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plant growth modeling

Qiang Zhao, Xiaohua Xiang, Dan Liu, Aiguo Yang, Yuanying Wang
Cold stress is a major environmental factor that impairs plant growth and development, geographic distribution, and crop productivity. The C-repeat binding factor (CBF) regulatory pathway has an essential role in response to cold stress. Here, we characterized a bHLH transcription factor from Nicotiana tabacum , NtbHLH123 , in response to cold stress (4°C). Overexpression of NtbHLH123 enhanced cold tolerance in transgenic tobacco plants. Based on yeast one-hybrid, chromatin immunoprecipitation PCR, and transient expression analysis assays, NtbHLH123 binds directly to the G-box/E-box motifs in the promoter of the NtCBF genes and positively regulates their expression...
2018: Frontiers in Plant Science
Haohan Wang, Bryon Aragam, Eric P Xing
A fundamental and important challenge in modern datasets of ever increasing dimensionality is variable selection, which has taken on renewed interest recently due to the growth of biological and medical datasets with complex, non-i.i.d. structures. Naïvely applying classical variable selection methods such as the Lasso to such datasets may lead to a large number of false discoveries. Motivated by genome-wide association studies in genetics, we study the problem of variable selection for datasets arising from multiple subpopulations, when this underlying population structure is unknown to the researcher...
November 2017: Proceedings
On Sun Lau, Zhuojun Song, Zimin Zhou, Kelli A Davies, Jessica Chang, Xin Yang, Shenqi Wang, Doris Lucyshyn, Irene Hui Zhuang Tay, Philip A Wigge, Dominique C Bergmann
Environmental factors shape the phenotypes of multicellular organisms. The production of stomata-the epidermal pores required for gas exchange in plants-is highly plastic and provides a powerful platform to address environmental influence on cell differentiation [1-3]. Rising temperatures are already impacting plant growth, a trend expected to worsen in the near future [4]. High temperature inhibits stomatal production, but the underlying mechanism is not known [5]. Here, we show that elevated temperature suppresses the expression of SPEECHLESS (SPCH), the basic-helix-loop-helix (bHLH) transcription factor that serves as the master regulator of stomatal lineage initiation [6, 7]...
April 4, 2018: Current Biology: CB
León Jesús German-Ponciano, Gilberto Uriel Rosas-Sánchez, Eduardo Rivadeneyra-Domínguez, Juan Francisco Rodríguez-Landa
Flavonoids are phenolic compounds found commonly in plants that protect them against the negative effects of environmental insults. These secondary metabolites have been widely studied in preclinical research because of their biological effects, particularly as antioxidant agents. Diverse flavonoids have been studied to explore their potential therapeutic effects in the treatment of disorders of the central nervous system, including anxiety and depression. The present review discusses advances in the study of some flavonoids as potential antidepressant agents...
2018: Scientifica
Cyril Charbonnel, Oleh Rymarenko, Olivier Da Ines, Fatiha Benyahya, Charles I White, Falk Butter, Simon Amiard
Despite intensive searches, few proteins involved in telomere homeostasis have been identified in plants. Here, we used pull-down assays to identify potential telomeric interactors in the model plant species Arabidopsis (Arabidopsis thaliana). We identified the candidate protein GH1-HMGA1 (also known as HON4), an uncharacterised linker histone protein of the high mobility group protein A (HMGA) family in plants. HMGAs are architectural transcription factors and have been suggested to function in DNA damage repair, but their precise biological roles remain unclear...
April 5, 2018: Plant Physiology
Kaikai Zhu, Xiaolong Wang, Jinyi Liu, Jun Tang, Qunkang Cheng, Jin-Gui Chen, Zong-Ming Max Cheng
Protein kinases (PKs) have evolved as the largest family of molecular switches that regulate protein activities associated with almost all essential cellular functions. Only a fraction of plant PKs, however, have been functionally characterized even in model plant species. In the present study, the entire grapevine kinome was identified and annotated using the most recent version of the grapevine genome. A total of 1168 PK-encoding genes were identified and classified into 20 groups and 121 families, with the RLK-Pelle group being the largest, with 872 members...
