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https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#1
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150414/constraints-on-statistical-learning-across-species
#2
REVIEW
Chiara Santolin, Jenny R Saffran
Both human and nonhuman organisms are sensitive to statistical regularities in sensory inputs that support functions including communication, visual processing, and sequence learning. One of the issues faced by comparative research in this field is the lack of a comprehensive theory to explain the relevance of statistical learning across distinct ecological niches. In the current review we interpret cross-species research on statistical learning based on the perceptual and cognitive mechanisms that characterize the human and nonhuman models under investigation...
November 14, 2017: Trends in Cognitive Sciences
https://www.readbyqxmd.com/read/29145972/cancer-immunotherapy-getting-brainy-visualizing-the-distinctive-cns-metastatic-niche-to-illuminate-therapeutic-resistance
#3
Mark Owyong, Niloufar Hosseini-Nassab, Gizem Efe, Alexander Honkala, Renske J E van den Bijgaart, Vicki Plaks, Bryan Ronain Smith
The advent of cancer immunotherapy (CIT) and its success in treating primary and metastatic cancer may offer substantially improved outcomes for patients. Despite recent advancements, many malignancies remain resistant to CIT, among which are brain metastases, a particularly virulent disease with no apparent cure. The immunologically unique niche of the brain has prompted compelling new questions in immuno-oncology such as the effects of tissue-specific differences in immune response, heterogeneity between primary tumors and distant metastases, and the role of spatiotemporal dynamics in shaping an effective anti-tumor immune response...
November 2017: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/29145667/planarians-customize-their-stem-cell-responses-following-genotoxic-stress-as-a-function-of-exposure-time-and-regenerative-state
#4
An-Sofie Stevens, Annelies Wouters, Jan-Pieter Ploem, Nicky Pirotte, Andromeda Van Roten, Maxime Willems, Niels Hellings, Carmen Franken, Gudrun Koppen, Tom Artois, Michelle Plusquin, Karen Smeets
Aiming to in vivo characterise the responses of pluripotent stem cells and regenerative tissues to carcinogenic stress, we employed the highly regenerative organism Schmidtea mediterranea. Its broad regenerative capacities are attributable to a large pool of pluripotent stem cells, which are considered key players in the lower vulnerability towards chemically-induced carcinogenesis observed in regenerative organisms. S. mediterranea is, therefore, an ideal model to study pluripotent stem cell responses with stem cells residing in their natural environment...
November 14, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29145456/regulation-of-the-bone-marrow-microenvironment-by-g-csf-effects-of-g-csf-on-acute-lymphoblastic-leukaemia
#5
Jordan Basnett, Vicki Xie, Adam Cisterne, Ken Bradstock, Linda Bendall
It has been suggested that disruption of the lymphoid niche by G-CSF may be of therapeutic benefit to patients with acute lymphoblastic leukaemia. We used a xenograft model to determine the effect of G-CSF on ALL progression in a minimal residual disease setting. Consistent with the effects on normal murine B cell progenitors, G-CSF slowed disease in the majority of ALL xenografts tested, suggesting that G-CSF may provide benefits beyond neutrophil recovery for ALL patients. However, two of eight xenografts demonstrated accelerated disease progression...
2017: PloS One
https://www.readbyqxmd.com/read/29145425/statistical-analysis-of-co-occurrence-patterns-in-microbial-presence-absence-datasets
#6
Kumar P Mainali, Sharon Bewick, Peter Thielen, Thomas Mehoke, Florian P Breitwieser, Shishir Paudel, Arjun Adhikari, Joshua Wolfe, Eric V Slud, David Karig, William F Fagan
Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy...
2017: PloS One
https://www.readbyqxmd.com/read/29141765/bionomics-and-spatial-distribution-of-triatomine-vectors-of-trypanosoma-cruzi-in-texas-and-other-southern-states-usa
#7
Rachel Curtis-Robles, Sarah A Hamer, Sage Lane, Michael Z Levy, Gabriel L Hamer
Defining spatial and temporal occurrences of triatomine vectors of Trypanosoma cruzi, the agent of Chagas disease, in the US is critical for public health protection. Through a citizen science program and field collections from 2012 to 2016, we collected 3,215 triatomines, mainly from Texas. Using morphological and molecular approaches, we identified seven Triatoma species and report sex, length, and blood engorgement status. Many citizen-collected triatomines (92.9%) were encountered indoors, in peridomestic settings, or in dog kennels and represent spillover transmission risk of T...
November 6, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29141657/local-estrogen-axis-in-the-human-bone-microenvironment-regulates-estrogen%C3%A2-receptor-positive%C3%A2-breast-cancer-cells
#8
Derek F Amanatullah, John S Tamaresis, Pauline Chu, Michael H Bachmann, Nhat M Hoang, Deborah Collyar, Aaron T Mayer, Robert B West, William J Maloney, Christopher H Contag, Bonnie L King
BACKGROUND: Approximately 70% of all breast cancers express the estrogen receptor, and are regulated by estrogen. While the ovaries are the primary source of estrogen in premenopausal women, most breast cancer is diagnosed following menopause, when systemic levels of this hormone decline. Estrogen production from androgen precursors is catalyzed by the aromatase enzyme. Although aromatase expression and local estrogen production in breast adipose tissue have been implicated in the development of primary breast cancer, the source of estrogen involved in the regulation of estrogen receptor-positive (ER+) metastatic breast cancer progression is less clear...
