ADHD Candidate Gene Study in a Population-Based Birth Cohort: Association with DBH and DRD2

ERIC Educational Resources Information Center

Nyman, Emma S.; Ogdie, Matthew N.; Loukola, Anu; Varilo, Teppo; Taanila, Anja; Hurtig, Tuula; Moilanen, Irma K.; Loo, Sandra K.; McGough, James J.; Jarvelin, Marjo-Riitta; Smalley, Susan L.

2007-01-01

A study aims to examine the genetic contribution if any to attention-deficit/hyperactivity disorder (ADHD). The results confirm the hypothesis and the association of dopamine [beta]-hydroxylase and dopamine receptor D2 genes with ADHD.

Moxd1 Is a Marker for Sexual Dimorphism in the Medial Preoptic Area, Bed Nucleus of the Stria Terminalis and Medial Amygdala

PubMed Central

Tsuneoka, Yousuke; Tsukahara, Shinji; Yoshida, Sachine; Takase, Kenkichi; Oda, Satoko; Kuroda, Masaru; Funato, Hiromasa

2017-01-01

The brain shows various sex differences in its structures. Various mammalian species exhibit sex differences in the sexually dimorphic nucleus of the preoptic area (SDN-POA) and parts of the extended amygdala such as the principal nucleus of the bed nucleus of the stria terminalis (BNSTpr) and posterodorsal part of the medial amygdala (MePD). The SDN-POA and BNSTpr are male-biased sexually dimorphic nuclei, and characterized by the expression of calbindin D-28K (calbindin 1). However, calbindin-immunoreactive cells are not restricted to the SDN-POA, but widely distributed outside of the SDN-POA. To find genes that are more specific to sexually dimorphic nuclei, we selected candidate genes by searching the Allen brain atlas and examined the detailed expressions of the candidate genes using in situ hybridization. We found that the strong expression of monooxygenase DBH-like 1 (Moxd1) was restricted to the SDN-POA, BNSTpr and MePD. The numbers of Moxd1-positive cells in the SDN-POA, BNSTpr and MePD in male mice were larger than those in female mice. Most of the Moxd1-positive cells in the SDN-POA and BNSTpr expressed calbindin. Neonatal castration of male mice reduced the number of Moxd1-positive cells in the SDN-POA, whereas gonadectomy in adulthood did not change the expression of the Moxd1 gene in the SDN-POA in both sexes. These results suggest that the Moxd1 gene is a suitable marker for sexual dimorphic nuclei in the POA, BNST and amygdala, which enables us to manipulate sexually dimorphic neurons to examine their roles in sex-biased physiology and behaviors. PMID:28396628

Moxd1 Is a Marker for Sexual Dimorphism in the Medial Preoptic Area, Bed Nucleus of the Stria Terminalis and Medial Amygdala.

PubMed

Tsuneoka, Yousuke; Tsukahara, Shinji; Yoshida, Sachine; Takase, Kenkichi; Oda, Satoko; Kuroda, Masaru; Funato, Hiromasa

2017-01-01

The brain shows various sex differences in its structures. Various mammalian species exhibit sex differences in the sexually dimorphic nucleus of the preoptic area (SDN-POA) and parts of the extended amygdala such as the principal nucleus of the bed nucleus of the stria terminalis (BNSTpr) and posterodorsal part of the medial amygdala (MePD). The SDN-POA and BNSTpr are male-biased sexually dimorphic nuclei, and characterized by the expression of calbindin D-28K (calbindin 1). However, calbindin-immunoreactive cells are not restricted to the SDN-POA, but widely distributed outside of the SDN-POA. To find genes that are more specific to sexually dimorphic nuclei, we selected candidate genes by searching the Allen brain atlas and examined the detailed expressions of the candidate genes using in situ hybridization. We found that the strong expression of monooxygenase DBH-like 1 ( Moxd1 ) was restricted to the SDN-POA, BNSTpr and MePD. The numbers of Moxd1 -positive cells in the SDN-POA, BNSTpr and MePD in male mice were larger than those in female mice. Most of the Moxd1 -positive cells in the SDN-POA and BNSTpr expressed calbindin. Neonatal castration of male mice reduced the number of Moxd1 -positive cells in the SDN-POA, whereas gonadectomy in adulthood did not change the expression of the Moxd1 gene in the SDN-POA in both sexes. These results suggest that the Moxd1 gene is a suitable marker for sexual dimorphic nuclei in the POA, BNST and amygdala, which enables us to manipulate sexually dimorphic neurons to examine their roles in sex-biased physiology and behaviors.

Methylation polymorphism influences practice effects in children during attention tasks1

PubMed Central

Voelker, Pascale; Sheese, Brad E.; Rothbart, Mary K.; Posner, Michael I.

2017-01-01

Epigenetic mechanisms mediate the influence of experience on gene expression. Methylation is a principal method for inducing epigenetic effects on DNA. In this paper, we examine alleles of the methylenetetrahydrofolate reductase (MTHFR) gene that vary enzyme activity, altering the availability of the methyl donor and thus changing the efficiency of methylation. We hypothesized that alleles of the MTHFR gene would influence behavior in an attention related task in conjunction with genes known to influence attention. We found that 7-year-old children homozygous for the C allele of MTHFR in interaction with the catechol O-methyltransferase (COMT) gene showed greater improvement in overall reaction time (RT) and in conflict resolution with practice on the Attention Network Test (ANT). This finding indicates that methylation may operate on or through genes that influence executive network operation. However, MTHFR T allele carriers showed faster overall RT and conflict resolution. Some children showed an initial improvement in ANT RT followed by a decline in performance, and we found that alleles of the dopamine beta-hydroxylase (DBH) gene were related to this performance decline. These results suggest a genetic dissociation between improvement while learning a skill and reduction in performance with continued practice. PMID:27050482

Noradrenergic Genotype Predicts Lapses in Sustained Attention

ERIC Educational Resources Information Center

Greene, Ciara M.; Bellgrove, Mark A.; Gill, Michael; Robertson, Ian H.

2009-01-01

Sustained attention is modulated by the neurotransmitter noradrenaline. The balance of dopamine and noradrenaline in the cortex is controlled by the DBH gene. The principal variant in this gene is a C/T change at position-1021, and the T allele at this locus is hypothesised to result in a slower rate of dopamine to noradrenaline conversion than…

Norepinephrine is required to promote wakefulness and for hypocretin-induced arousal in zebrafish

PubMed Central

Singh, Chanpreet; Oikonomou, Grigorios; Prober, David A

2015-01-01

Pharmacological studies in mammals suggest that norepinephrine (NE) plays an important role in promoting arousal. However, the role of endogenous NE is unclear, with contradicting reports concerning the sleep phenotypes of mice lacking NE due to mutation of dopamine β-hydroxylase (dbh). To investigate NE function in an alternative vertebrate model, we generated dbh mutant zebrafish. In contrast to mice, these animals exhibit dramatically increased sleep. Surprisingly, despite an increase in sleep, dbh mutant zebrafish have a reduced arousal threshold. These phenotypes are also observed in zebrafish treated with small molecules that inhibit NE signaling, suggesting that they are caused by the lack of NE. Using genetic overexpression of hypocretin (Hcrt) and optogenetic activation of hcrt-expressing neurons, we also find that NE is important for Hcrt-induced arousal. These results establish a role for endogenous NE in promoting arousal and indicate that NE is a critical downstream effector of Hcrt neurons. DOI: http://dx.doi.org/10.7554/eLife.07000.001 PMID:26374985

Chronic Inhibition of Dopamine β-Hydroxylase Facilitates Behavioral Responses to Cocaine in Mice

PubMed Central

Gaval-Cruz, Meriem; Liles, Larry Cameron; Iuvone, Paul Michael; Weinshenker, David

2012-01-01

The anti-alcoholism medication, disulfiram (Antabuse), decreases cocaine use in humans regardless of concurrent alcohol consumption and facilitates cocaine sensitization in rats, but the functional targets are unknown. Disulfiram inhibits dopamine β-hydroxylase (DBH), the enzyme that converts dopamine (DA) to norepinephrine (NE) in noradrenergic neurons. The goal of this study was to test the effects of chronic genetic or pharmacological DBH inhibition on behavioral responses to cocaine using DBH knockout (Dbh −/−) mice, disulfiram, and the selective DBH inhibitor, nepicastat. Locomotor activity was measured in control (Dbh +/−) and Dbh −/− mice during a 5 day regimen of saline+saline, disulfiram+saline, nepicastat+saline, saline+cocaine, disulfiram+cocaine, or nepicastat+cocaine. After a 10 day withdrawal period, all groups were administered cocaine, and locomotor activity and stereotypy were measured. Drug-naïve Dbh −/− mice were hypersensitive to cocaine-induced locomotion and resembled cocaine-sensitized Dbh +/− mice. Chronic disulfiram administration facilitated cocaine-induced locomotion in some mice and induced stereotypy in others during the development of sensitization, while cocaine-induced stereotypy was evident in all nepicastat-treated mice. Cocaine-induced stereotypy was profoundly increased in the disulfiram+cocaine, nepicastat+cocaine, and nepicastat+saline groups upon cocaine challenge after withdrawal in Dbh +/− mice. Disulfiram or nepicastat treatment had no effect on behavioral responses to cocaine in Dbh −/− mice. These results demonstrate that chronic DBH inhibition facilitates behavioral responses to cocaine, although different methods of inhibition (genetic vs. non-selective inhibitor vs. selective inhibitor) enhance qualitatively different cocaine-induced behaviors. PMID:23209785

DBH Prediction Using Allometry Described by Bivariate Copula Distribution

NASA Astrophysics Data System (ADS)

Xu, Q.; Hou, Z.; Li, B.; Greenberg, J. A.

2017-12-01

Forest biomass mapping based on single tree detection from the airborne laser scanning (ALS) usually depends on an allometric equation that relates diameter at breast height (DBH) with per-tree aboveground biomass. The incapability of the ALS technology in directly measuring DBH leads to the need to predict DBH with other ALS-measured tree-level structural parameters. A copula-based method is proposed in the study to predict DBH with the ALS-measured tree height and crown diameter using a dataset measured in the Lassen National Forest in California. Instead of exploring an explicit mathematical equation that explains the underlying relationship between DBH and other structural parameters, the copula-based prediction method utilizes the dependency between cumulative distributions of these variables, and solves the DBH based on an assumption that for a single tree, the cumulative probability of each structural parameter is identical. Results show that compared with the bench-marking least-square linear regression and the k-MSN imputation, the copula-based method obtains better accuracy in the DBH for the Lassen National Forest. To assess the generalization of the proposed method, prediction uncertainty is quantified using bootstrapping techniques that examine the variability of the RMSE of the predicted DBH. We find that the copula distribution is reliable in describing the allometric relationship between tree-level structural parameters, and it contributes to the reduction of prediction uncertainty.

Effects of chemical sympathectomy on the increases in plasma catecholamines and dopamine-beta-hydroxylase induced by forced immobilization and insulin-induced hypoglycemia: origin and fate of plasma dopamine-beta-hydroxylase.

PubMed

Israel, A S; Barbella, Y R; Cubeddu, L X

1982-06-01

The effect of acute stresses on plasma norepinephrine, epinephrine and dopamine-beta-hydroxylase (DBH) were evaluated in control and 6-hydroxydopamine-treated, awake cannulated guinea pigs. Forced immobolization for 1 hr caused a 3- and 5-fold increase in plasma DBH and norepinephrine, respectively. Pretreatment with 6-hydroxydopamine (23 mg/kg b.wt.i.a., 72 and 48 hr before stress) reduced by 70% the increase in plasma DBH and totally prevented the rise in plasma catecholamines evoked by the restraining stress. Injection of insulin (5 U/kg b.wt.i.a.) induced a 60% decrease in blood glucose, a 1-fold increase in plasma DBH and a selective 4-fold increase in plasma epinephrine; these effects were not modified by chemical sympathectomy. Our results indicate that forced immobilization and hypoglycemia produce a preferential activation of the sympathetic postganglionic nerves and of the adrenal medulla, respectively, and that in guinea pigs both stresses increase plasma DBH. The kinetics of disappearance of plasma DBH were studied after subjecting the guinea pigs for 1 hr to forced immobilization. Although 7 of 12 animals showed a biphasic rate of fall of plasma DBH, in each case there was a rapid initial fall possibly due to the "distribution" of the enzyme with a T1/2 of 1.65 hr. Similar findings were observed in 6-hydroxydopamine-treated guinea pigs. These results suggest that the distribution of DBH is the most important process in reducing the augmented plasma DBH levels elicited by a short-term stress and that this process is not dependent on the integrity of the sympathetic nerves nor on the adrenal or sympathetic origin of the enzyme. This study supports the view that the ratio, content of releasable DBH present in sympathetic nerves and adrenal glands/total circulating pool of DBH, is the factor that determines whether an increase in plasma DBH would occur in animals exposed to an acute stress.

Association of the DBH Polymorphism rs3025343 With Smoking Cessation in a Large Population-Based Sample.

PubMed

Hirvonen, Katariina; Korhonen, Tellervo; Salomaa, Veikko; Männistö, Satu; Kaprio, Jaakko

2017-09-01

Genetic variations in DBH-gene and its surroundings have been shown to associate with smoking behavior including smoking cessation in several studies. In this study we replicate and measure the effect size for association between DBH polymorphism rs3025343 and smoking cessation in a large population-based sample while examining environmental factors that could relate to the association. We studied 11 926 adult subjects from four surveys of the National FINRISK Study. The analysis was restricted to either current or former smokers. Logistic and linear regression analyses were conducted to investigate the relationships of the single nucleotide polymorphism (SNP), covariates, smoking cessation, and smoking severity (cotinine, CPD). Gene-environment interactions were tested by likelihood-ratio test. The association between rs3025343 and smoking cessation (prevalence odds ratio, OR = 1.12, p = .094, 95%CI = 0.98-1.30) was replicated identically with the GWAS study of The Tobacco and Genetics Consortium (OR = 1.12, 95%CI = 1.08-1.18). None of our tested phenotypes significantly influenced the association between rs3025343 and smoking cessation. Overall, marital status, education, depression, alcohol use, self-rated health, and chronic obstructive pulmonary disease (COPD) showed phenotypic associations with smoking cessation, but the association of various phenotypes with smoking cessation did not vary by genotype. The current study replicates the effect size for the association between rs3025343 and smoking cessation despite lack of overall significance due to smaller sample size. We could not show environmental influences on the association of rs3025343 with smoking cessation. Our study replicates the direction and strength of the association of DBH polymorphism rs3025343 with smoking cessation. We could not detect environmental influences on the strength of the association of rs3025343 with smoking cessation, but the limited power of our analysis needs to be taken into account. © The Author 2017. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

High Hydrostatic Pressure Extract of Ginger Exerts Antistress Effects in Immobilization-Stressed Rats.

PubMed

Moon, Sohee; Lee, Mak-Soon; Jung, Sunyoon; Kang, Bori; Kim, Seog-Young; Park, Seonyoung; Son, Hye-Yeon; Kim, Chong-Tai; Jo, Young-Hee; Kim, In-Hwan; Kim, Young Soon; Kim, Yangha

2017-09-01

Stress contributes to physiological changes such as weight loss and hormonal imbalances. The aim of the present study was to investigate antistress effects of high hydrostatic pressure extract of ginger (HPG) in immobilization-stressed rats. Male Sprague-Dawley rats (n = 24) were divided into three groups as follows: control (C), immobilization stress (2 h daily, for 2 weeks) (S), and immobilization stress (2 h daily, for 2 weeks) plus oral administration of HPG (150 mg/kg body weight/day) (S+G). Immobilization stress reduced the body weight gain and thymus weight by 50.2% and 31.3%, respectively, compared to the control group. The levels of serum aspartate transaminase, alanine transaminase, and corticosterone were significantly higher in the stress group, compared to the control group. Moreover, immobilization stress elevated the mRNA levels of tyrosine hydroxylase (Th), dopamine beta-hydroxylase (Dbh), and cytochrome P450 side-chain cleavage (P450scc), which are related to catecholamine and corticosterone synthesis in the adrenal gland. HPG administration also increased the body weight gain and thymus weight by 12.7% and 16.6%, respectively, compared to the stress group. Furthermore, the mRNA levels of Th, Dbh, phenylethanolamine-N-methyltransferase, and P450scc were elevated by the HPG treatment when compared to the stress group. These results suggest that HPG would have antistress effects partially via the reversal of stress-induced physiological changes and suppression of mRNA expression of genes related to corticosterone and catecholamine synthetic enzymes.

An initial investigation of associations between dopamine-linked genetic variation and smoking motives in African Americans.

PubMed

Bidwell, L C; McGeary, J E; Gray, J C; Palmer, R H C; Knopik, V S; MacKillop, J

2015-11-01

Nicotine dependence (ND) is a heterogeneous phenotype with complex genetic influences that may vary across ethnicities. The use of intermediate phenotypes may clarify genetic influences and reveal specific etiological pathways. Prior work in European Americans has found that the four Primary Dependence Motives (PDM) subscales (Automaticity, Craving, Loss of Control, and Tolerance) of the Wisconsin Inventory of Smoking Motives represent core features of nicotine dependence and are promising intermediate phenotypes for understanding genetic pathways to ND. However, no studies have examined PDM as an intermediate phenotype in African American smokers, an ethnic population that displays unique patterns of smoking and genetic variation. In the current study, 268 African American daily smokers completed a phenotypic assessment and provided a sample of DNA. Associations among haplotypes in the NCAM1-TTC12-ANKK1-DRD2 gene cluster, a dopamine-related gene region associated with ND, PDM intermediate phenotypes, and ND were examined. Dopamine-related genetic variation in the DBH and COMT genes was also considered on an exploratory basis. Mediational analysis was used to test the indirect pathway from genetic variation to smoking motives to nicotine dependence. NCAM1-TTC12-ANKK1-DRD2 region variation was significantly associated with the Automaticity subscale and, further, Automaticity significantly mediated associations among NCAM1-TTC12-ANKK1-DRD2 cluster variants and ND. DBH was also significantly associated with Automaticity, Craving, and Tolerance; Automaticity and Tolerance also served as mediators of the DBH-ND relationship. These results suggest that PDM, Automaticity in particular, may be a viable intermediate phenotype for understanding dopamine-related genetic influences on ND in African American smokers. Findings support a model in which putatively dopaminergic variants exert influence on ND through an effect on patterns of automatic routinized smoking. Copyright © 2015 Elsevier Inc. All rights reserved.

Identification of Common Differentially Expressed Genes in Urinary Bladder Cancer

PubMed Central

Zaravinos, Apostolos; Lambrou, George I.; Boulalas, Ioannis; Delakas, Dimitris; Spandidos, Demetrios A.

2011-01-01

Background Current diagnosis and treatment of urinary bladder cancer (BC) has shown great progress with the utilization of microarrays. Purpose Our goal was to identify common differentially expressed (DE) genes among clinically relevant subclasses of BC using microarrays. Methodology/Principal Findings BC samples and controls, both experimental and publicly available datasets, were analyzed by whole genome microarrays. We grouped the samples according to their histology and defined the DE genes in each sample individually, as well as in each tumor group. A dual analysis strategy was followed. First, experimental samples were analyzed and conclusions were formulated; and second, experimental sets were combined with publicly available microarray datasets and were further analyzed in search of common DE genes. The experimental dataset identified 831 genes that were DE in all tumor samples, simultaneously. Moreover, 33 genes were up-regulated and 85 genes were down-regulated in all 10 BC samples compared to the 5 normal tissues, simultaneously. Hierarchical clustering partitioned tumor groups in accordance to their histology. K-means clustering of all genes and all samples, as well as clustering of tumor groups, presented 49 clusters. K-means clustering of common DE genes in all samples revealed 24 clusters. Genes manifested various differential patterns of expression, based on PCA. YY1 and NFκB were among the most common transcription factors that regulated the expression of the identified DE genes. Chromosome 1 contained 32 DE genes, followed by chromosomes 2 and 11, which contained 25 and 23 DE genes, respectively. Chromosome 21 had the least number of DE genes. GO analysis revealed the prevalence of transport and binding genes in the common down-regulated DE genes; the prevalence of RNA metabolism and processing genes in the up-regulated DE genes; as well as the prevalence of genes responsible for cell communication and signal transduction in the DE genes that were down-regulated in T1-Grade III tumors and up-regulated in T2/T3-Grade III tumors. Combination of samples from all microarray platforms revealed 17 common DE genes, (BMP4, CRYGD, DBH, GJB1, KRT83, MPZ, NHLH1, TACR3, ACTC1, MFAP4, SPARCL1, TAGLN, TPM2, CDC20, LHCGR, TM9SF1 and HCCS) 4 of which participate in numerous pathways. Conclusions/Significance The identification of the common DE genes among BC samples of different histology can provide further insight into the discovery of new putative markers. PMID:21483740

Cubic-foot tree volume equations and tables for western juniper.

Treesearch

Judith M. Chittester; Colin D. MacLean

1984-01-01

This note presents cubic-foot volume equations and tables for western juniper (Juniperus occidentalis Hook. ). Total cubicfoot volume (ground to tip, excluding all branches (CVTS)) is expressed as a function of diameter at breast height (DBH) and total height. Utilizable cubic-foot volume (top of 12-inch stump to a 4-inch top, excluding all...

Applying and Individual-Based Model to Simultaneously Evaluate Net Ecosystem Production and Tree Diameter Increment

NASA Astrophysics Data System (ADS)

Fang, F. J.

2017-12-01

Reconciling observations at fundamentally different scales is central in understanding the global carbon cycle. This study investigates a model-based melding of forest inventory data, remote-sensing data and micrometeorological-station data ("flux towers" estimating forest heat, CO2 and H2O fluxes). The individual tree-based model FORCCHN was used to evaluate the tree DBH increment and forest carbon fluxes. These are the first simultaneous simulations of the forest carbon budgets from flux towers and individual-tree growth estimates of forest carbon budgets using the continuous forest inventory data — under circumstances in which both predictions can be tested. Along with the global implications of such findings, this also improves the capacity for forest sustainable management and the comprehensive understanding of forest ecosystems. In forest ecology, diameter at breast height (DBH) of a tree significantly determines an individual tree's cross-sectional sapwood area, its biomass and carbon storage. Evaluation the annual DBH increment (ΔDBH) of an individual tree is central to understanding tree growth and forest ecology. Ecosystem Carbon flux is a consequence of key ecosystem processes in the forest-ecosystem carbon cycle, Gross and Net Primary Production (GPP and NPP, respectively) and Net Ecosystem Respiration (NEP). All of these closely relate with tree DBH changes and tree death. Despite advances in evaluating forest carbon fluxes with flux towers and forest inventories for individual tree ΔDBH, few current ecological models can simultaneously quantify and predict the tree ΔDBH and forest carbon flux.

Predictive equations for dimensions and leaf area of coastal Southern California street trees

Treesearch

P.J. Peper; E.G. McPherson; S.M. Mori

2001-01-01

Tree height, crown height, crown width, diameter at breast height (dbh), and leaf area were measured for 16 species of commonly planted street trees in the coastal southern California city of Santa Monica, USA. The randomly sampled trees were planted from 1 to 44 years ago. Using number of years after planting or dbh as explanatory variables, mean values of dbh, tree...

Relative maxima of diameter and basal area

Treesearch

Thomas B. Lynch; Difei Zhang

2012-01-01

It has often been observed that maximum dbh growth occurs at an earlier age than maximum individual tree basal area growth. This can be deduced from the geometry of the tree stem, by observing that a dbh increment at a given radius will be associated with a larger basal area increment than an equal dbh increment occurring at a shorter radius from the stem center. Thus...

Diameter growth of individual hardwood trees

Treesearch

G.R., Jr. Trimble; G.R. Trimble

1969-01-01

Between 1959 and 1967 a study of d.b.h. growth rates was made on individual hardwood trees near Parsons, W. Va. From this study, we obtained information that will help foresters to predict growth. We learned that the correlation of the more easily used crown classification with d.b.h. growth is as good as or better than the correlation of vigor classes with d.b.h....

Modelling diameter distributions of two-cohort forest stands with various proportions of dominant species: a two-component mixture model approach.

Treesearch

Rafal Podlaski; Francis Roesch

2014-01-01

In recent years finite-mixture models have been employed to approximate and model empirical diameter at breast height (DBH) distributions. We used two-component mixtures of either the Weibull distribution or the gamma distribution for describing the DBH distributions of mixed-species, two-cohort forest stands, to analyse the relationships between the DBH components,...

Forest biomass and energy-wood potential in the southern United States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saucier, J.R.

1993-12-31

Timber resource data were compiled from the most recent USDA Forest Service inventory data for the 12 Southern States from Virginia to Texas. Timber resource inventories traditionally include only trees 5 inches dbh and greater and their volumes to the prevailing merchantable top diameter expressed in cubic feet, board feet, or cords. For this paper, conversion factors were developed to express timber inventories in weight and to expand the inventories to include the crowns of merchantable trees and trees less than 5 inches dbh. By so doing, the total aboveground biomass is estimated for the timberlands in the South. Themore » region contains 185 million acres of timberland. Some 14.6 billion green tons of woody biomass are present on southern timberland -- about 79 tons per acre. When mature stands are harvested, the average acre in the South has 22.2 tons of woody material left in crowns and sapling, and 5.1 tons in cull stems. Thus, an average of 27.3 green tons per acre of potential energy wood are left after conventional harvests. Conversion factors that are presented permit estimates for specific tracts, areas, counties, or states.« less

Xiao Yao San Improves Depressive-Like Behaviors in Rats with Chronic Immobilization Stress through Modulation of Locus Coeruleus-Norepinephrine System.

PubMed

Ding, Xiu-Fang; Zhao, Xiao-Hua; Tao, Yang; Zhong, Wei-Chao; Fan, Qin; Diao, Jian-Xin; Liu, Yuan-Liang; Chen, Yu-Yao; Chen, Jia-Xu; Lv, Zhi-Ping

2014-01-01

Most research focuses on the hypothalamic-pituitary-adrenal (HPA) axis, hypothalamus-pituitary-thyroid (HPT) axis, and hypothalamus-pituitary-gonadal (HPGA) axis systems of abnormalities of emotions and behaviors induced by stress, while no studies of Chinese herbal medicine such as Xiao Yao San (XYS) on the mechanisms of locus coeruleus-norepinephrine (LC-NE) system have been reported. Therefore, experiments were carried out to observe mechanism of LC-NE system in response to chronic immobilization stress (CIS) and explore the antidepressant effect of XYS. Rat model was established by CIS. LC morphology in rat was conducted. The serum norepinephrine (NE) concentrations and NE biosynthesis such as tyrosine hydroxylase (TH), dopamine-β-hydroxylase (DBH), and corticotrophin-releasing-factor (CRF) in LC were determined. Results showed that there were no discernible alterations in LC in rats. The serum NE concentrations, positive neurons, mean optical density (MOD), and protein levels of TH, DBH, and CRF in model group were significantly increased compared to the control group. But XYS-treated group displayed a significantly decreased in NE levels and expressions of TH, DBH, and CRF compared to the model group. In conclusion, CIS can activate LC-NE system to release NE and then result in a significant decrease in rats. XYS treatment can effectively improve depressive-like behaviors in rats through inhibition of LC-NE neurons activity.

Xiao Yao San Improves Depressive-Like Behaviors in Rats with Chronic Immobilization Stress through Modulation of Locus Coeruleus-Norepinephrine System

PubMed Central

Ding, Xiu-Fang; Zhao, Xiao-Hua; Tao, Yang; Zhong, Wei-Chao; Fan, Qin; Diao, Jian-Xin; Liu, Yuan-Liang; Chen, Yu-Yao; Chen, Jia-Xu; Lv, Zhi-Ping

2014-01-01

Most research focuses on the hypothalamic-pituitary-adrenal (HPA) axis, hypothalamus-pituitary-thyroid (HPT) axis, and hypothalamus-pituitary-gonadal (HPGA) axis systems of abnormalities of emotions and behaviors induced by stress, while no studies of Chinese herbal medicine such as Xiao Yao San (XYS) on the mechanisms of locus coeruleus-norepinephrine (LC-NE) system have been reported. Therefore, experiments were carried out to observe mechanism of LC-NE system in response to chronic immobilization stress (CIS) and explore the antidepressant effect of XYS. Rat model was established by CIS. LC morphology in rat was conducted. The serum norepinephrine (NE) concentrations and NE biosynthesis such as tyrosine hydroxylase (TH), dopamine-β-hydroxylase (DBH), and corticotrophin-releasing-factor (CRF) in LC were determined. Results showed that there were no discernible alterations in LC in rats. The serum NE concentrations, positive neurons, mean optical density (MOD), and protein levels of TH, DBH, and CRF in model group were significantly increased compared to the control group. But XYS-treated group displayed a significantly decreased in NE levels and expressions of TH, DBH, and CRF compared to the model group. In conclusion, CIS can activate LC-NE system to release NE and then result in a significant decrease in rats. XYS treatment can effectively improve depressive-like behaviors in rats through inhibition of LC-NE neurons activity. PMID:25610478

An Examination of the Behavioral and Neuropsychological Correlates of Three ADHD Candidate Gene Polymorphisms (DRD4 7+, DBH TaqI A2, and DAT1 40bp VNTR) in Hyperactive and Normal Children Followed to Adulthood

PubMed Central

Barkley, Russell A.; Smith, Karen M.; Fischer, Mariellen; Navia, Bradford

2008-01-01

Several candidate gene polymorphisms have been implicated in attention deficit hyperactivity disorder (ADHD), including DAT1 40bp VNTR, DRD4 7+, and DBH TaqI A2 alleles. We used the Milwaukee longitudinal study of hyperactive (N=122) and normal (N=67) children to compare participants with and without these respective polymorphisms on ADHD-related behavioral ratings at childhood, 8 years later in adolescence, and 13+ years later into young adulthood. Neuropsychological tests were given at the adolescent and young adulthood follow-up. No differences were found between the DRD4-7+ and 7- repeat polymorphism. The DBH TaqI A2 allele, when homozygous, was associated with being more hyperactive in childhood, having more pervasive behavior problems at adolescence, and earning less money on a Card Playing Task in adulthood. At adolescence, poorer test scores were also found only in the hyperactive group with homozygous for this allele. The DAT1 40bp VNTR heterozygous 9/10 repeat, however, differed from the 10/10 repeat pair in many respects, having greater ADHD and externalizing symptoms at all three follow-ups, more cross-situational behavioral problems at both childhood and adolescence, poorer mother-teen relations at adolescence, and lower class rankings in high school. Participants with the 9/10 pair in the control group also had lower work performance, a lower grade point average in high school, greater teacher rated externalizing symptoms at adolescence, and greater omission errors on a continuous performance test in adulthood. The DAT1 40bp VNTR 9/10 polymorphism pairing appears to be reliably associated with greater symptoms of ADHD and externalizing behavior from childhood to adulthood, and with family, educational, and occupational impairments. We also present a contrary view on the appropriate endophenotypes for use in behavioral genetic research on ADHD. PMID:16741944

Weighting factors for computing the relation between tree volume and d.b.h. in the Pacific Northwest.

Treesearch

Donald R. Gedney; Floyd A. Johnson

1959-01-01

Timber cruising is frequently made easier through use of local volume tables based on d.b.h. alone. These tables are made by establishing the relation between volume and d.b.h. from measurements (including height) made on sample trees in the stand. The sample-tree measurements are converted to volumes through use of standard volume tables, and a volume-diameter curve...

Using LiDAR to Estimate Total Aboveground Biomass of Redwood Stands in the Jackson Demonstration State Forest, Mendocino, California

NASA Astrophysics Data System (ADS)

Rao, M.; Vuong, H.

2013-12-01

The overall objective of this study is to develop a method for estimating total aboveground biomass of redwood stands in Jackson Demonstration State Forest, Mendocino, California using airborne LiDAR data. LiDAR data owing to its vertical and horizontal accuracy are increasingly being used to characterize landscape features including ground surface elevation and canopy height. These LiDAR-derived metrics involving structural signatures at higher precision and accuracy can help better understand ecological processes at various spatial scales. Our study is focused on two major species of the forest: redwood (Sequoia semperirens [D.Don] Engl.) and Douglas-fir (Pseudotsuga mensiezii [Mirb.] Franco). Specifically, the objectives included linear regression models fitting tree diameter at breast height (dbh) to LiDAR derived height for each species. From 23 random points on the study area, field measurement (dbh and tree coordinate) were collected for more than 500 trees of Redwood and Douglas-fir over 0.2 ha- plots. The USFS-FUSION application software along with its LiDAR Data Viewer (LDV) were used to to extract Canopy Height Model (CHM) from which tree heights would be derived. Based on the LiDAR derived height and ground based dbh, a linear regression model was developed to predict dbh. The predicted dbh was used to estimate the biomass at the single tree level using Jenkin's formula (Jenkin et al 2003). The linear regression models were able to explain 65% of the variability associated with Redwood's dbh and 80% of that associated with Douglas-fir's dbh.

Development and Evaluation of Models for the Relationship between Tree Height and Diameter at Breast Height for Chinese-Fir Plantations in Subtropical China.

PubMed

Li, Yan-qiong; Deng, Xiang-wen; Huang, Zhi-hong; Xiang, Wen-hua; Yan, Wen-de; Lei, Pi-feng; Zhou, Xiao-lu; Peng, Chang-hui

2015-01-01

Tree diameter at breast height (dbh) and height are the most important variables used in forest inventory and management as well as forest carbon-stock estimation. In order to identify the key stand variables that influence the tree height-dbh relationship and to develop and validate a suit of models for predicting tree height, data from 5961 tree samples aged from 6 years to 53 years and collected from 80 Chinese-fir plantation plots were used to fit 39 models, including 33 nonlinear models and 6 linear models, were developed and evaluated into two groups. The results showed that composite models performed better in height estimate than one-independent-variable models. Nonlinear composite Model 34 and linear composite Model 6 were recommended for predicting tree height in Chinese fir plantations with a dbh range between 4 cm and 40 cm when the dbh data for each tree and the quadratic mean dbh of the stand (Dq) and mean height of the stand (Hm) were available. Moreover, Hm could be estimated by using the formula Hm = 11.707 × l n(Dq)-18.032. Clearly, Dq was the primary stand variable that influenced the height-dbh relationship. The parameters of the models varied according to stand age and site. The inappropriate application of provincial or regional height-dbh models for predicting small tree height at local scale may result in larger uncertainties. The method and the recommended models developed in this study were statistically reliable for applications in growth and yield estimation for even-aged Chinese-fir plantation in Huitong and Changsha. The models could be extended to other regions and to other tree species only after verification in subtropical China.

Development and Evaluation of Models for the Relationship between Tree Height and Diameter at Breast Height for Chinese-Fir Plantations in Subtropical China

PubMed Central

Li, Yan-qiong; Deng, Xiang-wen; Huang, Zhi-hong; Xiang, Wen-hua; Yan, Wen-de; Lei, Pi-feng; Zhou, Xiao-lu; Peng, Chang-hui

2015-01-01

Tree diameter at breast height (dbh) and height are the most important variables used in forest inventory and management as well as forest carbon-stock estimation. In order to identify the key stand variables that influence the tree height-dbh relationship and to develop and validate a suit of models for predicting tree height, data from 5961 tree samples aged from 6 years to 53 years and collected from 80 Chinese-fir plantation plots were used to fit 39 models, including 33 nonlinear models and 6 linear models, were developed and evaluated into two groups. The results showed that composite models performed better in height estimate than one-independent-variable models. Nonlinear composite Model 34 and linear composite Model 6 were recommended for predicting tree height in Chinese fir plantations with a dbh range between 4 cm and 40 cm when the dbh data for each tree and the quadratic mean dbh of the stand (Dq) and mean height of the stand (Hm) were available. Moreover, Hm could be estimated by using the formula Hm=11.707×ln(Dq)-18.032. Clearly, Dq was the primary stand variable that influenced the height-dbh relationship. The parameters of the models varied according to stand age and site. The inappropriate application of provincial or regional height-dbh models for predicting small tree height at local scale may result in larger uncertainties. The method and the recommended models developed in this study were statistically reliable for applications in growth and yield estimation for even-aged Chinese-fir plantation in Huitong and Changsha. The models could be extended to other regions and to other tree species only after verification in subtropical China. PMID:25905458

Protection of individual ash trees from emerald ash borer (Coleoptera: Buprestidae) with basal soil applications of imidacloprid.

PubMed

Smitley, D R; Rebek, E J; Royalty, R N; Davis, T W; Newhouse, K F

2010-02-01

We conducted field trials at five different locations over a period of 6 yr to investigate the efficacy of imidacloprid applied each spring as a basal soil drench for protection against emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae). Canopy thinning and emerald ash borer larval density were used to evaluate efficacy for 3-4 yr at each location while treatments continued. Test sites included small urban trees (5-15 cm diameter at breast height [dbh]), medium to large (15-65 cm dbh) trees at golf courses, and medium to large street trees. Annual basal drenches with imidacloprid gave complete protection of small ash trees for three years. At three sites where the size of trees ranged from 23 to 37 cm dbh, we successfully protected all ash trees beginning the test with <60% canopy thinning. Regression analysis of data from two sites reveals that tree size explains 46% of the variation in efficacy of imidacloprid drenches. The smallest trees (<30 cm dbh) remained in excellent condition for 3 yr, whereas most of the largest trees (>38 cm dbh) declined to a weakened state and undesirable appearance. The five-fold increase in trunk and branch surface area of ash trees as the tree dbh doubles may account for reduced efficacy on larger trees, and suggests a need to increase treatment rates for larger trees.

