriaceae, 41.6% Aeromonadaceae, and 1.3% Pseudomonadaceae. The Enterobacteriaceae were more frequent in the raw effluent compared to the Aeromonadaceae, which in turn were more prevalent in the recycled activated sludge and final effluent. Environmental variables such as pH, oxygen, chemical oxygen demand, and temperature were significantly correlated with the quantification of carbapenem-resistant Enterobacteriaceae (CRE) at specific points in the WWTP. Interestingly, isolated K. pneumoniae harboring blaKPC-2 from the WWTPs were diverse and did not relate genetically to the hospital strains with which they were compared. In conclusion, these results confirm the worrying scenario of the dissemination and persistence of emerging contaminants such as CRGNB harboring blaKPC-2, and reinforce the need to establish strategies aimed at containing this problem using multifocal interventions.

Multidrug resistance and diversity of resistance profiles in carbapenem-resistant Gram-negative bacilli throughout a wastewater treatment plant in Colombia.

OBJECTIVES: Carbapenem-resistant Gram-negative bacilli (CRGNB) have been reported in different wastewater treatment plants (WWTPs) throughout the world; however, few studies have described the antimicrobial resistance profile in different CRGNB throughout WWTPs, information that would identify points of selection of resistant bacteria. The objective of this work was to characterize the resistance profile of CRGNB harbouring blaKPC-2 from a Colombian WWTP. METHODS: Six samples were taken from four points of a WWTP. CRGNB were selected in chromID® CARBA and identified by 16S rRNA. Carbapenemases were determined by polymerase chain reaction (PCR), and susceptibility was assessed using VITEK2. RESULTS: One hundred and forty-two CRGNB harbouring blaKPC-2 were detected: 41% corresponded to Aeromonas spp. (n = 58) and 59% to Enterobacteriaceae. To establish the resistance profile, 50% of the isolates were selected proportionally by family and sampling point (26 Aeromonadaceae and 45 Enterobacteriaceae). All Enterobacteriaceae showed resistance to carbapenems and penicillins + inhibitors, high percentages of resistance to ceftriaxone (88.9%), and ciprofloxacin (44.4%), and low resistance to other antibiotics (>30%). In Aeromonadaceae, 76.9% were resistant to ceftriaxone, 58% to carbapenems, and 65.4% to ciprofloxacin. Twenty-one resistance profiles were observed, the most common of which were resistant to penicillins + inhibitor, cephalosporins (third to fourth generation), and carbapenems (19%). The percentage of multidrug resistance was 91% and was similar at all points of the WWTP. CONCLUSIONS: The high frequency of multidrug resistance and great diversity of resistance profiles observed throughout the WWTP is of concern, and shows the role of WWTP as a reservoir and dissemination source of antimicrobial resistance to water sources.

High clonal diversity of multidrug-resistant and extended spectrum beta-lactamase-producing Escherichia coli in a wastewater treatment plant.

Increasing beta-lactam resistance has led to the exploration of different places, such as wastewater treatment plants (WWTPs) which have been considered to be reservoirs and sources of bacterial resistance. This work aims to determine the presence of beta-lactamase-producing-Enterobacteriaceae in different points of a WWTP in Colombia. Six samplings were carried out in 2017 in the raw influent, aeration tanks, recycled sludge and final effluent of a WWTP. The beta-lactamase-producing-Enterobacteriaceae were detected and identified using phenotypic and molecular methods. Of the 353 isolates included, 28.3% corresponded to enterobacteria. The most frequent microorganisms were Escherichia coli (83%), Citrobacter freundii (11%) and Enterobacter cloacae complex (4%). The 97% of enterobacteriaceae had at least one beta-lactamase, and the most prevalent were the blaTEM (43.8%) and blaCTX-M-1group (35.8%) which were detected specially in recycled sludge and final effluent sample points. High percentage of multidrug resistance (to beta-lactams and non-beta-lactam antibiotics) was detected in E. coli (63.2%). Additionally, the typing by PFGE and MLST showed high genotypic diversity and the presence of the successful ST131 clone, globally spread. This work highlights the strong role of E. coli as a vector for the dissemination of resistance and the beta-lactamases in aquatic environments.

Review article: the evidence that vancomycin is a therapeutic option for primary sclerosing cholangitis.

BACKGROUND AND AIMS: PSC is an autoimmune biliary inflammatory disorder that is often associated with inflammatory bowel disease (IBD), with 50%-75% of patients with PSC having coexisting IBD, most commonly ulcerative colitis. Currently, no medical therapies have been shown to improve the disease course or slow its progression. However, ongoing research has resulted in a growing interest in the use of antibiotics for treatment of PSC, of which vancomycin is the most studied. In this review, we summarise the current evidence on the use of vancomycin in PSC and comment on future research areas of interest. METHODS: A comprehensive PUBMED and EMBASE literature search for articles on vancomycin, PSC, therapeutic options and microbiome was performed. RESULTS: Two randomised clinical trials, three case series and two case reports were included in the study. These include uncontrolled data from at least 98 patients that include promising improvements in biochemistry and imaging. Optimal dosing regimens are unclear. CONCLUSION: Vancomycin is one of the most studied antibiotics used in the treatment of PSC with promising results. There is not currently sufficient evidence to support treatment recommendations. Further research is needed to establish if vancomycin is a PSC treatment.

