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niche modeling

Jana Jakubikova, Danka Cholujova, Teru Hideshima, Paulina Gronesova, Andrea Soltysova, Takeshi Harada, Jungnam Joo, Sun-Young Kong, Raphael E Szalat, Paul G Richardson, Nikhil C Munshi, David M Dorfman, Kenneth C Anderson
Specific niches within the tumor bone marrow (BM) microenvironment afford a sanctuary for multiple myeloma (MM) clones due to stromal cell-tumor cell interactions, which confer survival advantage and drug resistance. Defining the sequelae of tumor cell interactions within the MM niches on an individualized basis may provide the rationale for personalized therapies. To mimic the MM niche, we here describe a new 3D co-culture ex-vivo model in which primary MM patient BM cells are co-cultured with mesenchymal stem cells (MSC) in a hydrogel 3D system...
October 13, 2016: Oncotarget
Alberto Muñoz, Xavier Santos, Ángel M Felicísimo
Ecological Niche Models (ENMs) are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area...
2016: PeerJ
Jeffrey D Kline, Mark E Harmon, Thomas A Spies, Anita T Morzillo, Robert J Pabst, Brenda C McComb, Frank Schnekenburger, Keith A Olsen, Blair Csuti, Jody C Vogeler
Forest policymakers and managers have long sought ways to evaluate the capability of forest landscapes to jointly produce timber, habitat, and other ecosystem services in response to forest management. Currently, carbon is of particular interest as policies for increasing carbon storage on federal lands are being proposed. However, a challenge in joint production analysis of forest management is adequately representing ecological conditions and processes that influence joint production relationships. We used simulation models of vegetation structure, forest sector carbon, and potential wildlife habitat to characterize landscape-level joint production possibilities for carbon storage, timber harvest, and habitat for seven wildlife species across a range of forest management regimes...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
Guilherme V T Ribeiro, Alberto L Teixido, Newton P U Barbosa, Fernando A O Silveira
Sampling biases permeate ecological research and result in knowledge gaps that have vital consequences for conservation planning. The consequences of knowledge gaps on species identity and distribution (the Wallacean and Linnean shortfalls, respectively) have become apparent recently, but we know little about the extent that research biases and knowledge gaps on traits that influence species' niches (the Hutchinsonian shortfall) affect conservation policy. To examine whether knowledge of species' traits based on seed ecology is geographically, phylogenetically, and ecologically biased, we retrieved research data on seed germination, seed dormancy, seed dispersal, seed banks, seed predation, and seed removal from a database of 847 papers, 1648 species, and 5322 cases...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
Kimberly Cuevas, Amy Giles
Sensory preconditioning (SPC) is a form of latent learning in which preexposure to co-occurring neutral stimuli (S1 -S2 ) permits subsequent learning to be transferred from one stimulus (S1 ) to the other (S2 ). We examined whether human infants exhibit developmental transitions in the temporal parameters of SPC by manipulating the preexposure regimen. Infants received simultaneous or sequential preexposure to puppets S1 and S2 (Days 1-2); saw target actions modeled on S1 (Day 3); and were tested for deferred imitation with S2 (Day 4)...
November 2016: Developmental Psychobiology
Antonino Carbone, Annunziata Gloghini, Arnaldo Caruso, Paolo De Paoli, Riccardo Dolcetti
The pathogenesis of classical Hodgkin lymphoma (cHL) is still enigmatic, largely because its tumor cells, the so-called Hodgkin and Reed-Stenberg (HRS) cells, invariably reside in a prominent reactive microenvironment, are rare and therefore difficult to analyze. On the other hand, the broadly investigated cHL-derived cell lines are not unequivocally considered as suitable and representative models for this puzzling disease. Based on current knowledge, it appears that the cross talk between the tumour cells and the reactive infiltrate of the microenvironment is complex and that multiple mechanisms occur, making cHL a very heterogeneous disease...
October 17, 2016: International Journal of Cancer. Journal International du Cancer
Olga De Castro, Antonietta Di Maio, Mirko Di Febbraro, Gennaro Imparato, Michele Innangi, Errol Véla, Bruno Menale
The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae), which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM), present (CURR), near-future (FUT)} and (2) the possible influence of environmental variables on the genetic structure of this species in the current period...