Synthesis, photoluminescent, antibacterial activities and theoretical studies of 4-hydroxycoumarin derivatives

NASA Astrophysics Data System (ADS)

Li, Jing; Hou, Zheng; Li, Fen; Zhang, Zi-dan; Zhou, Ying; Luo, Xiao-xing; Li, Ming-kai

2014-10-01

Two new biscoumarin and epoxydicoumarin derivatives, namely, 3,3‧-(4-di-p-tolyl-amino-benzylidene)-bis-(4-hydroxycoumarin) (DBH) and 9-(4-di-p-tolyl-amino-phenyl)-1,8-dioxo-9H-dibenzo[c,h]-2,7,10-trioxanthene (DDT), were synthesized and characterized via IR, 1H NMR, HRMS, single crystal X-ray crystallography and UV-vis absorption spectra. The fluorescence behaviors of DBH and DDT in dichloromethane solutions were observed. The in vitro antibacterial activity of DBH and DDT against Staphylococcus aureus (S. aureus ATCC 29213), methicillin-resistant S. aureus (MRSA XJ 75302), vancomycin-intermediate S. aureus (Mu50 ATCC 700699), and USA 300 (Los Angeles County clone, LAC) was evaluated by observing the minimum inhibitory concentration. The results showed that compared with compound DDT, DBH exhibited better potent antibacterial activity.

Prognoses of diameter and height of trees of eucalyptus using artificial intelligence.

PubMed

Vieira, Giovanni Correia; de Mendonça, Adriano Ribeiro; da Silva, Gilson Fernandes; Zanetti, Sidney Sára; da Silva, Mayra Marques; Dos Santos, Alexandre Rosa

2018-04-01

Models of individual trees are composed of sub-models that generally estimate competition, mortality, and growth in height and diameter of each tree. They are usually adopted when we want more detailed information to estimate forest multiproduct. In these models, estimates of growth in diameter at 1.30m above the ground (DBH) and total height (H) are obtained by regression analysis. Recently, artificial intelligence techniques (AIT) have been used with satisfactory performance in forest measurement. Therefore, the objective of this study was to evaluate the performance of two AIT, artificial neural networks and adaptive neuro-fuzzy inference system, to estimate the growth in DBH and H of eucalyptus trees. We used data of continuous forest inventories of eucalyptus, with annual measurements of DBH, H, and the dominant height of trees of 398 plots, plus two qualitative variables: genetic material and site index. It was observed that the two AIT showed accuracy in growth estimation of DBH and H. Therefore, the two techniques discussed can be used for the prognosis of DBH and H in even-aged eucalyptus stands. The techniques used could also be adapted to other areas and forest species. Copyright © 2017 Elsevier B.V. All rights reserved.

Large variations in diurnal and seasonal patterns of sap flux among Aleppo pine trees in semi-arid forest reflect tree-scale hydraulic adjustments

NASA Astrophysics Data System (ADS)

Preisler, Yakir; Tatarinov, Fyodor; Rohatyn, Shani; Rotenberg, Eyal; Grünzweig, José M.; Klein, Tamir; Yakir, Dan

2015-04-01

Adjustments and adaptations of trees to drought vary across different biomes, species and habitats, with important implications for tree mortality and forest dieback associated with global climate change. The aim of this study was to investigate possible links between the patterns of variations in water flux dynamics and drought resistance in Aleppo pine (Pinus halepensis) trees in a semi-arid stand (Yatir forest, Israel). We measured sap flow (SF) and variations in stem diameter, complemented with short-term campaigns of leaf-scale measurements of water vapour and CO2 gas exchange, branch water potential and hydraulic conductivity, as well as eddy flux measurements of evapotranspiration (ET) from a permanent flux tower at the site. SF rates were well synchronized with ET, reaching maximum rates during midday in all trees during the rainy season (Dec-Apr). However, during the dry season (May-Nov), the daily trend in the rates of SF greatly varied among trees, allowing classification into three tree classes: 1) trees with SF maximum rate constantly occurring in mid-day (12:00-13:00); 2)trees showing a shift to an early morning SF peak (04:00-06:00); and 3) trees shifting their daily SF peak to the evening (16:00-18:00). This classification did not change during the four years study period, between 2010 and 2014. Checking for correlation of tree parameters as DBH, tree height, crown size, and competition indices with rates of SF, indicated that timing of maximum SF in summer was mainly related to tree size (DBH), when large trees tended to have a later SF maximum. Dendrometer measurements indicated that large trees (high DBH) had maximum daily diameter in the morning during summer and winter, while small trees typically had maximum daily diameter during midday and afternoon in winter and summer, respectively. Leaf-scale transpiration (T) measurements showed typical morning peak in all trees, and another peak in the afternoon in large trees only. Different diurnal curves observed during the dry season, indicated that water potential and hydraulic conductivity values in larger trees restored from midday depression earlier than in smaller ones. The results demonstrate large heterogeneity in the behaviour related to tree water relations among trees of the same species and in the same stand. The combination of diurnal leaf-scale measurements, SF and changes in DBH demonstrated the different strategies of individual trees of different sizes. Large trees with sufficient internal water storage can more freely manipulate their water storage capacity, with reduced dependence on environmental conditions (e.g., morning and afternoon peaks of T). On the other hand, during the dry summer small trees with insufficient internal water storage are strongly restricted by low soil water availability and extreme environmental conditions, which is expressed in only one peak of T, midday to afternoon shift of diurnal DBH maximum, and shift in SF to predawn when soil water potential is highest. Refilling of internal water storage seems to be in the afternoon/evening since T becomes smaller than SF and DBH increases. Reliance on external water availability in small trees might be insufficient during long drought episodes when soil water content decreases below threshold required for extraction by the trees, leading to increased tree mortality in small DBH trees.

Interim Regional Supplement to the Corps of Engineers Wetland Delineation Manual: Eastern Mountains and Piedmont Region

DTIC Science & Technology

2010-07-01

Sapling/ shrub stratum – Consists of woody plants, excluding vines , less than 3 in. DBH and greater than 3.28 ft (1 m) tall. 3. Herb stratum...excluding woody vines , approximately 20 ft (6 m) or more in height and less than 3 in. (7.6 cm) DBH. 3. Shrub stratum – Consists of woody plants...of height. Sapling/ Shrub – Woody plants, excluding vines , less than 3 in. DBH and greater than 3.28 ft (1 m) tall. Herb – All herbaceous (non

Estimating Dbh from Stump Diameter for 15 Southern Species

Treesearch

Carl V. Bylin

1982-01-01

Regression equations for predicting dbh from tree stump diameter inside and outside bark are presented for 15 southern species. Equations were certified on idependent test subsets using the F distrubution statistic with signigicance level of .05.

Complex Spatial Structure in a Population of Didymopanax pittieri, A Tree of Wind-Exposed Lower Montane Rain Forest

NASA Technical Reports Server (NTRS)

Lawton, Robert M.; Lawton, Robert O.

2010-01-01

Didymopanax pittieri is a common shade-intolerant tree colonizing treefall gaps in the elfin forests on windswept ridgecrests in the lower montane rain forests of the Cordillera de Tilarain, Costa Rica. All D. pittieri taller than > 0.5 m in a 5.2-ha elfin forested portion of a gridded study watershed in the Monteverde Cloud Forest Preserve were located, mapped, and measured. This local population of D. pittieri is spatially inhomogeneous, in that density increases with increasing wind exposure; D. pittieri are more abundant near ridge crests than lower on windward slopes. The important and ubiquitous phenomenon of spatial inhomogeneity in population density is addressed and corrected for in spatial analyses by the application of the inhomogeneous version of Ripley's K. The spatial patterns of four size classes of D. pittieri (<5 cm dbh, 5-10 cm dbh, 10-20 cm dbh, and> 20 cm dbh) were investigated. Within the large-scale trend in density driven by wind exposure, D. pittieri saplings are clumped at the scale of treefall gaps and at the scale of patches of aggregated gaps. D. pittieri 5-10 cm dbh are randomly distributed, apparently due to competitive thinning of sapling clumps during the early stages of gap-phase regeneration. D. pittieri larger than 10 cm dbh are overdispersed at a scale larger than that of patches of gaps. Natural disturbance can influence the distribution of shade intolerant tree populations at several different spatial scales, and can have discordant effects at different life history stages.

Vascular Epiphyte Diversity Differs with Host Crown Zone and Diameter, but Not Orientation in a Tropical Cloud Forest

PubMed Central

Wang, Xixi; Long, Wenxing; Schamp, Brandon S.; Yang, Xiaobo; Kang, Yong; Xie, Zhixu; Xiong, Menghui

2016-01-01

Vascular epiphytes are important components of biological diversity in tropical forests. We measured the species richness and abundance of vascular epiphytes along four vertical crown zones and five horizontal orientations on 376 trees, as well as the diameter at breast height (DBH) of host trees in tropical cloud forests in Bawangling, Hainan, China. The relationship between vascular epiphyte species richness and host tree DBH was assessed using a generalized linear model. There were 1,453 vascular individual epiphytes attributed to 9 families, 24 genera and 35 species, with orchids and pteridophytes dominating. Both the species richness and abundance of epiphytes significantly differed among the four crown zones for all collections and each host tree, suggesting that vertical microhabitats contribute to the distribution of epiphytes on host trees. Neither epiphyte abundance nor species richness differed among the eastern, southern, western, and northern orientations for all host trees; however, both richness and abundance were significantly higher for epiphytes that encircled host tree trunks. This suggests that morphological and physiological characteristics of the tree, but not microclimates probably contribute to the distribution of epiphytes on host trees. Epiphyte species richness was positively correlated with tree DBH across the six host tree species studied, with increases in DBH among smaller trees resulting in larger increases in richness, while increases in DBH among larger host trees resulting in more modest increases in ephiphyte richness. Our findings contribute support for a positive relationship between epiphyte species richness and host tree DBH and provide important guidance for future surveys of epiphyte community development. PMID:27391217

Azadirachtin: an effective systemic insecticide for control of Agrilus planipennis (Coleoptera: Buprestidae).

PubMed

McKenzie, Nicole; Helson, Blair; Thompson, Dean; Otis, Gard; McFarlane, John; Buscarini, Teresa; Meating, Joe

2010-06-01

The emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), an invasive pest discovered in North America in 2002, is now well established and threatens ash (Fraxinus spp.) trees throughout the continent. Experiments were conducted to 1) examine the efficacy of an alternative natural pesticide, azadirachtin, to control emerald ash borer, and 2) determine foliar uptake and dissipation patterns after systemic injections of azadirachtin into trunks of small (2.2 cm diameter at breast height [dbh]), uninfested green ash trees. We found no evidence of mortality of adult beetles. In contrast, fewer larvae completed their development at dose levels > or = 1.7 mg (AI)/cm dbh and development ceased beyond the second instar at dose levels > or = 13.6 mg (AI)/cm dbh. Substantial concentrations (11.2 microg/g dry mass [SD = 7.55]) of azadirachtin were present in leaves within 7 d of treatment. After rapid initial uptake, concentrations in leaves declined logarithmically during the 55 d after injection. A similar pattern was observed in a separate experiment that examined the uptake and translocation of azadirachtin in larger green ash trees (22 cm dbh) treated with 250 mg (AI) /cm dbh with the EcoJect injection system. In another experiment, recently infested plantation green ash trees treated with doses > or = 40 mg (AI)/cm dbh had significant reductions in adult emergence approximately 1 yr postinjection. Given the inhibition of larval development, reduction of adult emergence, and the occurrence of foliar residues at biologically active concentrations, we conclude that azadirachtin is effective in protecting ash trees from emerald ash borer.

Comparison of different tree sap flow up-scaling procedures using Monte-Carlo simulations

NASA Astrophysics Data System (ADS)

Tatarinov, Fyodor; Preisler, Yakir; Roahtyn, Shani; Yakir, Dan

2015-04-01

An important task in determining forest ecosystem water balance is the estimation of stand transpiration, allowing separating evapotranspiration into transpiration and soil evaporation. This can be based on up-scaling measurements of sap flow in representative trees (SF), which can be done by different mathematical algorithms. The aim of the present study was to evaluate the error associated with different up-scaling algorithms under different conditions. Other types of errors (such as, measurement error, within tree SF variability, choice of sample plot etc.) were not considered here. A set of simulation experiments using Monte-Carlo technique was carried out and three up-scaling procedures were tested. (1) Multiplying mean stand sap flux density based on unit sapwood cross-section area (SFD) by total sapwood area (Klein et al, 2014); (2) deriving of linear dependence of tree sap flow on tree DBH and calculating SFstand using predicted SF by DBH classes and stand DBH distribution (Cermak et al., 2004); (3) same as method 2 but using non-linear dependency. Simulations were performed under different SFD(DBH) slope (bs, positive, negative, zero); different DBH and SFD standard deviations (Δd and Δs, respectively) and DBH class size. It was assumed that all trees in a unit area are measured and the total SF of all trees in the experimental plot was taken as the reference SFstand value. Under negative bs all models tend to overestimate SFstand and the error increases exponentially with decreasing bs. Under bs >0 all models tend to underestimate SFstand, but the error is much smaller than for bs

Accuracy of tree diameter estimation from terrestrial laser scanning by circle-fitting methods

NASA Astrophysics Data System (ADS)

Koreň, Milan; Mokroš, Martin; Bucha, Tomáš

2017-12-01

This study compares the accuracies of diameter at breast height (DBH) estimations by three initial (minimum bounding box, centroid, and maximum distance) and two refining (Monte Carlo and optimal circle) circle-fitting methods The circle-fitting algorithms were evaluated in multi-scan mode and a simulated single-scan mode on 157 European beech trees (Fagus sylvatica L.). DBH measured by a calliper was used as reference data. Most of the studied circle-fitting algorithms significantly underestimated the mean DBH in both scanning modes. Only the Monte Carlo method in the single-scan mode significantly overestimated the mean DBH. The centroid method proved to be the least suitable and showed significantly different results from the other circle-fitting methods in both scanning modes. In multi-scan mode, the accuracy of the minimum bounding box method was not significantly different from the accuracies of the refining methods The accuracy of the maximum distance method was significantly different from the accuracies of the refining methods in both scanning modes. The accuracy of the Monte Carlo method was significantly different from the accuracy of the optimal circle method in only single-scan mode. The optimal circle method proved to be the most accurate circle-fitting method for DBH estimation from point clouds in both scanning modes.

Deficiency of Sustained Attention in ADHD and Its Potential Genetic Contributor MAOA.

PubMed

Liu, Lu; Cheng, Jia; Su, Yi; Ji, Ning; Gao, Qian; Li, Haimei; Yang, Li; Sun, Li; Qian, Qiujin; Wang, Yufeng

2015-03-17

To investigate the genetic contributors to ADHD sustained attention deficit among noradrenergic genes responsible for the synthesis (dopamine-β-hydroxylase gene, DBH), transport (norepinephrine transporter gene, NET1), reception (alpha-2A adrenergic receptor gene, ADRA2A), and metabolism (monoamine oxidase A gene, MAOA) of noradrenalin (NE). A total of 456 children with ADHD and 108 normal controls were included in a digit cancellation test (DCT). DNA was collected from 242 participants and genotyped for 14 single nucleotide polymorphisms (SNPs) of noradrenergic genes. Compared with normal controls, children with ADHD showed a lower total score and higher mean error rate in the DCT, indicating poorer sustained attention function. Analysis of covariance showed an association between MAOA genotypes and ADHD performance in DCT, with poorer performance in risk allele carriers. No association was found for other noradrenergic genes. Children with ADHD presented with a sustained attention deficit compared with normal controls. The sustained attention deficit of children with ADHD may be associated with genetic variant of MAOA. © 2015 SAGE Publications.

L-threo-dihydroxyphenylserine corrects neurochemical abnormalities in a Menkes disease mouse model.

PubMed

Donsante, Anthony; Sullivan, Patricia; Goldstein, David S; Brinster, Lauren R; Kaler, Stephen G

2013-02-01

Menkes disease is a lethal neurodegenerative disorder of infancy caused by mutations in a copper-transporting adenosine triphosphatase gene, ATP7A. Among its multiple cellular tasks, ATP7A transfers copper to dopamine beta hydroxylase (DBH) within the lumen of the Golgi network or secretory granules, catalyzing the conversion of dopamine to norepinephrine. In a well-established mouse model of Menkes disease, mottled-brindled (mo-br), we tested whether systemic administration of L-threo-dihydroxyphenylserine (L-DOPS), a drug used successfully to treat autosomal recessive norepinephrine deficiency, would improve brain neurochemical abnormalities and neuropathology. At 8, 10, and 12 days of age, wild-type and mo-br mice received intraperitoneal injections of 200μg/g body weight of L-DOPS, or mock solution. Five hours after the final injection, the mice were euthanized, and brains were removed. We measured catecholamine metabolites affected by DBH via high-performance liquid chromatography with electrochemical detection, and assessed brain histopathology. Compared to mock-treated controls, mo-br mice that received intraperitoneal L-DOPS showed significant increases in brain norepinephrine (p < 0.001) and its deaminated metabolite, dihydroxyphenylglycol (p < 0.05). The ratio of a non-beta-hydroxylated metabolite in the catecholamine biosynthetic pathway, dihydroxyphenylacetic acid, to the beta-hydroxylated metabolite, dihydroxyphenylglycol, improved equivalently to results obtained previously with brain-directed ATP7A gene therapy (p < 0.01). However, L-DOPS treatment did not arrest global brain pathology or improve somatic growth, as gene therapy had. We conclude that (1) L-DOPS crosses the blood-brain barrier in mo-br mice and corrects brain neurochemical abnormalities, (2) norepinephrine deficiency is not the cause of neurodegeneration in mo-br mice, and (3) L-DOPS treatment may ameliorate noradrenergic hypofunction in Menkes disease. Copyright © 2012 American Neurological Association.

L-DOPS corrects neurochemical abnormalities in a Menkes disease mouse model

PubMed Central

Donsante, Anthony; Sullivan, Patricia; Goldstein, David S.; Brinster, Lauren R.; Kaler, Stephen G.

2012-01-01

Objective Menkes disease is a lethal neurodegenerative disorder of infancy caused by mutations in a copper-transporting ATPase gene, ATP7A. Among its multiple cellular tasks, ATP7A transfers copper to dopamine-beta-hydroxylase (DBH) within the lumen of the Golgi network or secretory granules, catalyzing the conversion of dopamine to norepinephrine. In a well-established mouse model of Menkes disease, mottled-brindled, we tested whether systemic administration of L-threo-dihydroxyphenylserine (L-DOPS), a drug used successfully to treat autosomal recessive norepinephrine deficiency, would improve brain neurochemical abnormalities and neuropathology. Methods At 8, 10, and 12 days of age, wild type and mo-br mice received intraperi-toneal injections of 200μg/g body weight of L-DOPS, or mock solution. Five hours after the final injection, the mice were euthanized and brains removed. We measured catecholamine metabolites affected by DBH via high-performance liquid chromatography with electrochemical detection, and assessed brain histopathology. Results Compared to mock-treated controls, mo-br mice that received intraperitoneal L-DOPS showed significant increases in brain norepinephrine (P<0.001) and its deaminated metabolite, dihydroxyphenylglycol (DHPG, P<0.05). The ratio of a non-beta-hydroxylated metabolite in the catecholamine biosynthetic pathway, dihydroxyphenylacetic acid, to the beta-hydroxylated metabolite, dihydroxyphenylglycol, improved equivalently to results obtained previously with brain-directed ATP7A gene therapy (P<0.01). However, L-DOPS treatment did not arrest global brain pathology or improve somatic growth, as gene therapy had. Interpretation We conclude that 1) L-DOPS crosses the blood-brain barrier in mo-br mice and corrects brain neurochemical abnormalities, 2) norepinephrine deficiency is not the cause of neurodegeneration in mo-br mice, and 3) L-DOPS treatment may ameliorate noradrenergic hypofunction in Menkes disease. PMID:23224983

Cannabis and cocaine decrease cognitive impulse control and functional corticostriatal connectivity in drug users with low activity DBH genotypes.

PubMed

Ramaekers, J G; van Wel, J H; Spronk, D; Franke, B; Kenis, G; Toennes, S W; Kuypers, K P C; Theunissen, E L; Stiers, P; Verkes, R J

2016-12-01

The dopamine β-hydroxylase (DβH) enzyme transforms dopamine into noradrenaline. We hypothesized that individuals with low activity DBH genotypes (rs1611115 CT/TT) are more sensitive to the influence of cannabis and cocaine on cognitive impulse control and functional connectivity in the limbic 'reward' circuit because they experience a drug induced hyperdopaminergic state compared to individuals with high activity DBH genotypes (rs1611115 CC). Regular drug users (N = 122) received acute doses of cannabis (450 μg/kg THC), cocaine HCl 300 mg and placebo. Cognitive impulse control was assessed by means of the Matching Familiar Figures Test (MFFT). Resting state fMRI was measured in a subset of participants to determine functional connectivity between the nucleus accumbens (NAc) and (sub)cortical areas. The influence of cannabis and cocaine on impulsivity and functional connectivity significantly interacted with DBH genotype. Both drugs increased cognitive impulsivity in participants with CT/TT genotypes but not in CC participants. Both drugs also reduced functional connectivity between the NAc and the limbic lobe, prefrontal cortex, striatum and thalamus and primarily in individuals with CT/TT genotypes. Correlational analysis indicated a significant negative association between cognitive impulsivity and functional connectivity in subcortical areas of the brain. It is concluded that interference of cannabis and cocaine with cognitive impulse control and functional corticostriatal connectivity depends on DBH genotype. The present data provide a neural substrate and behavioral mechanism by which drug users can progress to drug seeking and may also offer a rationale for targeted pharmacotherapy in chronic drug users with high risk DBH genotypes.

[Spatial structural characteristics of natural Populus davidiana - Betula platyphylla secondary forest].

PubMed

Shao, Fang-Li; Yu, Xin-Xiao; Song, Si-Ming; Zhao, Yang

2011-11-01

This paper analyzed the spatial structural characteristics of natural Populus davidiana - Betula platyphylla secondary forest in a 4 hm2 plot of Mulan Paddock, based on the diameter distribution and the spatial structure parameters mingling degree, neighborhood comparison, and angle index. In the forest, the diameter distribution of the stands presented as an inverse 'J' curve, the average mingling degree was 0.4, with the individuals at weak and zero mingling degree reached 51.6%, and the average mingling degree of P. davidiana and B. platyphylla was 0.25 and 0.39, respectively. The neighborhood comparison based on the diameter at breast height (DBH) and tree height was almost the same, suggesting that the P. davidiana and B. platyphylla were in the transition state from subdominant to middle. The horizontal distribution pattern had a close relation to the minimum measured DBH, being clustered when the DBH was > or = 1 cm and < 6 cm, and random when the DBH was > or = 6 cm.

SPRUCE Tree Growth Assessments of Picea and Larix in S1-Bog Plots and SPRUCE Experimental Plots beginning in 2011

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanson, P.J.,; Phillips, J.R.; Wullschelger, S.D.

This data set reports tree growth measurements of mature Picea mariana and Larix laricina located in the S1-Bog permanent plots and the SPRUCE experimental study plots, Annual data collections were initiated in February of 2011and have been continued on an annual basis during mid-winter observation periods at the end of February or early March. Data collections are anticipated to continue through February of 2025 and this data set will be appended annually. Initial observations in 2011 included measurements of circumference at 1.3 m (diameter at breast height assessments; DBH) above the nominal bog hollow surface, tree heights and crown diameters.more » Subsequent annual measurements have focused on the measures of circumference at DBH. Circumference measurements to the nearest 0.1 cm are converted to DBH in cm and basal area at DBH in (cm2). Tree height and crown diameter are measured to the nearest 0.1 m.« less

Transcription factor activating protein 2 beta (TFAP2B) mediates noradrenergic neuronal differentiation in neuroblastoma.

PubMed

Ikram, Fakhera; Ackermann, Sandra; Kahlert, Yvonne; Volland, Ruth; Roels, Frederik; Engesser, Anne; Hertwig, Falk; Kocak, Hayriye; Hero, Barbara; Dreidax, Daniel; Henrich, Kai-Oliver; Berthold, Frank; Nürnberg, Peter; Westermann, Frank; Fischer, Matthias

2016-02-01

Neuroblastoma is an embryonal pediatric tumor that originates from the developing sympathetic nervous system and shows a broad range of clinical behavior, ranging from fatal progression to differentiation into benign ganglioneuroma. In experimental neuroblastoma systems, retinoic acid (RA) effectively induces neuronal differentiation, and RA treatment has been therefore integrated in current therapies. However, the molecular mechanisms underlying differentiation are still poorly understood. We here investigated the role of transcription factor activating protein 2 beta (TFAP2B), a key factor in sympathetic nervous system development, in neuroblastoma pathogenesis and differentiation. Microarray analyses of primary neuroblastomas (n = 649) demonstrated that low TFAP2B expression was significantly associated with unfavorable prognostic markers as well as adverse patient outcome. We also found that low TFAP2B expression was strongly associated with CpG methylation of the TFAP2B locus in primary neuroblastomas (n = 105) and demethylation with 5-aza-2'-deoxycytidine resulted in induction of TFAP2B expression in vitro, suggesting that TFAP2B is silenced by genomic methylation. Tetracycline inducible re-expression of TFAP2B in IMR-32 and SH-EP neuroblastoma cells significantly impaired proliferation and cell cycle progression. In IMR-32 cells, TFAP2B induced neuronal differentiation, which was accompanied by up-regulation of the catecholamine biosynthesizing enzyme genes DBH and TH, and down-regulation of MYCN and REST, a master repressor of neuronal genes. By contrast, knockdown of TFAP2B by lentiviral transduction of shRNAs abrogated RA-induced neuronal differentiation of SH-SY5Y and SK-N-BE(2)c neuroblastoma cells almost completely. Taken together, our results suggest that TFAP2B is playing a vital role in retaining RA responsiveness and mediating noradrenergic neuronal differentiation in neuroblastoma. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Development of population structure and spatial distribution patterns of a restored forest during 17-year succession (1993-2010) in Pingshuo opencast mine spoil, China.

PubMed

Zhao, Zhongqiu; Wang, Lianhua; Bai, Zhongke; Pan, Ziguan; Wang, Yun

2015-07-01

Afforestation of native tree species is often recommended for ecological restoration in mining areas, but the understanding of the ecological processes of restored vegetation is quite limited. In order to provide insight of the ecological processes of restored vegetation, in this study, we investigate the development of the population structure and spatial distribution patterns of restored Robinia pseudoacacia (ROPS) and Pinus tabuliformis (PITA) mixed forests during the 17 years of the mine spoil period of the Pingshuo opencast mine, Shanxi Province, China. After a 17-year succession, apart from the two planted species, Ulmus pumila (ULPU), as an invasive species, settled in the plot along with a large number of small diameter at breast height (DBH) size. In total, there are 10,062 living individual plants, much more than that at the plantation (5105), and ROPS had become the dominant species with a section area with a breast height of 9.40 m(2) hm(-2) and a mean DBH of 6.72 cm, much higher than both PITA and ULPU. The DBH size classes of all the total species showed inverted J-shaped distributions, which may have been a result of the large number of small regenerated ULPU trees. The DBH size classes of both ROPS and PITA showed peak-type structures with individuals mainly gathering in the moderate DBH size class, indicating a relatively healthy DBH size class structure. Meanwhile, invasive ULPU were distributed in a clear L shape, concentrating on the small DBH size class, indicating a relatively low survival rate for adult trees. Both ROPS and PITA species survival in the plantation showed uniform and aggregated distribution at small scales and random with scales increasing. ULPU showed a strong aggregation at small scales as well as random with scales increasing. Both the population structure and spatial distribution indicated that ROPS dominates and will continue to dominate the community in the future succession, which should be continuously monitored.

A patient with PMP22-related hereditary neuropathy and DBH-gene-related dysautonomia.

PubMed

Bartoletti-Stella, Anna; Chiaro, Giacomo; Calandra-Buonaura, Giovanna; Contin, Manuela; Scaglione, Cesa; Barletta, Giorgio; Cecere, Annagrazia; Garagnani, Paolo; Tieri, Paolo; Ferrarini, Alberto; Piras, Silvia; Franceschi, Claudio; Delledonne, Massimo; Cortelli, Pietro; Capellari, Sabina

2015-10-01

Recurrent focal neuropathy with liability to pressure palsies is a relatively frequent autosomal-dominant demyelinating neuropathy linked to peripheral myelin protein 22 (PMP22) gene deletions. The combination of PMP22 gene mutations with other genetic variants is known to cause a more severe phenotype than expected. We present the case of a patient with severe orthostatic hypotension since 12 years of age, who inherited a PMP22 gene deletion from his father. Genetic double trouble was suspected because of selective sympathetic autonomic disturbances. Through exome-sequencing analysis, we identified two novel mutations in the dopamine beta hydroxylase gene. Moreover, with interactome analysis, we excluded a further influence on the origin of the disease by variants in other genes. This case increases the number of unique patients presenting with dopamine-β-hydroxylase deficiency and of cases with genetically proven double trouble. Finding the right, complete diagnosis is crucial to obtain adequate medical care and appropriate genetic counseling.

Relationship of stump diameter to d.b.h. for sugar maple in the northeast

Treesearch

Frederick E. Hampf

1955-01-01

This is the second report on a series of studies (2) made show the relationship of stump diameter to diameter breast high (d.b.h.) for commercially important tree species in the Northeast. This report is for sugar maple (Acer saccharum).

Relationship of stump diameter to d.b.h. for white oak in the Northeast

Treesearch

Frederick E. Hampf

1957-01-01

This is the eighth report on a series of studies to show the relationship of stump diameter to diameter breast high (d.b.h.) for commercially important tree species in the Northeast. This report is for white oak (Quercus alba).

Relationship of stump diameter to d.b.h. for yellow birch in the Northeast

Treesearch

Frederick E. Hampf

1955-01-01

This is the fourth report on a series of studies to show the relationship of stump diameter to diameter breast high (d.b.h.) for commercially important tree species in the Northeast. This report is for yellow birch (Betula alleghaniensis).

Bald eagle winter roost characteristics in Lava Beds National Monument, California

USGS Publications Warehouse

Stohlgren, Thomas J.

1993-01-01

This study provided a survey of bald eagle (Haliaeetus leucocephalus) winter roost habitat (in 4 km2 of potential roost areas) in southern Lava Beds National Monument, California. A systematic-clustered sampling design (n=381 plots) was used to compare forest stand characteristics in two primary roost areas (Caldwell Butte and Eagle Nest Butte) and two potential roost areas (Hidden Valley and Island Butte). A 100 percent inventory of roost trees in Caldwell Butte (n=103 trees) and Eagle Nest Butte (n=44 trees) showed they were spatially clumped and restricted to 12.7 percent and 2.8 percent, respectively, of the study areas. Roost trees, primarily ponderosa pine (Pinus ponderosa), averaged 81.1 ± 1.3 cm dbh (mean ± 1 S.E.) compared to non-roost trees (>35 cm dbh) that averaged 52.2 ± 1.0 cm dbh. Roost trees were generally taller and more open-structured than non-roost trees. All four study sites had adequate numbers of mid-sized trees (10 to 50 cm dbh) to replace the current stock of older, larger roost trees. However, seedling and small trees (<10 cm dbh) in the roost areas were spatially clumped and few, suggesting that maintaining a continuous population of roost trees may be a problem in the distant future. Long-term studies of changing winter roost habitat and eagle use are essential to protect the bald eagle in the northwestern US.

Mechanism-based inactivation of dopamine beta-hydroxylase by p-cresol and related alkylphenols

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goodhart, P.J.; DeWolf, W.E. Jr.; Kruse, L.I.

1987-05-05

The mechanism-based inhibition of dopamine beta-hydroxylase by p-cresol (4-methylphenol) and other simple structural analogues of dopamine, which lack a basic side-chain nitrogen, is reported. p-Cresol binds DBH by a mechanism that is kinetically indistinguishable from normal dopamine substrate binding. Under conditions (pH 6.6) of random oxygen and phenethylamine substrate addition p-cresol adds randomly, whereas at pH 4.5 or in the presence of fumarate activator addition of p-cresol precedes oxygen binding as is observed with phenethylamine substrate. p-Cresol is shown to be a rapid (kinact = 2.0 min-1, pH 5.0) mechanism-based inactivator of DBH. This inactivation exhibits pseudo-first-order kinetics, is irreversible,more » is prevented by tyramine substrate or competitive inhibitor, and is dependent upon oxygen and ascorbic acid cosubstrates. Inhibition occurs with partial covalent incorporation of p-cresol into DBH. A plot of -log kinact vs. pH shows maximal inactivation occurs at pH 5.0 with dependence upon enzymatic groups with apparent pK values of 4.51 +/- 0.06 and 5.12 +/- 0.06. p-Cresol and related alkylphenols, unlike other mechanism-based inhibitors of DBH, lack a latent electrophile. These inhibitors are postulated to covalently modify DBH by a direct insertion of an aberrant substrate-derived benzylic radical into an active site residue.« less

Intertree competition in uneven-aged ponderosa pine stands

Treesearch

C.W. Woodall; C.E. Fiedler; K.S. Milner

2003-01-01

Intertree competition indices and effects were examined in 14 uneven-aged ponderosa pine (Pinus ponderosa var. scopulorum Engelm.) stands in eastern Montana. Location, height, diameter at breast height (DBH), basal area increment, crown ratio, and sapwood area were determined for each tree (DBH >3.8 cm) on one stem-mapped plot...

Relationship of stump diameter to d.b.h. for northern red oak in the Northeast

Treesearch

Frederick E. Hampf

1955-01-01

This is the fifth report on a series of studies to show the relationship of stump diameter to diameter breast high (d.b.h.) for commercially important tree species in the Northeast. This report is for northern red oak (Quercus rubra).

Genetic variations in the dopamine system and facial expression recognition in healthy chinese college students.

PubMed

Zhu, Bi; Chen, Chuansheng; Moyzis, Robert K; Dong, Qi; Chen, Chunhui; He, Qinghua; Stern, Hal S; Li, He; Li, Jin; Li, Jun; Lessard, Jared; Lin, Chongde

2012-01-01

This study investigated the relation between genetic variations in the dopamine system and facial expression recognition. A sample of Chinese college students (n = 478) was given a facial expression recognition task. Subjects were genotyped for 98 loci [96 single-nucleotide polymorphisms (SNPs) and 2 variable number tandem repeats] in 16 genes involved in the dopamine neurotransmitter system, including its 4 subsystems: synthesis (TH, DDC, and DBH), degradation/transport (COMT,MAOA,MAOB, and SLC6A3), receptors (DRD1,DRD2,DRD3,DRD4, and DRD5), and modulation (NTS,NTSR1,NTSR2, and NLN). To quantify the total contributions of the dopamine system to emotion recognition, we used a series of multiple regression models. Permutation analyses were performed to assess the posterior probabilities of obtaining such results. Among the 78 loci that were included in the final analyses (after excluding 12 SNPs that were in high linkage disequilibrium and 8 that were not in Hardy-Weinberg equilibrium), 1 (for fear), 3 (for sadness), 5 (for anger), 13 (for surprise), and 15 (for disgust) loci exhibited main effects on the recognition of facial expressions. Genetic variations in the dopamine system accounted for 3% for fear, 6% for sadness, 7% for anger, 10% for surprise, and 18% for disgust, with the latter surviving a stringent permutation test. Genetic variations in the dopamine system (especially the dopamine synthesis and modulation subsystems) made significant contributions to individual differences in the recognition of disgust faces. Copyright © 2012 S. Karger AG, Basel.

Why size matters: the interactive influences of tree diameter distribution and sap flow parameters on upscaled transpiration.

PubMed

Berry, Z Carter; Looker, Nathaniel; Holwerda, Friso; Gómez Aguilar, León Rodrigo; Ortiz Colin, Perla; González Martínez, Teresa; Asbjornsen, Heidi

2018-02-01

In stands with a broad range of diameters, a small number of very large trees can disproportionately influence stand basal area and transpiration (Et). Sap flow-based Et estimates may be particularly sensitive to large trees due to nonlinear relationships between tree-level water use (Q) and tree diameter at breast height (DBH). Because Q is typically predicted on the basis of DBH and sap flow rates measured in a subset of trees and then summed to obtain Et, we assessed the relative importance of DBH and sap flow variables (sap velocity, Vs, and sapwood depth, Rs) in determining the magnitude of Et and its dependence on large trees in a tropical montane forest ecosystem. Specifically, we developed a data-driven simulation framework to vary the relationship between DBH and Vs and stand DBH distribution and then calculate Q, Et and the proportion of Et contributed by the largest tree in each stand. Our results demonstrate that variation in how Rs is determined in the largest trees can alter estimates up to 26% of Et while variation in how Vs is determined can vary results by up to 132%. Taken together, these results highlight a great need to expand our understanding of water transport in large trees as this hinders our ability to predict water fluxes accurately from stand to catchment scales. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Individual tree size inequality enhances aboveground biomass in homegarden agroforestry systems in the dry zone of Sri Lanka.