Light pollution reduces activity, food consumption and growth rates in a sandy beach invertebrate.

The continued growth of human activity and infrastructure has translated into a widespread increase in light pollution. Natural daylight and moonlight cycles play a fundamental role for many organisms and ecological processes, so an increase in light pollution may have profound effects on communities and ecosystem services. Studies assessing ecological light pollution (ELP) effects on sandy beach organisms have lagged behind the study of other sources of disturbance. Hence, we assessed the influence of this stressor on locomotor activity, foraging behavior, absorption efficiency and growth rate of adults of the talitrid amphipod Orchestoidea tuberculata. In the field, an artificial light system was assembled to assess the local influence of artificial light conditions on the amphipod's locomotor activity and use of food patches in comparison to natural (ambient) conditions. Meanwhile in the laboratory, two experimental chambers were set to assess amphipod locomotor activity, consumption rates, absorption efficiency and growth under artificial light in comparison to natural light-dark cycles. Our results indicate that artificial light have significantly adverse effects on the activity patterns and foraging behavior of the amphipods, resulting on reduced consumption and growth rates. Given the steady increase in artificial light pollution here and elsewhere, sandy beach communities could be negatively affected, with unexpected consequences for the whole ecosystem.

Risk factors for atopy among school children in a rural area of Latin America.

BACKGROUND: Infection with common childhood infectious diseases including geohelminth infections may provide protection against the development of atopy and allergic disease. Few studies have investigated risk factors for atopy among children living in rural areas of Latin America. OBJECTIVE: To identify risk factors associated with atopy among school-age children in a rural area of Latin America. METHODS: Analytic cross-sectional study of school-age children conducted in seven rural schools in Pichincha Province in Ecuador. Detailed risk factor information was obtained by questionnaire, stool samples were collected for identification of geohelminth parasites, and Mantoux testing was performed to determine tuberculin sensitization. RESULTS: A total of 1002 children from seven rural schools were recruited. The prevalence of geohelminth infections was high (70.1% were infected with at least one geohelminth parasite) and the prevalence of allergic sensitization was high (20.0% had evidence of aeroallergen sensitization). Factors associated with significant protection against atopy in multivariate analyses were the presence of overcrowding in the child's home, low socio-economic level, and infection with geohelminth parasites, and the protective effects of the three factors were statistically independent. CONCLUSION: Low socio-economic level, overcrowding and geohelminth infection, are independently protective against atopy among school-age children living in a rural area of Latin America.

Genes influencing variation in serum osteocalcin concentrations are linked to markers on chromosomes 16q and 20q.

Osteocalcin (OC) is an important constituent of bone that is synthesized by osteoblasts. Serum levels of OC have been used as a biochemical marker of bone turnover. To identify the genes influencing variation in serum OC levels, we conducted a genome-wide scan in 429 individuals comprising 10 large multigenerational families. OC levels were measured by immunoassay, and genetic markers were typed at approximately 10-cM intervals across the genome. Quantitative trait linkage was tested using a multipoint analysis based on variance component methodology, adjusting for the effects of age, sex, and oral contraceptive use. Significance levels for linkage were obtained empirically, by Monte Carlo simulation. The heritability of OC levels in this population was 62 +/- 8%. We detected significant evidence for linkage between a quantitative trait locus influencing serum OC levels and markers on chromosome 16q, and suggestive evidence for linkage of OC levels with markers on chromosome 20q. The multipoint lod scores peaked at 3.35 on chromosome 16 and 2.78 on chromosome 20, corresponding to P values of 0.00004 and 0.00017, respectively. A potential candidate gene for bone formation in the linked region on chromosome 20 is CDMP1, which encodes cartilage-derived morphogenetic protein 1. Future studies should evaluate whether variation in CDMP1 or in other genes in the linked regions on chromosomes 16 and 20 influence the rate of bone turnover.

Speciation of inorganic and organic arsenic in marine sediments from La Coruña estuary.

The speciation of As(III), As(V), MMA and DMA in marine sediments from La Coruña estuary is described. The arsenic species have been separated by ion-exchange chromatography and detected by hydride generation atomic absorption spectrometry (HGAAS). The redox potential has been determined in order to relate the concentration of arsenic species to this parameter.

Porokeratosis of Mibelli and HIV-infection.

BACKGROUND: The exacerbation of porokeratosis of Mibelli associated with inmunosuppression has been well documented. MATERIALS AND METHODS: We describe the clinical and histologic data of three cases of HIV-infected patients, who developed porokeratosis following HIV-contact. RESULTS: The three reported patients were found to have the clinical and histologic features of porokeratosis of Mibelli. Either the exacerbation or development of the disease followed HIV infection. CONCLUSION: Although porokeratosis is not a disease indicative of AIDS, its flare-up or its presence in HIV-infected patients may serve as a marker of inmunodeficiency.