November 15, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29137633/bi-directional-exosome-driven-intercommunication-between-the-hepatic-niche-and-cancer-cells
#9
Nikolina Dioufa, Amanda M Clark, Bo Ma, Colin H Beckwitt, Alan Wells
BACKGROUND: Our understanding of the multiple roles exosomes play during tumor progression is still very poor and the contribution of the normal tissue derived exosomes in distant seeding and tumor outgrowth has also not been widely appreciated. METHODS: Using our all-human liver microphysiological system (MPS) platform as a model to closely recapitulate the early metastatic events, we isolated exosomes from both tumor cells and liver microenvironment. RESULTS: We observed that while priming of the hepatic niche (HepN) with MDA-231 breast cancer derived exosomes facilitated seeding of the cancer cells in the liver, subsequent tumor outgrowth was diminished; this was consistent with increased entry into dormancy...
November 14, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/29134056/semicircular-canals-in-anolis-lizards-ecomorphological-convergence-and-ecomorph-affinities-of-fossil-species
#10
Blake V Dickson, Emma Sherratt, Jonathan B Losos, Stephanie E Pierce
Anolis lizards are a model system for the study of adaptive radiation and convergent evolution. Greater Antillean anoles have repeatedly evolved six similar forms or ecomorphs: crown-giant, grass-bush, twig, trunk, trunk-crown and trunk-ground. Members of each ecomorph category possess a specific set of morphological, ecological and behavioural characteristics which have been acquired convergently. Here we test whether the semicircular canal system-the organ of balance during movement-is also convergent among ecomorphs, reflecting the shared sensory requirements of their ecological niches...
October 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/29132298/population-genetic-structure-is-shaped-by-historical-geographic-and-environmental-factors-in-the-leguminous-shrub-caragana-microphylla-on-the-inner-mongolia-plateau-of-china
#11
Bo Xu, Guoli Sun, Xuemin Wang, Jingwei Lu, Ian J Wang, Zan Wang
BACKGROUND: Understanding how landscape factors, including suites of geographic and environmental variables, and both historical and contemporary ecological and evolutionary processes shape the distribution of genetic diversity is a primary goal of landscape and conservation genetics and may be particularly consequential for species involved in ecological restoration. In this study, we examine the factors that shape the distribution of genetic variation in a leguminous shrub (Caragana microphylla) important for restoration efforts on the Mongolian Plateau in China...
November 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29131827/the-interplay-of-various-sources-of-noise-on-reliability-of-species-distribution-models-hinges-on-ecological-specialisation
#12
Alaaeldin Soultan, Kamran Safi
Digitized species occurrence data provide an unprecedented source of information for ecologists and conservationists. Species distribution model (SDM) has become a popular method to utilise these data for understanding the spatial and temporal distribution of species, and for modelling biodiversity patterns. Our objective is to study the impact of noise in species occurrence data (namely sample size and positional accuracy) on the performance and reliability of SDM, considering the multiplicative impact of SDM algorithms, species specialisation, and grid resolution...
2017: PloS One
https://www.readbyqxmd.com/read/29129979/hair-germ-model-in-vitro-via-human-postnatal-keratinocyte-dermal-papilla-interactions-impact-of-hyaluronic-acid
#13
Ekaterina Kalabusheva, Vasily Terskikh, Ekaterina Vorotelyak
Hair follicle (HF) reconstruction in vitro is a promising field in alopecia treatment and human HF development research. Here, we combined postnatal human dermal papilla (DP) cells and skin epidermal keratinocytes (KCs) in a hanging drop culture to develop an artificial HF germ. The method is based on DP cell hair-inducing properties and KC self-organization. We evaluated two protocols of aggregate assembling. Mixed HF germ-like structures demonstrated the initiation of epithelial-mesenchymal interaction, including WNT pathway activation and expression of follicular markers...
2017: Stem Cells International
https://www.readbyqxmd.com/read/29129690/monoterpenoid-perillyl-alcohol-impairs-metabolic-flexibility-of-candida-albicans-by-inhibiting-glyoxylate-cycle
#14
Moiz A Ansari, Zeeshan Fatima, Kamal Ahmad, Saif Hameed
The metabolic pathway such as glyoxylate cycle (GC) enables Candida albicans, to survive under glucose deficient conditions prevalent in the hostile niche. Thus its key enzymes (Isocitrate lyase; ICL and malate synthase; MLS) represent attractive targets against C. albicans. We have previously reported the antifungal potential of a natural monoterpenoid perillyl alcohol (PA). The present study uncovers additional role of PA as a potent GC inhibitor. We explored that PA phenocopied ICL1 deletion mutant and were hypersensitive under low carbon utilizing conditions...
