Extensive horizontal gene transfer in cheese-associated bacteria.

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities

Tailored for Real-World: A Whole Slide Image Classification System Validated on Uncurated Multi-Site Data Emulating the Prospective Pathology Workload.

Standard of care diagnostic procedure for suspected skin cancer is microscopic examination of hematoxylin & eosin stained tissue by a pathologist. Areas of high inter-pathologist discordance and rising biopsy rates necessitate higher efficiency and diagnostic reproducibility. We present and validate a deep learning system which classifies digitized dermatopathology slides into 4 categories. The system is developed using 5,070 images from a single lab, and tested on an uncurated set of 13,537 images from 3 test labs, using whole slide scanners manufactured by 3 different vendors. The system\u27s use of deep-learning-based confidence scoring as a criterion to consider the result as accurate yields an accuracy of up to 98%, and makes it adoptable in a real-world setting. Without confidence scoring, the system achieved an accuracy of 78%. We anticipate that our deep learning system will serve as a foundation enabling faster diagnosis of skin cancer, identification of cases for specialist review, and targeted diagnostic classifications

Central Neuroplasticity and Decreased Heart Rate Variability after Particulate Matter Exposure in Mice

BackgroundEpidemiologic studies show that exposure to fine particulate matter [aerodynamic diameter < or = 2.5 microm (PM(2.5))] increases the total daily cardiovascular mortality. Impaired cardiac autonomic function, which manifests as reduced heart rate variability (HRV), may be one of the underlying causes. However, the cellular mechanism(s) by which PM(2.5) exposure induces decreased HRV is not known.ObjectivesWe tested the hypothesis that exposure to PM(2.5) impairs HRV by decreasing the excitability of the cardiac vagal neurons in the nucleus ambiguus. We also determined the effect of iron on PM-exposure-induced decrease in HRV.MethodsWe measured 24-hr HRV in time domains from electrocardiogram telemetry recordings obtained in conscious, freely moving mice after 3 days of exposure to PM(2.5) in the form of soot only or iron-soot. In parallel studies, we determined the intrinsic properties of identified cardiac vagal neurons, retrogradely labeled with a fluorescent dye applied to the sinoatrial node.ResultsSoot-only exposure decreased short-term HRV (root mean square of successive difference). With the addition of iron, all HRV parameters were significantly reduced. In nonexposed mice, vagal blockade significantly reduced all HRV parameters, suggesting that HRV is, in part, under vagal regulation in mice. Iron-soot exposure had no significant effect on resting membrane potential but decreased spiking responses of the identified cardiac vagal neurons to depolarizations (p < 0.05). The decreased spiking response was accompanied with a higher minimal depolarizing current required to evoke spikes and a lower peak discharge frequency.ConclusionsThe data suggest that PM-induced neuroplasticity of cardiac vagal neurons may be one mechanism contributing to the cardiovascular consequences associated with PM(2.5) exposure seen in humans

The 5-HTTLPR variant in the serotonin transporter gene modifies degeneration of brain regions important for emotion in behavioral variant frontotemporal dementia

AbstractThe serotonin transporter length polymorphism (5-HTTLPR) short allele (5-HTTLPR-s) has been associated with differential susceptibility for anxiety and depression in multiple psychiatric disorders. 5-HTTLPR-s modifies the serotonergic systems that support emotion and behavioral regulation by reducing gene expression, which slows the reuptake of serotonin, and is associated with distinct morphological and functional effects. Serotonergic systems are also shown to be dysfunctional in behavioral variant frontotemporal dementia (bvFTD), a disease characterized by marked socioemotional dysfunction. However, studies of 5-HTTLPR-s effects in bvFTD have been inconsistent. Our objective was to investigate the patterns of gray matter volume by 5-HTTLPR-s genotype in both healthy older controls and bvFTD patients. We performed voxel-based morphometry of 179 cognitively normal older adults and 24 bvFTD cases to determine brain changes associated with dose (0/1/2) of 5-HTTLPR-s allele. 5-HTTLPR-s frequency did not differ between controls and bvFTD. We found a significant interaction effect whereby carrying more 5-HTTLPR-s alleles in bvFTD was associated with smaller volume in left inferior frontal gyrus (T = 4.86, PFWE = 0.03) and larger volume in right temporal lobe (T = 5.01, PFWE = 0.01). These results suggest that the 5-HTTLPR-s allele differentially influences brain morphology in bvFTD. We propose that patients with bvFTD and 5-HTTLPR-s have altered volumes in regions that support socioemotional behavior, which may be a developmental or disease-related compensation for altered serotonergic activity

3q26 Amplification is Rarely Present in Women Whose LSIL Cytology does not Represent CIN 2+ Disease

