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https://www.readbyqxmd.com/read/29354282/regulatory-feedback-response-mechanisms-to-phosphate-starvation-in-rice
#1
Ishan Ajmera, Jing Shi, Jitender Giri, Ping Wu, Dov J Stekel, Chungui Lu, T Charlie Hodgman
Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques...
2018: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/29353950/a-hybrid-three-scale-model-of-tumor-growth
#2
H L Rocha, R C Almeida, E A B F Lima, A C M Resende, J T Oden, T E Yankeelov
Cancer results from a complex interplay of different biological, chemical, and physical phenomena that span a wide range of time and length scales. Computational modeling may help to unfold the role of multiple evolving factors that exist and interact in the tumor microenvironment. Understanding these complex multiscale interactions is a crucial step towards predicting cancer growth and in developing effective therapies. We integrate different modeling approaches in a multiscale, avascular, hybrid tumor growth model encompassing tissue, cell, and sub-cell scales...
January 2018: Mathematical Models & Methods in Applied Sciences: M3AS
https://www.readbyqxmd.com/read/29351758/autophagy-promotes-metastasis-and-glycolysis-by-upregulating-mct1-expression-and-wnt-%C3%AE-catenin-signaling-pathway-activation-in-hepatocellular-carcinoma-cells
#3
Qing Fan, Liang Yang, Xiaodong Zhang, Yingbo Ma, Yan Li, Lei Dong, Zhihong Zong, Xiangdong Hua, Dongming Su, Hangyu Li, Jingang Liu
BACKGROUND: Autophagy is a dynamic physiological process that can generate energy and nutrients for cell survival during stress. Autophagy can regulate the migration and invasive ability in cancer cells. However, the connection between autophagy and metabolism is unclear. Monocarboxylate transporter 1 (MCT1) plays an important role in lactic acid transport and H+ clearance in cancer cells, and Wnt/β-catenin signaling can increase cancer cell glycolysis. We investigated whether autophagy promotes glycolysis in hepatocellular carcinoma (HCC) cells by activating the Wnt/β-catenin signaling pathway, accompanied by MCT1 upregulation...
January 19, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29349913/eukaryotic-phytoplankton-community-spatiotemporal-dynamics-as-identified-through-gene-expression-within-a-eutrophic-estuary
#4
Weida Gong, Hans Paerl, Adrian Marchetti
Over the span of a year, we investigated the interactions between biotic and abiotic factors within the eutrophic Neuse River Estuary (NRE). Through metatranscriptomic sequencing in combination with water quality measurements, we show that there are different metabolic strategies deployed along the NRE. In the upper estuary, taxonomically-resolved phytoplankton groups express more transcripts of genes for synthesis of cellular components and carbon metabolism whereas in the lower estuary, transcripts allocated to nutrient metabolism and transport were more highly expressed...