2016: PloS One
Flora Clément, Xinyi Xu, Caterina F Donini, Alice Clément, Soleilmane Omarjee, Emmanuel Delay, Isabelle Treilleux, Béatrice Fervers, Muriel Le Romancer, Pascale A Cohen, Véronique Maguer-Satta
Bone morphogenetic protein 2 (BMP2) and BMP4 are key regulators of the fate and differentiation of human mammary epithelial stem cells (SCs), as well as of their niches, and are involved in breast cancer development. We established that MCF10A immature mammary epithelial cells reliably reproduce the BMP response that we previously identified in human primary epithelial SCs. In this model, we observed that BMP2 promotes luminal progenitor commitment and expansion, whereas BMP4 prevents lineage differentiation...
October 14, 2016: Cell Death and Differentiation
Meghan Zuck, Tisha Ellis, Anthony Venida, Kevin Hybiske
The precise strategies that intracellular pathogens use to exit host cells have a direct impact on their ability to disseminate within a host, transmit to new hosts, and engage or avoid immune responses. The obligate intracellular bacterium Chlamydia trachomatis exits the host cell by two distinct exit strategies, lysis and extrusion. The defining characteristics of extrusions, and advantages gained by Chlamydia within this unique double-membrane structure are not well understood. Here, we define extrusions as being largely devoid of host organelles, comprised mostly of Chlamydia elementary bodies, and containing phosphatidylserine on the outer surface of the extrusion membrane...
October 14, 2016: Cellular Microbiology
Bryce A Richardson, Lindsay Chaney, Nancy L Shaw, Shannon M Still
Rising temperatures have begun to shift flowering time, but it is unclear whether phenotypic plasticity can accommodate projected temperature change for this century. Evaluating clines in phenological traits and the extent and variation in plasticity can provide key information on assessing risk of maladaptation and developing strategies to mitigate climate change. In this study, flower phenology was examined in 52 populations of big sagebrush (Artemisia tridentata) growing in three common gardens. Flowering date (anthesis) varied 91 days from late July to late November among gardens...
October 14, 2016: Global Change Biology
A Mas, L Stone, P M O'Connor, Q Yang, D T Kleven, C Simon, C L Walker, A Al-Hendy
Despite the high prevalence and major negative impact of uterine fibroids (UFs) on women's health, their pathogenesis remains largely unknown. While tumor initiating cells (TICs) have been previously isolated from UFs, the cell of origin for these tumors in normal myometrium has not been identified. We isolated cells with Stro1/CD44 surface markers from normal myometrium expressing stem cell markers Oct-4/c-kit/nanog that exhibited the properties of myometrial stem/progenitor-like cells (MSCs). Using a murine model for UFs, we showed that the cervix was a hypoxic "niche" and primary site (96%) for fibroid development in these animals...
October 14, 2016: Stem Cells
Judith Pérez-Velázquez, Jana L Gevertz, Aleksandra Karolak, Katarzyna A Rejniak
A tumor vasculature that is functionally abnormal results in irregular gradients of metabolites and drugs within the tumor tissue. Recently, significant efforts have been committed to experimentally examine how cellular response to anti-cancer treatments varies based on the environment in which the cells are grown. In vitro studies point to specific conditions in which tumor cells can remain dormant and survive the treatment. In vivo results suggest that cells can escape the effects of drug therapy in tissue regions that are poorly penetrated by the drugs...
2016: Advances in Experimental Medicine and Biology
Ardeshir Kianercy, Kenneth J Pienta
Bone, which includes several cell populations and numerous cytokines and chemokines that provide cell-cell signaling, is a common destination for many cancer metastases. Bone metastasis skews this signaling to develop vicious cycles between immune, bone and cancer populations that lead to abnormal bone remodeling during cancer niche construction. Temporal models utilize positive feedback systems as an integrative tool providing insights into the rate-limiting processes that determine multiple stages of the bone metastasis...
2016: Advances in Experimental Medicine and Biology
Ricardo Siqueira da Silva, Lalit Kumar, Farzin Shabani, Ezio Marques da Silva, Tarcisio Visintin da Silva Galdino, Marcelo Coutinho Picanço
Seasonal variations are important components in understanding the ecology of insect population of crops. Ecological studies through modeling may be a useful tool for enhancing knowledge of seasonal patterns of insects on field crops as well as seasonal patterns of favorable climatic conditions for species. Recently CLIMEX, a semi-mechanistic niche model, was upgraded and enhanced to consider spatio-temporal dynamics of climate suitability through time. In this study, attempts were made to determine monthly variations of climate suitability for Neoleucinodes elegantalis (Guenée) (Lepidoptera: Crambidae) in five commercial tomato crop localities through the latest version of CLIMEX...