Comparative Medicine - OneHealth and Comparative Medicine Poster SessionObjective: 10-17% of women with LSIL cytology truly have CIN 2+ disease at colposcopically directed biopsy and 20% of the CIN 2+ lesions derive from women with LSIL cytology. No molecular marker has yet been able to triage LSIL cytology effectively. If possible, the triage would spare women the referral to colposcopy. Irreversible chromosomal damage occurs during oncogenesis. Increasing cervical dysplastic severity occurs with increasing amplification of the 3q26 chromosomal region. The purpose of this study is to evaluate the test characteristics of 3q26 amplification in women whose routine cytology is reported as LSIL with emphasis on the negative predictive value for reassurance. Methods: We conducted a retrospective study using the available SurePath™ liquid cytology LSIL archival samples from women 17-59 years old which were linked to colposcopically directed biopsy samples taken on average 36 days after cytology sampling (3-90 day range). Nuclei from the LSIL samples were hybridized with a single-copy probe for the chromosome 3q26 region and a control probe for the centromeric alpha repeat sequence of chromosome 7, using standard FISH methods. Amplification was defined as five or more signals present in at least 2 cells. Results: Of the 68 paired cytology/biopsy samples, 3q26 amplification occurred in 40% of the women with CIN 2+ disease (sensitivity 95% CI: 12, 74). There was no amplification in 91% of women with less than CIN 2 disease (specificity 95% CI: 81, 97); and the negative predictive value was 90% (79, 96). Conclusions: The lack of 3q26 amplification in women with screening cytology LSIL results offers reassurance that CIN 2+ disease has not developed. Future prospective studies are ongoing

Muscle p70S6K phosphorylation in response to soy and dairy rich meals in middle aged men with metabolic syndrome: a randomised crossover trial

The mammalian target of rapamycin (mTOR) pathway is the primary regulator of muscle protein synthesis. Metabolic syndrome (MetS) is characterized by central obesity and insulin resistance; little is known about how MetS affects the sensitivity of the mTOR pathway to feeding

Dynamic Bayesian belief network to model the development of walking and cycling schemes

This paper aims to describe a model which represents the formulation of decision-making processes (over a number of years) affecting the step-changes of walking and cycling (WaC) schemes. These processes can be seen as being driven by a number of causal factors, many of which are associated with the attitudes of a variety of factors, in terms of both determining whether any scheme will be implemented and, if it is implemented, the extent to which it is used. The outputs of the model are pathways as to how the future might unfold (in terms of a number of future time steps) with respect to specific pedestrian and cyclist schemes. The transitions of the decision making processes are formulated using a qualitative simulation method, which describes the step-changes of the WaC scheme development. In this article a Bayesian belief network (BBN) theory is extended to model the influence between and within factors in the dynamic decision making process

Exploring Australian night shift workers’ food experiences within and outside of the workplace: A qualitative photovoice study

Abstract Objective: Night shift workers are at a 20 to 40% increased risk of metabolic diseases, which may be associated with their disrupted eating patterns. This qualitative study explores factors that influence night shift workers’ eating habits, within and outside of the workplace, to identify target areas for health promotion strategies. Participants & Setting: Eligible participants resided in Australia, working at least 3 overnight shifts per month. Design: The photovoice method was used, whereby participants were asked to take photos that represent their typical eating habits. These photos were incorporated as prompts in a semi-structured interview, which explored factors influencing eating habits on night shifts and days-off and perceptions and enablers to healthy eating. Results: Ten participants completed the study. Thematic analysis generated four main themes, which were mapped onto the Social Ecological Model (SEM). Aligned with the SEM, our results show night shift workers’ eating habits are influenced by intrapersonal, interpersonal and (work) organisational levels. Participants reported that at work, appropriate food preparation facilities are required to enable healthy food choices. Poor shift work rostering leads to prolonged fatigue on days-off, limiting their ability and motivation to engage in healthy eating. Consequently, night shift workers seem to require additional supports from their social networks and enhanced food literacy skills, in order to adopt/ maintain healthy eating behaviours. Conclusions: Night shift work creates individual and environmental barriers to healthy eating, which are present during and outside of work. Health promotion strategies for this population should include multiple approaches, targeting these barriers

Deep-sea microbes as tools to refine the rules of innate immune pattern recognition.

The assumption of near-universal bacterial detection by pattern recognition receptors is a foundation of immunology. The limits of this pattern recognition concept, however, remain undefined. As a test of this hypothesis, we determined whether mammalian cells can recognize bacteria that they have never had the natural opportunity to encounter. These bacteria were cultivated from the deep Pacific Ocean, where the genus Moritella was identified as a common constituent of the culturable microbiota. Most deep-sea bacteria contained cell wall lipopolysaccharide (LPS) structures that were expected to be immunostimulatory, and some deep-sea bacteria activated inflammatory responses from mammalian LPS receptors. However, LPS receptors were unable to detect 80% of deep-sea bacteria examined, with LPS acyl chain length being identified as a potential determinant of immunosilence. The inability of immune receptors to detect most bacteria from a different ecosystem suggests that pattern recognition strategies may be defined locally, not globally.R01 AI093589 - NIAID NIH HHS; P30 DK034854 - NIDDK NIH HHS; U19 AI133524 - NIAID NIH HHS; R01 AI147314 - NIAID NIH HHS; R01 AI116550 - NIAID NIH HHS; R37 AI116550 - NIAID NIH HHS; R01 AI123820 - NIAID NIH HHSAccepted manuscrip