Microbial biodiversity of the liquid fraction of rumen content from lactating cows

Host and dietary interactions with the rumen microbiome can affect the efficacy of supplements, and their effect on the composition of the bacterial population is still unknown. A 16S rRNA metagenomic approach and Next-Generation Sequencing (NGS) technology were used to investigate the bacterial microbiome composition in the liquid fraction of the rumen content collected via stomach tubing. To investigate biodiversity, samples were taken from three groups of four lactating dairy cows given a supplement of either 50 g of potato protein (Ctrl group), or 50 g of lyophilized Saccharomyces cerevisiae (LY group) or 50 g of dried S. cerevisiae (DY group) in a potato protein support. Rumen samples were collected after 15 days of dietary treatments and milk production was similar between the three groups. Taxonomic distribution analysis revealed a prevalence of the Firmicutes phylum in all cows (79.76%) and a significantly ( P<0.05) higher presence of the genus Bacillus in the DY group. Volatile fattyacid concentration was not significantly different between groups, possibly because of relatively high inter-animal variability or limited effect of the treatments or both, and the correlation analysis with bacterial taxa showed significant associations, in particular between many Firmicutes genera and butyrate. Limited differences were observed between dietary treatments, but the lack of microbiome data before yeast administration does not allow to draw firm conclusions on the effect of dietary treatments

Aberrant BLM cytoplasmic expressionassociates with DNA damage stress and hypersensitivity to DNA-damaging agents in colorectal cancer

Background Bloom syndrome is a rare and recessive disorder characterized by loss-of-function mutations of the BLM gene, which encodes a RecQ 30–50 DNA helicase. Despite its putative tumor suppressor function, the contribution of BLM to human sporadic colorectal cancer (CRC) remains poorly understood. Methods The transcriptional regulation mechanism underlying BLM and related DNA damage response regulation in independent CRC subsets and a panel of derived cell lines was investigated by bioinformatics analysis, the transcriptomic profile, a CpG island promoter methylation assay, Western blot, and an immunolocalization assay. Results In silico analysis of gene expression data sets revealed that BLM is overexpressed in poorly differentiated CRC and exhibits a close connection with shorter relapsefree survival even after adjustment for prognostic factors and pathways that respond to DNA damage response through ataxia telangiectasia mutated (ATM) signaling. Functional characterization demonstrated that CpG island promoter hypomethylation increases BLM expression and associates with cytoplasmic BLM mislocalization and increased DNA damage response both in clinical CRC samples and in derived cancer cell lines. The DNA-damaging agent S-adenosylmethionine suppresses BLM expression, leading to the inhibition of cell growth following accumulation of DNA damage. In tumor specimens, cytoplasmic accumulation of BLM correlates with DNA damage and cH2AX and phosphorylated ATM foci and predicts long-term progression-free survival in metastatic patients treated with irinotecan. Conclusions Taken together, the findings of this study provide the first evidence that cancer-linked DNA hypomethylation and cytosolic BLM mislocalization might reflect compromised levels of DNA-repair activity and enhanced hypersensitivity to DNA-damaging agents in CRC patients

Identification of five picorna-like viruses associated with the endangered cave-dwelling bivalve Congeria kusceri (Bole, 1962)

Congeria kusceri is a bivalve mollusk species endemic to the Dinaric Karst, which displays unique adaptations that have allowed its survival in the subterranean environment with small morphological changes compared with its fossil relatives. Anthropic activities have recently impacted the surface flow of the Neretva river, impairing the seasonal water cycle that has characterized the habitat of this species for hundreds of thousands of years. The lack of an adequate water supply, together with pollution from agricultural and farm water runoff, are posing a serious threat to C. kusceri, as evidenced by the sharp population decline observed in several locations during the past few decades. Due to the limited knowledge available about the basic biology of this filter-feeding species, the precise factors that may affect its health status and reproduction and therefore represent a hazard for its conservation are still unclear. Here, through a transcriptomic approach, we describe the nearly-complete genomes of five C. kusceri-associated RNA viruses belonging to the Picornaviridae family and phylogenetically related with picorna-like viruses previously described in other Mollusca. Although it is presently unknown whether these viruses may have a detrimental effect on bivalve health, we observed a significant increase of viral load during the summer seaso