PubMed

Ali, Arshad; Mattsson, Eskil

2017-01-01

Individual tree size variation, which is generally quantified by variances in tree diameter at breast height (DBH) and height in isolation or conjunction, plays a central role in ecosystem functioning in both controlled and natural environments, including forests. However, none of the studies have been conducted in homegarden agroforestry systems. In this study, aboveground biomass, stand quality, cation exchange capacity (CEC), DBH variation, and species diversity were determined across 45 homegardens in the dry zone of Sri Lanka. We employed structural equation modeling (SEM) to test for the direct and indirect effects of stand quality and CEC, via tree size inequality and species diversity, on aboveground biomass. The SEM accounted for 26, 8, and 1% of the variation in aboveground biomass, species diversity and DBH variation, respectively. DBH variation had the strongest positive direct effect on aboveground biomass (β=0.49), followed by the non-significant direct effect of species diversity (β=0.17), stand quality (β=0.17) and CEC (β=-0.05). There were non-significant direct effects of CEC and stand quality on DBH variation and species diversity. Stand quality and CEC had also non-significant indirect effects, via DBH variation and species diversity, on aboveground biomass. Our study revealed that aboveground biomass substantially increased with individual tree size variation only, which supports the niche complementarity mechanism. However, aboveground biomass was not considerably increased with species diversity, stand quality and soil fertility, which might be attributable to the adaptation of certain productive species to the local site conditions. Stand structure shaped by few productive species or independent of species diversity is a main determinant for the variation in aboveground biomass in the studied homegardens. Maintaining stand structure through management practices could be an effective approach for enhancing aboveground biomass in these dry zone homegarden agroforestry systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural insight of dopamine β-hydroxylase, a drug target for complex traits, and functional significance of exonic single nucleotide polymorphisms.

PubMed

Kapoor, Abhijeet; Shandilya, Manish; Kundu, Suman

2011-01-01

Human dopamine β-hydroxylase (DBH) is an important therapeutic target for complex traits. Several single nucleotide polymorphisms (SNPs) have also been identified in DBH with potential adverse physiological effect. However, difficulty in obtaining diffractable crystals and lack of a suitable template for modeling the protein has ensured that neither crystallographic three-dimensional structure nor computational model for the enzyme is available to aid rational drug design, prediction of functional significance of SNPs or analytical protein engineering. Adequate biochemical information regarding human DBH, structural coordinates for peptidylglycine alpha-hydroxylating monooxygenase and computational data from a partial model of rat DBH were used along with logical manual intervention in a novel way to build an in silico model of human DBH. The model provides structural insight into the active site, metal coordination, subunit interface, substrate recognition and inhibitor binding. It reveals that DOMON domain potentially promotes tetramerization, while substrate dopamine and a potential therapeutic inhibitor nepicastat are stabilized in the active site through multiple hydrogen bonding. Functional significance of several exonic SNPs could be described from a structural analysis of the model. The model confirms that SNP resulting in Ala318Ser or Leu317Pro mutation may not influence enzyme activity, while Gly482Arg might actually do so being in the proximity of the active site. Arg549Cys may cause abnormal oligomerization through non-native disulfide bond formation. Other SNPs like Glu181, Glu250, Lys239 and Asp290 could potentially inhibit tetramerization thus affecting function. The first three-dimensional model of full-length human DBH protein was obtained in a novel manner with a set of experimental data as guideline for consistency of in silico prediction. Preliminary physicochemical tests validated the model. The model confirms, rationalizes and provides structural basis for several biochemical data and claims testable hypotheses regarding function. It provides a reasonable template for drug design as well.

Development and Analysis of SRIC Harvesting Systems

Treesearch

Bryce J. Stokes; Bruce R. Hartsough

1993-01-01

This paper reviews several machine combinations for harvesting short-rotation, intensive-culture (SRIC) plantations. Productivity and cost information for individual machines was obtained from published sources. Three felling and skidding systems were analyzed for two stands, a 7.6-cm (3-in) average d.b.h. sycamore and a 15.2-cm (6-in) average d.b.h. eucalyptus. The...

Predicting logging residues: an interim equation for Appalachian oak sawtimber

Treesearch

A. Jeff Martin

1975-01-01

An equation, using dbh, dbh², bole length, and sawlog height to predict the cubic-foot volume of logging residue per tree, was developed from data collected on 36 mixed oaks in southwestern Virginia. The equation produced reliable results for small sawtimber trees, but additional research is needed for other species, sites, and utilization practices.

Development of height-volume relationships in second growth Abies grandis for use with aerial LiDAR

Treesearch

Wade T. Tinkham; Alistair M. S. Smith; David L. R. Affleck; Jarred D. Saralecos; Michael J. Falkowski; Chad M. Hoffman; Andrew T. Hudak; Michael A. Wulder

2016-01-01

Following typical forest inventory protocols, individual tree volume estimates are generally derived via diameter-at-breast-height (DBH)-based allometry. Although effective, measurement of DBH is time consuming and potentially a costly element in forest inventories. The capacity of airborne light detection and ranging (LiDAR) to provide individual tree-level...

Crown radius and diameter at breast height relationships for six bottomland hardwood species

Treesearch

Brian Roy Lockhart; Robert C. Weih; Keith M. Smith

2005-01-01

The relationship between a tree's crown radius and diameter at breast height (DBH) has a variety of uses including forest competition studies, tree crown densities, spacing and stocking relationships, wildlife habitat suitability models, and tree volume estimations. Estimating DBH from mean crown radius (MCR) is of interest to natural resource managers because MCR...

A benefit-cost analysis of ten tree species in Modesto, California, U.S.A

Treesearch

E.G. McPherson

2003-01-01

Tree work records for ten species were analyzed to estimate average annual management costs by dbh class for six activity areas. Average annual benefits were calculated by dbh class for each species with computer modeling. Average annual net benefits per tree were greatest for London plane (Platanus acerifolia) ($178.57), hackberry (...

Roosting habitat of Merriam's turkeys in the Black Hills, South Dakota

Treesearch

Mark A. Rumble

1992-01-01

Lack of roost habitat (trees >40 cm diameter breast height [dbh] and >18 m2/ha basal area) can limit populations of Merriam’s turkeys (Meleagris gallopavo merriami). The Black Hills region has relatively large populations of Merriam’s turkeys, yet trees >40 cm dbh are uncommon. Consequently, I studied...

Methylmercury causes epigenetic suppression of the tyrosine hydroxylase gene in an in vitro neuronal differentiation model.

PubMed

Go, Suzuna; Kurita, Hisaka; Matsumoto, Kana; Hatano, Manami; Inden, Masatoshi; Hozumi, Isao

2018-08-25

Methylmercury (MeHg) is the causative substance of Minamata disease, which is associated with various neurological disorders such as sensory disturbance and ataxia. It has been suggested low-level dietary intake of MeHg from MeHg-containing fish during gestation adversely affects the fetus. In our study, we investigated the toxicological effects of MeHg exposure on neuronal differentiation focusing on epigenetics. We used human fetal brain-derived immortalized cells (LUHMES cells) as a human neuronal differentiation model. Cell viability, neuronal, and catecholamine markers in LUHMES cells were assessed after exposure to MeHg (0-1000 nM) for 6 days (from day 2 to day 8 of neuronal differentiation). Cell viability on day 8 was not affected by exposure to 1 nM MeHg for 6 days. mRNA levels of AADC, DBH, TUJ1, and SYN1 also were unaffected by MeHg exposure. In contrast, levels of TH, the rate-limiting enzyme for dopamine synthesis, were significantly decreased after MeHg exposure. Acetylated histone H3, acetylated histone H3 lysine 9, and tri-methyl histone H3 lysine 9 levels at the TH gene promoter were not altered by MeHg exposure. However, tri-methylation of histone H3 lysine 27 levels, related to transcriptional repression, were significantly increased at the TH gene promotor after MeHg exposure. In summary, MeHg exposure during neuronal differentiation led to epigenetic changes that repressed TH gene expression. This study provides useful insights into the toxicological mechanisms underlying the effects of developmental MeHg exposure during neuronal differentiation. Copyright © 2018 Elsevier Inc. All rights reserved.

Biomass equations for major tree species of the Northeast

Treesearch

Louise M. Tritton; James W. Hornbeck

1982-01-01

Regression equations are used in both forestry and ecosystem studies to estimate tree biomass from field measurements of dbh (diameter at breast height) or a combination of dbh and height. Literature on biomass is reviewed, and 178 sets of publish equation for 25 species common to the Northeastern Unites States are listed. On the basis of these equations, estimates of...

User's Manual for Total-Tree Multiproduct Cruise Program

Treesearch

Alexander Clark; Thomas M. Burgan; Richard C. Field; Peter E. Dress

1985-01-01

This interactive computer program uses standard tree-cruise data to estimate the weight and volume of the total tree, saw logs, plylogs, chipping logs, pulpwood, crown firewood, and logging residue in timber stands.Input is cumulative cruise data for tree counts by d.b.h. and height. Output is in tables: board-foot volume by d.b.h.; total-tree and tree-component...

Equations for predicting diameter, height, crown width, and leaf area of San Joaquin Valley street trees

Treesearch

P.J. Peper; E.G. McPherson; S.M. Mori

2001-01-01

Although the modeling of energy-use reduction, air pollution uptake, rainfall interception, and microclimate modification associated with urban trees depends on data relating diameter at breast height (dbh) , crown height, crown diameter, and leaf area to tree age or dbh, scant information is available for common municipal tree species . I n this study , tree height ,...

Stand Parameters of 11- to 15-Year Old Green Ash Plantings

Treesearch

Roger M. Krinard

1989-01-01

Three green ash (Fraxinus pennsylvanica Marsh.) plantings, ages 11, 13, and 15, and a 13-year-old pumpkin ash (F. profunda (Bush) Bush) planting were sampled to determine d.b.h. and height development and survival of free-to-grow trees. On medium-textured (Commerce) and clay-capped (Bowdre and Tunica) soils, the average d.b.h...

Height-diameter equations for thirteen midwestern bottomland hardwood species

Treesearch

Kenneth C. Colbert; David R. Larsen; James R. Lootens

2002-01-01

Height-diameter equations are often used to predict the mean total tree height for trees when only diameter at breast height (dbh) is measured. Measuring dbh is much easier and is subject to less measurement error than total tree height. However, predicted heights only reflect the average height for trees of a particular diameter. In this study, we present a set of...

Butt log quality of trees in Pennsylvania oak stands

Treesearch

Martin E. Dale; Robert L. Brisbin; Robert L. Brisbin

1985-01-01

Describes the distribution of sawtimber trees by diameter at breast height (d.b.h.) and grade for eight hardwood species in upland oak stands of Pennsylvania. The proportion of trees by d.b.h. and grade revealed differences between species. The quality of northern red oak, white oak, and yellow-poplar appeared inherently better than that of red maple, chestnut oak, and...

Tree volume and biomass equations for the Lake States.

Treesearch

Jerold T. Hahn

1984-01-01

Presents species specific equations and methods for computing tree height, cubic foot, and board foot volume, and biomass for the Lake States (Michigan, Minnesota, and Wisconsin). Height equations compute either total or merchantable height to a variable top d.o.b. from d.b.h., site index, and basal area. Volumes and biomass are computed from d.b.h. and height.

MAOA, DBH and SLC6A4 variants in CHARGE: A case control study of autism spectrum disorders

PubMed Central

Tassone, Flora; Qi, Lihong; Zhang, Wenting; Hansen, Robin L; Pessah, Isaac N; Hertz-Picciotto, Irva

2011-01-01

Background Genetic factors are established to contribute to the development of autism. We examined three loci, serotonin transporter (SLC6A4), dopamine hydroxylase (DBH) and the variable number of tandem repeat promoter of the monoamine oxidase A (MAOA) for association with autism in participants from the CHARGE (CHildhood Autism Risks from Genetics and the Environment) Study, the first large-scale population-based case-control investigation of both environmental and genetic contributions to autism risk. Methods Among male children enrolled in the CHARGE study we tested associations between each of the three polymorphisms and autism (AU) (n=119), or a combined group of autism and other autism spectrum disorders (AU+ASD, which includes an additional n=53) as compared with typically developing controls (TD, n=137). Results The case-control association analysis showed neither SLC6A4 nor DBH to be statistically significantly associated with AU or ASD. However, the male children carrying 4 tandem repeats in the promoter region of the MAOA gene showed a 2-fold higher risk of AU (or AU+ASD) than those carrying allele 3, adjusted for confounders (OR = 2.02, 95% CI = 1.12, 3.65, p = 0.02 for AU vs. TD, and OR = 2.05, 95% CI = 1.19, 3.53, p = 0.01 for ASD vs. TD). In addition, mothers homozygous for the 4 tandem repeat allele showed at least a 3-fold higher risk of AU (or AU+ASD) than mothers homozygous for allele 3 (OR = 3.07, 95% CI = 1.19, 7.91, p = 0.02 for AU vs. TD, and OR = 3.26, 95% CI = 1.35, 7.89, p = 0.009 for AU+ASD vs. TD). Conclusions These results suggest a potential role of the functional MAOA promoter alleles in the male child, the mother, or both in autism spectrum disorders. PMID:21538940

Defense Health: Coordinating Authority Needed for Psychological Health and Traumatic Brain Injury Activities

DTIC Science & Technology

2012-01-01

Placebo-Controlled Trial of the Dopamine Beta Hydroxylase (DBH) Inhibitor, Nepicastat, for the Treatment of PTSD in Operation Iraqi Freedom (OIF...Operation Enduring Freedom (OEF) Veterans 1 A Randomized, Placebo-Controlled Trial of the Dopamine -?-Hydroxylase (DBH) Inhibitor, Nepicastat for the...Reduction: Predeployment Stress Inoculation Training 1 Combat, Sexual Assault, and Post-Traumatic Stress in OIF/OEF Military Women 1 Comparing

Age trends in genetic control of Juglans nigra L. height growth

Treesearch

George Rink; F. H. Kung

1995-01-01

Age-related trends in narrow-sense and family heritabilities for black walnut height and dbh from a southern Illinois open-pollinated progeny test are evaluated through age 20 years. Narrow-sense heritability for height tends to be relatively stable between ages 10 and 20 at 0.55 - 0.65 with similar patterns and values for family heritabilities for both height and dbh...

Understory-overstory relationships in ponderosa pine forests, Black Hills, South Dakota

Treesearch

Daniel W. Uresk; Kieth E. Severson

1989-01-01

Under-story-overstory relationships were examined over 7 different growing stock levels(GSLs) of 2 size classes(saplings,8-10 cm d.b.h. and poles, 15-18 cm d.b.h.) of ponderosa pine (Pinus ponderosa) in the Black Hills, South Dakota. Generally, production of graminoids, forbs, and shrubs was similar between sapling and pole stands. Trends among GSLs were also similar...

Dwarf mistletoe does not increase trunk taper in released red firs in California

Treesearch

Robert F. Scharpf

1977-01-01

Dwarf mistletoe had no noticeable effect on trunk taper of young, dominant and codominant red firs 4 to 22 inches (10.2 to 55.9 cm) d.b.h. Also, taper was not influenced by live crown ratio of infected and uninfected trees. Trees less than 7 inches d.b.h. had significantly more taper than larger trees, irrespective of dwarf mistletoe.

Modeling Caribbean tree stem diameters from tree height and crown width measurements

Treesearch

Thomas Brandeis; KaDonna Randolph; Mike Strub

2009-01-01

Regression models to predict diameter at breast height (DBH) as a function of tree height and maximum crown radius were developed for Caribbean forests based on data collected by the U.S. Forest Service in the Commonwealth of Puerto Rico and Territory of the U.S. Virgin Islands. The model predicting DBH from tree height fit reasonably well (R2 = 0.7110), with...

Estimating Dbh of Trees Employing Multiple Linear Regression of the best Lidar-Derived Parameter Combination Automated in Python in a Natural Broadleaf Forest in the Philippines

NASA Astrophysics Data System (ADS)

Ibanez, C. A. G.; Carcellar, B. G., III; Paringit, E. C.; Argamosa, R. J. L.; Faelga, R. A. G.; Posilero, M. A. V.; Zaragosa, G. P.; Dimayacyac, N. A.

2016-06-01

Diameter-at-Breast-Height Estimation is a prerequisite in various allometric equations estimating important forestry indices like stem volume, basal area, biomass and carbon stock. LiDAR Technology has a means of directly obtaining different forest parameters, except DBH, from the behavior and characteristics of point cloud unique in different forest classes. Extensive tree inventory was done on a two-hectare established sample plot in Mt. Makiling, Laguna for a natural growth forest. Coordinates, height, and canopy cover were measured and types of species were identified to compare to LiDAR derivatives. Multiple linear regression was used to get LiDAR-derived DBH by integrating field-derived DBH and 27 LiDAR-derived parameters at 20m, 10m, and 5m grid resolutions. To know the best combination of parameters in DBH Estimation, all possible combinations of parameters were generated and automated using python scripts and additional regression related libraries such as Numpy, Scipy, and Scikit learn were used. The combination that yields the highest r-squared or coefficient of determination and lowest AIC (Akaike's Information Criterion) and BIC (Bayesian Information Criterion) was determined to be the best equation. The equation is at its best using 11 parameters at 10mgrid size and at of 0.604 r-squared, 154.04 AIC and 175.08 BIC. Combination of parameters may differ among forest classes for further studies. Additional statistical tests can be supplemented to help determine the correlation among parameters such as Kaiser- Meyer-Olkin (KMO) Coefficient and the Barlett's Test for Spherecity (BTS).

Comparing RIEGL RiCOPTER UAV LiDAR Derived Canopy Height and DBH with Terrestrial LiDAR

PubMed Central

Bartholomeus, Harm M.; Kooistra, Lammert

2017-01-01

In recent years, LIght Detection And Ranging (LiDAR) and especially Terrestrial Laser Scanning (TLS) systems have shown the potential to revolutionise forest structural characterisation by providing unprecedented 3D data. However, manned Airborne Laser Scanning (ALS) requires costly campaigns and produces relatively low point density, while TLS is labour intense and time demanding. Unmanned Aerial Vehicle (UAV)-borne laser scanning can be the way in between. In this study, we present first results and experiences with the RIEGL RiCOPTER with VUX®-1UAV ALS system and compare it with the well tested RIEGL VZ-400 TLS system. We scanned the same forest plots with both systems over the course of two days. We derived Digital Terrain Models (DTMs), Digital Surface Models (DSMs) and finally Canopy Height Models (CHMs) from the resulting point clouds. ALS CHMs were on average 11.5 cm higher in five plots with different canopy conditions. This showed that TLS could not always detect the top of canopy. Moreover, we extracted trunk segments of 58 trees for ALS and TLS simultaneously, of which 39 could be used to model Diameter at Breast Height (DBH). ALS DBH showed a high agreement with TLS DBH with a correlation coefficient of 0.98 and root mean square error of 4.24 cm. We conclude that RiCOPTER has the potential to perform comparable to TLS for estimating forest canopy height and DBH under the studied forest conditions. Further research should be directed to testing UAV-borne LiDAR for explicit 3D modelling of whole trees to estimate tree volume and subsequently Above-Ground Biomass (AGB). PMID:29039755

Comparing RIEGL RiCOPTER UAV LiDAR Derived Canopy Height and DBH with Terrestrial LiDAR.

PubMed

Brede, Benjamin; Lau, Alvaro; Bartholomeus, Harm M; Kooistra, Lammert

2017-10-17

In recent years, LIght Detection And Ranging (LiDAR) and especially Terrestrial Laser Scanning (TLS) systems have shown the potential to revolutionise forest structural characterisation by providing unprecedented 3D data. However, manned Airborne Laser Scanning (ALS) requires costly campaigns and produces relatively low point density, while TLS is labour intense and time demanding. Unmanned Aerial Vehicle (UAV)-borne laser scanning can be the way in between. In this study, we present first results and experiences with the RIEGL RiCOPTER with VUX ® -1UAV ALS system and compare it with the well tested RIEGL VZ-400 TLS system. We scanned the same forest plots with both systems over the course of two days. We derived Digital Terrain Model (DTMs), Digital Surface Model (DSMs) and finally Canopy Height Model (CHMs) from the resulting point clouds. ALS CHMs were on average 11.5 c m higher in five plots with different canopy conditions. This showed that TLS could not always detect the top of canopy. Moreover, we extracted trunk segments of 58 trees for ALS and TLS simultaneously, of which 39 could be used to model Diameter at Breast Height (DBH). ALS DBH showed a high agreement with TLS DBH with a correlation coefficient of 0.98 and root mean square error of 4.24 c m . We conclude that RiCOPTER has the potential to perform comparable to TLS for estimating forest canopy height and DBH under the studied forest conditions. Further research should be directed to testing UAV-borne LiDAR for explicit 3D modelling of whole trees to estimate tree volume and subsequently Above-Ground Biomass (AGB).

Trading Habitat Patches for the Red Cockaded Woodpecker: Incorporating the Role of Landscape Structure and Uncertainty in Decision Making

DTIC Science & Technology

2007-06-11

to 35 cm dbh 2b. basal area of pines 25.4 to 35 cm dbh between 0 and 9.2 m2/ha PS1, PS4 , PS12 Small Pines No. pine stems/ha < 25.4 cm dbh...1Model A p-value Adj R2 AIC Fit = 2.50 + 0.0079 PS1 – 0.036 PM1 – 0.0102 PS4 – 0.019 HS12 0.063 0.033 426 Parameter p-value t-value Intercept...0.0001 8.23 PS1 0.125 1.54 PM1 0.038 -2.10 PS4 0.107 -1.62 HS12 0.063 -1.88 Model A – Most Parsimonious p-value Adj R2 AIC Fit = 2.02 – 0.03 PM1

Neurochemical coding of enteric neurons in the guinea pig stomach.

PubMed

Schemann, M; Schaaf, C; Mäder, M

1995-03-06

The aim of this study was to investigate the neurochemical coding of myenteric neurons in the guinea pig gastric corpus by using immunohistochemical methods. Antibodies and antisera against calbindin (CALB), calretinin (CALRET), choline acetyltransferase (ChAT), calcitonin gene-related peptide (CGRP), dopamine beta-hydroxylase (DBH), beta-endorphin (ENK), neuropeptide Y (NPY), neuron-specific enolase (NSE), nitric oxide synthase (NOS), protein gene product 9.5 (PGP), parvalbumin (PARV), serotonin (5-HT), somatostatin (SOM), substance P (SP), tyrosine hydroxylase (TH), and vasoactive intestinal peptide (VIP) were used. Double- and triple-labeling studies revealed colocalization of certain transmitters and enabled the identification of distinct subpopulations of gastric enteric neurons. NPY/VIP/NOS/ENK were present in 28% of all neurons, whereas 11% had NPY/VIP/DBH/ChAT; NOS-only neurons made up 2% of the population. The combination SP/ChAT/ENK occurred in 21% of the population, whereas SP/ChAT/ENK/CALRET and SP/CHAT/SOM/ +/- CALRET was identified in 5% and 6% of all cells, respectively. 5-HT-containing neurons comprised 2% of all cells and could be further classified by the presence of additional antigens as 5-HT/SP/(ChAT) or 5-HT/VIP/(ChAT). Approximately 21% of all neurons contained only ChAT with no additional antigen present and are referred to as ChAT/-. Gastric myenteric ganglion cells were not immunoreactive for CALB, PARV, CGRP, or TH. The results of this study indicate that gastric myenteric neurons can be characterized on the basis of different chemical coding. Neurochemical coding of corpus myenteric neurons revealed some similarities and significant differences in comparison with other regions of the gut. These differences might reflect adaptation of enteric nerves according to regional specialization and the distinct functions of the proximal stomach as a gastric reservoir.

Stand Parameters of a 27-Year-Old Water Oak Plantation on Old Field Loessial Soils

Treesearch

Roger M. Krinard; Robert L. Johnson

1988-01-01

At age 27, water oak (Quercus nigra L.) plantings on Macon Ridge old field loessial soil near Winnsboro, Louisiana, had per-acre stand values as follows: number of trees, 356; average d.b.h., 6.6 inches; basal area, 86 ft2; total volume from the stump to the tip (of trees with d.b.h. 25.0 in), 2,017 ft3...

Growth of Appalachian hardwoods kept free to grow from 2 to 12 years after clearcutting

Treesearch

H. Clay Smith

1983-01-01

Free-to-grow sapling-size, yellow-poplars of seedling origin outgrew similar black cherry and red oak in both dbh and total height (especially on good sites). Yellow-poplar consistently grew faster in dbh throughout the study, particularly on the better oak sites. Black cherry had an edge over yellow-poplar in total height during the early years of the study, but...

Stand Dynamics in an Old-Growth Hardwood Forest in Southern Illinois, USA

Treesearch

James J. Zaczek; John W. Groninger; J. W. Van Sambeek

2002-01-01

Kaskaskia Woods, a 7.4-ha old-growth hardwood forest in southern Illinois, USA, has been managed as a natural area and protected from disturbance since 1933. In 1935, eight 0.1-ha plots were installed and all trees 4 cm dbh or larger were tagged and inventoried. Trees were remeasured for survival, ingrowth (new trees >4 cm), and diameter (dbh) in 1940, 1958, 1965,...

Predicting diameter at breast height from total height and crown length

Treesearch

Quang V. Cao; Thomas J. Dean

2013-01-01

Tree diameter at breast height (d.b.h.) is often predicted from total height (model 1a) or both total height and number of trees per acre (model 1b). These approaches are useful when Light Detection and Ranging (LiDAR) data are available. LiDAR height data can be employed to predict tree d.b.h., and consequently individual tree volumes and volume/ ha can be obtained...

Modeling browse impacts on sapling and tree recruitment across forests in the northern United States

Treesearch

Matthew B. Russell; James A. Westfall; Christopher W. Woodall

2017-01-01

Understanding the patterns of tree recruitment is essential to quantifying the future health and productivity of forest ecosystems. Using national forest inventory information, we incorporated browse impact measurements into models of sapling (2.5–12.7 cm diameter at breast height (DBH)) and overstory tree (≥12.7 cm DBH) ingrowth across the northern United States....

Effects of timber harvesting on birds in the Black Hills of South Dakota and Wyoming, USA

Treesearch

Brian L. Dykstra; Mark A. Rumble; Lester D. Flake

1997-01-01

Timber harvest alters structural characteristics in ponderosa pine forests. In the Black Hills, harvested stands with 40-70% overstory canopy cover are managed as sapling/pole (3.0 - 22.9 cm dbh) or mature (> 22.9 cm dbh) stands. Changing the forest structure to two size classes has unknown effects on bird communities in this region. We counted birds in 20 harvested...

Prescribed Burning For Laurel and Rhodendron Control in the Southern appalachians

Treesearch

Ralph M. Hooper

1969-01-01

Prescribed fire shows promise as a tool for the control of laurel and rhododendron in the Southern Appalachian mountains. A recent prescribed fire killed the tops of 70 percent of ail laurel under 0.5 inch d.b.h. and 70 percent of the rhododendron under 1 inch d.b.h. Seventeen months after the bum, almost all of the top-killed laurel and rhododendron have...

The Relationship of Diameter at Breast Height and Crown Diameter for Four Species Groups in Hardin County, Tennessee

Treesearch

Lawrence R. Gering; Dennis M. May

1995-01-01

A set of simple linear regression models for predicting diameter at breast height (dbh) from crown diamter and a set of similar models for predicting crown diamter from dbh were developed for four species groups in Harding County, TN. Data were obtained from 557 trees measured during hte 1989 USDA Southern Forest Experiment Station survey of the forest of Tennessee,...

Spatial Characteristics of Tree Diameter Distributions in a Temperate Old-Growth Forest

PubMed Central

Zhao, Xiuhai; von Gadow, Klaus

2013-01-01

This contribution identifies spatial characteristics of tree diameter in a temperate forest in north-eastern China, based on a fully censused observational study area covering 500×600 m. Mark correlation analysis with three null hypothesis models was used to determine departure from expectations at different neighborhood distances. Tree positions are clumped at all investigated scales in all 37 studied species, while the diameters of most species are spatially negatively correlated, especially at short distances. Interestingly, all three cases showing short-distance attraction of dbh marks are associated with light-demanding shrub species. The short-distance attraction of dbh marks indicates spatially aggregated cohorts of stems of similar size. The percentage of species showing significant dbh suppression peaked at a 4 m distance under the heterogeneous Poisson model. At scales exceeding the peak distance, the percentage of species showing significant dbh suppression decreases sharply with increasing distances. The evidence from this large observational study shows that some of the variation of the spatial characteristics of tree diameters is related variations of topography and soil chemistry. However, an obvious interpretation of this result is still lacking. Thus, removing competitors surrounding the target trees is an effective way to avoid neighboring competition effects reducing the growth of valuable target trees in forest management practice. PMID:23527066

Spatial characteristics of tree diameter distributions in a temperate old-growth forest.

PubMed

Zhang, Chunyu; Wei, Yanbo; Zhao, Xiuhai; von Gadow, Klaus

2013-01-01

This contribution identifies spatial characteristics of tree diameter in a temperate forest in north-eastern China, based on a fully censused observational study area covering 500×600 m. Mark correlation analysis with three null hypothesis models was used to determine departure from expectations at different neighborhood distances. Tree positions are clumped at all investigated scales in all 37 studied species, while the diameters of most species are spatially negatively correlated, especially at short distances. Interestingly, all three cases showing short-distance attraction of dbh marks are associated with light-demanding shrub species. The short-distance attraction of dbh marks indicates spatially aggregated cohorts of stems of similar size. The percentage of species showing significant dbh suppression peaked at a 4 m distance under the heterogeneous Poisson model. At scales exceeding the peak distance, the percentage of species showing significant dbh suppression decreases sharply with increasing distances. The evidence from this large observational study shows that some of the variation of the spatial characteristics of tree diameters is related variations of topography and soil chemistry. However, an obvious interpretation of this result is still lacking. Thus, removing competitors surrounding the target trees is an effective way to avoid neighboring competition effects reducing the growth of valuable target trees in forest management practice.

Neural input is critical for arcuate hypothalamic neurons to mount intracellular signaling responses to systemic insulin and deoxyglucose challenges in male rats: implications for communication within feeding and metabolic control networks.

PubMed

Khan, Arshad M; Walker, Ellen M; Dominguez, Nicole; Watts, Alan G

2014-02-01

The hypothalamic arcuate nucleus (ARH) controls rat feeding behavior in part through peptidergic neurons projecting to the hypothalamic paraventricular nucleus (PVH). Hindbrain catecholaminergic (CA) neurons innervate both the PVH and ARH, and ablation of CA afferents to PVH neuroendocrine neurons prevents them from mounting cellular responses to systemic metabolic challenges such as insulin or 2-deoxy-d-glucose (2-DG). Here, we asked whether ablating CA afferents also limits their ARH responses to the same challenges or alters ARH connectivity with the PVH. We examined ARH neurons for three features: (1) CA afferents, visualized by dopamine-β-hydroxylase (DBH)- immunoreactivity; (2) activation by systemic metabolic challenge, as measured by increased numbers of neurons immunoreactive (ir) for phosphorylated ERK1/2 (pERK1/2); and (3) density of PVH-targeted axons immunoreactive for the feeding control peptides Agouti-related peptide and α-melanocyte-stimulating hormone (αMSH). Loss of PVH DBH immunoreactivity resulted in concomitant ARH reductions of DBH-ir and pERK1/2-ir neurons in the medial ARH, where AgRP neurons are enriched. In contrast, pERK1/2 immunoreactivity after systemic metabolic challenge was absent in αMSH-ir ARH neurons. Yet surprisingly, axonal αMSH immunoreactivity in the PVH was markedly increased in CA-ablated animals. These results indicate that (1) intrinsic ARH activity is insufficient to recruit pERK1/2-ir ARH neurons during systemic metabolic challenges (rather, hindbrain-originating CA neurons are required); and (2) rats may compensate for a loss of CA innervation to the ARH and PVH by increased expression of αMSH. These findings highlight the existence of a hierarchical dependence for ARH responses to neural and humoral signals that influence feeding behavior and metabolism.

Stochastically generating tree diameter lists to populate forest stands based on the linkage variables forest type and stand age

Treesearch

Bernard R. Parresol; F. Thomas Lloyd

2003-01-01

Forest inventory data were used to develop a standage-driven, stochastic predictor of unit-area, frequency weighted lists of breast high tree diameters (DBH). The average of mean statistics from 40 simulation prediction sets of an independent 78-plot validation dataset differed from the observed validation means by 0.5 cm for DBH, and by 12 trees/h for density. The 40...

Influences of Elevation on Overstory Species Composition in an Old-Growth Bottomland Hardwood-Loblolly Pine Forest in Southern Arkansas

Treesearch

Adrian G. Grell; Michael G. Shelton; Eric Heitzman

2004-01-01

Elevation was quantified in a 16.2-ha southern Arkansas bottomland forest using surveying equipment and survey-grade GPS units. Six 500-m2 plots were established in each of three 0.5-m elevation classes. Species and d.b.h. were determined for all trees ¡Ý9.1-cm d.b.h. Species importance values were calculated by plot. Twenty-four environmental...

The R. R. Reynolds Research Natural Area in Southeastern Arkansas: A 56-Year Case Study in Pine-Hardwood Overstory Sustainability

Treesearch

Michael D. Cain; Michael G. Shelton

1996-01-01

The R. R. Reynolds Research Natural Area is a 32-ha pine-hardwood forest in southeastern Arkansas, U.S.A. that originated from diameter-limit cutting of the virgin forest before 1915. In 1935, these 32 ha were reserved from timber management. Between 1937 and 1993, eight inventories were taken of all living trees > g-cm DBH, using 2.5-cm DBH classes within three...

Thirty-Eight Years of Autogenic, Woody Understory Dynamics in a Mature, Temperate Pine-Oak Forest

Treesearch

Michael D. Cain; Michael G. Shelton

1997-01-01

In 1935, 32 ha of a pine-hardwood forest were set aside from future timber management in southern Arkansas, U.S.A. Old-growth timber had been cut to a 36-cm stump diameter before 1915. Between 1952 and 1993, four inventories were made of the overstory and midstory components (number of live trees 29 cm in diameter breast height (DBH) taken at 1.37 m, by 2.54-cm DBH...

(1)H, (13)C, and (15)N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog.

PubMed

Moro, Sean L; Cocco, Melanie J

2015-10-01

The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the (15)N, (1)H, and (13)C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains.

Behavioural genetic differences between Chinese and European pigs.

PubMed

Chu, Qingpo; Liang, Tingting; Fu, Lingling; Li, Huizhi; Zhou, Bo

2017-09-01

Aggression is a heritable trait and genetically related to neurotransmitter-related genes. Behavioural characteristics of some pig breeds are different. To compare the genetic differences between breeds, backtest and aggressive behaviour assessments, and genotyped using Sequenom iPLEX platform were performed in 50 Chinese indigenous Mi pigs and 100 landrace-large white (LLW) cross pigs with 32 SNPs localized in 11 neurotransmitter-related genes. The genetic polymorphisms of 26 SNPs had notable differences (P < 0.05) between Mi and LLW. The most frequent haplotypes were different in DBH, HTR2A, GAD1, HTR2B,MAOA and MAOB genes between Mi and LLW. The mean of backtest scores was significantly lower (P < 0.001) for Mi than LLW pigs. Skin lesion scores were greater (P < 0.01) in LLW pigs than Mi pigs. In this study, we have confirmed that Chinese Mi pigs are less active and less aggressive than European LLW pigs, and the genetic polymorphisms of neurotransmitter-related genes, which have been proved previously associated with aggressive behaviour, have considerable differences between Mi and LLW pigs.

Determination of iodide with 1,3-dibromo-5,5-dimethylhydantoin (DBH) in comparison with the ICl-method. Analytical methods of pharmacopeias with DBH in respect to environmental and economical concern. Part 3.

PubMed

Hilp, M; Senjuk, S

2001-06-01

USP 1995 (The United States Pharmacopeia, 23rd Edit., (1995), potassium iodide p. 1265, sodium iodide p. 1424), PH. EUR. 1997 (European Pharmacopoeia, third ed., Council of Europe, Strasbourg, (1997), potassium iodide p. 1367, sodium iodide p. 1493) and JAP 1996 (The Japanes Pharmacopoeia, 13th ed. (1996), potassium iodide p. 578, sodium iodide p. 630) determine iodide with the ICl-method (J. Am. Chem. Soc. 25 (1903) 756-761; Z. Anorg. Chem. 36 (1903) 76-83; Fresenius Z. Anal. Chem. 106 (1936) 12-23; Arzneibuch-Kommentar, Wissenschaftliche Erläuterungen zum Europäischen Arzneibuch, Wissenschaftliche Verlagsgesellschaft mbH, Stuttgart, Govi-Verlag - Pharmazeutischer Verlag GmbH, Eschborn, 12th suppl. (1999), K10 p. 2), using chloroform, which is toxic and hazardous to environment. Without the application of chlorinated hydrocarbons USP 2000 (The United State Pharmacopeia, 24th ed. (2000), potassium iodide p. 1368, sodium iodide p. 1535) and Brit 1999 (British Pharmacopoeia London, (1999), Appendix VIII C, p. A162) titrate iodide with the redox indicator amaranth. A titration with potentiometric indication giving two end-points at the step of I(2) and [ICl(2)](-) is described. Due to the high concentration of hydrochloric acid required for the ICl-method, the determination with DBH (1,3-dibromo-5,5-dimethylhydantoin; 1,3-dibromo-5,5-dimethyl-2,4-imidazolidinedione) can be recommended and is performed easily. Similarly, the iodide content of gallamine triethiodide may be analyzed with DBH by application of a visual two-phase titration in water and ethyl acetate or with potentiometric indication in a mixture of 2-propanol and water. During the removal of the excess of DBH 4-bromo-triethylgallamine (2,2',2"-[1-bromo-benzene-2,3,4-triyltris(oxy)]N,N,N-triethylethanium) is formed.

