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Land use/land cover change from forested to developed land is a major threat to freshwater biodiversity globally. However, existing research has focused on high-density development in urban centers. We know less about how low-density development affects stream biodiversity, even though increases in low-density development have been documented across the globe and may be tied to the homogenization of stream biotic assemblages. Here, we investigated the diversity (alpha and beta) and assemblage composition of algal diatoms and fish over a ten-year period at three points in time (2000, 2005, 2010) in forested watersheds (n = 4) and watersheds experiencing increasing low-density development (“developing watersheds”; n = 4) in the southern Appalachian Mountains of western North Carolina, USA. We employed a repeated snapshot sampling approach for the data collection. In developing watersheds, we observed higher alpha diversity and different species assemblages for both diatoms and fishes compared to forested watersheds. These differences were attributed to the establishment and/or higher abundances of cosmopolitan diatoms (e.g., Achnanthidium rivulare Potapova and Ponader, Navicula spp., Nitzschia spp.) as well as fishes (e.g., Creek Chub [Semotilus atromaculatus] and Blacknose Dace [Rhinichthys atratulus]). Most endemic species persisted in developing reaches, but in lower abundances (e.g., diatoms: Meridion alansmithii Brant; fishes: Mottled Sculpin [Cottus bairdi]). Diatom beta diversity within developing reaches was lower compared to forested reaches, and lower in 2005 and 2010 compared to 2000. Diatom assemblage composition also changed over time in developing reaches but remained stable in forested reaches. In contrast, fish beta diversity showed no significant differences between watershed types or among years, suggesting that diatom assemblages may respond more quickly or to lower levels of watershed development than fish assemblages. We conclude that biotic assemblages in streams draining developing watersheds in southern Appalachia show evidence of homogenization, but not yet extirpation of endemic taxa. Our study demonstrates the importance of understanding the effects of low-density development on biodiversity in stream ecosystems around the world before native species are lost.

Abstract Background Weaning stress reduces growth performance and health of young pigs due in part to an abrupt change in diets from highly digestible milk to fibrous plant-based feedstuffs. This study investigated whether dietary galactooligosaccharide (GOS), supplemented both pre- and post-weaning, could improve growth performance and intestinal health via alterations in the hindgut microbial community. Methods Using a 3 × 2 factorial design, during farrowing 288 piglets from 24 litters received either no creep feed (FC), creep without GOS (FG–) or creep with 5% GOS (FG+) followed by a phase 1 nursery diet without (NG–) or with 3.8% GOS (NG+). Pigs were sampled pre- (D22) and post-weaning (D31) to assess intestinal measures. Results Creep fed pigs grew 19% faster than controls (P

Abstract Red blood cells (RBCs) stored in blood bags develop a storage lesion that include structural, metabolic, and morphologic transformations resulting in a progressive loss of RBC deformability. The speed of RBC deformability loss is donor‐dependent, which if properly characterized, could be used as a biomarker to select high‐quality RBC units for sensitive recipients or to provide customized storage timelines depending on the donor. We used the microfluidic ratchet device to measure the deformability of red blood cells stored in blood bags every 14 days over a span of 56 days. We observed that storage in blood bags generally prevented RBC deformability loss over the current standard 42‐day storage window. However, between 42 and 56 days, the deformability loss profile varied dramatically between donors. In particular, we observed accelerated RBC deformability loss for a majority of male donors, but for none of the female donors. Together, our results suggest that RBC deformability loss could be used to screen for donors who can provide stable RBCs for sensitive transfusion recipients or to identify donors capable of providing RBCs that could be stored for longer than the current 42‐day expiration window.