Međudjelovanje atmosfere s morem u Jadranu: simulacije bure i juga

Two simulations of the response of Adriatic Sea to severe wind performed by an atmosphere-ocean coupled model and the comparisons with observed data and modelled fields published in literature are presented. The model RAMS-DieCAST was applied to simulate the variations of sea currents and temperature profiles, from surface to bottom, induced by two episodes of intense wind over the Adriatic sea: a Bora wind event that occurred in January 1995 and a Sirocco wind event in November 2002. The results of the simulations are compared with observed data at the sea surface. In the Bora episode, the computed surface temperatures are compared with satellite SSTs and in situ observed temperatures; in the Sirocco event the simulated surface currents and temperatures are compared with experimental data collected by surface drifters released in different regions of the Adriatic Sea during the same Sirocco event. In both episodes the simulated temperature trends agree with the observed values and during the Sirocco episode the current fields are in quite good agreement with the drifter data. The modelled sea temperature and velocity fields show also a good concordance with other simulation results in literature.Dvije simulacije jakog vjetra nad Jadranom simuliraju se združenim atmosfersko-oceanografskim modelom te se analiziraju i uspoređuju s mjerenjima i drugim objavljenim modeliranim poljima. U tu svrhu se koristi model RAMS-DieCAST za simulaciju promjena morskih struja i temperaturnih profila po vertikali, uzrokovanih dvjema epizodama intenzivnog vjetra nad Jadranom: burom u siječnju 1995. godine i jugom u studenom 2002. godine. Rezultati simulacija se uspoređuju s opažanjima na morskoj površini. Tijekom bure, modelirana površinska temperatura uspoređuje se s površinskom temperaturom mora dobivene satelitskim mjerenjima i mjerenjima temperature u određenim točkama prostora. Tijekom juga, simulirane površinske struje i temperature se uspoređuju s eksperimentalnim mjerenjima dobivenih na temelju površinskih driftera koji su pušteni u različitim dijelovima Jadrana za istu epizodu. U obje epizode trendovi simulirane temperature dobro se podudaraju s opažanjima. Također se tijekom juga, površinske struje dobro podudaraju s mjerenjima driftera. Modelirana temperatura mora kao i vektorsko polje brzina pokazuju dobro slaganje s rezultatima sličnih simulacija u literaturi

Međudjelovanje atmosfere s morem u Jadranu: simulacije bure i juga

Two simulations of the response of Adriatic Sea to severe wind performed by an atmosphere-ocean coupled model and the comparisons with observed data and modelled fields published in literature are presented. The model RAMS-DieCAST was applied to simulate the variations of sea currents and temperature profiles, from surface to bottom, induced by two episodes of intense wind over the Adriatic sea: a Bora wind event that occurred in January 1995 and a Sirocco wind event in November 2002. The results of the simulations are compared with observed data at the sea surface. In the Bora episode, the computed surface temperatures are compared with satellite SSTs and in situ observed temperatures; in the Sirocco event the simulated surface currents and temperatures are compared with experimental data collected by surface drifters released in different regions of the Adriatic Sea during the same Sirocco event. In both episodes the simulated temperature trends agree with the observed values and during the Sirocco episode the current fields are in quite good agreement with the drifter data. The modelled sea temperature and velocity fields show also a good concordance with other simulation results in literature.Dvije simulacije jakog vjetra nad Jadranom simuliraju se združenim atmosfersko-oceanografskim modelom te se analiziraju i uspoređuju s mjerenjima i drugim objavljenim modeliranim poljima. U tu svrhu se koristi model RAMS-DieCAST za simulaciju promjena morskih struja i temperaturnih profila po vertikali, uzrokovanih dvjema epizodama intenzivnog vjetra nad Jadranom: burom u siječnju 1995. godine i jugom u studenom 2002. godine. Rezultati simulacija se uspoređuju s opažanjima na morskoj površini. Tijekom bure, modelirana površinska temperatura uspoređuje se s površinskom temperaturom mora dobivene satelitskim mjerenjima i mjerenjima temperature u određenim točkama prostora. Tijekom juga, simulirane površinske struje i temperature se uspoređuju s eksperimentalnim mjerenjima dobivenih na temelju površinskih driftera koji su pušteni u različitim dijelovima Jadrana za istu epizodu. U obje epizode trendovi simulirane temperature dobro se podudaraju s opažanjima. Također se tijekom juga, površinske struje dobro podudaraju s mjerenjima driftera. Modelirana temperatura mora kao i vektorsko polje brzina pokazuju dobro slaganje s rezultatima sličnih simulacija u literaturi