2018: Horticulture Research
Sara Ramió-Pujol, Ramon Ganigué, Lluís Bañeras, Jesús Colprim
Research efforts aimed at increasing ethanol and butanol productivity from syngas are currently gaining attention. For most model carboxydotrophic bacteria, production rates, yields and maximum product titers have been studied in detail, but little is known on alcohol toxicity in these bacteria. The aim of this work was to investigate the inhibitory effects of ethanol and butanol on the growth of Clostridium ljungdahlii PETC, Clostridium carboxidivorans P7, and 'Butyribacterium methylotrophicum DSM3468'. Experiments to determine inhibitory effects due to product accumulation were carried out using a synthetic mixture of CO:CO2:H2 as a substrate...
March 29, 2018: FEMS Microbiology Letters
Jun Luo, Daixia Yin, Hao Cheng, William Davison, Hao Zhang
Changes in soil rhizosphere properties after growing the Cd hyperaccumulator Noccaea caerulescens and the Ni hyperaccumulator Thlaspi goesingense were investigated. Dissolved organic carbon content increased in the rhizosphere, but there were no significant changes in the solution concentrations of Cd and Ni. Concentrations of these metals extracted by NH4Cl and EDTA decreased in the rhizosphere, as did DGT-measured concentrations, indicating a depletion of labile metal in the solid phase. The results could be explained by the increased DOC in the rhizosphere maintaining a higher proportion of the labile metal in solution through complexation, with the overall depletion of metals only manifest in the solid phase...
April 4, 2018: Environmental Science & Technology
Young Koung Lee, Ji Ye Rhee, Seong Hee Lee, Gap Chae Chung, Soon Ju Park, Shoji Segami, Masayohi Maeshima, Giltsu Choi
In this work, we genetically characterized the function of Arabidopsis thaliana, LONGIFOLIA (LNG1), LNG2, LNG3, LNG4, their contribution to regulate vegetative architecture in plant. We used molecular and biophysical approaches to elucidate a gene function that regulates vegetative architecture, as revealed by the leaf phenotype and later effects on flowering patterns in Arabidopsis loss-of-function mutants. As a result, LNG genes play an important role in polar cell elongation by turgor pressure controlling the activation of XTH17 and XTH24...
April 3, 2018: Plant Molecular Biology
Konstantin Ochs, Rui P Rivaes, Teresa Ferreira, Gregory Egger
Mediterranean rivers in intensive agricultural watersheds usually display outgrowths of macrophytes - notably alien species - due to a combination of high concentrations of nutrients in the water runoff and low flows resulting from water abstraction for irrigation. Standard mechanical and chemical control is used to mitigate the problems associated with excessive growth of plant biomass: mainly less drainage capacity and higher flood risk. However, such control measures are cost and labor-intensive and do not present long-term efficiency...
2018: Frontiers in Plant Science
Arthur Zwaenepoel, Tim Diels, David Amar, Thomas Van Parys, Ron Shamir, Yves Van de Peer, Oren Tzfadia
Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms...
2018: Frontiers in Plant Science
Mateusz Matuszkiewicz, Miroslaw Sobczak, Javier Cabrera, Carolina Escobar, Stanislaw Karpiński, Marcin Filipecki
Cyst-forming plant-parasitic nematodes are common pests of many crops. They inject secretions into host cells to induce the developmental and metabolic reprogramming that leads to the formation of a syncytium, which is the sole food source for growing nematodes. As in other host-parasite models, avirulence leads to rapid and local programmed cell death (PCD) known as the hypersensitive response (HR), whereas in the case of virulence, PCD is still observed but is limited to only some cells. Several regulators of PCD were analyzed to understand the role of PCD in compatible plant-nematode interactions...
2018: Frontiers in Plant Science
Wendy Berthi, Alexa González, Alexandra Rios, Silvia Blair, Álvaro Cogollo, Adriana Pabón
BACKGROUND: Malaria is an infectious disease caused by parasites of the genus Plasmodium, of which Plasmodium vivax and Plasmodium falciparum are the major species that cause the disease in humans. As there are relatively few alternatives for malaria treatment, it is necessary to search for new chemotherapeutic options. Colombia possesses a great diversity of plants, which are potential sources of new compounds of medical interest. Thus, in this study the antiplasmodial effect of extracts from two species of plants from the families Simaroubaceae and Picramniaceae (Picramnia latifolia and Picrolemma huberi) was evaluated in vitro and in vivo...