Monoamine Oxidase and Dopamine β-Hydroxylase Inhibitors from the Fruits of Gardenia jasminoides

PubMed Central

Kim, Ji Ho; Kim, Gun Hee; Hwang, Keum Hee

2012-01-01

This research was designed to determine what components of Gardenia jasminoides play a major role in inhibiting the enzymes related antidepressant activity of this plant. In our previous research, the ethyl acetate fraction of G. jasminosides fruits inhibited the activities of both monoamine oxidase-A (MAO-A) and monoamine oxidase-B (MAO-B), and oral administration of the ethanolic extract slightly increased serotonin concentrations in the brain tissues of rats and decreased MAO-B activity. In addition, we found through in vitro screening test that the ethyl acetate fraction showed modest inhibitory activity on dopamine-β hydroxylase (DBH). The bioassay-guided fractionation led to the isolation of five bio-active compounds, protocatechuic acid (1), geniposide (2), 6'-O-trans-p-coumaroylgeniposide (3), 3,5-d-ihydroxy-1,7-bis (4-hydroxyphenyl) heptanes (4), and ursolic acid (5), from the ethyl acetate fraction of G. jasminoides fruits. The isolated compounds showed different inhibitory potentials against MAO-A, -B, and DBH. Protocatechuic acid showed potent inhibition against MAO-B (IC50 300 μmol/L) and DBH (334 μmol/L), exhibiting weak MAO-A inhibition (2.41 mmol/L). Two iridoid glycosides, geniposide (223 μmol/L) and 6'-O-trans-p-coumaroylgeniposide (127μmol/L), were selective MAO-B inhibitor. Especially, 6'-O-trans-p-coumaroylgeniposide exhibited more selective MAO-B inhibition than deprenyl, well-known MAO-B inhibitor for the treatment of early-stage Parkinson’s disease. The inhibitory activity of 3,5-di-hydroxy-1,7-bis (4-hydroxyphenyl) heptane was strong for MAO-B (196 μmol/L), modest for MAO-A (400 μmol/L), and weak for DBH (941 μmol/L). Ursolic acid exhibited significant inhibition of DBH (214 μmol/L), weak inhibition of MAO-B (780 μmol/L), and no inhibition against MAO-A. Consequently, G. jasminoides fruits are considerable for development of biofunctional food materials for the combination treatment of depression and neurodegenerative disorders. PMID:24116298

Removal or retention of unmerchantable saplings in Allegheny hardwoods: effect on regeneration after clearcutting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marquis, D.A.

1981-01-01

Merchantable trees in an old growth stand (mainly beech, (Fagus grandifolia) and supar maple) in NW Pennsylvania were clear felled in September and October 1937, and 4 plots set up containing (a) large (d.b.h. over 1.5 inch), and small residual saplings, (b) primarily small residuals (1-inch d.b.h.) and (c) plots as (a) and (b) but with saplings over 0.5 inch d.b.h. chopped down (moved) in April and May 1938. Plots were tallied in 1938 after mowing, and in 1942, 1947, 1957 and 1972. After 35 years, the 2 mowed plots (c) were dominated by fast-growing, shade-intolerant black cherry (Prunus serotina)more » which accounted for 65% of the b.a. The plot with treatment (a) had fewer, larger trees with some sawtimber size maple and beech. Cherry accounted for 32% b.a. The plot with treatment (b) had trees intermediate in size and composition (cherry 53% b.a.). (Refs. 10).« less

Tree competition and species coexistence in a Quercus--Betula forest in the Dongling Mountains in northern China

NASA Astrophysics Data System (ADS)

Hou, Ji-hua; Mi, Xiang-cheng; Liu, Can-ran; Ma, Ke-ping

2006-09-01

The population size structure, growth dynamics and mode of competition among adult trees (≥ 4 cm DBH) of six abundant tree species in a 5 ha study plot of a temperate deciduous forest in the Dongling Mountains in northern China were investigated using diffusion and growth dynamics models. In the year of 2000, two dominant species, Quercus liaotungensis and Betula dahurica accounted for ca. 68.69% of the total basal area and 52.71% of the total density of adult plants. Q. liaotungensis, Populus davidiana and Acer mono exhibited inverse J-shaped DBH distributions whereas Betula dahurica, B. platyphylla and Salix caprea had unimodal DBH distributions. One-sided interspecific competition was detected between some species combinations at the scale of the 5 ha study plot, and the competitive effect was mainly size-dependent rather than from species-specific interactions with large individuals in the canopy layer out competing smaller individuals in the understory. Symmetric competition was found between Q. liaotungensis and A. mono only. However, considering the straight line relationship of G ( t, x) - √{D(t, x)}, which suggests that competitive asymmetry is very low or absent, combined with the relatively low mortality of trees with a DBH larger than 4 cm, we speculate that asymmetric interspecific competition was not important in structuring this tree community. Regeneration characteristics of each species are most likely important in regulating species coexistence and stand dynamics in this forest.

[Growth effect of eucalyptus-acacia mixed plantation in South China].

PubMed

Yang, Zeng-Jiang; Xu, Da-Ping; Chen, Wen-Ping; Huang, Lie-Jian; Li, Shang-Jun; Chen, Yuan

2009-10-01

Eucalyptus U6 and Acacia crassicarpa were mixed planted with different ratios and modes to investigate the growth parameters of the two tree species. In the 2-3 years old mixed plantation, the wind-throw of A. crassicarpa decreased markedly with increasing ratio of Eucalyptus U6, the decrement being 26.14% when the Eucalyptus U6/A. crassicarpa ratio was 3 : 1, but the survival rates of Eucalyptus U6 and A. crassicarpa had no significant difference under different planting modes. Mixed planting retarded the A. crassicarpa growth to some extent, with the DBH being 90% of that in pure A. crassicarpa stand. The mixed planting had little effects on the height growth of Eucalyptus U6, but promoted its DBH growth markedly, and the beneficial effect increased with increasing ratio of A. crassicarpa. In the 6 years old 1 : 1 Eucalyptus U6/A. crassicarpa plantation, the Eucalyptus U6 individuals with DBH > 15 cm occupied 32.1%; while in pure Eucalyptus U6 stand, they only accounted for 5.83%. Mixed planting with 2 : 1 Eucalyptus U6/A. crassicarpa could obtain a maximum total biomass of 198.8 m3 x hm(-2), which was 118.8% of the total biomass in pure Eucalyptus U6 stand, or 169.9% of that in pure A. crassicarpa stand. Mixture of Eucalyptus with Acacia would be a good choice to produce Eucalyptus trees with larger DBH.

Copper-containing monooxygenases: enzymatic and biomimetic studies of the O-atom transfer catalysis.

PubMed

Blain, Ingrid; Slama, Patrick; Giorgi, Michel; Tron, Thierry; Réglier, Marius

2002-04-01

This review reports our recent studies or the mechanism of O-atom transfer to a benzylic C-H bond promoted by Dopamine beta-Hydroxylase (DBH) and its biomimetic models. We demonstrate that it is possible to carry out parallel and comparative studies on this enzyme (DBH) and its biomimetic models with the same substrate: 2-aminoindane (3). It was chosen because its two stereogenic centers, both in benzylic positions, make it very powerful for studying the stereochemistry of an O-atom transfer reaction. DBH-catalyzed hydroxylation of 3 produced exclusively 14% of trans-(1S,2S)-2-amino-1-indanol (4) (93% ee). Studies with stereospecifically deuterium-labeled 2-aminoindanes (1R,2S)-3b and (1S,2S)-3a showed that the formation of 4 was the rcsult of an overall process with retention of configuration where an O-atom is stereospecifically inserted in the trans pro-S position of the substrate. With copper(I) and (II) complexes of IndPY2 ligands we studied the reaction with dioxygen and observed an O-atom transfer to a benzylic C-H bond which was performed in the same manner as that of DBH. With the deuterium-labeled cis-2-d-IndPY2 ligand, we demonstrated that the reaction occurs by a stereospecific process with retention of configuration. In both cases (enzymatic vs. biomimetic) the O-atom transfers occur in a two-step process involving radical intermediates.

Neuro-psychopharmacogenetics and Neurological Antecedents of Posttraumatic Stress Disorder: Unlocking the Mysteries of Resilience and Vulnerability

PubMed Central

Bowirrat, Abdalla; Chen, Thomas J.H.; Blum, Kenneth; Madigan, Margaret; Bailey, John A.; Chuan Chen, Amanda Lih; Downs, B. William; Braverman, Eric R.; Radi, Shahien; Waite, Roger L.; Kerner, Mallory; Giordano, John; Morse, Siohban; Oscar-Berman, Marlene; Gold, Mark

2010-01-01

Background and Hypothesis: Although the biological underpinnings of immediate and protracted trauma-related responses are extremely complex, 40 years of research on humans and other mammals have demonstrated that trauma (particularly trauma early in the life cycle) has long-term effects on neurochemical responses to stressful events. These effects include the magnitude of the catecholamine response and the duration and extent of the cortisol response. In addition, a number of other biological systems are involved, including mesolimbic brain structures and various neurotransmitters. An understanding of the many genetic and environmental interactions contributing to stress-related responses will provide a diagnostic and treatment map, which will illuminate the vulnerability and resilience of individuals to Posttraumatic Stress Disorder (PTSD). Proposal and Conclusions: We propose that successful treatment of PTSD will involve preliminary genetic testing for specific polymorphisms. Early detection is especially important, because early treatment can improve outcome. When genetic testing reveals deficiencies, vulnerable individuals can be recommended for treatment with “body friendly” pharmacologic substances and/or nutrients. Results of our research suggest the following genes should be tested: serotoninergic, dopaminergic (DRD2, DAT, DBH), glucocorticoid, GABAergic (GABRB), apolipoprotein systems (APOE2), brain-derived neurotrophic factor, Monamine B, CNR1, Myo6, CRF-1 and CRF-2 receptors, and neuropeptide Y (NPY). Treatment in part should be developed that would up-regulate the expression of these genes to bring about a feeling of well being as well as a reduction in the frequency and intensity of the symptoms of PTSD. PMID:21629442

Variable coupling between sap-flow and transpiration in pine trees under drought conditions

NASA Astrophysics Data System (ADS)

Preisler, Yakir; Tatarinov, Fyodor; Rohatyn, Shani; Rotenberg, Eyal; Grunzweig, Jose M.; Yakir, Dan

2016-04-01

Changes in diurnal patterns in water transport and physiological activities in response to changes in environmental conditions are important adjustments of trees to drought. The rate of sap flow (SF) in trees is expected to be in agreement with the rate of tree-scale transpiration (T) and provides a powerful measure of water transport in the soil-plant-atmosphere system. The aim of this five-years study was to investigate the temporal links between SF and T in Pinus halepensis exposed to extreme seasonal drought in the Yatir forest in Israel. We continuously measured SF (20 trees), the daily variations in stem diameter (ΔDBH, determined with high precision dendrometers; 8 trees), and ecosystem evapotranspiration (ET; eddy covariance), which were complemented with short-term campaigns of leaf-scale measurements of H2O and CO2 gas exchange, water potentials, and hydraulic conductivity. During the rainy season, tree SF was well synchronized with ecosystem ET, reaching maximum rates during midday in all trees. However, during the dry season, the daily SF trends greatly varied among trees, allowing a classification of trees into three classes: 1) Trees that remain with SF maximum at midday, 2) trees that advanced their SF peak to early morning, and 3) trees that delayed their SF peak to late afternoon hours. This classification remained valid for the entire study period (2010-2015), and strongly correlated with tree height and DBH, and to a lower degree with crown size and competition index. In the dry season, class 3 trees (large) tended to delay the timing of SF maximum to the afternoon, and to advance their maximum diurnal DBH to early morning, while class 2 trees (smaller) advanced their SF maximum to early morning and had maximum daily DBH during midday and afternoon. Leaf-scale transpiration (T), measurements showed a typical morning peak in all trees, irrespective of classification, and a secondary peak in the afternoon in large trees only. Water potential and hydraulic conductivity in larger trees recovered faster from midday depression than in smaller ones. We concluded that the observed changes in the patterns of water flow into and out of the trees reflected differences in the utilization of external and internal 'water storage'. Large trees appear to rely on sufficient internal water storage that filled up in the morning (max DBH) and supported transpiration both in the morning and the afternoon, while SF increased throughout the day to compensate for the depletion in water storage (SF maximum in the afternoon). In contrast, small trees with insufficient internal water storage must rely on soil water availability and maximize SF in the morning to support concurrent tree transpiration, achieving some internal storage only in the afternoon, when T declines and maximum daily DBH is observed. The results indicated also that trees with insufficient internal storage, as can be detected by the simultaneous SF and DBH patterns, are likely to be more vulnerable to drought-related mortality since soil water availability may not be sufficient to support transpiration and stomata opening.

Impaired cardiac energy metabolism in embryos lacking adrenergic stimulation.

PubMed

Baker, Candice N; Gidus, Sarah A; Price, George F; Peoples, Jessica N R; Ebert, Steven N

2015-03-01

As development proceeds from the embryonic to fetal stages, cardiac energy demands increase substantially, and oxidative phosphorylation of ADP to ATP in mitochondria becomes vital. Relatively little, however, is known about the signaling mechanisms regulating the transition from anaerobic to aerobic metabolism that occurs during the embryonic period. The main objective of this study was to test the hypothesis that adrenergic hormones provide critical stimulation of energy metabolism during embryonic/fetal development. We examined ATP and ADP concentrations in mouse embryos lacking adrenergic hormones due to targeted disruption of the essential dopamine β-hydroxylase (Dbh) gene. Embryonic ATP concentrations decreased dramatically, whereas ADP concentrations rose such that the ATP/ADP ratio in the adrenergic-deficient group was nearly 50-fold less than that found in littermate controls by embryonic day 11.5. We also found that cardiac extracellular acidification and oxygen consumption rates were significantly decreased, and mitochondria were significantly larger and more branched in adrenergic-deficient hearts. Notably, however, the mitochondria were intact with well-formed cristae, and there was no significant difference observed in mitochondrial membrane potential. Maternal administration of the adrenergic receptor agonists isoproterenol or l-phenylephrine significantly ameliorated the decreases in ATP observed in Dbh-/- embryos, suggesting that α- and β-adrenergic receptors were effective modulators of ATP concentrations in mouse embryos in vivo. These data demonstrate that adrenergic hormones stimulate cardiac energy metabolism during a critical period of embryonic development. Copyright © 2015 the American Physiological Society.

Physiogenomic analysis of localized FMRI brain activity in schizophrenia.

PubMed

Windemuth, Andreas; Calhoun, Vince D; Pearlson, Godfrey D; Kocherla, Mohan; Jagannathan, Kanchana; Ruaño, Gualberto

2008-06-01

The search for genetic factors associated with disease is complicated by the complexity of the biological pathways linking genotype and phenotype. This analytical complexity is particularly concerning in diseases historically lacking reliable diagnostic biological markers, such as schizophrenia and other mental disorders. We investigate the use of functional magnetic resonance imaging (fMRI) as an intermediate phenotype (endophenotype) to identify physiogenomic associations to schizophrenia. We screened 99 subjects, 30 subjects diagnosed with schizophrenia, 13 unaffected relatives of schizophrenia patients, and 56 unrelated controls, for gene polymorphisms associated with fMRI activation patterns at two locations in temporal and frontal lobes previously implied in schizophrenia. A total of 22 single nucleotide polymorphisms (SNPs) in 15 genes from the dopamine and serotonin neurotransmission pathways were genotyped in all subjects. We identified three SNPs in genes that are significantly associated with fMRI activity. SNPs of the dopamine beta-hydroxylase (DBH) gene and of the dopamine receptor D4 (DRD4) were associated with activity in the temporal and frontal lobes, respectively. One SNP of serotonin-3A receptor (HTR3A) was associated with temporal lobe activity. The results of this study support the physiogenomic analysis of neuroimaging data to discover associations between genotype and disease-related phenotypes.

The mutational landscape of MYCN, Lin28b and ALK F1174L driven murine neuroblastoma mimics human disease.

PubMed

De Wilde, Bram; Beckers, Anneleen; Lindner, Sven; Kristina, Althoff; De Preter, Katleen; Depuydt, Pauline; Mestdagh, Pieter; Sante, Tom; Lefever, Steve; Hertwig, Falk; Peng, Zhiyu; Shi, Le-Ming; Lee, Sangkyun; Vandermarliere, Elien; Martens, Lennart; Menten, Björn; Schramm, Alexander; Fischer, Matthias; Schulte, Johannes; Vandesompele, Jo; Speleman, Frank

2018-02-02

Genetically engineered mouse models have proven to be essential tools for unraveling fundamental aspects of cancer biology and for testing novel therapeutic strategies. To optimally serve these goals, it is essential that the mouse model faithfully recapitulates the human disease. Recently, novel mouse models for neuroblastoma have been developed. Here, we report on the further genomic characterization through exome sequencing and DNA copy number analysis of four of the currently available murine neuroblastoma model systems ( ALK, Th- MYCN, Dbh- MYCN and Lin28b ). The murine tumors revealed a low number of genomic alterations - in keeping with human neuroblastoma - and a positive correlation of the number of genetic lesions with the time to onset of tumor formation was observed. Gene copy number alterations are the hallmark of both murine and human disease and frequently affect syntenic genomic regions. Despite low mutational load, the genes mutated in murine disease were found to be enriched for genes mutated in human disease. Taken together, our study further supports the validity of the tested mouse models for mechanistic and preclinical studies of human neuroblastoma.

Automatic tree parameter extraction by a Mobile LiDAR System in an urban context.

PubMed

Herrero-Huerta, Mónica; Lindenbergh, Roderik; Rodríguez-Gonzálvez, Pablo

2018-01-01

In an urban context, tree data are used in city planning, in locating hazardous trees and in environmental monitoring. This study focuses on developing an innovative methodology to automatically estimate the most relevant individual structural parameters of urban trees sampled by a Mobile LiDAR System at city level. These parameters include the Diameter at Breast Height (DBH), which was estimated by circle fitting of the points belonging to different height bins using RANSAC. In the case of non-circular trees, DBH is calculated by the maximum distance between extreme points. Tree sizes were extracted through a connectivity analysis. Crown Base Height, defined as the length until the bottom of the live crown, was calculated by voxelization techniques. For estimating Canopy Volume, procedures of mesh generation and α-shape methods were implemented. Also, tree location coordinates were obtained by means of Principal Component Analysis. The workflow has been validated on 29 trees of different species sampling a stretch of road 750 m long in Delft (The Netherlands) and tested on a larger dataset containing 58 individual trees. The validation was done against field measurements. DBH parameter had a correlation R2 value of 0.92 for the height bin of 20 cm which provided the best results. Moreover, the influence of the number of points used for DBH estimation, considering different height bins, was investigated. The assessment of the other inventory parameters yield correlation coefficients higher than 0.91. The quality of the results confirms the feasibility of the proposed methodology, providing scalability to a comprehensive analysis of urban trees.

Hypnotic hypersensitivity to volatile anesthetics and dexmedetomidine in dopamine β-hydroxylase knockout mice.

PubMed

Hu, Frances Y; Hanna, George M; Han, Wei; Mardini, Feras; Thomas, Steven A; Wyner, Abraham J; Kelz, Max B

2012-11-01

Multiple lines of evidence suggest that the adrenergic system can modulate sensitivity to anesthetic-induced immobility and anesthetic-induced hypnosis as well. However, several considerations prevent the conclusion that the endogenous adrenergic ligands norepinephrine and epinephrine alter anesthetic sensitivity. Using dopamine β-hydroxylase knockout (Dbh) mice genetically engineered to lack the adrenergic ligands and their siblings with normal adrenergic levels, we test the contribution of the adrenergic ligands upon volatile anesthetic induction and emergence. Moreover, we investigate the effects of intravenous dexmedetomidine in adrenergic-deficient mice and their siblings using both righting reflex and processed electroencephalographic measures of anesthetic hypnosis. We demonstrate that the loss of norepinephrine and epinephrine and not other neuromodulators co-packaged in adrenergic neurons is sufficient to cause hypersensitivity to induction of volatile anesthesia. However, the most profound effect of adrenergic deficiency is retarding emergence from anesthesia, which takes two to three times as long in Dbh mice for sevoflurane, isoflurane, and halothane. Having shown that Dbh mice are hypersensitive to volatile anesthetics, we further demonstrate that their hypnotic hypersensitivity persists at multiple doses of dexmedetomidine. Dbh mice exhibit up to 67% shorter latencies to loss of righting reflex and up to 545% longer durations of dexmedetomidine-induced general anesthesia. Central rescue of adrenergic signaling restores control-like dexmedetomidine sensitivity. A novel continuous electroencephalographic analysis illustrates that the longer duration of dexmedetomidine-induced hypnosis is not due to a motor confound, but occurs because of impaired anesthetic emergence. Adrenergic signaling is essential for normal emergence from general anesthesia. Dexmedetomidine-induced general anesthesia does not depend on inhibition of adrenergic neurotransmission.

Automatic tree parameter extraction by a Mobile LiDAR System in an urban context

PubMed Central

Lindenbergh, Roderik; Rodríguez-Gonzálvez, Pablo

2018-01-01

In an urban context, tree data are used in city planning, in locating hazardous trees and in environmental monitoring. This study focuses on developing an innovative methodology to automatically estimate the most relevant individual structural parameters of urban trees sampled by a Mobile LiDAR System at city level. These parameters include the Diameter at Breast Height (DBH), which was estimated by circle fitting of the points belonging to different height bins using RANSAC. In the case of non-circular trees, DBH is calculated by the maximum distance between extreme points. Tree sizes were extracted through a connectivity analysis. Crown Base Height, defined as the length until the bottom of the live crown, was calculated by voxelization techniques. For estimating Canopy Volume, procedures of mesh generation and α-shape methods were implemented. Also, tree location coordinates were obtained by means of Principal Component Analysis. The workflow has been validated on 29 trees of different species sampling a stretch of road 750 m long in Delft (The Netherlands) and tested on a larger dataset containing 58 individual trees. The validation was done against field measurements. DBH parameter had a correlation R2 value of 0.92 for the height bin of 20 cm which provided the best results. Moreover, the influence of the number of points used for DBH estimation, considering different height bins, was investigated. The assessment of the other inventory parameters yield correlation coefficients higher than 0.91. The quality of the results confirms the feasibility of the proposed methodology, providing scalability to a comprehensive analysis of urban trees. PMID:29689076

Growth process and model simulation of three different classes of Schima superba in a natural subtropical forest in China

NASA Astrophysics Data System (ADS)

Wei, Hui; Deng, Xiangwen; Ouyang, Shuai; Chen, Lijun; Chu, Yonghe

2017-01-01

Schima superba is an important fire-resistant, high-quality timber species in southern China. Growth in height, diameter at breast height (DBH), and volume of the three different classes (overtopped, average and dominant) of S. superba were examined in a natural subtropical forest. Four growth models (Richards, edited Weibull, Logistic and Gompertz) were selected to fit the growth of the three different classes of trees. The results showed that there was a fluctuation phenomenon in height and DBH current annual growth process of all three classes. Multiple intersections were found between current annual increment (CAI) and mean annual increment (MAI) curves of both height and DBH, but there was no intersection between volume CAI and MAI curves. All selected models could be used to fit the growth of the three classes of S. superba, with determinant coefficients above 0.9637. However, the edited Weibull model performed best with the highest R2 and the lowest root of mean square error (RMSE). S. superba is a fast-growing tree with a higher growth rate during youth. The height and DBH CAIs of overtopped, average and dominant trees reached growth peaks at ages 5-10, 10-15 and 15-20 years, respectively. According to model simulation, the volume CAIs of overtopped, average and dominant trees reached growth peaks at ages 17, 55 and 76 years, respectively. The biological rotation ages of the overtopped, average and dominant trees of S. superba were 29, 85 and 128 years, respectively.

Breeding of Acrocomia aculeata using genetic diversity parameters and correlations to select accessions based on vegetative, phenological, and reproductive characteristics.

PubMed

Coser, S M; Motoike, S Y; Corrêa, T R; Pires, T P; Resende, M D V

2016-10-17

Macaw palm (Acrocomia aculeata) is a promising species for use in biofuel production, and establishing breeding programs is important for the development of commercial plantations. The aim of the present study was to analyze genetic diversity, verify correlations between traits, estimate genetic parameters, and select different accessions of A. aculeata in the Macaw Palm Germplasm Bank located in Universidade Federal de Viçosa, to develop a breeding program for this species. Accessions were selected based on precocity (PREC), total spathe (TS), diameter at breast height (DBH), height of the first spathe (HFS), and canopy area (CA). The traits were evaluated in 52 accessions during the 2012/2013 season and analyzed by restricted estimation maximum likelihood/best linear unbiased predictor procedures. Genetic diversity resulted in the formation of four groups by Tocher's clustering method. The correlation analysis showed it was possible to have indirect and early selection for the traits PREC and DBH. Estimated genetic parameters strengthened the genetic variability verified by cluster analysis. Narrow-sense heritability was classified as moderate (PREC, TS, and CA) to high (HFS and DBH), resulting in strong genetic control of the traits and success in obtaining genetic gains by selection. Accuracy values were classified as moderate (PREC and CA) to high (TS, HFS, and DBH), reinforcing the success of the selection process. Selection of accessions for PREC, TS, and HFS by the rank-average method permits selection gains of over 100%, emphasizing the successful use of the accessions in breeding programs and obtaining superior genotypes for commercial plantations.

Comparing the accuracy of terrestrial laser scanner in measuring forest inventory variables to enhance better decision making for potential fire hazards

NASA Astrophysics Data System (ADS)

Ghimire, Suman; Xystrakis, Fotios; Koutsias, Nikos

2017-04-01

Forest inventory variables are essential in accessing the potential of wildfire hazard, obtaining above ground biomass and carbon sequestration which helps developing strategies for sustainable management of forests. Effective management of forest resources relies on the accuracy of such inventory variables. This study aims to compare the accuracy in obtaining the forest inventory variables like diameter at breast height (DBH) and tree height from Terrestrial Laser Scanner (Faro Focus 3D X 330) with that from the traditional forest inventory techniques in the Mediterranean forests of Greece. The data acquisition was carried out on an area of 9,539.8 m2 with six plots each of radius 6 m. Computree algorithm was applied for automatic detection of DBH from terrestrial laser scanner data. Similarly, tree height was estimated manually using CloudCompare software for the terrestrial laser scanner data. The field estimates of DBH and tree height was carried out using calipers and Nikon Forestry 550 Laser Rangefinder. The comparison of DBH measured between field estimates and Terrestrial Laser Scanner (TLS), resulted in R squared values ranging from 0.75 to 0.96 at the plot level. An average R2 and RMSE value of 0.80 and 1.07 m respectively was obtained when comparing the tree height between TLS and field data. Our results confirm that terrestrial laser scanner can provide nondestructive, high-resolution, and precise determination of forest inventory for better decision making in sustainable forest management and assessing potential of forest fire hazards.

Data for developing allometric models and evaluating carbon stocks of the Zambezi Teak Forests in Zambia.

PubMed

Ngoma, Justine; Moors, Eddy; Kruijt, Bart; Speer, James H; Vinya, Royd; Chidumayo, Emmanuel N; Leemans, Rik

2018-04-01

This paper presents data on carbon stocks of tropical tree species along a rainfall gradient. The data was generated from the Sesheke, Namwala, and Kabompo sites in Zambia. Though above-ground data was generated for all these three sites, we uprooted trees to determine below-ground biomass from the Sesheke site only. The vegetation was assessed in all three sites. The data includes tree diameter at breast height (DBH), total tree height, wood density, wood dry weight and root dry weight for large (≥ 5 cm DBH) and small (< 5 cm DBH) trees. We further presented Root-to-Shoot Ratios of uprooted trees. Data on the importance-value indices of various species for large and small trees are also determined. Below and above-ground carbon stocks of the surveyed tree species are presented per site. This data were used by Ngoma et al. (2018) [1] to develop above and below-ground biomass models and the reader is referred to this study for additional information, interpretation, and reflection on applying this data.

An immunohistochemical screening of neurochemical markers in fungiform papillae and taste buds of the anterior rat tongue.

PubMed

Astbäck, J; Arvidson, K; Johansson, O

1997-02-01

The occurrence and distribution of several neurochemical markers were investigated. Numerous nerve fibres were shown, using antibodies to protein gene product (PGP) 9.5, neurone-specific enolase, calcitonin gene-related peptide (CGRP), substance P. neurokinin A or protein S-100. The presence of vasoactive intestinal polypeptide (VIP), peptide histidine isoleucine amide (PHI), neuropeptide tyrosine, dopamine-beta-hydroxylase (DBH), cholecystokinin/gastrin, glutamate and galanin was more scarce. Nerve fibres containing these above-mentioned markers were found at several locations, i.e. in the epithelium, connective tissue, and around blood vessels. In the taste buds, numerous PGP 9.5, neurone-specific enolase-, CGRP-, substance P-, neurokinin A- and protein S-100-containing structures were found, but few VIP and galanin ones. No immunoreactivity was found with antibodies against somatostatin, bombesin, enkephalin or dynorphin. These findings extend knowledge about the general as well as the neurochemical messenger-based innervation of rat fungiform papillae, forming a firm basis for future functional investigations of normal, experimental and also clinical materials.

Tradeoffs in basal area growth and reproduction shift over the lifetime of a long-lived tropical species.

PubMed

Staudhammer, Christina L; Wadt, Lúcia H O; Kainer, Karen A

2013-09-01

Understanding of the extent to which reproductive costs drive growth largely derives from reproductively mature temperate trees in masting and non-masting years. We modeled basal area increment (BAI) and explored current growth-reproduction tradeoffs and changes in such allocation over the life span of a long-lived, non-masting tropical tree. We integrated rainfall and soil variables with data from 190 Bertholletia excelsa trees of different diameter at breast height (DBH) sizes, crown characteristics, and liana loads, quantifying BAI and reproductive output over 4 and 6 years, respectively. While rainfall explains BAI in all models, regardless of DBH class or ontogenic stage, light (based on canopy position and crown form) is most critical in the juvenile (5 cm ≤ DBH < 50 cm) phase. Suppressed trees are only present as juveniles and grow ten times slower (1.45 ± 2.73 m(2) year(-1)) than trees in dominant and co-dominant positions (13.25 ± 0.82 and 12.90 ± 1.35 m(2) year(-1), respectively). Additionally, few juvenile trees are reproductive, and those that are, demonstrate reduced growth, as do reproductive trees in the next 50 to 100 cm DBH class, suggesting growth-reproduction tradeoffs. Upon reaching the canopy, however, and attaining a sizeable girth, this pattern gradually shifts to one where BAI and reproduction are influenced independently by variables such as liana load, crown size and soil properties. At this stage, BAI is largely unaffected by fruit production levels. Thus, while growth-reproduction tradeoffs clearly exist during early life stages, effects of reproductive allocation diminish as B. excelsa increases in size and maturity.

Effectiveness of differing trap types for the detection of emerald ash borer (Coleoptera: Buprestidae).

PubMed

Marshall, Jordan M; Storer, Andrew J; Fraser, Ivich; Beachy, Jessica A; Mastro, Victor C

2009-08-01

The early detection of populations of a forest pest is important to begin initial control efforts, minimizing the risk of further spread and impact. Emerald ash borer (Agrilus planipennis Fairmaire) is an introduced pestiferous insect of ash (Fraxinus spp. L.) in North America. The effectiveness of trapping techniques, including girdled trap trees with sticky bands and purple prism traps, was tested in areas with low- and high-density populations of emerald ash borer. At both densities, large girdled trap trees (>30 cm diameter at breast height [dbh], 1.37 m in height) captured a higher rate of adult beetles per day than smaller trees. However, the odds of detecting emerald ash borer increased as the dbh of the tree increased by 1 cm for trap trees 15-25 cm dbh. Ash species used for the traps differed in the number of larvae per cubic centimeter of phloem. Emerald ash borer larvae were more likely to be detected below, compared with above, the crown base of the trap tree. While larval densities within a trap tree were related to the species of ash, adult capture rates were not. These results provide support for focusing state and regional detection programs on the detection of emerald ash borer adults. If bark peeling for larvae is incorporated into these programs, peeling efforts focused below the crown base may increase likelihood of identifying new infestations while reducing labor costs. Associating traps with larger trees ( approximately 25 cm dbh) may increase the odds of detecting low-density populations of emerald ash borer, possibly reducing the time between infestation establishment and implementing management strategies.

Age trends of genetic parameters, early selection and family by site interactions for growth traits in Larix kaempferi open-pollinated families.

PubMed

Diao, Shu; Hou, Yimei; Xie, Yunhui; Sun, Xiaomei

2016-07-07

Japanese larch (Larix kaempferi) as a successful exotic species has become one of the most important economic and ecological conifers in China. In order to broaden the genetic resource of Larix kaempferi, an effort was made in 1996 to introduce 128 families from seven seed orchards in Japan, with which to establish two progeny trials in climatically different environments. The experiment was aimed to determine the strategy of early selection, particularly important for long-rotated Japanese larch, and the optimal breeding program for specific environments. Growth trajectories revealed different growth performances of stem height (HGT) and diameter at breast height (DBH) in two different environments, Hubei and Liaoning. In both sites, there were marked variabilities in HGT, DBH and volume (VOL) among families at each year. The trends of individual and family heritability and age-age correlations were found to follow a certain dynamic pattern. Based on these trends, the optimum selection age was determined at four years for HGT and five years for DBH in Hubei and Liaoning. Genetic gains for VOL were 34.4 and 6.04 % in Hubei and Liaoning respectively when selection ratio was 10 % at age 16. Type-B correlations were less than 0.67 and rank correlations of breeding value were less than 0.4 for HGT, DBH and VOL between the two sites, revealing that there exist pronounced family-by-site interactions for the growth traits of Larix kaempferi. Early selection for Larix kaempferi is an effective strategy to overcome its long rotation age. In early selection, dual growth trait selection is more effective than single one. Regionalization deployment should be considered in Larix. kaempferi breeding program based on different environmental factors.

The trait contribution to wood decomposition rates of 15 Neotropical tree species.

PubMed

van Geffen, Koert G; Poorter, Lourens; Sass-Klaassen, Ute; van Logtestijn, Richard S P; Cornelissen, Johannes H C

2010-12-01

The decomposition of dead wood is a critical uncertainty in models of the global carbon cycle. Despite this, relatively few studies have focused on dead wood decomposition, with a strong bias to higher latitudes. Especially the effect of interspecific variation in species traits on differences in wood decomposition rates remains unknown. In order to fill these gaps, we applied a novel method to study long-term wood decomposition of 15 tree species in a Bolivian semi-evergreen tropical moist forest. We hypothesized that interspecific differences in species traits are important drivers of variation in wood decomposition rates. Wood decomposition rates (fractional mass loss) varied between 0.01 and 0.31 yr(-1). We measured 10 different chemical, anatomical, and morphological traits for all species. The species' average traits were useful predictors of wood decomposition rates, particularly the average diameter (dbh) of the tree species (R2 = 0.41). Lignin concentration further increased the proportion of explained inter-specific variation in wood decomposition (both negative relations, cumulative R2 = 0.55), although it did not significantly explain variation in wood decomposition rates if considered alone. When dbh values of the actual dead trees sampled for decomposition rate determination were used as a predictor variable, the final model (including dead tree dbh and lignin concentration) explained even more variation in wood decomposition rates (R2 = 0.71), underlining the importance of dbh in wood decomposition. Other traits, including wood density, wood anatomical traits, macronutrient concentrations, and the amount of phenolic extractives could not significantly explain the variation in wood decomposition rates. The surprising results of this multi-species study, in which for the first time a large set of traits is explicitly linked to wood decomposition rates, merits further testing in other forest ecosystems.

Tyrosine hydroxylase (TH), its cofactor tetrahydrobiopterin (BH4), other catecholamine-related enzymes, and their human genes in relation to the drug and gene therapies of Parkinson's disease (PD): historical overview and future prospects.

PubMed

Nagatsu, Toshiharu; Nagatsu, Ikuko

2016-11-01

Tyrosine hydroxylase (TH), which was discovered at the National Institutes of Health (NIH) in 1964, is a tetrahydrobiopterin (BH4)-requiring monooxygenase that catalyzes the first and rate-limiting step in the biosynthesis of catecholamines (CAs), such as dopamine, noradrenaline, and adrenaline. Since deficiencies of dopamine and noradrenaline in the brain stem, caused by neurodegeneration of dopamine and noradrenaline neurons, are mainly related to non-motor and motor symptoms of Parkinson's disease (PD), we have studied human CA-synthesizing enzymes [TH; BH4-related enzymes, especially GTP-cyclohydrolase I (GCH1); aromatic L-amino acid decarboxylase (AADC); dopamine β-hydroxylase (DBH); and phenylethanolamine N-methyltransferase (PNMT)] and their genes in relation to PD in postmortem brains from PD patients, patients with CA-related genetic diseases, mice with genetically engineered CA neurons, and animal models of PD. We purified all human CA-synthesizing enzymes, produced their antibodies for immunohistochemistry and immunoassay, and cloned all human genes, especially the human TH gene and the human gene for GCH1, which synthesizes BH4 as a cofactor of TH. This review discusses the historical overview of TH, BH4-, and other CA-related enzymes and their genes in relation to the pathophysiology of PD, the development of drugs, such as L-DOPA, and future prospects for drug and gene therapy for PD, especially the potential of induced pluripotent stem (iPS) cells.