Drug resistance in B and non-B subtypes amongst subjects recently diagnosed as primary/recent or chronic HIV-infected over the period 2013–2016: Impact on susceptibility to first-line strategies including integrase strand-transfer inhibitors

Objectives To characterize the prevalence of transmitted drug resistance mutations (TDRMs) by plasma analysis of 750 patients at the time of HIV diagnosis from January 1, 2013 to November 16, 2016 in the Veneto region (Italy), where all drugs included in the recommended first line therapies were prescribed, included integrase strand transfer inhibitors (InNSTI). Methods TDRMs were defined according to the Stanford HIV database algorithm. Results Subtype B was the most prevalent HIV clade (67.3%). A total of 92 patients (12.3%) were expected to be resistant to one drug at least, most with a single class mutation (60/68–88.2% in subtype B infected subjectsand 23/24–95.8% in non-B subjects) and affecting mainly NNRTIs. No significant differences were observed between the prevalence rates of TDRMs involving one or more drugs, except for the presence of E138A quite only in patients with B subtype and other NNRTI in subjects with non-B infection. The diagnosis of primary/recent infection was made in 73 patients (9.7%): they had almost only TDRMs involving a single class. Resistance to InSTI was studied in 484 subjects (53 with primary-recent infection), one patient had 143C in 2016, a total of thirteen 157Q mutations were detected (only one in primary/recent infection). Conclusions Only one major InSTI-TDRM was identified but monitoring of TDRMs should continue in the light of continuing presence of NNRTI-related mutation amongst newly diagnosed subjects, sometime impacting also to modern NNRTI drugs recommended in first-line therapy

Red mark syndrome: Is the aquaculture water microbiome a keystone for understanding the disease aetiology?

Aquaculture significantly contributes to the growing demand for food worldwide. However, diseases associated with intensive aquaculture conditions, especially the skin related syndromes, may have significant implications on fish health and industry. In farmed rainbow trout, red mark syndrome (RMS), which consists of multiple skin lesions, currently lacks recognized aetiological agents, and increased efforts are needed to elucidate the onset of these conditions. Most of the past studies were focused on analyzing skin lesions, but no study focused on water, a medium constantly interacting with fish. Indeed, water tanks are environmental niches colonized by microbial communities, which may be implicated in the onset of the disease. Here, we present the results of water and sediment microbiome analyses performed in an RMS-affected aquaculture facility, bringing new knowledge about the environmental microbiomes harbored under these conditions. On the whole, no significant differences in the bacterial community structure were reported in RMS-affected tanks compared to the RMS-free ones. However, we highlighted significant differences in microbiome composition when analyzing different samples source (i.e., water and sediments). Looking at the finer scale, we measured significant changes in the relative abundances of specific taxa in RMS-affected tanks, especially when analyzing water samples. Our results provide worthwhile insight into a mostly uncharacterized ecological scenario, aiding future studies on the aquaculture built environment for disease prevention and monitoring

Eye fluke infection changes diet composition in juvenile European perch (Perca fluviatilis)

Intraspecific diet specialization, usually driven by resource availability, competition and predation, is common in natural populations. However, the role of parasites on diet specialization of their hosts has rarely been studied. Eye flukes can impair vision ability of their hosts and have been associated with alterations of fish feeding behavior. Here it was assessed whether European perch (Perca fluviatilis) alter their diet composition as a consequence of infection with eye flukes. Young-of-the-year (YOY) perch from temperate Lake Müggelsee (Berlin, Germany) were sampled in two years, eye flukes counted and fish diet was evaluated using both stomach content and stable isotope analyses. Perch diet was dominated by zooplankton and benthic macroinvertebrates. Both methods indicated that with increasing eye fluke infection intensity fish had a more selective diet, feeding mainly on the benthic macroinvertebrate Dikerogammarus villosus, while less intensively infected fish appeared to be generalist feeders showing no preference for any particular prey type. Our results show that infection with eye flukes can indirectly affect interaction of the host with lower trophic levels by altering the diet composition and highlight the underestimated role of parasites in food web studies.Leibniz-AssociationPeer Reviewe