January 19, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29347735/spreading-of-nonmotile-bacteria-on-a-hard-agar-plate-comparison-between-agent-based-and-stochastic-simulations
#5
Navdeep Rana, Pushpita Ghosh, Prasad Perlekar
We study spreading of a nonmotile bacteria colony on a hard agar plate by using agent-based and continuum models. We show that the spreading dynamics depends on the initial nutrient concentration, the motility, and the inherent demographic noise. Population fluctuations are inherent in an agent-based model, whereas for the continuum model we model them by using a stochastic Langevin equation. We show that the intrinsic population fluctuations coupled with nonlinear diffusivity lead to a transition from a diffusion limited aggregation type of morphology to an Eden-like morphology on decreasing the initial nutrient concentration...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347664/morphodynamics-of-a-growing-microbial-colony-driven-by-cell-death
#6
Pushpita Ghosh, Herbert Levine
Bacterial cells can often self-organize into multicellular structures with complex spatiotemporal morphology. In this work, we study the spatiotemporal dynamics of a growing microbial colony in the presence of cell death. We present an individual-based model of nonmotile bacterial cells which grow and proliferate by consuming diffusing nutrients on a semisolid two-dimensional surface. The colony spreads by growth forces and sliding motility of cells and undergoes cell death followed by subsequent disintegration of the dead cells in the medium...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347525/network-patterns-in-exponentially-growing-two-dimensional-biofilms
#7
Cameron Zachreson, Xinhui Yap, Erin S Gloag, Raz Shimoni, Cynthia B Whitchurch, Milos Toth
Anisotropic collective patterns occur frequently in the morphogenesis of two-dimensional biofilms. These patterns are often attributed to growth regulation mechanisms and differentiation based on gradients of diffusing nutrients and signaling molecules. Here, we employ a model of bacterial growth dynamics to show that even in the absence of growth regulation or differentiation, confinement by an enclosing medium such as agar can itself lead to stable pattern formation over time scales that are employed in experiments...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29343844/determinants-of-population-responses-to-environmental-fluctuations
#8
Jose M G Vilar, J Miguel Rubi
Environmental fluctuations, such as changing conditions and variable nutrient availability, are an unavoidable component of the dynamics of virtually all populations. They affect populations in ways that are often difficult to predict and sometimes lead to paradoxical outcomes. Here, we present a general analytical approach to examine how populations respond to fluctuations. We show that there exist general explicit conditions that determine to what extent fluctuations propagate to the variability of the responses and how they change the behavior of the system, including whether they promote proliferation or death and whether they facilitate coexistence or exclusion of competing species...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29341143/loss-of-alkaline-ceramidase-inhibits-autophagy-in-arabidopsis-and-plays-an-important-role-during-environmental-stress-response
#9
Ping Zheng, Jian-Xin Wu, Sunil Kumar Sahu, Hong-Yun Zeng, Li-Qun Huang, Zhe Liu, Shi Xiao, Nan Yao
Sphingolipids, a class of bioactive lipids found in cell membranes, can modulate the biophysical properties of the membranes and play a critical role in signal transduction. Sphingolipids are involved in autophagy in humans and yeast, but their role in autophagy in plants is not well understood. In this study, we reported that the AtACER, an alkaline ceramidase that hydrolyzes ceramide to LCB, functions in autophagy process in Arabidopsis. Our empirical data showed that the loss of AtACER inhibited autophagy, while its overexpression promoted autophagy under nutrient, salinity, and oxidative stresses...
January 17, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29338217/unprecedented-synergistic-effects-of-nanoscale-nutrients-on-growth-productivity-of-sweet-sorghum-sorghum-bicolor-l-moench-and-nutrient-biofortification
#10
Naseeruddin Ramapuram, Sumathi V, Nvkv Prasad Tollamadugu, P Sudhakar, Chandrika V, Balam Ravindra Reddy
Evidence based synergistic effects of nanoscale materials (size <100 nm in at least one dimension) were scantly documented in agriculture at field scale. Herein, we report for the first time on effects of nanoscale zinc oxide (n-ZnO), calcium oxide (n-CaO) and magnesium oxide (n-MgO) on growth and productivity of sweet sorghum (Sorghum bicolor (L.) Moench). Modified sol-gel method was used to prepare nanoscale materials under study. Characterization was done using Electron microscopy (TEM & SEM), X-ray diffraction (XRD) and dynamic light scattering (DLS)...
January 16, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29337889/reactive-oxygen-species-and-mitochondrial-dynamics-the-yin-and-yang-of-mitochondrial-dysfunction-and-cancer-progression
#11
REVIEW
Jan Ježek, Katrina F Cooper, Randy Strich
Mitochondria are organelles with a highly dynamic ultrastructure maintained by a delicate equilibrium between its fission and fusion rates. Understanding the factors influencing this balance is important as perturbations to mitochondrial dynamics can result in pathological states. As a terminal site of nutrient oxidation for the cell, mitochondrial powerhouses harness energy in the form of ATP in a process driven by the electron transport chain. Contemporaneously, electrons translocated within the electron transport chain undergo spontaneous side reactions with oxygen, giving rise to superoxide and a variety of other downstream reactive oxygen species (ROS)...