Analysis of vegetation changes in Rock Creek Park, 1991-2007

USGS Publications Warehouse

Hatfield, Jeff S.; Krafft, Cairn

2009-01-01

Vegetation data collected at Rock Creek Park every 4 years during 1991-2007 were analyzed for differences among 3 regions within the park and among years. The variables measured and analyzed were percentage of twigs browsed, percentage of canopy cover, species richness of herbaceous plants, number of tree seedlings in each of 7 height classes, tree seedling stocking rate for low deer density and high deer density areas, percentage of tree and shrub cover < 2 m in height, mean diameter at breast height (DBH) of trees > 1 cm DBH, number of tree stems > 1 cm DBH, species richness of trees and shrubs, and mean height of the 5 tallest trees in each plot quadrant. Repeated measures analysis of variance (ANOVA) was used to test for differences and, except for some differences in tree species composition among the 3 regions, no differences (P > 0.01) were found among the 3 regions in the variables discussed above. Many of the variables showed very significant differences (P < 0.01) among years, and causative factors should be investigated further. In addition, importance values were calculated for the 10 most important tree species in each region and changes over time were reported. Future sampling recommendations are also discussed.

Predicting spatial variations of tree species richness in tropical forests from high-resolution remote sensing.

PubMed

Fricker, Geoffrey A; Wolf, Jeffrey A; Saatchi, Sassan S; Gillespie, Thomas W

2015-10-01

There is an increasing interest in identifying theories, empirical data sets, and remote-sensing metrics that can quantify tropical forest alpha diversity at a landscape scale. Quantifying patterns of tree species richness in the field is time consuming, especially in regions with over 100 tree species/ha. We examine species richness in a 50-ha plot in Barro Colorado Island in Panama and test if biophysical measurements of canopy reflectance from high-resolution satellite imagery and detailed vertical forest structure and topography from light detection and ranging (lidar) are associated with species richness across four tree size classes (>1, 1-10, >10, and >20 cm dbh) and three spatial scales (1, 0.25, and 0.04 ha). We use the 2010 tree inventory, including 204,757 individuals belonging to 301 species of freestanding woody plants or 166 ± 1.5 species/ha (mean ± SE), to compare with remote-sensing data. All remote-sensing metrics became less correlated with species richness as spatial resolution decreased from 1.0 ha to 0.04 ha and tree size increased from 1 cm to 20 cm dbh. When all stems with dbh > 1 cm in 1-ha plots were compared to remote-sensing metrics, standard deviation in canopy reflectance explained 13% of the variance in species richness. The standard deviations of canopy height and the topographic wetness index (TWI) derived from lidar were the best metrics to explain the spatial variance in species richness (15% and 24%, respectively). Using multiple regression models, we made predictions of species richness across Barro Colorado Island (BCI) at the 1-ha spatial scale for different tree size classes. We predicted variation in tree species richness among all plants (adjusted r² = 0.35) and trees with dbh > 10 cm (adjusted r² = 0.25). However, the best model results were for understory trees and shrubs (dbh 1-10 cm) (adjusted r² = 0.52) that comprise the majority of species richness in tropical forests. Our results indicate that high-resolution remote sensing can predict a large percentage of variance in species richness and potentially provide a framework to map and predict alpha diversity among trees in diverse tropical forests.

Restoration thinning and influence of tree size and leaf area to sapwood area ratio on water relations of Pinus ponderosa.

PubMed

Simonin, K; Kolb, T E; Montes-Helu, M; Koch, G W

2006-04-01

Ponderosa pine (Pinus ponderosa Dougl. ex P. Laws) forest stand density has increased significantly over the last century (Covington et al. 1997). To understand the effect of increased intraspecific competition, tree size (height and diameter at breast height (DBH)) and leaf area to sapwood area ratio (A(L):A(S)) on water relations, we compared hydraulic conductance from soil to leaf (kl) and transpiration per unit leaf area (Q(L)) of ponderosa pine trees in an unthinned plot to trees in a thinned plot in the first and second years after thinning in a dense Arizona forest. We calculated kl and Q(L) based on whole- tree sap flux measured with heat dissipation sensors. Thinning increased tree predawn water potential within two weeks of treatment. Effects of thinning on kl and Q(L) depended on DBH, A(L):A(S) and drought severity. During severe drought in the first growing season after thinning, kl and Q(L) of trees with low A(L):A(S) (160-250 mm DBH; 9-11 m height) were lower in the thinned plot than the unthinned plot, suggesting a reduction in stomatal conductance (g(s)) or reduced sapwood specific conductivity (K(S)), or both, in response to thinning. In contrast kl and Q(L) were similar in the thinned plot and unthinned plot for trees with high A(L):A(S) (260-360 mm DBH; 13-16 m height). During non-drought periods, kl and Q(L) were greater in the thinned plot than in the unthinned plot for all but the largest trees. Contrary to previous studies of ponderosa pine, A(L):A(S) was positively correlated with tree height and DBH. Furthermore, kl and Q(L) showed a weak negative correlation with tree height and a strong negative correlation with A(S) and thus A(L):A(S) in both the thinned and unthinned plots, suggesting that trees with high A(L):A(S) had lower g(s). Our results highlight the important influence of stand competitive environment on tree-size-related variation in A(L):A(S) and the roles of A(L):A(S) and drought on whole-tree water relations in response to thinning.

Norepinephrine-deficient mice lack responses to antidepressant drugs, including selective serotonin reuptake inhibitors

PubMed Central

Cryan, John F.; O'Leary, Olivia F.; Jin, Sung-Ha; Friedland, Julie C.; Ouyang, Ming; Hirsch, Bradford R.; Page, Michelle E.; Dalvi, Ashutosh; Thomas, Steven A.; Lucki, Irwin

2004-01-01

Mice unable to synthesize norepinephrine (NE) and epinephrine due to targeted disruption of the dopamine β-hydroxylase gene, Dbh, were used to critically test roles for NE in mediating acute behavioral changes elicited by different classes of antidepressants. To this end, we used the tail suspension test, one of the most widely used paradigms for assessing antidepressant activity and depression-related behaviors in normal and genetically modified mice. Dbh–/– mice failed to respond to the behavioral effects of various antidepressants, including the NE reuptake inhibitors desipramine and reboxetine, the monoamine oxidase inhibitor pargyline, and the atypical antidepressant bupropion, even though they did not differ in baseline immobility from Dbh+/– mice, which have normal levels of NE. Surprisingly, the effects of the selective serotonin reuptake inhibitors (SSRIs) fluoxetine, sertraline, and paroxetine were also absent or severely attenuated in the Dbh–/– mice. In contrast, citalopram (the most selective SSRI) was equally effective at reducing immobility in mice with and without NE. Restoration of NE by using l-threo-3,4-dihydroxyphenylserine reinstated the behavioral effects of both desipramine and paroxetine in Dbh–/– mice, thus demonstrating that the reduced sensitivity to antidepressants is related to NE function, as opposed to developmental abnormalities resulting from chronic NE deficiency. Microdialysis studies demonstrated that the ability of fluoxetine to increase hippocampal serotonin was blocked in Dbh–/– mice, whereas citalopram's effect was only partially attenuated. These data show that NE plays an important role in mediating acute behavioral and neurochemical actions of many antidepressants, including most SSRIs. PMID:15148402

Physiogenomic Analysis of Localized fMRI Brain Activity in Schizophrenia

PubMed Central

Windemuth, Andreas; Calhoun, Vince D.; Pearlson, Godfrey D.; Kocherla, Mohan; Jagannathan, Kanchana; Ruaño, Gualberto

2009-01-01

The search for genetic factors associated with disease is complicated by the complexity of the biological pathways linking genotype and phenotype. This analytical complexity is particularly concerning in diseases historically lacking reliable diagnostic biological markers, such as schizophrenia and other mental disorders. We investigate the use of functional magnetic resonance imaging (fMRI) as an intermediate phenotype (endophenotype) to identify physiogenomic associations to schizophrenia. We screened 99 subjects, 30 subjects diagnosed with schizophrenia, 13 unaffected relatives of schizophrenia patients, and 56 unrelated controls, for gene polymorphisms associated with fMRI activation patterns at two locations in temporal and frontal lobes previously implied in schizophrenia. A total of 22 single nucleotide polymorphisms (SNPs) in 15 genes from the dopamine and serotonin neurotransmission pathways were genotyped in all subjects. We identified three SNPs in genes that are significantly associated with fMRI activity. SNPs of the dopamine beta-hydroxylase (DBH) gene and of the dopamine receptor D4 (DRD4) were associated with activity in the temporal and frontal lobes, respectively. One SNP of serotonin-3A receptor (HTR3A) was associated with temporal lobe activity. The results of this study support the physiogenomic analysis of neuroimaging data to discover associations between genotype and disease-related phenotypes. PMID:18330705

Hamartomas from patients with tuberous sclerosis show loss of heterozygosity for chromosome 9q34

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, A.J.; Sepp, T.; Yates, J.R.W.

1994-09-01

We have previously shown allele loss in hamartomas from cases of tuberous sclerosis (TSC) for markers in the region of the recently characterized TSC2 gene on chromosome 16p13.3. Germline deletions in the TSC2 gene have been shown in 5% of patients with TSC. These data strongly suggest that the TSC2 gene acts as a tumor suppressor gene. We hypothesised that hamartomas from patients with TSC can also show allele loss for markers on chromosome 9q34 in the region of the TSC1 gene. We studied 7 hamartomas (3 renal angiomyolipomas, 3 giant cell astrocytomas, and a cardiac rhabdomyoma) from 7 casesmore » of TSC, none of which showed allele loss for markers on chromosome 16p13.3. Eight microsatellite markers were analyzed, comprising from centromeric to telomeric, ASS - D9S64 - D9S149 -D9S150 - DBH - D9S66 - D9S114 - D9S67. Two hamartomas (one renal angiomyolipoma and one giant cell astrocytoma) showed allele loss for at least two markers. The region of allele loss involved the TSC1 locus, but did not include D9S149 or D9S67. We have shown allele loss in two of seven TSC hamartomas in the region of the TSC1 gene on 9q34. Based on this deletion mapping, we suggest that the TSC1 gene on 9a34, like the TSC2 gene, acts as a tumor suppressor gene.« less

Working memory brain activity and capacity link MAOA polymorphism to aggressive behavior during development.

PubMed

Ziermans, T; Dumontheil, I; Roggeman, C; Peyrard-Janvid, M; Matsson, H; Kere, J; Klingberg, T

2012-02-28

A developmental increase in working memory capacity is an important part of cognitive development, and low working memory (WM) capacity is a risk factor for developing psychopathology. Brain activity represents a promising endophenotype for linking genes to behavior and for improving our understanding of the neurobiology of WM development. We investigated gene-brain-behavior relationships by focusing on 18 single-nucleotide polymorphisms (SNPs) located in six dopaminergic candidate genes (COMT, SLC6A3/DAT1, DBH, DRD4, DRD5, MAOA). Visuospatial WM (VSWM) brain activity, measured with functional magnetic resonance imaging, and VSWM capacity were assessed in a longitudinal study of typically developing children and adolescents. Behavioral problems were evaluated using the Child Behavior Checklist (CBCL). One SNP (rs6609257), located ~6.6 kb downstream of the monoamine oxidase A gene (MAOA) on human chromosome X, significantly affected brain activity in a network of frontal, parietal and occipital regions. Increased activity in this network, but not in caudate nucleus or anterior prefrontal regions, was correlated with VSWM capacity, which in turn predicted externalizing (aggressive/oppositional) symptoms, with higher WM capacity associated with fewer externalizing symptoms. There were no direct significant correlations between rs6609257 and behavioral symptoms. These results suggest a mediating role of WM brain activity and capacity in linking the MAOA gene to aggressive behavior during development.

Tree Height and DBH Growth Model Establishment of Main Tree Species in Wuling Mountain Small Watershed

NASA Astrophysics Data System (ADS)

Luo, Jia; Zhang, Min; Zhou, Xiaoling; Chen, Jianhua; Tian, Yuxin

2018-01-01

Taken 4 main tree species in the Wuling mountain small watershed as research objects, 57 typical sample plots were set up according to the stand type, site conditions and community structure. 311 goal diameter-class sample trees were selected according to diameter-class groups of different tree-height grades, and the optimal fitting models of tree height and DBH growth of main tree species were obtained by stem analysis using Richard, Logistic, Korf, Mitscherlich, Schumacher, Weibull theoretical growth equations, and the correlation coefficient of all optimal fitting models reached above 0.9. Through the evaluation and test, the optimal fitting models possessed rather good fitting precision and forecast dependability.

Towards Coleoptera-specific high-throughput screening systems for compounds with ecdysone activity: development of EcR reporter assays using weevil (Anthonomus grandis)-derived cell lines and in silico analysis of ligand binding to A. grandis EcR ligand-binding pocket.

PubMed

Soin, Thomas; Iga, Masatoshi; Swevers, Luc; Rougé, Pierre; Janssen, Colin R; Smagghe, Guy

2009-08-01

Molting in insects is regulated by ecdysteroids and juvenile hormones. Several synthetic non-steroidal ecdysone agonists are on the market as insecticides. These ecdysone agonists are dibenzoylhydrazine (DBH) analogue compounds that manifest their toxicity via interaction with the ecdysone receptor (EcR). Of the four commercial available ecdysone agonists, three (tebufenozide, methoxyfenozide and chromafenozide) are highly lepidopteran specific, one (halofenozide) is used to control coleopteran and lepidopteran insects in turf and ornamentals. However, compared to the very high binding affinity of these DBH analogues to lepidopteran EcRs, halofenozide has a low binding affinity for coleopteran EcRs. For the discovery of ecdysone agonists that target non-lepidopteran insect groups, efficient screening systems that are based on the activation of the EcR are needed. We report here the development and evaluation of two coleopteran-specific reporter-based screening systems to discover and evaluate ecdysone agonists. The screening systems are based on the cell lines BRL-AG-3A and BRL-AG-3C that are derived from the weevil Anthonomus grandis, which can be efficiently transduced with an EcR reporter cassette for evaluation of induction of reporter activity by ecdysone agonists. We also cloned the almost full length coding sequence of EcR expressed in the cell line BRL-AG-3C and used it to make an initial in silico 3D-model of its ligand-binding pocket docked with ponasterone A and tebufenozide.

3D Forest: An application for descriptions of three-dimensional forest structures using terrestrial LiDAR

PubMed Central

Krůček, Martin; Vrška, Tomáš; Král, Kamil

2017-01-01

Terrestrial laser scanning is a powerful technology for capturing the three-dimensional structure of forests with a high level of detail and accuracy. Over the last decade, many algorithms have been developed to extract various tree parameters from terrestrial laser scanning data. Here we present 3D Forest, an open-source non-platform-specific software application with an easy-to-use graphical user interface with the compilation of algorithms focused on the forest environment and extraction of tree parameters. The current version (0.42) extracts important parameters of forest structure from the terrestrial laser scanning data, such as stem positions (X, Y, Z), tree heights, diameters at breast height (DBH), as well as more advanced parameters such as tree planar projections, stem profiles or detailed crown parameters including convex and concave crown surface and volume. Moreover, 3D Forest provides quantitative measures of between-crown interactions and their real arrangement in 3D space. 3D Forest also includes an original algorithm of automatic tree segmentation and crown segmentation. Comparison with field data measurements showed no significant difference in measuring DBH or tree height using 3D Forest, although for DBH only the Randomized Hough Transform algorithm proved to be sufficiently resistant to noise and provided results comparable to traditional field measurements. PMID:28472167

Specialized disaster behavioral health training: Its connection with response, practice, trauma health, and resilience

PubMed Central

Atkins, Christiana D.; Burnett,, Harvey J.

2016-01-01

Abstract This study examined the relationship between having training in key disaster behavioral health (DBH) interventions and trauma health (compassion fatigue, burnout and compassion satisfaction), resilience, the number of crisis responses participated in within the last year, and the frequency of assembling to practice crisis interventions skills. Data was collected from a convenience sample of disaster behavioral health responders (N = 139) attending a training conference in Michigan. Measures included the Professional Quality of Life Scale, the 14-item Resilience Scale, and a demographic questionnaire. Point biserial correlations revealed that having training in large and small group crisis interventions and individual and peer crisis interventions was significantly correlated with higher resilience and lower levels of burnout. Psychological First Aid was not significantly associated with any of the trauma health variables or with resilience. Compassion fatigue and compassion satisfaction were not significantly associated with DBH training. Chi-square tests for independence found no significant association between key DBH training strategies and the number of crisis responses participated in within the past year and the frequency of assembling to practice crisis interventions skills. These findings suggest that completing training in both, large and small group and individual and peer crisis intervention techniques may help to increase resiliency and reduce burnout among disaster behavioral health providers. PMID:28229015

Birch Stands Growth Increase in Western Siberia

NASA Technical Reports Server (NTRS)

Kharuk, Viacheslav I.; Kuzmichev, Valeriy V.; Im, Sergey T.; Ranson, Kenneth J.

2014-01-01

Birch (Betula pendula Roth) growth within the Western Siberia forest-steppe was analyzed based on long-term (1897-2006) inventory data (height, diameter at breast height [dbh], and stand volume). Analysis of biometry parameters showed increased growth at the beginning of twenty-first century compared to similar stands (stands age = 40-60 years) at the end of nineteenth century. Mean height, dbh, and stem volume increased from 14 to 20 m, from 16 to 22 cm, and from approx. 63 to approx. 220 cu m/ha, respectively. Significant correlations were found between the stands mean height, dbh, and volume on the one hand, and vegetation period length (r(sub s) = 0.71 to 0.74), atmospheric CO2 concentration (r(sub s) = 0.71 to 0.76), and drought index (Standardized Precipitation-Evapotranspiration Index, r(sub s) = -0.33 to -0.51) on the other hand. The results obtained have revealed apparent climate-induced impacts (e.g. increase of vegetation period length and birch habitat drying due to drought increase) on the stands growth. Along with this, a high correlation of birch biometric parameters and [CO2] in ambient air indicated an effect of CO2 fertilization. Meanwhile, further drought increase may switch birch stand growth into decline and greater mortality as has already been observed within the Trans-Baikal forest-steppe ecotone.

Below and above-ground carbon distribution along a rainfall gradient. A case of the Zambezi teak forests, Zambia

NASA Astrophysics Data System (ADS)

Ngoma, Justine; Moors, Eddy; Kruijt, Bart; Speer, James H.; Vinya, Royd; Chidumayo, Emmanuel N.; Leemans, Rik

2018-02-01

Understanding carbon (C) stocks or biomass in forests is important to examine how forests mitigate climate change. To estimate biomass in stems, branches and roots takes intensive fieldwork to uproot, cut and weigh the mass of each component. Different models or equations are also required. Our research focussed on the dry tropical Zambezi teak forests and we studied their structure at three sites following a rainfall gradient in Zambia. We sampled 3558 trees at 42 plots covering a combined area of 15ha. Using data from destructive tree samples, we developed mixed-species biomass models to estimate above ground biomass for small (<5 cm diameter at breast height (DBH, 1.3 m above-ground)) and large (≥5 cm DBH) trees involving 90 and 104 trees respectively, that belonged to 12 species. A below-ground biomass model was developed from seven trees of three species (16-44 cm DBH) whose complete root systems were excavated. Three stump models were also derived from these uprooted trees. Finally, we determined the C fractions from 194 trees that belonged to 12 species. The analysis revealed that DBH was the only predictor that significantly correlated to both above-ground and below-ground biomass. We found a mean root-to-shoot ratio of 0.38:0.62. The C fraction in leaves ranged from 39% to 42%, while it varied between 41% and 46% in wood. The C fraction was highest at the Kabompo site that received the highest rainfall, and lowest at the intermediate Namwala site. The C stocks varied between 15 and 36 ton C ha-1 and these stocks where highest at the wetter Kabompo site and lowest at the drier Sesheke site. Our results indicate that the projected future rainfall decrease for southern Africa, will likely reduce the C storage potential of the Zambezi teak forests, thereby adversely affecting their mitigating role in climate change.

Innervation pattern of the preocular human central retinal artery.

PubMed

Bergua, Antonio; Kapsreiter, Markus; Neuhuber, Winfried L; Reitsamer, Herbert A; Schrödl, Falk

2013-05-01

The central retinal artery (CRA) is the main vessel for inner retinal oxygen and nutrition supply. While the intraocular branches lack autonomic innervation, the innervation pattern of the extra-ocular part of this vessel along its course within the optic nerve is poorly investigated. This part however is essential for maintenance of retinal blood supply, in physiological and pathological conditions. Therefore, the aim of this study was the characterization of the autonomic innervation of the preocular CRA in humans with morphological methods. Meeting the Declaration of Helsinki, eyes of body or cornea donors were processed for single or double immunohistochemistry against tyrosine hydroxilase (TH), dopamine-β-hydroxylase (DBH), choline acetyl-transferase (ChAT), vesicular acetylcholine transporter (VAChT), neuronal nitric oxide synthase (nNOS), calcitonin gene-related peptide (CGRP), substance P (SP), vasoactive intestinal polypeptide (VIP), and cytochemistry for NADPH-diaphorase (NADPH-d). For documentation, light-, fluorescence-, and confocal laser-scanning microscopy were used. TH and DBH immunoreactive nerve fibres were detected in the CRA vessel wall, although a distinct perivascular plexus was missing. Further, nerve fibres immunoreactive for ChAT and VAChT were found, while CGRP, SP, and VIP were not detected. NADPH-d staining revealed scattered nerve fibres in the adventitia of the CRA and in close vicinity; however, nNOS-immunostaining could not confirm this finding. The CRA receives adrenergic and cholinergic innervations, indicating sympathetic and parasympathetic components, respectively. Remarkably, a peptidergic primary afferent innervation was missing. Since clinical results suggest an autoregulation of intraretinal vessels, further studies are needed to clarify the impact of CRA innervation for retinal perfusion. Copyright © 2012 Elsevier Ltd. All rights reserved.

Biodegradation of dichlorodiphenyltrichloroethane: intermediates in dichlorodiphenylacetic acid metabolism by aerobacter aerogenes

USGS Publications Warehouse

Wedemeyer, Gary

1967-01-01

The final product of dichlorodiphenyltrichloroethane (DDT) degradation by vertebrates is commonly considered to be dichlorodiphenylacetic acid, DDA. Recently, certain organisms have been found to degrade further DDA to dichlorobenzophenone (DBP), but the possibility that such degradation was due to microbial action could not be excluded. Significantly, dichlorobenzhydrol (DBH), dichlorophenylmethane (DPM), and dichlorodiphenylethylene (DDE) have been tentatively identified in rats fed DDA. Since DDA as well as DDT is degraded by the ubiquitous microorganism Aerobacter aerogenes, it seemed reasonable that the intestinal microflora might be involved in DBP formation, DPM and DBH being intermediates in its pathway from DDA. Since DDA is a (3,y-unsaturated acid, ketone formation via an alkene and an alcohol would be expected.

Working memory brain activity and capacity link MAOA polymorphism to aggressive behavior during development

PubMed Central

Ziermans, T; Dumontheil, I; Roggeman, C; Peyrard-Janvid, M; Matsson, H; Kere, J; Klingberg, T

2012-01-01

A developmental increase in working memory capacity is an important part of cognitive development, and low working memory (WM) capacity is a risk factor for developing psychopathology. Brain activity represents a promising endophenotype for linking genes to behavior and for improving our understanding of the neurobiology of WM development. We investigated gene–brain–behavior relationships by focusing on 18 single-nucleotide polymorphisms (SNPs) located in six dopaminergic candidate genes (COMT, SLC6A3/DAT1, DBH, DRD4, DRD5, MAOA). Visuospatial WM (VSWM) brain activity, measured with functional magnetic resonance imaging, and VSWM capacity were assessed in a longitudinal study of typically developing children and adolescents. Behavioral problems were evaluated using the Child Behavior Checklist (CBCL). One SNP (rs6609257), located ∼6.6 kb downstream of the monoamine oxidase A gene (MAOA) on human chromosome X, significantly affected brain activity in a network of frontal, parietal and occipital regions. Increased activity in this network, but not in caudate nucleus or anterior prefrontal regions, was correlated with VSWM capacity, which in turn predicted externalizing (aggressive/oppositional) symptoms, with higher WM capacity associated with fewer externalizing symptoms. There were no direct significant correlations between rs6609257 and behavioral symptoms. These results suggest a mediating role of WM brain activity and capacity in linking the MAOA gene to aggressive behavior during development. PMID:22832821

MOXD2, a Gene Possibly Associated with Olfaction, Is Frequently Inactivated in Birds

PubMed Central

Goh, Chul Jun; Choi, Dongjin; Park, Dong-Bin; Kim, Hyein; Hahn, Yoonsoo

2016-01-01

Vertebrate MOXD2 encodes a monooxygenase DBH-like 2 protein that could be involved in neurotransmitter metabolism, potentially during olfactory transduction. Loss of MOXD2 in apes and whales has been proposed to be associated with evolution of olfaction in these clades. We analyzed 57 bird genomes to identify MOXD2 sequences and found frequent loss of MOXD2 in 38 birds. Among the 57 birds, 19 species appeared to have an intact MOXD2 that encoded a full-length protein; 32 birds had a gene with open reading frame-disrupting point mutations and/or exon deletions; and the remaining 6 species did not show any MOXD2 sequence, suggesting a whole-gene deletion. Notably, among 10 passerine birds examined, 9 species shared a common genomic deletion that spanned several exons, implying the gene loss occurred in a common ancestor of these birds. However, 2 closely related penguin species, each of which had an inactive MOXD2, did not share any mutation, suggesting an independent loss after their divergence. Distribution of the 38 birds without an intact MOXD2 in the bird phylogenetic tree clearly indicates that MOXD2 loss is widespread and independent in bird lineages. We propose that widespread MOXD2 loss in some bird lineages may be implicated in the evolution of olfactory perception in these birds. PMID:27074048

MOXD2, a Gene Possibly Associated with Olfaction, Is Frequently Inactivated in Birds.

PubMed

Goh, Chul Jun; Choi, Dongjin; Park, Dong-Bin; Kim, Hyein; Hahn, Yoonsoo

2016-01-01

Vertebrate MOXD2 encodes a monooxygenase DBH-like 2 protein that could be involved in neurotransmitter metabolism, potentially during olfactory transduction. Loss of MOXD2 in apes and whales has been proposed to be associated with evolution of olfaction in these clades. We analyzed 57 bird genomes to identify MOXD2 sequences and found frequent loss of MOXD2 in 38 birds. Among the 57 birds, 19 species appeared to have an intact MOXD2 that encoded a full-length protein; 32 birds had a gene with open reading frame-disrupting point mutations and/or exon deletions; and the remaining 6 species did not show any MOXD2 sequence, suggesting a whole-gene deletion. Notably, among 10 passerine birds examined, 9 species shared a common genomic deletion that spanned several exons, implying the gene loss occurred in a common ancestor of these birds. However, 2 closely related penguin species, each of which had an inactive MOXD2, did not share any mutation, suggesting an independent loss after their divergence. Distribution of the 38 birds without an intact MOXD2 in the bird phylogenetic tree clearly indicates that MOXD2 loss is widespread and independent in bird lineages. We propose that widespread MOXD2 loss in some bird lineages may be implicated in the evolution of olfactory perception in these birds.

Estimation of Tree Position and STEM Diameter Using Simultaneous Localization and Mapping with Data from a Backpack-Mounted Laser Scanner

NASA Astrophysics Data System (ADS)

Holmgren, J.; Tulldahl, H. M.; Nordlöf, J.; Nyström, M.; Olofsson, K.; Rydell, J.; Willén, E.

2017-10-01

A system was developed for automatic estimations of tree positions and stem diameters. The sensor trajectory was first estimated using a positioning system that consists of a low precision inertial measurement unit supported by image matching with data from a stereo-camera. The initial estimation of the sensor trajectory was then calibrated by adjustments of the sensor pose using the laser scanner data. Special features suitable for forest environments were used to solve the correspondence and matching problems. Tree stem diameters were estimated for stem sections using laser data from individual scanner rotations and were then used for calibration of the sensor pose. A segmentation algorithm was used to associate stem sections to individual tree stems. The stem diameter estimates of all stem sections associated to the same tree stem were then combined for estimation of stem diameter at breast height (DBH). The system was validated on four 20 m radius circular plots and manual measured trees were automatically linked to trees detected in laser data. The DBH could be estimated with a RMSE of 19 mm (6 %) and a bias of 8 mm (3 %). The calibrated sensor trajectory and the combined use of circle fits from individual scanner rotations made it possible to obtain reliable DBH estimates also with a low precision positioning system.

Habitat relationships and nest site characteristics of cavity-nesting birds in cottonwood floodplains

USGS Publications Warehouse

Sedgwick, James A.; Knopf, Fritz L.

1990-01-01

We examined habitat relationships and nest site characteristics for 6 species of cavity-nesting birds--American kestrel (Falco sparverius), northern flicker (Colaptes auratus), red-headed woodpecker (Melanerpes erythrocephalus), black-capped chickadee (Parus atricapillus), house wren (Troglodytes aedon), and European starling (Sturnus vulgaris)--in a mature plains cottonwood (Populus sargentii) bottomland along the South Platte River in northeastern Colorado in 1985 and 1986. We examined characteristics of cavities, nest trees, and the habitat surrounding nest trees. Density of large trees (>69 cm dbh), total length of dead limbs ≥10 cm diameter (TDLL), and cavity density were the most important habitat variables; dead limb length (DLL), dbh, and species were the most important tree variables; and cavity height, cavity entrance diameter, and substrate condition at the cavity (live vs. dead) were the most important cavity variables in segregating cavity nesters along habitat, tree, and cavity dimensions, respectively. Random sites differed most from cavity-nesting bird sites on the basis of dbh, DLL, limb tree density (trees with ≥1 m dead limbs ≥10 cm diameter), and cavity density. Habitats of red-headed woodpeckers and American kestrels were the most unique, differing most from random sites. Based on current trends in cottonwood demography, densities of cavity-nesting birds will probably decline gradually along the South Platte River, paralleling a decline in DLL, limb tree density, snag density, and the concurrent lack of cottonwood regeneration.

Estimation of carbon storage based on individual tree detection in Pinus densiflora stands using a fusion of aerial photography and LiDAR data.

PubMed

Kim, So-Ra; Kwak, Doo-Ahn; Lee, Woo-Kyun; oLee, Woo-Kyun; Son, Yowhan; Bae, Sang-Won; Kim, Choonsig; Yoo, Seongjin

2010-07-01

The objective of this study was to estimate the carbon storage capacity of Pinus densiflora stands using remotely sensed data by combining digital aerial photography with light detection and ranging (LiDAR) data. A digital canopy model (DCM), generated from the LiDAR data, was combined with aerial photography for segmenting crowns of individual trees. To eliminate errors in over and under-segmentation, the combined image was smoothed using a Gaussian filtering method. The processed image was then segmented into individual trees using a marker-controlled watershed segmentation method. After measuring the crown area from the segmented individual trees, the individual tree diameter at breast height (DBH) was estimated using a regression function developed from the relationship observed between the field-measured DBH and crown area. The above ground biomass of individual trees could be calculated by an image-derived DBH using a regression function developed by the Korea Forest Research Institute. The carbon storage, based on individual trees, was estimated by simple multiplication using the carbon conversion index (0.5), as suggested in guidelines from the Intergovernmental Panel on Climate Change. The mean carbon storage per individual tree was estimated and then compared with the field-measured value. This study suggested that the biomass and carbon storage in a large forest area can be effectively estimated using aerial photographs and LiDAR data.

Development and evaluation of height diameter at breast models for native Chinese Metasequoia.

PubMed

Liu, Mu; Feng, Zhongke; Zhang, Zhixiang; Ma, Chenghui; Wang, Mingming; Lian, Bo-Ling; Sun, Renjie; Zhang, Li

2017-01-01

Accurate tree height and diameter at breast height (dbh) are important input variables for growth and yield models. A total of 5503 Chinese Metasequoia trees were used in this study. We studied 53 fitted models, of which 7 were linear models and 46 were non-linear models. These models were divided into two groups of single models and multivariate models according to the number of independent variables. The results show that the allometry equation of tree height which has diameter at breast height as independent variable can better reflect the change of tree height; in addition the prediction accuracy of the multivariate composite models is higher than that of the single variable models. Although tree age is not the most important variable in the study of the relationship between tree height and dbh, the consideration of tree age when choosing models and parameters in model selection can make the prediction of tree height more accurate. The amount of data is also an important parameter what can improve the reliability of models. Other variables such as tree height, main dbh and altitude, etc can also affect models. In this study, the method of developing the recommended models for predicting the tree height of native Metasequoias aged 50-485 years is statistically reliable and can be used for reference in predicting the growth and production of mature native Metasequoia.

Development and evaluation of height diameter at breast models for native Chinese Metasequoia

PubMed Central

Feng, Zhongke; Zhang, Zhixiang; Ma, Chenghui; Wang, Mingming; Lian, Bo-ling; Sun, Renjie; Zhang, Li

2017-01-01

Accurate tree height and diameter at breast height (dbh) are important input variables for growth and yield models. A total of 5503 Chinese Metasequoia trees were used in this study. We studied 53 fitted models, of which 7 were linear models and 46 were non-linear models. These models were divided into two groups of single models and multivariate models according to the number of independent variables. The results show that the allometry equation of tree height which has diameter at breast height as independent variable can better reflect the change of tree height; in addition the prediction accuracy of the multivariate composite models is higher than that of the single variable models. Although tree age is not the most important variable in the study of the relationship between tree height and dbh, the consideration of tree age when choosing models and parameters in model selection can make the prediction of tree height more accurate. The amount of data is also an important parameter what can improve the reliability of models. Other variables such as tree height, main dbh and altitude, etc can also affect models. In this study, the method of developing the recommended models for predicting the tree height of native Metasequoias aged 50–485 years is statistically reliable and can be used for reference in predicting the growth and production of mature native Metasequoia. PMID:28817600

The Spatial Pattern and Interactions of Woody Plants on the Temperate Savanna of Inner Mongolia, China: The Effects of Alternating Seasonal Grazing-Mowing Regimes

PubMed Central

2015-01-01

Ulmus pumila tree-dominated temperate savanna, which is distributed widely throughout the forest-steppe ecotone on the Mongolian Plateau, is a relatively stable woody-herbaceous complex ecosystem in northern China. Relatively more attention has been paid to the degradation of typical steppe areas, whereas less focus has been placed on the succession of this typical temperate savanna under the present management regime. In this study, we established 3 sample plots 100 m×100 m in size along a gradient of fixed distances from one herder’s stationary site and then surveyed all the woody plants in these plots. A spatial point pattern analysis was employed to clarify the spatial distribution and interaction of these woody plants. The results indicated that old U. pumila trees (DBH ≥ 20 cm) showed a random distribution and that medium U. pumila trees (5 cm ≤ DBH < 20 cm) showed an aggregated distribution at a smaller scale and a random distribution at a larger scale; few or no juvenile trees (DBH < 5 cm) were present, and seedlings (without DBH) formed aggregations in all 3 plots. These findings can be explained by an alternate seasonal grazing-mowing regime (exclosure in summer, mowing in autumn and grazing in winter and spring); the shrubs in all 3 plots exist along a grazing gradient that harbors xerophytic and mesophytic shrubs. Of these shrubs, xerophytic shrubs show significant aggregation at a smaller scale (0-5.5 m), whereas mesophytic shrubs show significant aggregation at a larger scale (0-25 m), which may be the result of the dual effects of grazing pressure and climate change. Medium trees and seedlings significantly facilitate the distributions of xerophytic shrubs and compete significantly with mesophytic shrubs due to differences in water use strategies. We conclude that the implementation of an alternative grazing-mowing regime results in xerophytic shrub encroachment or existence, breaking the chain of normal succession in a U. pumila tree community in this typical temperate savanna ecosystem. This might eventually result in the degradation of the original tree-dominated savanna to a xerophytic shrub-dominated savanna. PMID:26196956

Relationships of tree height and diameter at breast height revisited: analyses of stem growth using 20-year data of an even-aged Chamaecyparis obtusa stand

PubMed Central

Sumida, Akihiro; Miyaura, Tomiyasu; Torii, Hitoshi

2013-01-01

Stem diameter at breast height (DBH) and tree height (H) are commonly used measures of tree growth. We examined patterns of height growth and diameter growth along a stem using a 20-year record of an even-aged hinoki cypress (Chamaecyparis obtusa (Siebold & Zucc.) Endl.) stand. In the region of the stem below the crown (except for the butt swell), diameter growth rates (ΔD) at different heights tended to increase slightly from breast height upwards. This increasing trend was pronounced in suppressed trees, but not as much as the variation in ΔD among individual trees. Hence, ΔD below the crown can be regarded as generally being represented by the DBH growth rate (ΔDBH) of a tree. Accordingly, the growth rate of the stem cross-sectional area increased along the stem upwards in suppressed trees, but decreased in dominant trees. The stem diameter just below the crown base (DCB), the square of which is an index of the amount of leaves on a tree, was an important factor affecting ΔDBH. DCB also had a strong positive relationship with crown length. Hence, long-term changes in the DCB of a tree were associated with long-term changes in crown length, determined by the balance between the height growth rate (ΔH) and the rising rate of the crown base (ΔHCB). Within the crown, ΔD's were generally greater than the rates below the crown. Even dying trees (ΔD ≈ 0 below the crown) maintained ΔD > 0 within the crown and ΔH > 0 until about 5 years before death. This growth within the crown may be related to the need to produce new leaves to compensate for leaves lost owing to the longevity of the lower crown. These results explain the different time trajectories in DBH–H relationships among individual trees, and also the long-term changes in the DBH–H relationships. The view that a rise in the crown base is strongly related to leaf turnover helps to interpret DBH–H relationships. PMID:23303367

Dendrometric measurements reveal stages leading to tree mortality in a semiarid pine forest

NASA Astrophysics Data System (ADS)

Tatarinov, Fyodor; Preisler, Yakir; Klein, Tamir; Rotenberg, Eyal; Yakir, Dan

2017-04-01

Increasing frequency and intensity of climatic extreme events, such as droughts may lead to increasing vulnerability of forests, especially in semi-arid regions. In the spring of 2016 mortality was observed among trees used for sap flow (SF) and dendrometry measurements in the semi-arid Fluxnet pine forest site of Yatir in Israel (280mm annual mean precipitation). This was accompanied by bark-beetle attack, and with visual drying of needles starting in April 2016. Comparative analysis of dendrometry and sap flux (SF) measurements in 31 trees of which 7 died and 24 survived permitted identification of the stages leading to tree mortality. Distinction between dying and surviving trees was identified in the dendrometric measurements from Nov. 2015, about five months before visual mortality signs: First, clear decline in diameter (DBH) was observed in all dying trees, whereas DBH of living trees remained constant until the first rain in January 2016 followed by growth. Second, the diurnal patterns in DBH showed a gradual shift of the diurnal DBH maximum from noon-time to early morning from the summer of 2015 to the spring of 2016 in surviving trees, whereas in dying trees it remained stable around noontime. Third, the diurnal swelling/shrinkage dynamics, assumed to reflect water use and storage dynamics, showed clear decline in magnitude, down to near zero, in the dying trees while regular daily cycle continued in the surviving trees. In September 2015 Shoot measurements showed midnight minimum of leaf water potential, lower than in living trees (-4.5 vs. -3.6 MPa respectively). Sap flow measurements were not sufficiently sensitive during the non-active season (fall and early winter) and indicated changes only after the first rain in January 2016. At this time, SF showed dramatic increase in SF with typical midday maximum in the surviving trees, whereas in dying trees SF remained low and irregular. The results show that indicators of mortality can be detected at least 5 months before visual signs are observed, and demonstrate the interacting effects of carbon economy (growth) and tree water management (radial water movement and storage) on the development of mortality in Aleppo pine trees.