April 4, 2018: Malaria Journal
Yoshiyuki Miyazawa, Sheng Du, Takeshi Taniguchi, Norikazu Yamanaka, Tomo'omi Kumagai
The mesic-origin plantation species Robinia pseudoacacia L. has been successfully grown in many arid land plantations around the world but often exhibits dieback and reduced growth due to drought. Therefore, to explore the behavior of this species under changing environmental conditions, we examined the relationship between ecophysiological traits, gas exchange and plant hydraulics over a 3-year period in trees that experienced reduced plant hydraulic conductance (Gp) in summer. We found that the transpiration rate, stomatal conductance (Gs) and minimum leaf water potential (Ψlmin) decreased in early summer in response to a decrease in Gp, and that Gp did not recover until the expansion of new leaves in spring...
March 28, 2018: Tree Physiology
P Andrus, R Rae
The genetic mechanisms of how free-living nematodes evolved into parasites are unknown. Current genetic model nematodes (e.g. Caenorhabditis elegans) are not well suited to provide the answer, and mammalian parasites are expensive and logistically difficult to maintain. Here we propose the terrestrial gastropod parasite Phasmarhabditis hermaphrodita as a new alternative to study the evolution of parasitism, and outline the methodology of how to keep P. hermaphrodita in the lab for genetic experiments. We show that P...
April 2, 2018: Journal of Helminthology
Rida Batool, Asma Kalsoom, Iqra Akbar, Najma Arshad, Nazia Jamil
The present study was proposed to investigate the toxicological and prophylactic potential of ethanolic extracts of Rosa damascena and Nymphaea alba and their mixture in albino mice. For toxicity study, three different doses of plant extracts were orally administrated to three groups of mice for 14 successive days. Blood biochemistry and histological examinations of liver and kidney revealed that these extracts had no harmful effects up to 1000 mg/kg. To determine the prophylactic effects of Rosa damascena , Nymphaea alba , and their mixture, an infection model of Listeria monocytogenes was established in a pilot study...
2018: BioMed Research International
Matthew E Akalusi, Charles P-A Bourque
The extent of the effect of projected changes in climate on trees remains unclear. This study investigated the effect of climatic variation on morphological traits of balsam fir [ Abies balsamea (L.) Mill.] provenances sourced from locations spanning latitudes from 44° to 51°N and longitudes from 53° to 102°W across North America, growing in a common garden in eastern Canada. Lower latitude provenances performed significantly better than higher latitude provenances ( p < .05) with regard to diameter at breast height (DBH), height (H), and crown width (CW), a distinction indicative of genotypic control of these traits...
March 2018: Ecology and Evolution
Philippe Lherminier
We distinguish two types of predations: the predation of matter-energy equals the food chain, and the informative predation is the capture of the information brought by the sexual partners. The cell or parent consumes energy and matter to grow, multiply and produce offspring. A fixed amount of resources is divided by the number of organisms, so individual growth and numerical multiplication are limited by depletion resources of the environment. Inversely, fertilization does not destroy information, but instead produces news...
March 29, 2018: Comptes Rendus Biologies
Silvina Mangano, Javier Martínez Pacheco, Cristina Marino-Buslje, José M Estevez
Polar growth in root hairs and pollen tubes is an excellent model for investigating plant cell size regulation. While linear plant growth is historically explained by the acid growth theory, which considers that auxin triggers apoplastic acidification by activating plasma membrane P-type H+ -ATPases (AHAs) along with cell wall relaxation over long periods, the apoplastic pH (apo pH) regulatory mechanisms are unknown for polar growth. Polar growth is a fast process mediated by rapid oscillations that repeat every ∼20-40s...
March 28, 2018: Trends in Plant Science
Lydia Zeibich, Oliver Schmidt, Harold L Drake
Earthworms are a dominant macro-fauna in soil ecosystems and have determinative effects on soil fertility and plant growth. These invertebrates feed on ingested material, and gizzard-linked disruption of ingested fungal and bacterial cells is conceived to provide diverse biopolymers in the anoxic alimentary canal of earthworms. Fermentation in the gut is likely important to the utilization of ingested biopolymer-derived compounds by the earthworm. This study therefore examined the fermentative response of gut content-associated microbes of the model earthworm Lumbricus terrestris to (a) microbial cell-lysate (to simulate gizzard-disrupted cells) and (b) dominate biopolymers of such biomass, protein and RNA...
March 30, 2018: Applied and Environmental Microbiology
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