October 13, 2016: International Journal of Biometeorology
Denada Dibra, Abhisek Mitra, Melissa Newman, Xueqing Xia, Camille Keenan, Jeffry J Cutrera, J Michael Mathis, Xiao-Jing Wang, Jeffrey Myers, Shulin Li
Establishment of a permissive pre-malignant niche in concert with mutant stem are key triggers to initiate skin carcinogenesis. An understudied area of research is finding upstream regulators of both these triggers. IL27, a pleiotropic cytokine with both pro- and anti-inflammatory properties, was found to be a key regulator of both. Two step skin carcinogenesis model and K15-KRASG12D mouse model were used to understand the role of IL27 in skin tumors. CD11b-/- mice and small-molecule of ETAR signaling (ZD4054) inhibitor were used in vivo to understand mechanistically how IL27 promotes skin carcinogenesis...
October 12, 2016: Oncotarget
Madhav V Dhodapkar
All cases of multiple myeloma (MM) are preceded by precursor states termed as monoclonal gammopathy of undetermined significance (MGUS) or smoldering myeloma (SMM). Genetic analyses of MGUS cells have provided evidence that it is a genetically advanced lesion wherein tumor cells carry many of the genetic changes found in MM cells. Intraclonal heterogeneity is also established early during the MGUS phase. While the genetic features of MGUS or SMM cells at baseline may predict disease risk, transition to MM involves altered growth of pre-existing clones...
October 13, 2016: Blood
Luciana Cristina Vitorino, Matheus S Lima-Ribeiro, Levi Carina Terribile, Rosane G Collevatti
BACKGROUND: We studied the phylogeography and demographical history of Tabebuia serratifolia (Bignoniaceae) to understand the disjunct geographical distribution of South American seasonally dry tropical forests (SDTFs). We specifically tested if the multiple and isolated patches of SDTFs are current climatic relicts of a widespread and continuously distributed dry forest during the last glacial maximum (LGM), the so called South American dry forest refugia hypothesis, using ecological niche modelling (ENM) and statistical phylogeography...
October 13, 2016: BMC Evolutionary Biology
Paula Villa Martín, Jorge Hidalgo, Rafael Rubio de Casas, Miguel A Muñoz
Evolutionary and ecosystem dynamics are often treated as different processes -operating at separate timescales- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field experiment has explicitly shown that communities of competing plant species can experience very fast phenotypic diversification, and that this gives rise to enhanced complementarity in resource exploitation and to enlarged ecosystem-level productivity. Here, we build on progress made in recent years in the integration of eco-evolutionary dynamics, and present a computational approach aimed at describing these empirical findings in detail...
October 2016: PLoS Computational Biology
Sarah L Crittenden, Hannah S Seidel, Judith Kimble
The Caenorhabditis elegans germline is an excellent model for studying the regulation of a pool of stem cells and progression of cells from a stem cell state to a differentiated state. At the tissue level, the germline is organized in an assembly line with the germline stem cell (GSC) pool at one end and differentiated cells at the other. A simple mesenchymal niche caps the GSC region of the germline and maintains GSCs in an undifferentiated state by signaling through the conserved Notch pathway. Downstream of Notch signaling, key regulators include novel LST-1 and SYGL-1 proteins and a network of RNA regulatory proteins...
2017: Methods in Molecular Biology
Antonella Antonelli, Willy A Noort, Jenny Jaques, Bauke de Boer, Regina de Jong-Korlaar, Annet Z Brouwers-Vos, Linda Lubbers-Aalders, Jeroen F van Velzen, Andries C Bloem, Huipin Yuan, Joost D de Bruijn, Gert J Ossenkoppele, Anton C M Martens, Edo Vellenga, Richard W J Groen, Jan Jacob Schuringa
In order to begin to understand mechanisms that regulate self-renewal, differentiation and transformation of human hematopoietic stem cells, or to evaluate the efficacy of novel treatment modalities, stem cells need to be studied in their own species-specific microenvironment. By implanting ceramic scaffolds coated with human mesenchymal stromal cells (MSCs) into immune deficient mice we mimic the human bone marrow niche. Thus, we have established a human leukemia xenograft mouse model in which a large cohort of patient samples successfully engrafted covering all important genetic and risk subgroups...
October 12, 2016: Blood
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