Selective inhibition of dopamine-beta-hydroxylase enhances dopamine release from noradrenergic terminals in the medial prefrontal cortex.

PubMed

Devoto, Paola; Flore, Giovanna; Saba, Pierluigi; Frau, Roberto; Gessa, Gian L

2015-10-01

Disulfiram has been claimed to be useful in cocaine addiction therapy, its efficacy being attributed to dopamine-beta-hydroxylase (DBH) inhibition. Our previous results indicate that disulfiram and the selective DBH inhibitor nepicastat increase extracellular dopamine (DA) in the rat medial prefrontal cortex (mPFC), and markedly potentiated cocaine-induced increase. Concomitantly, in rats with cocaine self-administration history, cocaine-seeking behavior induced by drug priming was prevented, probably through overstimulation of D1 receptors due to the DA increase. The present research was aimed at studying the neurochemical mechanisms originating the enhanced DA release. Noradrenergic system ablation was attained by intracerebroventricular (i.c.v.) administration of the neurotoxin anti-DBH-saporin (aDBH-sap). DA, noradrenaline (NA), and DOPAC were assessed by HPLC after ex vivo tissue extraction or in vivo microdialysis. Control and denervated rats were subjected to microdialysis in the mPFC and caudate nucleus to evaluate the effect of nepicastat-cocaine combination on extracellular DA levels and their regulation by α2-adrenoceptors. Fifteen days after neurotoxin or its vehicle administration, tissue and extracellular NA were reduced to less than 2% the control value, while extracellular DA was increased by approximately 100%. In control rats, nepicastat given alone and in combination with cocaine increased extracellular DA by about 250% and 1100%, respectively. In denervated rats, nepicastat slightly affected extracellular DA, while in combination with cocaine increased extracellular DA by 250%. No differences were found in the caudate nucleus. Clonidine almost totally reversed the extracellular DA elevation produced by nepicastat-cocaine combination, while it was ineffective in denervated rats. This research shows that the increase of extracellular DA produced by nepicastat alone or in combination with cocaine was prevented by noradrenergic denervation. The results indicate that nepicastat enhances DA release from noradrenergic terminals supposedly by removing NA from α2-autoreceptors. In addition to the inhibition of DA uptake, the latter mechanism may explain the synergistic effect of cocaine on nepicastat-induced DA release.

Trading Habitat Patches for the Red Cockaded Woodpecker: Incorporating the Role of Landscape Structure and Uncertainty in Decision Making

DTIC Science & Technology

2007-06-11

basal area of pines 25.4 to 35 cm dbh between 0 and 9.2 m2/ha PS1, PS4 , PS12 Small Pines No. pine stems/ha < 25.4 cm dbh NA HL1, HL4...value Adj R2 AIC Fit = 2.50 + 0.0079 PS1 – 0.036 PM1 – 0.0102 PS4 – 0.019 HS12 0.063 0.033 426 Parameter p-value t-value Intercept ɘ.0001 8.23 PS1...0.125 1.54 PM1 0.038 -2.10 PS4 0.107 -1.62 HS12 0.063 -1.88 Model A – Most Parsimonious p-value Adj R2 AIC Fit = 2.02 – 0.03 PM1 0.053 0.018 427

Forest Resource Measurements by Combination of Terrestrial Laser Scanning and Drone Use

NASA Astrophysics Data System (ADS)

Cheung, K.; Katoh, M.; Horisawa, M.

2017-10-01

Using terrestrial laser scanning (TLS), forest attributes such as diameter at breast height (DBH) and tree location can be measured accurately. However, due to low penetration of laser pulses to tree tops, tree height measurements are typically underestimated. In this study, data acquired by TLS and drones were combined; DBH and tree locations were determined by TLS, and tree heights were measured by drone use. The average tree height error and root mean square error (RMSE) of tree height were 0.8 and 1.2 m, respectively, for the combined method, and -0.4 and 1.7 m using TLS alone. The tree height difference was compared using airborne laser scanning (ALS). Furthermore, a method to acquire 100 % tree detection rate based on TLS data is suggested in this study.

Structure of the Epiphyte Community in a Tropical Montane Forest in SW China

PubMed Central

Zhao, Mingxu; Geekiyanage, Nalaka; Xu, Jianchu; Khin, Myo Myo; Nurdiana, Dian Ridwan; Paudel, Ekananda; Harrison, Rhett Daniel

2015-01-01

Vascular epiphytes are an understudied and particularly important component of tropical forest ecosystems. However, owing to the difficulties of access, little is known about the properties of epiphyte-host tree communities and the factors structuring them, especially in Asia. We investigated factors structuring the vascular epiphyte-host community and its network properties in a tropical montane forest in Xishuangbanna, SW China. Vascular epiphytes were surveyed in six plots located in mature forests. Six host and four micro-site environmental factors were investigated. Epiphyte diversity was strongly correlated with host size (DBH, diameter at breast height), while within hosts the highest epiphyte diversity was in the middle canopy and epiphyte diversity was significantly higher in sites with canopy soil or a moss mat than on bare bark. DBH, elevation and stem height explained 22% of the total variation in the epiphyte species assemblage among hosts, and DBH was the most important factor which alone explained 6% of the variation. Within hosts, 51% of the variation in epiphyte assemblage composition was explained by canopy position and substrate, and the most important single factor was substrate which accounted for 16% of the variation. Analysis of network properties indicated that the epiphyte host community was highly nested, with a low level of epiphyte specialization, and an almost even interaction strength between epiphytes and host trees. Together, these results indicate that large trees harbor a substantial proportion of the epiphyte community in this forest. PMID:25856457

Epistasis between neurochemical gene polymorphisms and risk for ADHD

PubMed Central

Segurado, Ricardo; Bellgrove, Mark A; Manconi, Francesca; Gill, Michael; Hawi, Ziarah

2011-01-01

A number of genes with function related to synaptic neurochemistry have been genetically associated with attention deficit/hyperactivity disorder. However, susceptibility to the development of common psychiatric disorders by single variants acting alone, can so far only explain a small proportion of the heritability of the phenotype. It has been postulated that the unexplained ‘dark heritability' may at least in part be due to epistatic effects, which may account for the small observed marginal associations, and the difficulties with replication of positive findings. We undertook a comprehensive exploration of pair-wise interactions between genetic variants in 24 candidate genic regions involved in monoaminergic catabolism, anabolism, release, re-uptake and signal transmission in a sample of 177 parent-affected child trios using a case-only design and a case–pseudocontrol design using conditional logistic regression. Marker-pairs thresholded on interaction odds ratio (OR) and P-value are presented. We detected a number of interaction ORs >4.0, including an interesting correlation between markers in the ADRA1B and DBH genes in affected individuals, and several further interesting but smaller effects. These effects are no larger than you would expect by chance under the assumption of independence of all pair-wise relations; however, independence is unlikely. Furthermore, the size of these effects is of interest and attempts to replicate these results in other samples are anticipated. PMID:21368917

The effect of interactions between genetics and cannabis use on neurocognition. A review.

PubMed

Cosker, E; Schwitzer, T; Ramoz, N; Ligier, F; Lalanne, L; Gorwood, P; Schwan, R; Laprévote, V

2018-03-02

Cannabis is one of the most widely-used drugs in industrialized countries. It is now well established that cannabis use impacts neurocognition. In the intoxication period time episodic memory, working memory and attention are impacted and impulsivity is increased. The long-term effects of cannabis use tend to be similar. Various internal factors, such as sex differences, modulate this impact. It is unclear whether genetic variations can also influence the impact of cannabis on neurocognition. We set out to examine the impact of genetic variations on neurocognition in cannabis users. We conducted a search via the PubMed, Web of Science, and ScienceDirect databases to identify studies measuring neurocognition and assessing genotypes in the context of cannabis use. We included 13 articles. We found that working memory, verbal and visual memory and sustained attention are more impacted during intoxication in subjects with the Val COMT allele. COMT gene could also modulate sustained attention in regular use. The CNR1, AKT1, DBH and 5-HTT/SLC6A4 genes may also modulate effects. Most of these genes are linked to schizophrenia. A fuller understanding of their impact on the effects of cannabis on neurocognition would thus help elucidate the mechanisms linking cannabis and psychosis. However, evidence is still scant, and more research is needed. Copyright © 2017. Published by Elsevier Inc.

[Age structure and dynamics of Quercus wutaishanica population in Lingkong Mountain of Shanxi Province, China].

PubMed

Zhang, Jie; Shangguan, Tie-Liang; Duan, Yi-Hao; Guo, Wei; Liu, Wei-Hua; Guo, Dong-Gang

2014-11-01

Using the plant survivorship theory, the age structure, and the relationship between tree height and diameter (DBH) of Quercus wutaishanica population in Lingkong Mountain were analyzed, and the static life table was compiled and the survival curve plotted. The shuttle shape in age structure of Q. wutaishanica population suggested its temporal stability. The linear regression significantly fitted the positive correlation between tree height and DBH. The maximal life expectancy was observed among the trees beyond the age of the highest mortality and coincided with the lowest point of mortality density, suggesting the strong vitality of the seedlings and young trees that survived in the natural selection and intraspecific competition. The population stability of the Q. wutaishanica population was characterized by the Deevey-II of the survival curve. The dynamic pattern was characterized by the recession in the early phase, growth in the intermediate phase, and stability in the latter phase.

Synthesis of geminal difluorides by oxidative desulfurization-difluorination of alkyl aryl thioethers with halonium electrophiles in the presence of fluorinating reagents and its application for 18F-radiolabeling.

PubMed

Hugenberg, Verena; Wagner, Stefan; Kopka, Klaus; Schober, Otmar; Schäfers, Michael; Haufe, Günter

2010-09-17

Various ω-substituted 1,1-difluoroalkanes are synthesized in good yields from alkyl aryl thioethers by a new oxidative desulfurization-difluorination protocol with the reagents combination of 1,3-dibromo-5,5-dimethylhydantoin (DBH) as an oxidizer and pyridine·9HF (Py·9HF) as a fluoride source. The reaction proceeds via a fluoro-Pummerer-type rearrangement followed by an oxidative desulfurization-fluorination step. Starting from α-fluorinated thioethers, this reaction is promising for (18)F-labeling (τ(1/2) = 110 min) of ligands applicable for positron emission tomography (PET). Using the combination of DBH and carrier-added Py·9H[(18)F]F, an (18)F-labeled difluoride was synthesized from the corresponding α-fluoro thioether with a radiochemical yield of 9%.

BOREAS HYD-3 Tree Measurements

NASA Technical Reports Server (NTRS)

Hardy, Janet P.; Hall, Forrest G. (Editor); Knapp, David E. (Editor); David Robert E.; Smith, David E. (Technical Monitor)

2000-01-01

The BOREAS HYD-3 team collected several data sets related to the hydrology of forested areas. This data set contains measurements of canopy density (closure), stem density, and DBH from a variety of sites. Canopy density measurements were made during the FFC-W and FFC-T 1994 in both the SSA and the NSA. Stem density measurements were made during FFC-W 1996 in the SSA only. Canopy density measurements were made using a forest densiometer, while measurements of stem density and DBH were made using standard techniques. This study was undertaken to predict spatial distributions of energy transfer, snow properties important to the hydrology, remote sensing signatures, and transmissivity of gases through the snow and their relation to forests in boreal ecosystems. The data are available in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884) or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

Involvement of catecholaminergic neurons in motor innervation of striated muscle in the mouse esophagus.

PubMed

van der Keylen, Piet; Garreis, Fabian; Steigleder, Ruth; Sommer, Daniel; Neuhuber, Winfried L; Wörl, Jürgen

2016-05-01

Enteric co-innervation is a peculiar innervation pattern of striated esophageal musculature. Both anatomical and functional data on enteric co-innervation related to various transmitters have been collected in different species, although its function remains enigmatic. However, it is unclear whether catecholaminergic components are involved in such a co-innervation. Thus, we examined to identify catecholaminergic neuronal elements and clarify their relationship to other innervation components in the esophagus, using immunohistochemistry with antibodies against tyrosine hydroxylase (TH), vesicular acetylcholine transporter (VAChT), choline acetyltransferase (ChAT) and protein gene product 9.5 (PGP 9.5), α-bungarotoxin (α-BT) and PCR with primers for amplification of cDNA encoding TH and dopamine-β-hydroxylase (DBH). TH-positive nerve fibers were abundant throughout the myenteric plexus and localized on about 14% of α-BT-labelled motor endplates differing from VAChT-positive vagal nerve terminals. TH-positive perikarya represented a subpopulation of only about 2.8% of all PGP 9.5-positive myenteric neurons. Analysis of mRNA showed both TH and DBH transcripts in the mouse esophagus. As ChAT-positive neurons in the compact formation of the nucleus ambiguus were negative for TH, the TH-positive nerve varicosities on motor endplates are presumably of enteric origin, although a sympathetic origin cannot be excluded. In the medulla oblongata, the cholinergic ambiguus neurons were densely supplied with TH-positive varicosities. Thus, catecholamines may modulate vagal motor innervation of esophageal-striated muscles not only at the peripheral level via enteric co-innervation but also at the central level via projections to the nucleus ambiguus. As Parkinson's disease, with a loss of central dopaminergic neurons, also affects the enteric nervous system and dysphagia is prevalent in patients with this disease, investigation of intrinsic catecholamines in the esophagus may be worthwhile to understand such a symptom.

Carbon Sequestration Estimation of Street Trees Based on Point Cloud from Vehicle-Borne Laser Scanning System

NASA Astrophysics Data System (ADS)

Zhao, Y.; Hu, Q.

2017-09-01

Continuous development of urban road traffic system requests higher standards of road ecological environment. Ecological benefits of street trees are getting more attention. Carbon sequestration of street trees refers to the carbon stocks of street trees, which can be a measurement for ecological benefits of street trees. Estimating carbon sequestration in a traditional way is costly and inefficient. In order to solve above problems, a carbon sequestration estimation approach for street trees based on 3D point cloud from vehicle-borne laser scanning system is proposed in this paper. The method can measure the geometric parameters of a street tree, including tree height, crown width, diameter at breast height (DBH), by processing and analyzing point cloud data of an individual tree. Four Chinese scholartree trees and four camphor trees are selected for experiment. The root mean square error (RMSE) of tree height is 0.11m for Chinese scholartree and 0.02m for camphor. Crown widths in X direction and Y direction, as well as the average crown width are calculated. And the RMSE of average crown width is 0.22m for Chinese scholartree and 0.10m for camphor. The last calculated parameter is DBH, the RMSE of DBH is 0.5cm for both Chinese scholartree and camphor. Combining the measured geometric parameters and an appropriate carbon sequestration calculation model, the individual tree's carbon sequestration will be estimated. The proposed method can help enlarge application range of vehicle-borne laser point cloud data, improve the efficiency of estimating carbon sequestration, construct urban ecological environment and manage landscape.

[Short-term death dynamics of trees in natural secondary poplar-birch forest in Changbai Mountains of Northeast China].

PubMed

Zhang, Zhao-Chen; Hao, Zhan-Qing; Ye, Ji; Lin, Fei; Yuan, Zuo-Qiang; Xing, Ding-Liang; Shi, Shuai; Wang, Xu-gao

2013-02-01

Taking the 5 hm2 sampling plot in the natural secondary poplar-birch forest in Changbai Mountains as test object, and based on the two census data in 2005 and 2010, an analysis was made on the main tree species composition and quantity, size class distribution of dead individuals, and regeneration characteristics of the main tree species in different habitat types of the plot in 2005-2010. In the five years, the species number of the individuals with DBH> or = 1 cm increased from 46 to 47, among which, 3 species were newly appeared, and 2 species were disappeared. The number of the individuals changed from 16509 to 15027, among which, 2150 individuals died, accounting for 13% of the whole individuals in 2005, and 668 individuals were newly increased. The basal area of the trees increased from 28.79 m2.m-2 to 30.55 m2.m-2, with that of 41 species increased while that of 6 species decreased. The decrease of the basal area of Betula platyphylla and Populus davidiana accounted for 72.3% of the total decrease. Small individuals had higher mortality, as compared with large ones, and the mortality of the individuals with DBH<5 cm occupied 65% of the total. B. platyphylla and P. davidiana contributed most in the dead individuals with large DBH. No difference was observed in the tree mortality among different habitat types, but the mortality of the individuals with different size classes showed greater variation.

Modern pollen-rain characteristics of tall terra firme moist evergreen forest, southern Amazonia

NASA Astrophysics Data System (ADS)

Gosling, William D.; Mayle, Francis E.; Tate, Nicholas J.; Killeen, Timothy J.

2005-11-01

The paucity of modern pollen-rain data from Amazonia constitutes a significant barrier to understanding the Late Quaternary vegetation history of this globally important tropical forest region. Here, we present the first modern pollen-rain data for tall terra firme moist evergreen Amazon forest, collected between 1999 and 2001 from artificial pollen traps within a 500 × 20 m permanent study plot (14°34'50″S, 60°49'48″W) in Noel Kempff Mercado National Park (NE Bolivia). Spearman's rank correlations were performed to assess the extent of spatial and inter-annual variability in the pollen rain, whilst statistically distinctive taxa were identified using Principal Components Analysis (PCA). Comparisons with the floristic and basal area data of the plot (stems ≥10 cm d.b.h.) enabled the degree to which taxa are over/under-represented in the pollen rain to be assessed (using R-rel values). Moraceae/Urticaceae dominates the pollen rain (64% median abundance) and is also an important constituent of the vegetation, accounting for 16% of stems ≥10 cm d.b.h. and ca. 11% of the total basal area. Other important pollen taxa are Arecaceae (cf. Euterpe), Melastomataceae/Combretaceae, Cecropia, Didymopanax, Celtis, and Alchornea. However, 75% of stems and 67% of the total basal area of the plot ≥10 cm d.b.h. belong to species which are unidentified in the pollen rain, the most important of which are Phenakospermum guianensis (a banana-like herb) and the key canopy-emergent trees, Erisma uncinatum and Qualea paraensis.

Chemoenzymatic synthesis and cannabinoid activity of a new diazabicyclic amide of phenylacetylricinoleic acid.

PubMed

López-Ortíz, Manuel; Herrera-Solís, Andrea; Luviano-Jardón, Axel; Reyes-Prieto, Nidia; Castillo, Ivan; Monsalvo, Ivan; Demare, Patricia; Méndez-Díaz, Mónica; Regla, Ignacio; Prospéro-García, Oscar

2010-06-01

Endocannabinoids (eCBs) are endogenous neuromodulators of synaptic transmission. Their dysfunction may cause debilitating disorders of diverse clinical manifestation. For example, drug addiction, lack of sex desire, eating disorders, such as anorexia or bulimia and dyssomnias. eCBs also participate in the regulation of core temperature and pain perception. In this context, it is important to recognize the utility of cannabinoid receptor 1 (CB1R) agonists, natural as Delta(9)-tetrahydrocannabinol (THC) or synthetic as Nabilone as useful drugs to alleviate this kind of patients' suffering. Therefore, we have developed a new drug, (R,Z)-18-((1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl)-18-oxooctadec-9-en-7-yl phenylacetate (PhAR-DBH-Me), that appears to bind and activate the CB1R. This diazabicyclic amide was synthesized from phenylacetylricinoleic acid and (1S,4S)-2,5-diazabicyclo[2.2.1]heptane. To test its cannabinergic properties we evaluated its effects on core temperature, pain perception, and the sleep-waking cycle of rats. Results indicate that 20 and 40mg/kg of PhAR-DBH-Me readily reduced core temperature and increased pain perception threshold. In addition, 20mg/kg increased REM sleep in otherwise normal rats. All these effects were prevented or attenuated by AM251, a CB1R antagonist. Place preference conditioning studies indicated that this molecule does not produce rewarding effects. These results strongly support that PhAR-DBH-Me possesses cannabinoid activity without the reinforcement effects. Copyright 2010 Elsevier Ltd. All rights reserved.

A ketogenic diet as a potential novel therapeutic intervention in amyotrophic lateral sclerosis.

PubMed

Zhao, Zhong; Lange, Dale J; Voustianiouk, Andrei; MacGrogan, Donal; Ho, Lap; Suh, Jason; Humala, Nelson; Thiyagarajan, Meenakshisundaram; Wang, Jun; Pasinetti, Giulio M

2006-04-03

The cause of neuronal death in amyotrophic lateral sclerosis (ALS) is uncertain but mitochondrial dysfunction may play an important role. Ketones promote mitochondrial energy production and membrane stabilization. SOD1-G93A transgenic ALS mice were fed a ketogenic diet (KD) based on known formulations for humans. Motor performance, longevity, and motor neuron counts were measured in treated and disease controls. Because mitochondrial dysfunction plays a central role in neuronal cell death in ALS, we also studied the effect that the principal ketone body, D-beta-3 hydroxybutyrate (DBH), has on mitochondrial ATP generation and neuroprotection. Blood ketones were > 3.5 times higher in KD fed animals compared to controls. KD fed mice lost 50% of baseline motor performance 25 days later than disease controls. KD animals weighed 4.6 g more than disease control animals at study endpoint; the interaction between diet and change in weight was significant (p = 0.047). In spinal cord sections obtained at the study endpoint, there were more motor neurons in KD fed animals (p = 0.030). DBH prevented rotenone mediated inhibition of mitochondrial complex I but not malonate inhibition of complex II. Rotenone neurotoxicity in SMI-32 immunopositive motor neurons was also inhibited by DBH. This is the first study showing that diet, specifically a KD, alters the progression of the clinical and biological manifestations of the G93A SOD1 transgenic mouse model of ALS. These effects may be due to the ability of ketone bodies to promote ATP synthesis and bypass inhibition of complex I in the mitochondrial respiratory chain.

DBH deficiency in an elderly patient: efficacy and safety of chronic droxidopa.

PubMed

Despas, Fabien; Pathak, A; Berry, M; Cagnac, R; Massabuau, P; Liozon, E; Galinier, M; Senard, J M

2010-06-01

We describe the effects of chronic droxidopa in a patient with Dopamine beta-hydroxylase deficiency diagnosed at the age of 73. Investigations were performed to assess sympathetic activity (MIBG scintigraphy, catecholamines) and cardiovascular droxidopa safety.

Bark thickness related to tree diameter in sugar maple (Acer saccharum Marsh.)

Treesearch

H. Clay Smith

1969-01-01

Bark thickness for sugar maple trees in Vermont was found to be related to tree diameter at breast height (d.b.h.). The relationship was positive-as the diameter increased, the bark thickness increased.

Early Yields Of Slash Pine Planted On a Cutover Site At Various Spacings

Treesearch

W.F. Mann

1971-01-01

Tabulates basal areas, cordwood and cubic-foot volumes, average d.b.h., and diameter distributions for 14-year-old slash pine planted in central Louisiana. Also gives regression equations developed to predict these parameters.

Liana habitat and host preferences in northern temperate forests

USGS Publications Warehouse

Leicht-Young, S. A.; Pavlovic, N.B.; Frohnapple, K.J.; Grundel, R.

2010-01-01

Lianas and other climbers are important ecological and structural components of forest communities. Like other plants, their abundance in a given habitat depends on a variety of factors, such as light, soil moisture and nutrients. However, since lianas require external support, host tree characteristics also influence their distribution. Lianas are conspicuous life forms in tropical regions, but in temperate areas, where they are less prominent, little is known about factors that control their distributions in these forests. We surveyed the climbing plant species in 20 mature (100 years and greater) forested habitats in the Midwest USA at a variety of levels from simple presence/absence, to ground layer abundances, to those species that had ascended trees. We also examined attributes of the tree species with climbers attached to them. Using cluster analysis, we distinguished five different tree communities in our survey locations. We determined that 25% of the trees we surveyed had one or more lianas attached to it, with Parthenocissus quinquefolia (Virginia creeper) the most common climbing species encountered. Canopy cover and soil attributes both influenced climber species presence/absence and ground layer climber abundance. The proportion of liana species of a given climbing type (roots, stem twiner, tendril climber) was significantly related to the DBH of the host tree, with more root climbers and fewer stem and tendril climbers on large trees. In general, the DBH of climbing lianas had a significant positive relationship to the DBH of the host tree; however this varied by the identity of the liana and the tree species. The greater the DBH of the host tree, the higher the probability that it was colonized by one or more lianas, with tree species such as Pinus banksiana (jack pine) and Quercus alba (white oak) being more susceptible to liana colonization than others. Finally, some liana species such as Celastrus scandens (American bittersweet) showed a preference for certain tree species (i.e., P. banksiana) as hosts. The information obtained about the relationship between the tree and climber community in this study provides insight into some of the factors that influence liana distributions in understudied temperate forest habitats and how lianas contribute to the structure of these mature forests. In addition, these data can provide a point of comparison to other liana communities in both temperate and tropical regions.

Interplanting woody nurse crops promotes differential growth of black walnut saplings

Treesearch

J. O. Dawson; J. W. Van Sambeek

1993-01-01

Interplanting black walnut (Juglans nigra) with four different nitrogen fixing, woody nurse crops (Alnus glutinosa, Elaeagnus umbellata, E. angustifolia or Caragana arborescens) increased annual walnut height and stem diameter (dbh) growth overall by as much as 50% and...

Elimination of scattered residual saplings left after clearcut harvesting of Appalachian hardwoods

Treesearch

G. R., Jr. Trimble; R. L. Rosier

1972-01-01

Basal-spraying and power-saw felling were compared as methods for eliminating the 1- to 5-inch d.b.h. understory stems left after clearcutting. Felling leaves the area more esthetically acceptable, and costs are lower.

[Associations between chronotype, road accidents and polymorphisms in genes linked with biological clock and dopaminergic system].

PubMed

Taranov, A O; Puchkova, A N; Slominsky, P A; Tupitsyna, T V; Dementiyenko, V V; Dorokhov, V B

2017-01-01

Public transport driving is a highly demanding activity requiring high skills and responsibility. Shift work, problems with regular sleep schedule negatively impact psychomotor reactions, cognitive functions and ability to react appropriately to the changing environment. For professional drivers all these factors may lead to the increased risk of a road accident. Individual differences in chronotype, cognitive and emotional control are partially genetically determined. Our study aimed to investigate the possible associations between chronotype parameters, traffic accident history and single nucleotide polymorphisms (SNPs) in a number of genes: RORA (rs1159814), CLOCK (rs12649507), PER3 (rs2640909), NPSR1 (rs324981), NPAS2 (rs4851377), DRD3 (rs6280), SLC6A3 (rs6347), DBH (rs1611125). We have studied 303 professional bus drivers working on rolling shifts in the Moscow region who had a recorded history of road accidents. The studied group was genotyped on selected SNPs and has filled out two chronotype questionnaires: MCTQ and shortened SWPAQ (Putilov A.A, 2014). A mixed chronotype with high levels of morning and evening alertness prevailed in the group. A prominent social jetlag caused by shift work was found. For SNP in PER3 gene there was an association with morning activation. SNP in CLOCK gene was associated with social jetlag and the risk to cause a crash. Minor alleles of SNPs in NPSR1and SLC6A3 correlated with later chronotype and increased risk of a road accident. We suppose that these polymorphisms may be amongst the genetic factors connecting chronotype and road accident risk.

Reversible and irreversible drought-induced changes in the anther proteome of rice (Oryza sativa L.) genotypes IR64 and Moroberekan.

PubMed

Liu, Jian-Xiang; Bennett, John

2011-01-01

Crop yield is most sensitive to water deficit during the reproductive stage. For rice, the most sensitive yield component is spikelet fertility and the most sensitive stage is immediately before heading. Here, we examined the effect of drought on the anther proteome of two rice genotypes: Moroberekan and IR64. Water was withheld for 3 d before heading (3DBH) in well watered controls for 5 d until the flag leaf relative water content (RWC) had declined to 45-50%. Plants were then re-watered and heading occurred 2-3 d later, representing a delay of 4-5 d relative to controls. The anther proteins were separated at 3 DBH, at the end of the stress period, and at heading in stressed/re-watered plants and controls by two-dimensional (2-D) gel electrophoresis, and 93 protein spots were affected reproducibly in abundance by drought during the experiment across two rice genotypes. After drought stress, upon re-watering, expressions of 24 protein spots were irreversible in both genotypes, 60 protein spots were irreversible in IR64 but reversible in Moroberekan, only nine protein spots were irreversible in Moroberekan while reversible in IR64. Among them, there were 14 newly drought-induced protein spots in IR64; none of them was reversible on re-watering. However, there were 13 newly drought-induced protein spots in Moroberekan, 10 of them were reversible on re-watering, including six drought-induced protein spots that were not reversed in IR64. Taken together, our proteomics data reveal that drought-tolerant genotype Moroberekan possessed better recovery capability following drought and re-watering at the anther proteome level than the drought-sensitive genotype IR64. The disruptions of drought to rice anther development and pollen cell functions are also discussed in the paper.

Photosynthetic capacity peaks at intermediate size in temperate deciduous trees.

PubMed

Thomas, Sean C

2010-05-01

Studies of age-related changes in leaf functional biology have generally been based on dichotomous comparisons of young and mature individuals (e.g., saplings and mature canopy trees), with little data available to describe changes through the entire ontogeny of trees, particularly of broadleaf angiosperms. Leaf-level gas-exchange and morphological parameters were quantified in situ in the upper canopy of trees acclimated to high light conditions, spanning a wide range of ontogenetic stages from saplings (approximately 1 cm in stem diameter) to trees >60 cm d.b.h. and nearing their maximum lifespan, in three temperate deciduous tree species in central Ontario, Canada. Traits associated with growth performance, including leaf photosynthetic capacity (expressed on either an area, mass or leaf N basis), stomatal conductance, leaf size and leaf N content, generally showed a unimodal ('hump-shaped') pattern, with peak values at an intermediate ontogenetic stage. In contrast, leaf mass per area (LMA) and related morphological parameters (leaf thickness, leaf tissue density, leaf C content) increased monotonically with tree size, as did water-use efficiency; these monotonic relationships were well described by simple allometric functions of the form Y = aX(b). For traits showing unimodal patterns, tree size corresponding to the trait maximum differed markedly among traits: all three species showed a similar pattern in which the peak for leaf size occurred in trees approximately 2-6 cm d.b.h., followed by leaf chemical traits and photosynthetic capacity on a mass or leaf N basis and finally by photosynthetic capacity on a leaf area basis, which peaked approximately at the size of reproductive onset. It is argued that ontogenetic increases in photosynthetic capacity and related traits early in tree ontogeny are general among relatively shade-tolerant tree species that have a low capacity for leaf-level acclimation, as are declines in this set of traits late in tree ontogeny.

Ecological Requirements of Chigger Mites.

DTIC Science & Technology

1982-03-31

our mature forest sites were in riverbottom hardwood forest, dominated by Acer negundo, Betula nigra and Liquidambar styraciflua with DBH greater than...Res. Malaysia , 16:1-67. Nutting, W. R. 1968. Host specificity in parasitic acarines. Acarolgia 10:165-180. Ott, Lyman. 1977. An introduction to

Volume Equations for Plantation Cottonwood Trees (Populusdeltoides)

Treesearch

Roger M. Krinard

1988-01-01

Equations and tables for cubic-foot volume of outside bark to the top of the tree and inside bark to a3-inchtop are given for plantation-grown cottonwoods (Populus delfoidesBartr. ex Marsh.) from 5 to 22 inches in d.b.h.

Ecological Importance of Small-Diameter Trees to the Structure, Diversity and Biomass of a Tropical Evergreen Forest at Rabi, Gabon.

PubMed

Memiaghe, Hervé R; Lutz, James A; Korte, Lisa; Alonso, Alfonso; Kenfack, David

2016-01-01

Tropical forests have long been recognized for their biodiversity and ecosystem services. Despite their importance, tropical forests, and particularly those of central Africa, remain understudied. Until recently, most forest inventories in Central Africa have focused on trees ≥10 cm in diameter, even though several studies have shown that small-diameter tree population may be important to demographic rates and nutrient cycling. To determine the ecological importance of small-diameter trees in central African forests, we used data from a 25-ha permanent plot that we established in the rainforest of Gabon to study the diversity and dynamics of these forests. Within the plot, we censused 175,830 trees ≥1 cm dbh from 54 families, 192 genera, and 345 species. Average tree density was 7,026 trees/ha, basal area 31.64 m2/ha, and above-ground biomass 369.40 Mg/ha. Fabaceae, Ebenaceae and Euphorbiaceae were the most important families by basal area, density and above-ground biomass. Small-diameter trees (1 cm ≥ dbh <10 cm) comprised 93.7% of the total tree population, 16.5% of basal area, and 4.8% of the above-ground biomass. They also had diversity 18% higher at family level, 34% higher at genus level, and 42% higher at species level than trees ≥10 cm dbh. Although the relative contribution of small-diameter trees to biomass was comparable to other forests globally, their contribution to forest density, and diversity was disproportionately higher. The high levels of diversity within small-diameter classes may give these forests high levels of structural resilience to anthropogenic/natural disturbance and a changing climate.

Ecological Importance of Small-Diameter Trees to the Structure, Diversity and Biomass of a Tropical Evergreen Forest at Rabi, Gabon

PubMed Central

Memiaghe, Hervé R.; Lutz, James A.; Korte, Lisa; Alonso, Alfonso; Kenfack, David

2016-01-01

Tropical forests have long been recognized for their biodiversity and ecosystem services. Despite their importance, tropical forests, and particularly those of central Africa, remain understudied. Until recently, most forest inventories in Central Africa have focused on trees ≥10 cm in diameter, even though several studies have shown that small-diameter tree population may be important to demographic rates and nutrient cycling. To determine the ecological importance of small-diameter trees in central African forests, we used data from a 25-ha permanent plot that we established in the rainforest of Gabon to study the diversity and dynamics of these forests. Within the plot, we censused 175,830 trees ≥1 cm dbh from 54 families, 192 genera, and 345 species. Average tree density was 7,026 trees/ha, basal area 31.64 m2/ha, and above-ground biomass 369.40 Mg/ha. Fabaceae, Ebenaceae and Euphorbiaceae were the most important families by basal area, density and above-ground biomass. Small-diameter trees (1 cm ≥ dbh <10 cm) comprised 93.7% of the total tree population, 16.5% of basal area, and 4.8% of the above-ground biomass. They also had diversity 18% higher at family level, 34% higher at genus level, and 42% higher at species level than trees ≥10 cm dbh. Although the relative contribution of small-diameter trees to biomass was comparable to other forests globally, their contribution to forest density, and diversity was disproportionately higher. The high levels of diversity within small-diameter classes may give these forests high levels of structural resilience to anthropogenic/natural disturbance and a changing climate. PMID:27186658

Soil base saturation combines with Beech Bark Disease to influence composition and structure of Sugar Maple-Beech forests in an acid rain-impacted region

USGS Publications Warehouse

Lawrence, Gregory B.; McDonnell, Todd C.; Sullivan, Timothy J.; Dovciak, Martin; Bailey, Scott W.; Antidormi, Michael; Zarfos, Michael R.