January 16, 2018: Antioxidants (Basel, Switzerland)
https://www.readbyqxmd.com/read/29337611/interactions-between-parasites-and-the-bacterial-microbiota-of-chickens
#12
Rüdiger Hauck
Except for the important role coccidia have as predisposing factors of necrotic enteritis, the role parasites play in the dynamics of a healthy microbiota of chickens is not well explored. This review describes the interactions of relevant intestinal parasites of chickens with bacteria. Infection with Eimeria spp. favor the growth of Clostridium perfringens and suppress the growth of many other bacteria by increasing viscosity and passage time of the ingesta, and by causing lesions to the intestinal mucosa that improve the availability of nutrients for C...
December 2017: Avian Diseases
https://www.readbyqxmd.com/read/29337437/canonical-signaling-and-nuclear-activity-of-mtor-a-teamwork-effort-to-regulate-metabolism-and-cell-growth
#13
REVIEW
Vincent Giguère
Mechanistic (or mammalian) target of rapamycin (mTOR) is a kinase that regulates almost all functions related to cell growth and metabolism in response to extra- and intracellular stimuli such as availability of nutrients, presence of growth factors or the energy status of the cell. As part of two distinct protein complexes, mTORC1 and mTORC2, the kinase has been shown to influence cell growth and proliferation by controlling ribosome biogenesis, mRNA translation, carbohydrate and lipid metabolism, protein degradation, autophagy as well as microtubule and actin dynamics...
January 16, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29337262/longitudinal-patterns-and-response-lengths-of-algae-in-riverine-ecosystems-a-model-analysis-emphasising-benthic-pelagic-interactions
#14
Christoph G Jäger, Dietrich Borchardt
In riverine ecosystems primary production is principally possible in two habitats: in the benthic layer by sessile algae and in the surface water by planktonic algae being transported downstream. The relevance of these two habitats generally changes along the rivers' continuum. However, analyses of the interaction of algae in these two habitats and their controlling factors in riverine ecosystems are, so far, very rare. We use a simplified advection-diffusion model system combined with ecological process kinetics to analyse the interaction of benthic and planktonic algae and nutrients along idealised streams and rivers at regional to large scales...
January 11, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29335637/expression-profiling-of-host-and-virus-during-a-coccolithophore-bloom-provides-insights-into-the-role-of-viral-infection-in-promoting-carbon-export
#15
Uri Sheyn, Shilo Rosenwasser, Yoav Lehahn, Noa Barak-Gavish, Ron Rotkopf, Kay D Bidle, Ilan Koren, Daniella Schatz, Assaf Vardi
The cosmopolitan coccolithophore Emiliania huxleyi is a unicellular eukaryotic alga that forms vast blooms in the oceans impacting large biogeochemical cycles. These blooms are often terminated due to infection by the large dsDNA virus, E. huxleyi virus (EhV). It was recently established that EhV-induced modulation of E. huxleyi metabolism is a key factor for optimal viral infection cycle. Despite the huge ecological importance of this host-virus interaction, the ability to assess its spatial and temporal dynamics and its possible impact on nutrient fluxes is limited by current approaches that focus on quantification of viral abundance and biodiversity...
January 15, 2018: ISME Journal
https://www.readbyqxmd.com/read/29335635/the-emergence-of-metabolic-heterogeneity-and-diverse-growth-responses-in-isogenic-bacterial-cells
#16
Emrah Şimşek, Minsu Kim
Microorganisms adapt to frequent environmental changes through population diversification. Previous studies demonstrated phenotypic diversity in a clonal population and its important effects on microbial ecology. However, the dynamic changes of phenotypic composition have rarely been characterized. Also, cellular variations and environmental factors responsible for phenotypic diversity remain poorly understood. Here, we studied phenotypic diversity driven by metabolic heterogeneity. We characterized metabolic activities and growth kinetics of starved Escherichia coli cells subject to nutrient upshift at single-cell resolution...