IntroductionBeta diversity represents changes in community composition among locations across a landscape. While the effects of human activities on beta diversity are becoming clearer, few studies have considered human effects on the three dimensions of beta diversity: taxonomic, functional, and phylogenetic. Including anthropogenic factors and multiple dimensions of biodiversity may explain additional variation in stream fish beta diversity, providing new insight into how metacommunities are structured within different spatial delineations.MethodsIn this study, we used a 350 site stream fish abundance dataset from South Carolina, United States to quantify beta diversity explainable by spatial, natural environmental, and anthropogenic variables. We investigated three spatial delineations: (1) a single whole-state metacommunity delineated by political boundaries, (2) two metacommunities delineated by a natural geomorphic break separating uplands from lowlands, and (3) four metacommunities delineated by natural watershed boundaries. Within each metacommunity we calculated taxonomic, functional, and phylogenetic beta diversity and used variation partitioning to quantify spatial, natural environmental, and anthropogenic contributions to variations in beta diversity.ResultsWe explained 25–81% of the variation in stream fish beta diversity. The importance of these three factors in structuring metacommunities differed among the diversity dimensions, providing complementary perspectives on the processes shaping beta diversity in fish communities. The effect of spatial, natural environmental, and anthropogenic factors varied among the spatial delineations, which indicate conclusions drawn from variation partitioning may depend on the spatial delineation chosen by researchers.DiscussionOur study highlights the importance of considering human effects on metacommunity structure, quantifying multiple dimensions of beta diversity, and careful consideration of user-defined metacommunity boundaries in beta diversity analyses.

Manual analysis of human high-resolution colonic manometry data is time consuming, non-standardized and subject to laboratory bias. In this article we present a technique for spectral analysis and statistical inference of quasiperiodic spatiotemporal signals recorded during colonic manometry procedures. Spectral analysis is achieved by computing the continuous wavelet transform and cross-wavelet transform of these signals. Statistical inference is achieved by modeling the resulting time-averaged amplitudes in the frequency and frequency-phase domains as Gaussian processes over a regular grid, under the influence of categorical and numerical predictors specified by the experimental design as a functional mixed-effects model. Parameters of the model are inferred with Hamiltonian Monte Carlo. Using this method, we re-analyzed our previously published colonic manometry data, comparing healthy controls and patients with slow transit constipation. The output from our automated method, supports and adds to our previous manual analysis. To obtain these results took less than two days. In comparison the manual analysis took 5 weeks. The proposed mixed-effects model approach described here can also be used to gain an appreciation of cyclical activity in individual subjects during control periods and in response to any form of intervention.

Neisseria meningitidis bacteria bind to host proteins CD147 and β2-adrenergic receptor on the surface of endothelial cells. Here, Maïssa et al. show that the two proteins interact with each other forming clusters that increase the binding strength of the bacteria to endothelial cells.

Understanding rumen plant–microbe interactions is central for development of novel methodologies allowing improvements in ruminant nutrient use efficiency. This study investigated rumen bacterial colonization of fresh plant material and changes in plant chemistry over a period of 24 h period using three different fresh forages: Lolium perenne (perennial ryegrass; PRG), Lotus corniculatus (bird’s foot trefoil; BFT) and Trifolium pratense (red clover; RC). We show using 16S rRNA gene ion torrent sequencing that plant epiphytic populations present pre-incubation (0 h) were substantially different to those attached post incubations in the presence of rumen fluid on all forages. Thereafter primary and secondary colonization events were evident as defined by changes in relative abundances of attached bacteria and changes in plant chemistry, as assessed using Fourier transform infrared (FTIR) spectroscopy. For PRG colonization, primary colonization occurred for up to 4 h and secondary colonization from 4 h onward. The changes from primary to secondary colonization occurred significantly later with BFT and RC, with primary colonization being up to 6 h and secondary colonization post 6 h of incubation. Across all 3 forages the main colonizing bacteria present at all time points post-incubation were Prevotella, Pseudobutyrivibrio, Ruminococcus, Olsenella, Butyrivibrio, and Anaeroplasma (14.2, 5.4, 1.9, 2.7, 1.8, and 2.0% on average respectively), with Pseudobutyrivibrio and Anaeroplasma having a higher relative abundance during secondary colonization. Using CowPI, we predict differences between bacterial metabolic function during primary and secondary colonization. Specifically, our results infer an increase in carbohydrate metabolism in the bacteria attached during secondary colonization, irrespective of forage type. The CowPI data coupled with the FTIR plant chemistry data suggest that attached bacterial function is similar irrespective of forage type, with the main changes occurring between primary and secondary colonization. These data suggest that the sward composition of pasture may have major implications for the temporal availability of nutrients for animal.