2018-01-01

Sugar maple, an abundant and highly valued tree species in eastern North America, has experienced decline from soil calcium (Ca) depletion by acidic deposition, while beech, which often coexists with sugar maple, has been afflicted with beech bark disease (BBD) over the same period. To investigate how variations in soil base saturation combine with effects of BBD in influencing stand composition and structure, measurements of soils, canopy, subcanopy, and seedlings were taken in 21 watersheds in the Adirondack region of NY (USA), where sugar maple and beech were the predominant canopy species and base saturation of the upper B horizon ranged from 4.4 to 67%. The base saturation value corresponding to the threshold for Al mobilization (16.8%) helped to define the species composition of canopy trees and seedlings. Canopy vigor and diameter at breast height (DBH) were positively correlated (P < 0.05) with base saturation for sugar maple, but unrelated for beech. However, beech occupied lower canopy positions than sugar maple, and as base saturation increased, the average canopy position of beech decreased relative to sugar maple (P < 0.10). In low-base saturation soils, soil-Ca depletion and BBD may have created opportunities for gap-exploiting species such as red maple and black cherry, whereas in high-base saturation soils, sugar maple dominated the canopy. Where soils were beginning to recover from acidic deposition effects, sugar maple DBH and basal area increased progressively from 2000 to 2015, whereas for beech, average DBH did not change and basal area did not increase after 2010.

Local-scale drivers of tree survival in a temperate forest.

PubMed

Wang, Xugao; Comita, Liza S; Hao, Zhanqing; Davies, Stuart J; Ye, Ji; Lin, Fei; Yuan, Zuoqiang

2012-01-01

Tree survival plays a central role in forest ecosystems. Although many factors such as tree size, abiotic and biotic neighborhoods have been proposed as being important in explaining patterns of tree survival, their contributions are still subject to debate. We used generalized linear mixed models to examine the relative importance of tree size, local abiotic conditions and the density and identity of neighbors on tree survival in an old-growth temperate forest in northeastern China at three levels (community, guild and species). Tree size and both abiotic and biotic neighborhood variables influenced tree survival under current forest conditions, but their relative importance varied dramatically within and among the community, guild and species levels. Of the variables tested, tree size was typically the most important predictor of tree survival, followed by biotic and then abiotic variables. The effect of tree size on survival varied from strongly positive for small trees (1-20 cm dbh) and medium trees (20-40 cm dbh), to slightly negative for large trees (>40 cm dbh). Among the biotic factors, we found strong evidence for negative density and frequency dependence in this temperate forest, as indicated by negative effects of both total basal area of neighbors and the frequency of conspecific neighbors. Among the abiotic factors tested, soil nutrients tended to be more important in affecting tree survival than topographic variables. Abiotic factors generally influenced survival for species with relatively high abundance, for individuals in smaller size classes and for shade-tolerant species. Our study demonstrates that the relative importance of variables driving patterns of tree survival differs greatly among size classes, species guilds and abundance classes in temperate forest, which can further understanding of forest dynamics and offer important insights into forest management.

Intra-specific competition (crowding) of giant sequoias (Sequoiadendron giganteum)

USGS Publications Warehouse

Stohlgren, Thomas J.

1993-01-01

Information on the size and location of 1916 giant sequoias (Sequoiadendron giganteum (Lindl.) Buchholz) in Muir Grove, Sequoia National Park, in the southern Sierra Nevada of California was used to assess intra-specific crowding. Study objectives were to: (1) determine which parameters associated with intra-specific competition (i.e. size and distance to nearest neighbor, crowding/root system area overlap, or number of neighbors) might be important in spatial pattern development, growth, and survivorship of established giant sequoias; (2) quantify the level of intra-specific crowding of different sized live sequoias based on a model of estimated overlapping root system areas (i.e. an index of relative crowding); (3) compare the level of intra-specific crowding of similarly sized live and dead giant sequoias (less than 30 cm diameter at breast height (dbh) at the time of inventory (1969). Mean distances to the nearest live giant sequoia neighbor were not significantly different (at α = 0.05) for live and dead sequoias in similar size classes. A zone of influence competition model (i.e. index of crowding) based on horizontal overlap of estimated root system areas was developed for 1753 live sequoias. The model, based only on the spatial arrangement of live sequoias, was then tested on dead sequoias of less than 30 cm dbh (n = 163 trees; also recorded in 1969). The dead sequoias had a significantly higher crowding index than 561 live trees of similar diameter. Results showed that dead sequoias of less than 16.6 cm dbh had a significantly greater mean number of live neighbors and mean crowding index than live sequoias of similar size. Intra-specific crowding may be an important mechanism in determining the spatial distribution of sequoias in old-growth forests.

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa

DOE PAGES

Healey, Adam L.; Lee, David J.; Lupoi, Jason S.; ...

2016-11-18

In order for a lignocellulosic bioenergy feedstock to be considered sustainable,it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application,it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin,glucan,and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7–21.3%) amongmore » parental and hybrid populations,whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28–38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age,with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase),and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%,respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass,with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass,respectively),with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate,biomass composition,and further optimization of enzymatic saccharification yield,high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production.« less

The Importance of Large-Diameter Trees to Forest Structural Heterogeneity

PubMed Central

Lutz, James A.; Larson, Andrew J.; Freund, James A.; Swanson, Mark E.; Bible, Kenneth J.

2013-01-01

Large-diameter trees dominate the structure, dynamics and function of many temperate and tropical forests. However, their attendant contributions to forest heterogeneity are rarely addressed. We established the Wind River Forest Dynamics Plot, a 25.6 ha permanent plot within which we tagged and mapped all 30,973 woody stems ≥1 cm dbh, all 1,966 snags ≥10 cm dbh, and all shrub patches ≥2 m2. Basal area of the 26 woody species was 62.18 m2/ha, of which 61.60 m2/ha was trees and 0.58 m2/ha was tall shrubs. Large-diameter trees (≥100 cm dbh) comprised 1.5% of stems, 31.8% of basal area, and 17.6% of the heterogeneity of basal area, with basal area dominated by Tsuga heterophylla and Pseudotsuga menziesii. Small-diameter subpopulations of Pseudotsuga menziesii, Tsuga heterophylla and Thuja plicata, as well as all tree species combined, exhibited significant aggregation relative to the null model of complete spatial randomness (CSR) up to 9 m (P≤0.001). Patterns of large-diameter trees were either not different from CSR (Tsuga heterophylla), or exhibited slight aggregation (Pseudotsuga menziesii and Thuja plicata). Significant spatial repulsion between large-diameter and small-diameter Tsuga heterophylla suggests that large-diameter Tsuga heterophylla function as organizers of tree demography over decadal timescales through competitive interactions. Comparison among two forest dynamics plots suggests that forest structural diversity responds to intermediate-scale environmental heterogeneity and disturbances, similar to hypotheses about patterns of species richness, and richness- ecosystem function. Large mapped plots with detailed within-plot environmental spatial covariates will be required to test these hypotheses. PMID:24376579

The importance of large-diameter trees to forest structural heterogeneity.

PubMed

Lutz, James A; Larson, Andrew J; Freund, James A; Swanson, Mark E; Bible, Kenneth J

2013-01-01

Large-diameter trees dominate the structure, dynamics and function of many temperate and tropical forests. However, their attendant contributions to forest heterogeneity are rarely addressed. We established the Wind River Forest Dynamics Plot, a 25.6 ha permanent plot within which we tagged and mapped all 30,973 woody stems ≥ 1 cm dbh, all 1,966 snags ≥ 10 cm dbh, and all shrub patches ≥ 2 m(2). Basal area of the 26 woody species was 62.18 m(2)/ha, of which 61.60 m(2)/ha was trees and 0.58 m(2)/ha was tall shrubs. Large-diameter trees (≥ 100 cm dbh) comprised 1.5% of stems, 31.8% of basal area, and 17.6% of the heterogeneity of basal area, with basal area dominated by Tsuga heterophylla and Pseudotsuga menziesii. Small-diameter subpopulations of Pseudotsuga menziesii, Tsuga heterophylla and Thuja plicata, as well as all tree species combined, exhibited significant aggregation relative to the null model of complete spatial randomness (CSR) up to 9 m (P ≤ 0.001). Patterns of large-diameter trees were either not different from CSR (Tsuga heterophylla), or exhibited slight aggregation (Pseudotsuga menziesii and Thuja plicata). Significant spatial repulsion between large-diameter and small-diameter Tsuga heterophylla suggests that large-diameter Tsuga heterophylla function as organizers of tree demography over decadal timescales through competitive interactions. Comparison among two forest dynamics plots suggests that forest structural diversity responds to intermediate-scale environmental heterogeneity and disturbances, similar to hypotheses about patterns of species richness, and richness- ecosystem function. Large mapped plots with detailed within-plot environmental spatial covariates will be required to test these hypotheses.

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Healey, Adam L.; Lee, David J.; Lupoi, Jason S.

In order for a lignocellulosic bioenergy feedstock to be considered sustainable,it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application,it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin,glucan,and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7–21.3%) amongmore » parental and hybrid populations,whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28–38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age,with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase),and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%,respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass,with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass,respectively),with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate,biomass composition,and further optimization of enzymatic saccharification yield,high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production.« less

Estimating potential emerald ash borer (Coleoptera: Buprestidae) populations using ash inventory data.

PubMed

McCullough, Deborah G; Siegert, Nathan W

2007-10-01

Emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), a phloem-feeding pest native to Asia, was identified in June 2002 as the cause of widespread ash (Fraxinus spp.), mortality in southeastern Michigan and Windsor, Ontario, Canada. Localized populations of A. planipennis have since been found across lower Michigan and in areas of Ohio, Indiana, Illinois, Maryland, and Ontario. Officials working to contain A. planipennis and managers of forestlands near A. planipennis infestations must be able to compare alternative strategies to allocate limited funds efficiently and effectively. Empirical data from a total of 148 green ash, Fraxinus pennsylvanica Marsh., and white ash, Fraxinus americana L., trees were used to develop models to estimate surface area of the trunk and branches by using tree diameter at breast height (dbh). Data collected from 71 additional F. pennsylvanica and F. americana trees killed by A. planipennis showed that on average, 88.9 +/- 4.6 beetles developed and emerged per m2 of surface area. Models were applied to ash inventory data collected at two outlier sites to estimate potential production of A. planipennis beetles at each site. Large trees of merchantable size (dbh > or = 26 cm) accounted for roughly 6% of all ash trees at the two sites, but they could have contributed 55-65% of the total A. planipennis production at both sites. In contrast, 75- 80% of the ash trees at the outlier sites were < or =13 cm dbh, but these small trees could have contributed only < or =12% of the potential A. planipennis production at both sites. Our results, in combination with inventory data, can be used by regulatory officials and resource managers to estimate potential A. planipennis production and to compare options for reducing A. planipennis density and slowing the rate of spread for any area of interest.

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa.

PubMed

Healey, Adam L; Lee, David J; Lupoi, Jason S; Papa, Gabriella; Guenther, Joel M; Corno, Luca; Adani, Fabrizio; Singh, Seema; Simmons, Blake A; Henry, Robert J

2016-01-01

In order for a lignocellulosic bioenergy feedstock to be considered sustainable, it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application, it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin, glucan, and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7-21.3%) among parental and hybrid populations, whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28-38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age, with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase), and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%, respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass, with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass, respectively), with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate, biomass composition, and further optimization of enzymatic saccharification yield, high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production.

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa

PubMed Central

Healey, Adam L.; Lee, David J.; Lupoi, Jason S.; Papa, Gabriella; Guenther, Joel M.; Corno, Luca; Adani, Fabrizio; Singh, Seema; Simmons, Blake A.; Henry, Robert J.

2016-01-01

In order for a lignocellulosic bioenergy feedstock to be considered sustainable, it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application, it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin, glucan, and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7–21.3%) among parental and hybrid populations, whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28–38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age, with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase), and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%, respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass, with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass, respectively), with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate, biomass composition, and further optimization of enzymatic saccharification yield, high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production. PMID:27917179

Role of P-glycoprotein and permeability upon the brain distribution and pharmacodynamics of etamicastat: a comparison with nepicastat.

PubMed

Loureiro, Ana I; Bonifácio, Maria João; Fernandes-Lopes, Carlos; Pires, Nuno; Igreja, Bruno; Wright, Lyndon C; Soares-da-Silva, Patrício

2015-01-01

1. This study explores the impact of permeability and P-glycoprotein (P-gp) efflux, upon brain exposure to etamicastat, a new dopamine-β-hydroxylase (DBH) inhibitor and consequently brain levels of catecholamines. 2. Brain exposure to etamicastat (10 mg/kg), following intravenous administration to mice, was residual and upon oral administration of the same dose no compound was detected, concurring with the absence of effects upon brain catecholamines. The intravenous co-administration of elacridar (1.0 mg/kg), a known P-gp/BCRP dual modulator, significantly increased brain etamicastat exposure, but the levels attained were very low when compared to those of nepicastat, a centrally active DBH inhibitor. 3. In vitro permeability studies from apical-to-basal direction conducted in Caco-2 cells and MDCK-II cells showed that etamicastat apparent permeability was 1.2 × 10(-5) and 1.1 × 10(-6 )cm/s, respectively, 5- and 50-fold lower as compared to nepicastat. The secretory efflux ratio in MDCK-II cells overexpressing human P-gp showed an efflux ratio greater than 2, for both compounds, which was significantly decreased by elacridar. Despite its lower bioavailability and higher clearance, as compared to nepicastat, etamicastat showed preferential distribution to peripheral tissues and high plasma free fraction (15.5%), which may explain its effects upon peripheral DBH and catecholamine levels. 4. Though P-gp-mediated efflux may contribute to the limited brain penetration of etamicastat, the low permeability along with the pharmacokinetic properties of etamicastat may be perceived as the main contributors for its peripheral selectivity, which is advantageous for a cardiovascular drug candidate.

Regulation of water flux through tropical forest canopy trees: do universal rules apply?

PubMed

Meinzer, F C; Goldstein, G; Andrade, J L

2001-01-01

Tropical moist forests are notable for their richness in tree species. The presence of such a diverse tree flora presents potential problems for scaling up estimates of water use from individual trees to entire stands and for drawing generalizations about physiological regulation of water use in tropical trees. We measured sapwood area or sap flow, or both, in 27 co-occurring canopy species in a Panamanian forest to determine the extent to which relationships between tree size, sapwood area and sap flow were species-specific, or whether they were constrained by universal functional relationships between tree size, conducting xylem area, and water use. For the 24 species in which active xylem area was estimated over a range of size classes, diameter at breast height (DBH) accounted for 98% of the variation in sapwood area and 67% of the variation in sapwood depth when data for all species were combined. The DBH alone also accounted for > or = 90% of the variation in both maximum and total daily sap flux density in the outermost 2 cm of sapwood for all species taken together. Maximum sap flux density measured near the base of the tree occurred at about 1,400 h in the largest trees and 1,130 h in the smallest trees studied, and DBH accounted for 93% of the variation in the time of day at which maximum sap flow occurred. The shared relationship between tree size and time of maximum sap flow at the base of the tree suggests that a common relationship between diurnal stem water storage capacity and tree size existed. These results are consistent with a recent hypothesis that allometric scaling of plant vascular systems, and therefore water use, is universal.

Local-Scale Drivers of Tree Survival in a Temperate Forest

PubMed Central

Wang, Xugao; Comita, Liza S.; Hao, Zhanqing; Davies, Stuart J.; Ye, Ji; Lin, Fei; Yuan, Zuoqiang

2012-01-01

Tree survival plays a central role in forest ecosystems. Although many factors such as tree size, abiotic and biotic neighborhoods have been proposed as being important in explaining patterns of tree survival, their contributions are still subject to debate. We used generalized linear mixed models to examine the relative importance of tree size, local abiotic conditions and the density and identity of neighbors on tree survival in an old-growth temperate forest in northeastern China at three levels (community, guild and species). Tree size and both abiotic and biotic neighborhood variables influenced tree survival under current forest conditions, but their relative importance varied dramatically within and among the community, guild and species levels. Of the variables tested, tree size was typically the most important predictor of tree survival, followed by biotic and then abiotic variables. The effect of tree size on survival varied from strongly positive for small trees (1–20 cm dbh) and medium trees (20–40 cm dbh), to slightly negative for large trees (>40 cm dbh). Among the biotic factors, we found strong evidence for negative density and frequency dependence in this temperate forest, as indicated by negative effects of both total basal area of neighbors and the frequency of conspecific neighbors. Among the abiotic factors tested, soil nutrients tended to be more important in affecting tree survival than topographic variables. Abiotic factors generally influenced survival for species with relatively high abundance, for individuals in smaller size classes and for shade-tolerant species. Our study demonstrates that the relative importance of variables driving patterns of tree survival differs greatly among size classes, species guilds and abundance classes in temperate forest, which can further understanding of forest dynamics and offer important insights into forest management. PMID:22347996

Understory and small trees contribute importantly to stemflow of a lower montane cloud forest

NASA Astrophysics Data System (ADS)

González Martínez, T. M.; Wiliams-Linera, G.; Holwerda, F.

2016-12-01

Stemflow (Sf) measurements in rainforests and montane forests dominated by large trees rarely include the understory and small trees. In the present study, contributions of woody understory (> 1 m height and < 5 cm DBH), small trees (5 < DBH < 10 cm) and upper canopy trees (> 10 cm DBH) to overall Sf of a lower montane cloud forest in central Veracruz, Mexico, were quantified. Incident precipitation (P), Sf volume and vegetation structure were measured. Subsequently, stemflow funneling ratios (SFR) were calculated, and allometric relationships between tree basal area and Sf volume were used to scale up measurements from individual trees to the stand level. Additionally, two other common methods to calculate areal Sf were used for comparative purposes. Understory woody plants, small trees and upper canopy trees represented 96, 2 and 2 %, respectively, of the total density. Upper canopy trees had the lowest SFRs (1.6 ± 0.5 on average), while the lower understory (> 1 m and < 2 m height) had the highest (36.1 ± 6.4). Small trees and upper understory (> 2 m) presented similar SFRs (22.9 ± 5.4 and 20.2 ± 3.9, respectively). Different scaling methods yielded very similar results for all but the upper understory. Overall areal Sf during the study period was 19 mm (3.8 % of rainfall), to which the understory contributed 66.3 % (12.6 mm), small trees 12.6 % (2.4 mm) and upper canopy trees 21.1 % (4.0 mm). Our results suggest that woody understory vegetation and small trees can have an important role in Sf generation of tall humid tropical forests, provided that the density of plants in these groups is high enough.

Diameter increase in second-growth Appalachian hardwood stands - a comparison of species

Treesearch

George R., Jr. Trimble

1967-01-01

A study of growth at d.b.h. among eight hardwood species after partial cutting in second-growth stands. Red oak grew fastest, followed in order by yellow-poplar, sugar maple, basswood, black cherry, white ash, beech, and chestnut oak.

Expanding options for reforestation of the Cumberland Plateau

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGee, C.E.

1980-01-01

Stems of d.b.h. 4 inches or greater in a low quality stand in Tennessee dominated by white and scarlet oak (Quercus coccinea) were sheared in September-November 1976, chipped, and removed. Sawtimber quality trees (30) in the 37-acre area were felled separately by conventional methods. Residual trees (2-3 inches d.b.h., ht. over 4.5 ft) in some areas were injected with herbicide. One-acre plots were planted with 1+0 loblolly pine, 2+0 white pine (Pinus strobus), or 1+0 yellow poplar, or left to regenerate naturally. After 2 years, survival of all trees was good (83% or over) and average height of loblolly pine,more » yellow poplar and desirable natural stems (white, scarlet or black oak, Quercus velutina) was 3.3 ft, significantly different from that of white pine (1.5 ft). It is concluded that poor quality stands can be cheaply improved by this method, although release from competing vegetation may be necessary, especially in the case of white pine.« less

Newly-derived neuroblastoma cell lines propagated in serum-free media recapitulate the genotype and phenotype of primary neuroblastoma tumours.

PubMed

Bate-Eya, Laurel T; Ebus, Marli E; Koster, Jan; den Hartog, Ilona J M; Zwijnenburg, Danny A; Schild, Linda; van der Ploeg, Ida; Dolman, M Emmy M; Caron, Huib N; Versteeg, Rogier; Molenaar, Jan J

2014-02-01

Recently protocols have been devised for the culturing of cell lines from fresh tumours under serum-free conditions in defined neural stem cell medium. These cells, frequently called tumour initiating cells (TICs) closely retained characteristics of the tumours of origin. We report the isolation of eight newly-derived neuroblastoma TICs from six primary neuroblastoma tumours and two bone marrow metastases. The primary tumours from which these TICs were generated have previously been fully typed by whole genome sequencing (WGS). Array comparative genomic hybridisation (aCGH) analysis showed that TIC lines retained essential characteristics of the primary tumours and exhibited typical neuroblastoma chromosomal aberrations such as MYCN amplification, gain of chromosome 17q and deletion of 1p36. Protein analysis showed expression for neuroblastoma markers MYCN, NCAM, CHGA, DBH and TH while haematopoietic markers CD19 and CD11b were absent. We analysed the growth characteristics and confirmed tumour-forming potential using sphere-forming assays, subcutaneous and orthotopic injection of these cells into immune-compromised mice. Affymetrix mRNA expression profiling of TIC line xenografts showed an expression pattern more closely mimicking primary tumours compared to xenografts from classical cell lines. This establishes that these neuroblastoma TICs cultured under serum-free conditions are relevant and useful neuroblastoma tumour models. Copyright © 2013 Elsevier Ltd. All rights reserved.

Tables for predicting the slash weight of shortleaf pine.

Treesearch

Duane R. Freeman; Peter J. Roussopoulos

1983-01-01

The tables provided here estimate crown weights of shortleaf pine (Pinus echinata Mill.) from measurements of diameter (d.b.h) and crown ratio, for both a 3-inch and a 4-inch merchantable top. Crown component fractions for standard fuel size classes are also presented.

Relationship of stump diameter to d.b.h. for pitch pine in the northeast

Treesearch

Frederick E. Hampf

1957-01-01

This is the seventh report on a series of studies to show the relationship of stump diameter to diameter breast high (d. b. h.) for commercially important tree species in the Northeast. This report is for pitch pine (Pinus rigida).

Interactive effects of frequent burning and timber harvesting on above ground carbon biomass in temperate eucalypt forests

NASA Astrophysics Data System (ADS)

Collins, Luke; Penman, Trent; Ximenes, Fabiano; Bradstock, Ross

2015-04-01

The sequestration of carbon has been identified as an important strategy to mitigate the effects of climate change. Fuel reduction burning and timber harvesting are two common co-occurring management practices within forests. Frequent burning and timber harvesting may alter forest carbon pools through the removal and redistribution of biomass and demographic and structural changes to tree communities. Synergistic and antagonistic interactions between frequent burning and harvesting are likely to occur, adding further complexity to the management of forest carbon stocks. Research aimed at understanding the interactive effects of frequent fire and timber harvesting on carbon biomass is lacking. This study utilised data from two long term (25 - 30 years) manipulative burning experiments conducted in southern Australia in temperate eucalypt forests dominated by resprouting canopy species. Specifically we examined the effect of fire frequency and harvesting on (i) total biomass of above ground carbon pools and (ii) demographic and structural characteristics of live trees. We also investigated some of the mechanisms driving these changes. Frequent burning reduced carbon biomass by up to 20% in the live tree carbon pool. Significant interactions occurred between fire and harvesting, whereby the reduction in biomass of trees >20 cm diameter breast height (DBH) was amplified by increased fire frequency. The biomass of trees <20 cm DBH increased with harvesting intensity in frequently burnt areas, but was unaffected by harvesting intensity in areas experiencing low fire frequency. Biomass of standing and fallen coarse woody debris was relatively unaffected by logging and fire frequency. Fire and harvesting significantly altered stand structure over the study period. Comparison of pre-treatment conditions to current conditions revealed that logged sites had a significantly greater increase in the number of small trees (<40 cm DBH) than unlogged sites. Logged sites showed a significant decrease in the number of large trees (>60 cm DBH) over the study period, while unlogged sites showed an increase. Frequently burnt logged sites showed the greatest reduction in large trees, presumably due to increased fire related mortality and collapse. Analysis of tree survival and growth data suggest that mortality rate is increased and growth rate reduced in frequently burnt areas compared to unburnt areas. Our findings suggest that future shifts towards more frequent fire (both prescribed fire and wildfire) could potentially lead to broad scale reductions in carbon sequestration in temperate forests and woodlands dominated by resprouting canopy species. Reductions in carbon sequestration associated with frequent burning will potentially be amplified in intensively harvested landscapes.

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery

PubMed Central

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-01-01

Background DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. Results GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. Conclusion GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at . PMID:19728865

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.

PubMed

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-09-03

DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at http://cgs.pharm.kyoto-u.ac.jp/services/network.

Expression of Multiple Resistance Genes Enhances Tolerance to Environmental Stressors in Transgenic Poplar (Populus × euramericana ‘Guariento’)

PubMed Central

Su, Xiaohua; Chu, Yanguang; Li, Huan; Hou, Yingjie; Zhang, Bingyu; Huang, Qinjun; Hu, Zanmin; Huang, Rongfeng; Tian, Yingchuan

2011-01-01

Commercial and non-commercial plants face a variety of environmental stressors that often cannot be controlled. In this study, transgenic hybrid poplar (Populus × euramericana ‘Guariento’) harboring five effector genes (vgb, SacB, JERF36, BtCry3A and OC-I) were subjected to drought, salinity, waterlogging and insect stressors in greenhouse or laboratory conditions. Field trials were also conducted to investigate long-term effects of transgenic trees on insects and salt tolerance in the transformants. In greenhouse studies, two transgenic lines D5-20 and D5-21 showed improved growth, as evidenced by greater height and basal diameter increments and total biomass relative to the control plants after drought or salt stress treatments. The improved tolerance to drought and salt was primarily attributed to greater instantaneous water use efficiency (WUEi) in the transgenic trees. The chlorophyll concentrations tended to be higher in the transgenic lines under drought or saline conditions. Transformed trees in drought conditions accumulated more fructan and proline and had increased Fv/Fm ratios (maximum quantum yield of photosystem II) under waterlogging stress. Insect-feeding assays in the laboratory revealed a higher total mortality rate and lower exuviation index of leaf beetle [Plagiodera versicolora (Laicharting)] larvae fed with D5-21 leaves, suggesting enhanced insect resistance in the transgenic poplar. In field trials, the dominance of targeted insects on 2-year-old D5-21 transgenic trees was substantially lower than that of the controls, indicating enhanced resistance to Coleoptera. The average height and DBH (diameter at breast height) of 2.5-year-old transgenic trees growing in naturally saline soil were 3.80% and 4.12% greater than those of the control trees, but these increases were not significant. These results suggested that multiple stress-resistance properties in important crop tree species could be simultaneously improved, although additional research is needed to fully understand the relationships between the altered phenotypes and the function of each transgene in multigene transformants. PMID:21931776

Neighboring Genes Show Correlated Evolution in Gene Expression

PubMed Central

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

Generational Association Studies of Dopaminergic Genes in Reward Deficiency Syndrome (RDS) Subjects: Selecting Appropriate Phenotypes for Reward Dependence Behaviors

PubMed Central

Blum, Kenneth; Chen, Amanda L. C.; Oscar-Berman, Marlene; Chen, Thomas J. H.; Lubar, Joel; White, Nancy; Lubar, Judith; Bowirrat, Abdalla; Braverman, Eric; Schoolfield, John; Waite, Roger L.; Downs, Bernard W.; Madigan, Margaret; Comings, David E.; Davis, Caroline; Kerner, Mallory M.; Knopf, Jennifer; Palomo, Tomas; Giordano, John J.; Morse, Siobhan A.; Fornari, Frank; Barh, Debmalya; Femino, John; Bailey, John A.

2011-01-01

Abnormal behaviors involving dopaminergic gene polymorphisms often reflect an insufficiency of usual feelings of satisfaction, or Reward Deficiency Syndrome (RDS). RDS results from a dysfunction in the “brain reward cascade,” a complex interaction among neurotransmitters (primarily dopaminergic and opioidergic). Individuals with a family history of alcoholism or other addictions may be born with a deficiency in the ability to produce or use these neurotransmitters. Exposure to prolonged periods of stress and alcohol or other substances also can lead to a corruption of the brain reward cascade function. We evaluated the potential association of four variants of dopaminergic candidate genes in RDS (dopamine D1 receptor gene [DRD1]; dopamine D2 receptor gene [DRD2]; dopamine transporter gene [DAT1]; dopamine beta-hydroxylase gene [DBH]). Methodology: We genotyped an experimental group of 55 subjects derived from up to five generations of two independent multiple-affected families compared to rigorously screened control subjects (e.g., N = 30 super controls for DRD2 gene polymorphisms). Data related to RDS behaviors were collected on these subjects plus 13 deceased family members. Results: Among the genotyped family members, the DRD2 Taq1 and the DAT1 10/10 alleles were significantly (at least p < 0.015) more often found in the RDS families vs. controls. The TaqA1 allele occurred in 100% of Family A individuals (N = 32) and 47.8% of Family B subjects (11 of 23). No significant differences were found between the experimental and control positive rates for the other variants. Conclusions: Although our sample size was limited, and linkage analysis is necessary, the results support the putative role of dopaminergic polymorphisms in RDS behaviors. This study shows the importance of a nonspecific RDS phenotype and informs an understanding of how evaluating single subset behaviors of RDS may lead to spurious results. Utilization of a nonspecific “reward” phenotype may be a paradigm shift in future association and linkage studies involving dopaminergic polymorphisms and other neurotransmitter gene candidates. PMID:22408582

Gene-gene interactions of CYP2A6 and MAOA polymorphisms on smoking behavior in Chinese male population.

PubMed

Tang, Xun; Guo, Song; Sun, Hongqiang; Song, Xuemei; Jiang, Zuonin; Sheng, Lixiang; Zhou, Dongfeng; Hu, Yonghua; Chen, Dafang

2009-05-01

Nicotine is the major psychoactive ingredient in tobacco, and is responsible for dependence through the nicotine-stimulated reward pathway mediated by the central dopaminergic system. Consequently, genetic polymorphisms in both nicotine metabolism and dopamine catabolism genes may influence smoking behavior, and interact with each other resulting in risk modulation. In this study, we investigated the association and multilocus gene-gene interactions of cytochrome P450 2A6 (CYP2A6), dopamine beta-hydroxylase (DBH), catechol O-methyl transferase (COMT), and monoamine oxidase A (MAOA) polymorphisms with smoking behavior in a community-based Chinese male population. The polymorphisms were genotyped in 203 current smokers, 66 former smokers, and 102 never smokers. Multivariate logistic regression models and the multifactor dimensionality reduction method were used to analyze the association and multilocus gene-gene interactions. Statistically significant trends were shown for increased risk of smoking initiation in participants with CYP2A6*1B/CYP2A6*1B genotypes compared with those with CYP2A6*1A/CYP2A6*1A genotypes [odds ratio (OR)=3.5, 95% confidence interval (CI)= 1.5-8.1], and participants with CYP2A6*1/CYP2A6*1 genotypes were at higher risk of smoking initiation (OR=2.4, 95% CI=1.2-4.5) and smoking persistence (OR=4.0, 95% CI=1.5-10.3) than those who have CYP2A6*4C genotypes. Moreover, the best model involved a gene-gene interaction between MAOA and CYP2A6 was characterized by the multifactor dimensionality reduction method (64.11% accuracy, P<0.001), and indicated that carriers of the combined 1460 T/O genotype for MAOA EcoRV and CYP2A6*1/CYP2A6*1 genotypes were at higher risk of smoking (OR=15.4, 95% CI=4.5-52.5). These findings suggested a substantial influence of CYP2A6 polymorphism as well as the interaction with MAOA resulting in risk modulation on smoking behavior in Chinese male population.

Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

PubMed Central

Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

2013-01-01

The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

Neighboring Genes Show Correlated Evolution in Gene Expression.

PubMed

Ghanbarian, Avazeh T; Hurst, Laurence D

2015-07-01

When considering the evolution of a gene's expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sawtimber by Prescription - The Sudden Sawlog Story Through Age 33

Treesearch

J.D. Burton

1982-01-01

Presents total and net yield, standing volume, volume harvested, and natural mortality, in cubic feet i.b. to a 3-inch top d.i.b., and in board feet Int. ¼ to an 8-inch and to a 6-inch top, together with dbh distribution at various ages.

Relationship of stump diameter to d.b.h. for American beech in the Northeast

Treesearch

Frederick E. Hampf

1955-01-01

This is the third report on a series of studies (2, 3) made to show the relationship of stump diameter to diameter breast high (d. b. h.) for commercially important tree species in the Northeast. This report is for American beech (Fagus grandifolia).

Above-ground weights for tamarack in northeastern Minnesota.

Treesearch

Eugene M. Carpenter

1983-01-01

We used trees from natural uneven-aged stands in northeastern Minnesota to develop prediction equations to estimate total tree, stem, crown, live and dead branch weight. Presented here are specific gravity and moisture content by d.b.h. and height in tree, as well as bark, sapwood, and heartwood ratios.

Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods.

PubMed

Chang, Dan; Duda, Thomas F

2014-06-05

Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components ('conotoxins'), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species' 'venom gene space'. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species. We modified community phylogenetics approaches to incorporate phylogenetic history and disparity of genes and their expression profiles to determine patterns of venom gene space utilization. Less than half of the A-superfamily gene repertoire of these species is expressed, and only a few orthologous genes are coexpressed among species. Species exhibit substantially distinct expression strategies, with some expressing sets of closely related loci ('under-dispersed' expression of available genes) while others express sets of more disparate genes ('over-dispersed' expression). In addition, expressed genes show higher dN/dS values than either unexpressed or ancestral genes; this implies that expression exposes genes to selection and facilitates rapid evolution of these genes. Few recent lineage-specific gene duplicates are expressed simultaneously, suggesting that expression divergence among redundant gene copies may be established shortly after gene duplication. Our study demonstrates that venom gene space is explored differentially by Conus species, a process that effectively permits the independent and rapid evolution of venoms in these species.

FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data.

PubMed

Manijak, Mieszko P; Nielsen, Henrik B

2011-06-11

Although, systematic analysis of gene annotation is a powerful tool for interpreting gene expression data, it sometimes is blurred by incomplete gene annotation, missing expression response of key genes and secondary gene expression responses. These shortcomings may be partially circumvented by instead matching gene expression signatures to signatures of other experiments. To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700 Arabidopsis microarray experiments. Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. The server is available at http://www.cbs.dtu.dk/services/faro/.

Digital gene expression analysis of the zebra finch genome

PubMed Central

2010-01-01

Background In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates. PMID:20359325

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data.

PubMed

Bikel, Shirley; Jacobo-Albavera, Leonor; Sánchez-Muñoz, Fausto; Cornejo-Granados, Fernanda; Canizales-Quinteros, Samuel; Soberón, Xavier; Sotelo-Mundo, Rogerio R; Del Río-Navarro, Blanca E; Mendoza-Vargas, Alfredo; Sánchez, Filiberto; Ochoa-Leyva, Adrian

2017-01-01

In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays. We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6-10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR). From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment. Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments.

Differential gene expression analysis in glioblastoma cells and normal human brain cells based on GEO database.

PubMed

Wang, Anping; Zhang, Guibin

2017-11-01

The differentially expressed genes between glioblastoma (GBM) cells and normal human brain cells were investigated to performed pathway analysis and protein interaction network analysis for the differentially expressed genes. GSE12657 and GSE42656 gene chips, which contain gene expression profile of GBM were obtained from Gene Expression Omniub (GEO) database of National Center for Biotechnology Information (NCBI). The 'limma' data packet in 'R' software was used to analyze the differentially expressed genes in the two gene chips, and gene integration was performed using 'RobustRankAggreg' package. Finally, pheatmap software was used for heatmap analysis and Cytoscape, DAVID, STRING and KOBAS were used for protein-protein interaction, Gene Ontology (GO) and KEGG analyses. As results: i) 702 differentially expressed genes were identified in GSE12657, among those genes, 548 were significantly upregulated and 154 were significantly downregulated (p<0.01, fold-change >1), and 1,854 differentially expressed genes were identified in GSE42656, among the genes, 1,068 were significantly upregulated and 786 were significantly downregulated (p<0.01, fold-change >1). A total of 167 differentially expressed genes including 100 upregulated genes and 67 downregulated genes were identified after gene integration, and the genes showed significantly different expression levels in GBM compared with normal human brain cells (p<0.05). ii) Interactions between the protein products of 101 differentially expressed genes were identified using STRING and expression network was established. A key gene, called CALM3, was identified by Cytoscape software. iii) GO enrichment analysis showed that differentially expressed genes were mainly enriched in 'neurotransmitter:sodium symporter activity' and 'neurotransmitter transporter activity', which can affect the activity of neurotransmitter transportation. KEGG pathway analysis showed that the differentially expressed genes were mainly enriched in 'protein processing in endoplasmic reticulum', which can affect protein processing in endoplasmic reticulum. The results showed that: i) 167 differentially expressed genes were identified from two gene chips after integration; and ii) protein interaction network was established, and GO and KEGG pathway analyses were successfully performed to identify and annotate the key gene, which provide new insights for the studies on GBN at gene level.