January 15, 2018: ISME Journal
https://www.readbyqxmd.com/read/29335481/bioimpedimetric-analysis-in-conjunction-with-growth-dynamics-to-differentiate-aggressiveness-of-cancer-cells
#17
Aditya Parekh, Debanjan Das, Subhayan Das, Santanu Dhara, Karabi Biswas, Mahitosh Mandal, Soumen Das
Determination of cancer aggressiveness is mainly assessed in tissues by looking at the grade of cancer. There is a lack of specific method to determine aggressiveness of cancer cells in vitro. In our present work, we have proposed a bio-impedance based non-invasive method to differentiate aggressive property of two breast cancer cell lines. Real-time impedance analysis of MCF-7 (less aggressive) and MDA-MB-231 cells (more aggressive) demonstrated unique growth pattern. Detailed slope-analysis of impedance curves at different growth phases showed that MDA-MB-231 had higher proliferation rate and intrinsic resistance to cell death, when allowed to grow in nutrient and space limiting conditions...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29332945/the-human-skin-microbiome
#18
REVIEW
Allyson L Byrd, Yasmine Belkaid, Julia A Segre
Functioning as the exterior interface of the human body with the environment, skin acts as a physical barrier to prevent the invasion of foreign pathogens while providing a home to the commensal microbiota. The harsh physical landscape of skin, particularly the desiccated, nutrient-poor, acidic environment, also contributes to the adversity that pathogens face when colonizing human skin. Despite this, the skin is colonized by a diverse microbiota. In this Review, we describe amplicon and shotgun metagenomic DNA sequencing studies that have been used to assess the taxonomic diversity of microorganisms that are associated with skin from the kingdom to the strain level...
January 15, 2018: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29331242/species-specific-response-to-sulfide-intrusion-in-native-and-exotic-mediterranean-seagrasses-under-stress
#19
Eugenia T Apostolaki, Marianne Holmer, Veronica Santinelli, Ioannis Karakassis
We explored the sulfur dynamics and the relationships between sediment sulfur and nutrient pools, seagrass structural and physiological variables and sulfide intrusion in native (Posidonia oceanica, Cymodocea nodosa) and exotic (Halophila stipulacea) Mediterranean seagrasses at six sites affected by cumulative anthropogenic pressures to understand the factors controlling sulfide intrusion in seagrass. Sensitive indicators of seagrass stress (leaf TN, δ15N, TS, Fsulfide) were increased at several sites, implying that seagrasses are under pressure...
December 25, 2017: Marine Environmental Research
https://www.readbyqxmd.com/read/29328931/biostimulation-and-bioaugmentation-of-native-microbial-community-accelerated-bioremediation-of-oil-refinery-sludge
#20
Ajoy Roy, Avishek Dutta, Siddhartha Pal, Abhishek Gupta, Jayeeta Sarkar, Ananya Chatterjee, Anumeha Saha, Poulomi Sarkar, Pinaki Sar, Sufia K Kazy
Scope for developing an engineered bioremediation strategy for the treatment of hydrocarbon-rich petroleum refinery waste was investigated through biostimulation and bioaugmentation approaches. Enhanced (46-55%) total petroleum hydrocarbon (TPH) attenuation was achieved through phosphate, nitrate or nitrate+phosphate amendment in the sludge with increased (upto 12%) abundance of fermentative, hydrocarbon degrading, sulfate-reducing, CO2-assimilating and methanogenic microorganisms (Bacillus, Coprothermobacter, Rhodobacter, Pseudomonas, Achromobacter, Desulfitobacter, Desulfosporosinus, T78, Methanobacterium, Methanosaeta, etc)...
January 3, 2018: Bioresource Technology
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