Measuring three-dimensional (3D) localization of hematopoietic stem cells (HSCs) within the bone marrow microenvironment using intravital microscopy is a rapidly expanding research theme. This approach holds the key to understanding the detail of HSC-niche interactions, which are critical for appropriate stem cell function. Due to the complex tissue architecture of the bone marrow and to the progressive introduction of scattering and signal loss at increasing imaging depths, there is no ready-made software to handle efficient segmentation and unbiased analysis of the data. To address this, we developed an automated image analysis tool that simplifies and standardizes the biological interpretation of 3D HSC microenvironment images. The algorithm identifies HSCs and measures their localization relative to surrounding osteoblast cells and bone collagen. We demonstrate here the effectiveness, consistency, and accuracy of the proposed approach compared to current manual analysis and its wider applicability to analyze other 3D bone marrow components.

Abstract Forty‐two cell lines recapitulating mammary carcinoma heterogeneity were profiled for all‐trans retinoic acid (ATRA) sensitivity. Luminal and ER+ (estrogen‐receptor‐positive) cell lines are generally sensitive to ATRA, while refractoriness/low sensitivity is associated with a Basal phenotype and HER2 positivity. Indeed, only 2 Basal cell lines (MDA‐MB157 and HCC‐1599) are highly sensitive to the retinoid. Sensitivity of HCC‐1599 cells is confirmed in xenotransplanted mice. Short‐term tissue‐slice cultures of surgical samples validate the cell‐line results and support the concept that a high proportion of Luminal/ER+ carcinomas are ATRA sensitive, while triple‐negative (Basal) and HER2‐positive tumors tend to be retinoid resistant. Pathway‐oriented analysis of the constitutive gene‐expression profiles in the cell lines identifies RARα as the member of the retinoid pathway directly associated with a Luminal phenotype, estrogen positivity and ATRA sensitivity. RARα3 is the major transcript in ATRA‐sensitive cells and tumors. Studies in selected cell lines with agonists/antagonists confirm that RARα is the principal mediator of ATRA responsiveness. RARα over‐expression sensitizes retinoid‐resistant MDA‐MB453 cells to ATRA anti‐proliferative action. Conversely, silencing of RARα in retinoid‐sensitive SKBR3 cells abrogates ATRA responsiveness. All this is paralleled by similar effects on ATRA‐dependent inhibition of cell motility, indicating that RARα may mediate also ATRA anti‐metastatic effects. We define gene sets of predictive potential which are associated with ATRA sensitivity in breast cancer cell lines and validate them in short‐term tissue cultures of Luminal/ER+ and triple‐negative tumors. In these last models, we determine the perturbations in the transcriptomic profiles afforded by ATRA. The study provides fundamental information for the development of retinoid‐based therapeutic strategies aimed at the stratified treatment of breast cancer subtypes.

PTEN controls three-dimensional (3D) glandular morphogenesis by coupling juxtamembrane signaling to mitotic spindle machinery. While molecular mechanisms remain unclear, PTEN interacts through its C2 membrane-binding domain with the scaffold protein β-Arrestin1. Because β-Arrestin1 binds and suppresses the Cdc42 GTPase-activating protein ARHGAP21, we hypothesize that PTEN controls Cdc42 -dependent morphogenic processes through a β-Arrestin1-ARHGAP21 complex. Here, we show that PTEN knockdown (KD) impairs β-Arrestin1 membrane localization, β-Arrestin1-ARHGAP21 interactions, Cdc42 activation, mitotic spindle orientation and 3D glandular morphogenesis. Effects of PTEN deficiency were phenocopied by β-Arrestin1 KD or inhibition of β-Arrestin1-ARHGAP21 interactions. Conversely, silencing of ARHGAP21 enhanced Cdc42 activation and rescued aberrant morphogenic processes of PTEN-deficient cultures. Expression of the PTEN C2 domain mimicked effects of full-length PTEN but a membrane-binding defective mutant of the C2 domain abrogated these properties. Our results show that PTEN controls multicellular assembly through a membrane-associated regulatory protein complex composed of β-Arrestin1, ARHGAP21 and Cdc42.