November 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29129523/higher-order-kidney-organogenesis-from-pluripotent-stem-cells
#15
Atsuhiro Taguchi, Ryuichi Nishinakamura
Organogenesis generates higher-order structures containing functional subunits, connective components, and progenitor niches. Despite recent advances in organoid-based modeling of tissue development, recapitulating these complex configurations from pluripotent stem cells (PSCs) has remained challenging. In this study, we report assembly of kidney organoids that recapitulate embryonic branching morphogenesis. By studying the distinct origins and developmental processes of the ureteric bud, which contains epithelial kidney progenitors that undergo branching morphogenesis and thereby plays a central role in orchestrating organ geometry, and neighboring mesenchymal nephron progenitors, we established a protocol for differential induction of each lineage from mouse and human PSCs...
November 4, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/29128951/insights-from-the-genomes-of-microbes-thriving-in-uranium-enriched-sediments
#16
Brodie Sutcliffe, Anthony A Chariton, Andrew J Harford, Grant C Hose, Sarah Stephenson, Paul Greenfield, David J Midgley, Ian T Paulsen
Elevated uranium dose (4 g kg(-1)) causes a shift in billabong sediment communities that result in the enrichment of five bacterial species. These taxa include Geobacter, Geothrix and Dyella species, as well as a novel-potentially predatory-Bacteroidetes species, and a new member of class Anaerolineae (Chloroflexi). Additionally, a population of methanogenic Methanocella species was also identified. Genomic reconstruction and metabolic examination of these taxa reveal a host of divergent life strategies and putative niche partitioning...
November 11, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/29126191/evolution-of-exploitative-interactions-during-diversification-in-bacillus-subtilis-biofilms
#17
Anna Dragoš, Nivedha Lakshmanan, Marivic Martin, Balázs Horváth, Gergely Maróti, Carolina Falcón García, Oliver Lieleg, Ákos T Kovács
Microbial biofilms are tightly packed, heterogeneous structures that serve as arenas for social interactions. Studies on Gram negative models reveal that during evolution in structured environments like biofilms, isogenic populations commonly diversify into phenotypically and genetically distinct variants. These variants can settle in alternative biofilm niches and develop new types of interactions that greatly influence population productivity. Here, we explore the evolutionary diversification of pellicle biofilms of the Gram positive, spore-forming bacterium Bacillus subtilis...
November 8, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29125596/contrasting-the-relative-importance-of-species-sorting-and-dispersal-limitation-in-shaping-marine-bacterial-versus-protist-communities
#18
Wenxue Wu, Hsiao-Pei Lu, Akash Sastri, Yi-Chun Yeh, Gwo-Ching Gong, Wen-Chen Chou, Chih-Hao Hsieh
A central challenge in microbial ecology is to understand the underlying mechanisms driving community assembly, particularly in the continuum of species sorting and dispersal limitation. However, little is known about the relative importance of species sorting and dispersal limitation in shaping marine microbial communities; especially, how they are related to organism types/traits and water depth. Here, we used variation partitioning and null model analysis to compare mechanisms driving bacterial and protist metacommunity dynamics at the basin scale in the East China Sea, based on MiSeq paired-end sequencing of 16S ribosomal DNA (rDNA) and 18S rDNA, respectively, in surface, deep chlorophyll maximum and bottom layers...
November 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/29124854/thermoacclimation-and-genome-adaptation-of-the-membrane-lipidome-in-marine-synechococcus
#19
Justine Pittera, Juliette Jouhet, Solène Breton, Laurence Garczarek, Frédéric Partensky, Éric Maréchal, Ngoc An Nguyen, Hugo Doré, Morgane Ratin, Frances D Pitt, David J Scanlan, Christophe Six
The marine cyanobacteria of the genus Synechococcus are important primary producers, displaying a wide latitudinal distribution that is underpinned by diversification into temperature ecotypes. The physiological basis underlying these ecotypes is poorly known. In many organisms, regulation of membrane fluidity is crucial for acclimating to variations in temperature. Here, we reveal the detailed composition of the membrane lipidome of the model strain Synechococcus sp. WH7803 and its response to temperature variation...
November 10, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29124393/the-systemic-environment-at-the-interface-of-aging-and-adult-neurogenesis
#20
REVIEW
Lucas K Smith, Charles W White, Saul A Villeda
Aging results in impaired neurogenesis in the two neurogenic niches of the adult mammalian brain, the dentate gyrus of the hippocampus and the subventricular zone of the lateral ventricle. While significant work has characterized intrinsic cellular changes that contribute to this decline, it is increasingly apparent that the systemic environment also represents a critical driver of brain aging. Indeed, emerging studies utilizing the model of heterochronic parabiosis have revealed that immune-related molecular and cellular changes in the aging systemic environment negatively regulate adult neurogenesis...
November 9, 2017: Cell and Tissue Research
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