Discovery and validation of a glioblastoma co-expressed gene module

PubMed Central

Dunwoodie, Leland J.; Poehlman, William L.; Ficklin, Stephen P.; Feltus, Frank Alexander

2018-01-01

Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors. Among the proneural, neural, mesenchymal, and classical glioblastoma subtypes, these genes are most-highly expressed in the mesenchymal subtype. Furthermore, high expression of these genes is associated with decreased survival across each glioblastoma subtype. These genes are of interest to glioblastoma biology and our gene interaction discovery and validation workflow can be used to discover and validate co-expressed gene modules derived from any co-expression network. PMID:29541392

Discovery and validation of a glioblastoma co-expressed gene module.

PubMed

Dunwoodie, Leland J; Poehlman, William L; Ficklin, Stephen P; Feltus, Frank Alexander

2018-02-16

Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors. Among the proneural, neural, mesenchymal, and classical glioblastoma subtypes, these genes are most-highly expressed in the mesenchymal subtype. Furthermore, high expression of these genes is associated with decreased survival across each glioblastoma subtype. These genes are of interest to glioblastoma biology and our gene interaction discovery and validation workflow can be used to discover and validate co-expressed gene modules derived from any co-expression network.

Gender-Specific Gene Expression in Post-Mortem Human Brain: Localization to Sex Chromosomes

PubMed Central

Vawter, Marquis P; Evans, Simon; Choudary, Prabhakara; Tomita, Hiroaki; Meador-Woodruff, Jim; Molnar, Margherita; Li, Jun; Lopez, Juan F; Myers, Rick; Cox, David; Watson, Stanley J; Akil, Huda; Jones, Edward G; Bunney, William E

2011-01-01

Gender differences in brain development and in the prevalence of neuropsychiatric disorders such as depression have been reported. Gender differences in human brain might be related to patterns of gene expression. Microarray technology is one useful method for investigation of gene expression in brain. We investigated gene expression, cell types, and regional expression patterns of differentially expressed sex chromosome genes in brain. We profiled gene expression in male and female dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum using the Affymetrix oligonucleotide microarray platform. Differentially expressed genes between males and females on the Y chromosome (DBY, SMCY, UTY, RPS4Y, and USP9Y) and X chromosome (XIST) were confirmed using real-time PCR measurements. In situ hybridization confirmed the differential expression of gender-specific genes and neuronal expression of XIST, RPS4Y, SMCY, and UTY in three brain regions examined. The XIST gene, which silences gene expression on regions of the X chromosome, is expressed in a subset of neurons. Since a subset of neurons express gender-specific genes, neural subpopulations may exhibit a subtle sexual dimorphism at the level of differences in gene regulation and function. The distinctive pattern of neuronal expression of XIST, RPS4Y, SMCY, and UTY and other sex chromosome genes in neuronal subpopulations may possibly contribute to gender differences in prevalence noted for some neuropsychiatric disorders. Studies of the protein expression of these sex- chromosome-linked genes in brain tissue are required to address the functional consequences of the observed gene expression differences. PMID:14583743

ABO Blood Type and Personality Traits in Healthy Japanese Subjects.

PubMed

Tsuchimine, Shoko; Saruwatari, Junji; Kaneda, Ayako; Yasui-Furukori, Norio

2015-01-01

There is no scientific consensus that a relationship exists between the ABO blood group and personality traits. However, a recent study hypothesized that the dopamine beta-hydroxylase (DBH) gene is in linkage with the ABO gene. The sample population consisted of 1,427 healthy Japanese subjects who completed the Temperament and Character Inventory (TCI). Each subject's ABO blood type was determined by genotyping the rs8176719 and rs8176746 ABO gene single-nucleotide polymorphisms (SNPs) using a TaqMan genotyping assay. The relationships between the six ABO genotypes or four ABO phenotypes and personality traits were examined using a multivariate analysis of covariance (MANCOVA), controlling for age and sex. The MANCOVA data showed a significant difference in TCI scores among the ABO genotype groups (F [7, 1393] = 3.354, p = 0.001). A subsequent univariate analysis showed a significant difference in the mean scores for Persistence among the genotype groups (F = 2.680, partial η2 = 0.010, p = 0.020). Similarly, dividing the ABO blood type into four phenotypes revealed a significant difference among the phenotype groups (F [7, 1397] = 2.529, p = 0.014). A subsequent univariate analysis showed a significant difference among the phenotype groups in the mean scores for Persistence (F = 2.952, partial η2= 0.006, p = 0.032). We observed a significant association between ABO blood group genotypes and personality traits in a large number of healthy Japanese subjects. However, these results should be regarded as preliminary and should be interpreted with caution because it is possible that the association between ABO blood group genotype and the Persistence trait is relatively weak.

Is Knowledge Random? Introducing Sampling and Bias through Outdoor Inquiry

ERIC Educational Resources Information Center

Stier, Sam

2010-01-01

Sampling, very generally, is the process of learning about something by selecting and assessing representative parts of that population or object. In the inquiry activity described here, students learned about sampling techniques as they estimated the number of trees greater than 12 cm dbh (diameter at breast height) in a wooded, discrete area…

Biological response of plantation cottonwood to spacing, pruning and thinning

Treesearch

R. J. Gascon; R. M. Krinard

1976-01-01

A literature review and a sampling of data obtained from cottonwood growers of the biological response of plantation-grown cottonwood trees to initial spacings in the Midsouth have indicated the following trends: as spacing increased, dbh increased, height of dominants not practically affected, total cubic volume decreased, basal area decreased, natural pruning...

Predicting mortality for five California conifers following wildfire

Treesearch

Sharon M. Hood; Sheri L. Smith; Daniel R. Cluck

2010-01-01

Fire injury was characterized and survival monitored for 5677 trees >25cm DBH from five wildfires in California that occurred between 2000 and 2004. Logistic regression models for predicting the probability of mortality 5-years after fire were developed for incense cedar (Calocedrus decurrens (Torr.) Florin), white fir (Abies concolor (Gord. & Glend.) Lindl. ex...

Feasibility of harvesting southern hardwood trees by extraction

Treesearch

Donald L. Sirois

1977-01-01

A Rome TXH Tree Extractor was used to explore the harvesting of four species of southern hardwoods by extraction. The test indicate that harvesting by extraction is feasible for harvestang, if tree size is limited to 9 inches DBH or less. Stump and below ground biomass averaged 18 percent of total tree biomass.

Inga paterno Harms

Treesearch

Nadia Navarrete-Tindall; Hugo Aragon

2002-01-01

Inga paterno is native to southern Mexico and Central America (Zarucchi 1986). Inga paterno is a fast-growing tree, reaching 10 m to 20 m in height and 44 cm d.b.h. Inga paterno has pinnately compound leaves with four to five elongated and entire leaflets (Guzmin 1980). Leaves are copper-red and soft when young,...

Updated generalized biomass equations for North American tree species

Treesearch

David C. Chojnacky; Linda S. Heath; Jennifer C. Jenkins

2014-01-01

Historically, tree biomass at large scales has been estimated by applying dimensional analysis techniques and field measurements such as diameter at breast height (dbh) in allometric regression equations. Equations often have been developed using differing methods and applied only to certain species or isolated areas. We previously had compiled and combined (in meta-...

The longevity of large pine snags in eastern Texas

Treesearch

Richard N. Conner; Daniel Saenz

2005-01-01

Habitat for cavity-nesting wildlife is closely tied to the availability of standing dead trees (snags). Large snags (>40 cm dbh) are particularly important because they provide cavity- excavation substrate for both large and small cavity excavators. Historically in the southern United States, common belief has been that the utility of pine (Pinus...

Diameter Measurement in Bald Cypress

Treesearch

Bernard R. Parresol; James E. Hotvedt

1990-01-01

The usual practice of measuring diameter at 4.5 feet ( 1.3 m) or Dbh is meaningless in wetland tree species such as bald cypress (Taxodium distichum (L.) Rich.), due to the presence of fluted basal swells. Since buttress dimensions usually have no consistent relation to volume or form in the tree, the current practice among...

Tree diameter at breast height in relation to stump diameter by species group

Treesearch

Arthur G. Horn; Richard C. Keller

1957-01-01

A stump tally is one method of determining the volume of timber previously removed from an area in a logging operation. To estimate volume of standing timber from stumps, foresters must first know the relationship between stump diameters and tree diameters at breast height (d.b.h.).

Individual tree diameter, height, and volume functions for longleaf pine

Treesearch

Carlos A. Gonzalez-Benecke; Salvador A. Gezan; Timothy A. Martin; Wendell P. Cropper; Lisa J. Samuelson; Daniel J. Leduc

2014-01-01

Currently, little information is available to estimate individual tree attributes for longleaf pine (Pinus palustris Mill.), an important tree species of the southeastern United States. The majority of available models are local, relying on stem diameter outside bark at breast height (dbh, cm) and not including stand-level parameters. We developed...

Performance of Loblolly Pine Seed Sources in Argentina

Treesearch

Timothy La Farge; Floyd E. Bridgwater; Mirta N. Baez

1999-01-01

Four test series of loblolly pine (Pinus taeda L.) were evaluated to determine the performance in northeastern Argentina of seed sources from three breeding populations in the southeastern United States. Three half-sib progeny tests of seed sources from Florida and Louisiana demonstrated strong genetic gains for height, dbh, and volume growth....

Regeneration patterns of northern white cedar, an old-growth forest dominant

USGS Publications Warehouse

Scott, Michael L.; Murphy, Peter G.

1987-01-01

Regeneration of Thuja occidentalis L. was examined in an old-growth dune forest on South Manitou Island, Michigan. To estimate the current status of cedar regeneration, we determined size structure of seedlings and stems and analyzed present patterns of establishment and persistence relative to substrate type. There has been a shift in the pattern of cedar establishment from soil to log substrates. While 97% of all stems ≥15 cm dbh are associated with a soil substrate, 81% of stems ≥2.5cm-25 cm tall. There was no significant relationship between the state of log decay and the density of seedlings >25 cm in height, indicating that long-term survival is not dependent on the degree of log decomposition. However, survival on logs is associated with canopy openings. Seedlings >25 cm tall were associated with gaps, and 78% of cedar stems (≥2.5 cm dbh) on logs were associated with a single windthrow gap. Thus, current cedar regeneration in this old-growth forest depends on logs and the canopy openings associated with them.

Development and analysis of SRIC harvesting systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stokes, B.J.; Hartsough, B.R.

1993-12-31

This paper reviews several machine combinations for harvesting short-rotation, intensive-culture (SRIC) plantations. Productivity and cost information for individual machines was obtained from published sources. Three felling and skidding systems were analyzed for two stands, a 7.6-cm (3-in) average d.b.h. sycamore and a 15.2-cm (6-in) average d.b.h. eucalyptus. The analyses assumed that whole trees were chipped at roadside. Costs and production were summarized for each system. The systems were: (1) Continuous-travel feller-buncher, skidder, and chipper; (2) 3-wheel feller-buncher, skidder, and chipper; (3) chainsaw, skidder, and chipper. In the 7.6-cm stand, system productivities were 9.9, 7.3, and 7.5 BDLT/SMH, and costs weremore » $20.9, $20.8, and $18.0 per BDLT for the three systems, respectively. System production rates for the 15.2-cm stand were 24.3, 10.2, and 12.5 BDLT/SMH, and costs were $8.7, $10.9, and $13.2 for systems 1, 2 and 3, respectively.« less

A feasibility study on the measurement of tree trunks in forests using multi-scale vertical images

NASA Astrophysics Data System (ADS)

Berveglieri, A.; Oliveira, R. O.; Tommaselli, A. M. G.

2014-06-01

The determination of the Diameter at Breast Height (DBH) is an important variable that contributes to several studies on forest, e.g., environmental monitoring, tree growth, volume of wood, and biomass estimation. This paper presents a preliminary technique for the measurement of tree trunks using terrestrial images collected with a panoramic camera in nadir view. A multi-scale model is generated with these images. Homologue points on the trunk surface are measured over the images and their ground coordinates are determined by intersection of rays. The resulting XY coordinates of each trunk, defining an arc shape, can be used as observations in a circle fitting by least squares. Then, the DBH of each trunk is calculated using an estimated radius. Experiments were performed in two urban forest areas to assess the approach. In comparison with direct measurements on the trunks taken with a measuring tape, the discrepancies presented a Root Mean Square Error (RMSE) of 1.8 cm with a standard deviation of 0.7 cm. These results demonstrate compatibility with manual measurements and confirm the feasibility of the proposed technique.

Treatment of an old-growth stand and its effects on birds, ants, and large woody debris: A case study. Forest Service general technical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bull, E.L.; Torgersen, T.R.; Blumton, A.K.

1995-09-01

An old-structure stand with large amounts of tree mortality was treated to accelerate regeneration and reduce fuel loads but still maintain its function as old growth for selected bird species. The smll-diameter (less than 15 inches in diameter at breast height (d.b.h.)), dead trees were removed as was some of the down wood less than 15 inches in diameter at the large end. All live trees of any size and all dead trees equal to or greater than 15 inches d.b.h. were retained. Vaux`s swifts (Chaetura vauxi) and pileated woodpeckers (Dryocopus pileatus) continued to use the stand after harvest formore » nesting and roosting. Brown-headed cowbirds (molothrus ater) were more than twice as common in the treated stand as in an adjacent unlogged, control stand. In a comparison before and after harvest in the treated stand, the number of logs increased, the number of logs with ants increased, but the percentage of logs with ants decreased.« less

A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases

PubMed Central

2011-01-01

Y-family DNA polymerases are characterized by low-fidelity synthesis on undamaged DNA and ability to catalyze translesion synthesis over the damaged DNA. Their translocation along the DNA template is an important event during processive DNA synthesis. In this work we present a Brownian ratchet model for this translocation, where the directed translocation is rectified by the nucleotide binding to the polymerase. Using the model, different features of the available structures for Dpo4, Dbh and polymerase ι in binary and ternary forms can be easily explained. Other dynamic properties of the Y-family polymerases such as the fast translocation event upon dNTP binding for Dpo4 and the considerable variations of the processivity among the polymerases can also be well explained by using the model. In addition, some predicted results of the DNA synthesis rate versus the external force acting on Dpo4 and Dbh polymerases are presented. Moreover, we compare the effect of the external force on the DNA synthesis rate of the Y-family polymerase with that of the replicative DNA polymerase. PMID:21699732

Neurochemical markers of human fungiform papillae and taste buds.

PubMed

Astbäck, J; Arvidson, K; Johansson, O

1995-11-10

The presence of distribution of several neurochemical markers in human fungiform papillae and taste buds were investigated by the immunohistochemical technique. The gustatory cells of the taste buds are in synaptic contact with sensory nerve endings, and considering the taste buds strictly as specialized sensory organs, the amounts and distribution of some of the neurochemical markers were different to what we expected. For example, few structures showed immunoreactivity to the tachykinins substance P (SP), calcitonin gene-related peptide (CGRP), and neurokinin A (NKA) also for the peptides vasoactive intestinal polypeptide (VIP), neuropeptide tyrosine (NPY) and galanin, low amounts of immunoreactivity occurred. On the other hand, using antibodies to protein gene product 9.5 (PGP 9.5), protein S-100, and glutamate, numerous nerve fibres and/or immunoreactive cells were found in the fungiform papillae, in the epithelium, in the connective tissue and around blood vessels, as well as in or near taste buds. Incubation with the antibodies against somatostatin, enkephalin, bombesin, peptide histidine isoleucine amide (PHI), cholecystokinin (CCK)/gastrin and dopamine-beta-hydroxylase (DBH) was negative for the fungiform papillae. In conclusion, the present study has shown several immunoreactive structures using antibodies against certain neurochemical markers. Further investigations will hopefully correlate these morphological findings with functional taste perception data. Future studies of patients with taste disorders or other pathological changes correlated with taste and tongue will also be of utmost importance.

Gene expression variability in human hepatic drug metabolizing enzymes and transporters.

PubMed

Yang, Lun; Price, Elvin T; Chang, Ching-Wei; Li, Yan; Huang, Ying; Guo, Li-Wu; Guo, Yongli; Kaput, Jim; Shi, Leming; Ning, Baitang

2013-01-01

Interindividual variability in the expression of drug-metabolizing enzymes and transporters (DMETs) in human liver may contribute to interindividual differences in drug efficacy and adverse reactions. Published studies that analyzed variability in the expression of DMET genes were limited by sample sizes and the number of genes profiled. We systematically analyzed the expression of 374 DMETs from a microarray data set consisting of gene expression profiles derived from 427 human liver samples. The standard deviation of interindividual expression for DMET genes was much higher than that for non-DMET genes. The 20 DMET genes with the largest variability in the expression provided examples of the interindividual variation. Gene expression data were also analyzed using network analysis methods, which delineates the similarities of biological functionalities and regulation mechanisms for these highly variable DMET genes. Expression variability of human hepatic DMET genes may affect drug-gene interactions and disease susceptibility, with concomitant clinical implications.

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data

PubMed Central

Bikel, Shirley; Jacobo-Albavera, Leonor; Sánchez-Muñoz, Fausto; Cornejo-Granados, Fernanda; Canizales-Quinteros, Samuel; Soberón, Xavier; Sotelo-Mundo, Rogerio R.; del Río-Navarro, Blanca E.; Mendoza-Vargas, Alfredo; Sánchez, Filiberto

2017-01-01

Background In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays. Methods We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6–10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR). Results From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment. Discussion Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments. PMID:29230367

Stand structural diversity rather than species diversity enhances aboveground carbon storage in secondary subtropical forests in Eastern China

NASA Astrophysics Data System (ADS)

Ali, Arshad; Yan, En-Rong; Chen, Han Y. H.; Chang, Scott X.; Zhao, Yan-Tao; Yang, Xiao-Dong; Xu, Ming-Shan

2016-08-01

Stand structural diversity, typically characterized by variances in tree diameter at breast height (DBH) and total height, plays a critical role in influencing aboveground carbon (C) storage. However, few studies have considered the multivariate relationships of aboveground C storage with stand age, stand structural diversity, and species diversity in natural forests. In this study, aboveground C storage, stand age, tree species, DBH and height diversity indices, were determined across 80 subtropical forest plots in Eastern China. We employed structural equation modelling (SEM) to test for the direct and indirect effects of stand structural diversity, species diversity, and stand age on aboveground C storage. The three final SEMs with different directions for the path between species diversity and stand structural diversity had a similar goodness of fit to the data. They accounted for 82 % of the variation in aboveground C storage, 55-59 % of the variation in stand structural diversity, and 0.1 to 9 % of the variation in species diversity. Stand age demonstrated strong positive total effects, including a positive direct effect (β = 0.41), and a positive indirect effect via stand structural diversity (β = 0.41) on aboveground C storage. Stand structural diversity had a positive direct effect on aboveground C storage (β = 0.56), whereas there was little total effect of species diversity as it had a negative direct association with, but had a positive indirect effect, via stand structural diversity, on aboveground C storage. The negligible total effect of species diversity on aboveground C storage in the forests under study may have been attributable to competitive exclusion with high aboveground biomass, or a historical logging preference for productive species. Our analyses suggested that stand structural diversity was a major determinant for variations in aboveground C storage in the secondary subtropical forests in Eastern China. Hence, maintaining tree DBH and height diversity through silvicultural operations might constitute an effective approach for enhancing aboveground C storage in these forests.

PVC--as flooring material--and its association with incident asthma in a Swedish child cohort study.

PubMed

Larsson, M; Hägerhed-Engman, L; Kolarik, B; James, P; Lundin, F; Janson, S; Sundell, J; Bornehag, C G

2010-12-01

The Dampness in Buildings and Health study (DBH) started in the year 2000 in Värmland, Sweden, with a baseline questionnaire sent to all children (n = 14,077) aged 1-6. Five years later, a follow-up questionnaire was sent to the children who were 1-3 years at baseline. A total of 4779 children participated in both the baseline and the follow-up studies and constitute the study population in this cohort study. The aim of this study was to examine the association between exposure to PVC-flooring in the child's and parent's bedroom in homes of children aged 1-3 and the incidence of asthma, rhinitis, and eczema during the following 5-year period. Adjusted analyses showed that the incidence of asthma among children was associated with PVC-flooring in the child's bedroom (AOR 1.52; 95% CI 0.99-2.35) and in the parent's bedroom (1.46; 0.96-2.23). The found risks were on borderline of significance and should therefore be interpreted with caution. There was further a positive relationship between the number of rooms with PVC-flooring and the cumulative incidence of asthma. PVC-flooring was found to be a stronger risk factor for incident asthma in multifamily homes when compared with single-family houses and in smoking families compared with non-smoking families and in women. These longitudinal data from the DBH study found an association between the presence of PVC-flooring in the home and incident asthma in children. However, earlier results from the DBH study have shown that PVC-flooring is one important source for phthalates in indoor dust, and exposure to such phthalates was found to be associated with asthma and allergy among children. This emphasizes the need for prospective studies that focus on the importance of prenatal and neonatal exposure to phthalates in the development of asthma and allergy in children. © 2010 John Wiley & Sons A/S.

Effects of Harvesting Intensity and Herbivory by White-tailed Deer on Vegetation and Nutrient Uptake in a Northern Hardwood Forest

NASA Astrophysics Data System (ADS)

Yorks, T. E.; Leopold, D. J.; Raynal, D. J.; Murdoch, P. S.; Burns, D. A.

2003-12-01

We quantified the response of vegetation and nutrient uptake in a northern hardwood forest in southeastern New York for three to four years after three intensities of harvesting: clearcutting, heavy timber stand improvement (TSI), light TSI (97, 29, and 10% basal area reductions, respectively). We also quantified effects of white-tailed deer (Odocoileus virginianus) herbivory on nutrient retention by vegetation. Total biomass and nutrient accumulation in vegetation was higher after TSI than clearcutting in the first two years but was highest in the fenced clearcut in subsequent years, indicating that TSI or partial harvesting is a viable management tool for harvesting timber while consistently maintaining high rates of nutrient retention. After clearcutting, biomass and nutrient retention were initially dominated by woody stems <1.4 m tall and herbaceous vegetation, but saplings 0.1-5.0 cm DBH became the most important contributors to biomass and nutrient accumulation within four years. However, after both intensities of TSI, trees >5.0 cm DBH continued to account for most biomass and nutrient accumulation whereas understory vegetation accumulated little biomass or nutrients. Heavy TSI resulted in increased regeneration of only two tree species (Acer pensylvanicum, Fagus grandifolia), but clearcutting allowed these two species, mature forest species (A. saccharum, Betula alleghaniensis), and the early successional Prunus pensylvanica to regenerate. Several early successional shrub and herbaceous species were also important to nutrient retention after clearcutting, including Polygonum cilinode, Rubus spp., and Sambucus racemosa. Herbivory by white-tailed deer dramatically reduced biomass and nutrient accumulation by woody stems <5 cm DBH after clearcutting (5.5 vs. 0.7 Mg biomass/ha and 30.4 vs. 6.3 kg N/ha on fenced and unfenced clearcut sites, respectively, after four years), indicating the important influence this herbivore can have on nutrient retention in recently disturbed forests.

Genome-wide association study of smoking behaviors in COPD patients

PubMed Central

Siedlinski, Mateusz; Cho, Michael H.; Bakke, Per; Gulsvik, Amund; Lomas, David A.; Anderson, Wayne; Kong, Xiangyang; Rennard, Stephen I.; Beaty, Terri H.; Hokanson, John E.; Crapo, James D.; Silverman, Edwin K.

2012-01-01

Background Cigarette smoking is a major risk factor for COPD and COPD severity. Previous genome-wide association studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs) associated with the number of cigarettes smoked per day (CPD) and a Dopamine Beta-Hydroxylase (DBH) locus associated with smoking cessation in multiple populations. Objective To identify SNPs associated with lifetime average and current CPD, age at smoking initiation, and smoking cessation in COPD subjects. Methods GWAS were conducted in 4 independent cohorts encompassing 3,441 ever-smoking COPD subjects (GOLD stage II or higher). Untyped SNPs were imputed using HapMap (phase II) panel. Results from all cohorts were meta-analyzed. Results Several SNPs near the HLA region on chromosome 6p21 and in an intergenic region on chromosome 2q21 showed associations with age at smoking initiation, both with the lowest p=2×10−7. No SNPs were associated with lifetime average CPD, current CPD or smoking cessation with p<10−6. Nominally significant associations with candidate SNPs within alpha-nicotinic acetylcholine receptors 3/5 (CHRNA3/CHRNA5; e.g. p=0.00011 for SNP rs1051730) and Cytochrome P450 2A6 (CYP2A6; e.g. p=2.78×10−5 for a nonsynonymous SNP rs1801272) regions were observed for lifetime average CPD, however only CYP2A6 showed evidence of significant association with current CPD. A candidate SNP (rs3025343) in the DBH was significantly (p=0.015) associated with smoking cessation. Conclusion We identified two candidate regions associated with age at smoking initiation in COPD subjects. Associations of CHRNA3/CHRNA5 and CYP2A6 loci with CPD and DBH with smoking cessation are also likely of importance in the smoking behaviors of COPD patients. PMID:21685187

Determinants of Tree Assemblage Composition at the Mesoscale within a Subtropical Eucalypt Forest

PubMed Central

Hero, Jean-Marc; Butler, Sarah A.; Lollback, Gregory W.; Castley, James G.

2014-01-01

A variety of environmental processes, including topography, edaphic and disturbance factors can influence vegetation composition. The relative influence of these patterns has been known to vary with scale, however, few studies have focused on environmental drivers of composition at the mesoscale. This study examined the relative importance of topography, catchment flow and soil in influencing tree assemblages in Karawatha Forest Park; a South-East Queensland subtropical eucalypt forest embedded in an urban matrix that is part of the Terrestrial Ecosystem Research Network South-East Queensland Peri-urban SuperSite. Thirty-three LTER plots were surveyed at the mesoscale (909 ha), where all woody stems ≥1.3 m high rooted within plots were sampled. Vegetation was divided into three cohorts: small (≥1–10 cm DBH), intermediate (≥10–30 cm DBH), and large (≥30 cm DBH). Plot slope, aspect, elevation, catchment area and location and soil chemistry and structure were also measured. Ordinations and smooth surface modelling were used to determine drivers of vegetation assemblage in each cohort. Vegetation composition was highly variable among plots at the mesoscale (plots systematically placed at 500 m intervals). Elevation was strongly related to woody vegetation composition across all cohorts (R2: 0.69–0.75). Other topographic variables that explained a substantial amount of variation in composition were catchment area (R2: 0.43–0.45) and slope (R2: 0.23–0.61). Soil chemistry (R2: 0.09–0.75) was also associated with woody vegetation composition. While species composition differed substantially between cohorts, the environmental variables explaining composition did not. These results demonstrate the overriding importance of elevation and other topographic features in discriminating tree assemblage patterns irrespective of tree size. The importance of soil characteristics to tree assemblages was also influenced by topography, where ridge top sites were typically drier and had lower soil nutrient levels than riparian areas. PMID:25501866

Micellar induced regioselectivity in the two-step consecutive reaction of SO3(2-) with Br-(CH2CH2)n-Br (n=2-5).

PubMed

Currie, Fredrik; Jarvoll, Patrik; Holmberg, Krister; Romsted, Laurence S; Gunaseelan, Krishnan

2007-08-15

High field (800 MHz) (1)H NMR was used to monitor the two-step consecutive reaction of excess SO(3)(2-) with symmetrical bifunctional alpha,omega-dibromoalkanes with butane (DBB), hexane (DBH), octane (DBO), and decane (DBD) chains in CTAB micelles at 25 degrees C. The first-order rate constant for the first substitution step for DBB and DBH is about 5 times faster than for the second, but the kinetics for DBO and DBD were not cleanly first-order. After 40 min, the solution contained about 80% of the intermediate bromoalkanesulfonate from DBB and DBH and the remainder is alkanedisulfonate and unreacted starting material. The same reactions were carried out in homogeneous MeOH/D(2)O solutions at 50 degrees C. The rate constants for all four alpha,omega-dibromoalkanes were first-order throughout the time course of the reaction and the same within +/-10%. However, because micellar solutions are organized on the nanoscale and bring together lipophilic and hydrophilic reactants into a small reaction volume at the micellar interface, they speed this substitution reaction considerably compared to reaction in MeOH/D(2)O. The CTAB micelles also induce a significant regioselectivity in product formation by speeding the first step of the consecutive reaction more than the second. The results are consistent with the bromoalkanesulfonate intermediates having a radial orientation within the micelles with the -CH(2)SO(3)(-) group in the interfacial region and the -CH(2)Br group directed into the micellar core such that the concentration of -CH(2)Br groups in the reactive zone, i.e., the micellar interface, is significantly reduced. These results provide the first example of self-assembled surfactant system altering the relative rates of the reaction steps of a consecutive reaction and, in doing so, enhancing monosubstitution of a symmetrically disubstituted species.

Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior.

PubMed

Schrader, Lukas; Helanterä, Heikki; Oettler, Jan

2017-03-01

Plastic gene expression underlies phenotypic plasticity and plastically expressed genes evolve under different selection regimes compared with ubiquitously expressed genes. Social insects are well-suited models to elucidate the evolutionary dynamics of plastic genes for their genetically and environmentally induced discrete polymorphisms. Here, we study the evolution of plastically expressed genes in the ant Cardiocondyla obscurior-a species that produces two discrete male morphs in addition to the typical female polymorphism of workers and queens. Based on individual-level gene expression data from 28 early third instar larvae, we test whether the same evolutionary dynamics that pertain to plastically expressed genes in adults also pertain to genes with plastic expression during development. In order to quantify plasticity of gene expression over multiple contrasts, we develop a novel geometric measure. For genes expressed during development, we show that plasticity of expression is positively correlated with evolutionary rates. We furthermore find a strong correlation between expression plasticity and expression variation within morphs, suggesting a close link between active and passive plasticity of gene expression. Our results support the notion of relaxed selection and neutral processes as important drivers in the evolution of adaptive plasticity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Dopamine-Secreting Paraganglioma in the Retroperitoneum.

PubMed

Matsuda, Yusuke; Kimura, Noriko; Yoshimoto, Takanobu; Sekiguchi, Yoshihiro; Tomoishi, Junzo; Kasahara, Ichiro; Hara, Yoshihito; Ogawa, Yoshihiro

2017-03-01

Pheochromocytomas and paragangliomas, which exclusively produce dopamine, are very rare. Herein, we report for the first time a Japanese case of an exclusively dopamine-producing paraganglioma accompanied by detailed immunohistochemical analyses. A 70-year-old Japanese woman was referred to our hospital for functional examination of her left retroperitoneal mass. Her adrenal functions were normal, except for excessive dopamine secretion. After the tumorectomy, her dopamine level normalized. The histopathological diagnosis of the tumor was paraganglioma; this was confirmed by positive immunostaining of chromogranin A (CgA), tyrosine hydroxylase (TH), dopamine β-hydroxylase (DBH), and succinate dehydrogenase gene subunit B (SDHB). However, the immunostaining of CgA in the tumor cells showed peculiar dot-like staining located corresponding to Golgi complex in the perinuclear area, rather than the diffuse cytoplasmic staining usually observed in epinephrine- or norepinephrine-producing functional pheochromocytomas and paragangliomas. The immunohistochemical results suggested that the tumor cells had sparse neuroendocrine granules in the cytoplasm, resulting in inhibition of catecholamine synthesis from dopamine to norepinephrine in neurosecretory granules. This may be the mechanism responsible for exclusive dopamine secretion in the present case.

Analysis of multiplex gene expression maps obtained by voxelation.

PubMed

An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

2009-04-29

Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum. The experimental results confirm the hypothesis that genes with similar gene expression maps might have similar gene functions. The voxelation data takes into account the location information of gene expression level in mouse brain, which is novel in related research. The proposed approach can potentially be used to predict gene functions and provide helpful suggestions to biologists.

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.

PubMed

Li, Lin; Briskine, Roman; Schaefer, Robert; Schnable, Patrick S; Myers, Chad L; Flagel, Lex E; Springer, Nathan M; Muehlbauer, Gary J

2016-11-04

Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant subgenome. However, the landscape of co-expression network divergence of duplicate genes in maize is still largely uncharacterized. To address the consequence of gene duplication on co-expression network divergence, we developed a gene co-expression network from RNA-seq data derived from 64 different tissues/stages of the maize reference inbred-B73. WGD, tandem and inserted gene duplications exhibited distinct regulatory divergence. Inserted duplicate genes were more likely to be singletons in the co-expression networks, while WGD duplicate genes were likely to be co-expressed with other genes. Tandem duplicate genes were enriched in the co-expression pattern where co-expressed genes were nearly identical for the duplicates in the network. Older gene duplications exhibit more extensive co-expression variation than younger duplications. Overall, non-syntenic genes primarily from inserted duplications show more co-expression divergence. Also, such enlarged co-expression divergence is significantly related to duplication age. Moreover, subgenome dominance was not observed in the co-expression networks - maize1 and maize2 exhibit similar levels of intra subgenome correlations. Intriguingly, the level of inter subgenome co-expression was similar to the level of intra subgenome correlations, and genes from specific subgenomes were not likely to be the enriched in co-expression network modules and the hub genes were not predominantly from any specific subgenomes in maize. Our work provides a comprehensive analysis of maize co-expression network divergence for three different types of gene duplications and identifies potential relationships between duplication types, duplication ages and co-expression consequences.

Tissue Non-Specific Genes and Pathways Associated with Diabetes: An Expression Meta-Analysis.

PubMed

Mei, Hao; Li, Lianna; Liu, Shijian; Jiang, Fan; Griswold, Michael; Mosley, Thomas

2017-01-21

We performed expression studies to identify tissue non-specific genes and pathways of diabetes by meta-analysis. We searched curated datasets of the Gene Expression Omnibus (GEO) database and identified 13 and five expression studies of diabetes and insulin responses at various tissues, respectively. We tested differential gene expression by empirical Bayes-based linear method and investigated gene set expression association by knowledge-based enrichment analysis. Meta-analysis by different methods was applied to identify tissue non-specific genes and gene sets. We also proposed pathway mapping analysis to infer functions of the identified gene sets, and correlation and independent analysis to evaluate expression association profile of genes and gene sets between studies and tissues. Our analysis showed that PGRMC1 and HADH genes were significant over diabetes studies, while IRS1 and MPST genes were significant over insulin response studies, and joint analysis showed that HADH and MPST genes were significant over all combined data sets. The pathway analysis identified six significant gene sets over all studies. The KEGG pathway mapping indicated that the significant gene sets are related to diabetes pathogenesis. The results also presented that 12.8% and 59.0% pairwise studies had significantly correlated expression association for genes and gene sets, respectively; moreover, 12.8% pairwise studies had independent expression association for genes, but no studies were observed significantly different for expression association of gene sets. Our analysis indicated that there are both tissue specific and non-specific genes and pathways associated with diabetes pathogenesis. Compared to the gene expression, pathway association tends to be tissue non-specific, and a common pathway influencing diabetes development is activated through different genes at different tissues.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

PubMed

Hurst, Laurence D; Ghanbarian, Avazeh T; Forrest, Alistair R R; Huminiecki, Lukasz

2015-12-01

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

PubMed Central

Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R. R.; Huminiecki, Lukasz

2015-01-01

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution. PMID:26685068

Validating internal controls for quantitative plant gene expression studies.

PubMed

Brunner, Amy M; Yakovlev, Igor A; Strauss, Steven H

2004-08-18

Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression levels for reference genes are adequately consistent among the samples used, nor compare alternative genes to assess which are most reliable for the experimental conditions analyzed. Using real-time RT-PCR to study the expression of 10 poplar (genus Populus) housekeeping genes, we demonstrate a simple method for determining the degree of stability of gene expression over a set of experimental conditions. Based on a traditional method for analyzing the stability of varieties in plant breeding, it defines measures of gene expression stability from analysis of variance (ANOVA) and linear regression. We found that the potential internal control genes differed widely in their expression stability over the different tissues, developmental stages and environmental conditions studied. Our results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression. The method we demonstrated facilitates statistical and graphical evaluation of gene expression stability. Selection of the best reference gene for a given set of experimental conditions should enable detection of biologically significant changes in gene expression that are too small to be revealed by less precise methods, or when highly variable reference genes are unknowingly used in real-time RT-PCR experiments.

General statistics of stochastic process of gene expression in eukaryotic cells.

PubMed Central

Kuznetsov, V A; Knott, G D; Bonner, R F

2002-01-01

Thousands of genes are expressed at such very low levels (< or =1 copy per cell) that global gene expression analysis of rarer transcripts remains problematic. Ambiguity in identification of rarer transcripts creates considerable uncertainty in fundamental questions such as the total number of genes expressed in an organism and the biological significance of rarer transcripts. Knowing the distribution of the true number of genes expressed at each level and the corresponding gene expression level probability function (GELPF) could help resolve these uncertainties. We found that all observed large-scale gene expression data sets in yeast, mouse, and human cells follow a Pareto-like distribution model skewed by many low-abundance transcripts. A novel stochastic model of the gene expression process predicts the universality of the GELPF both across different cell types within a multicellular organism and across different organisms. This model allows us to predict the frequency distribution of all gene expression levels within a single cell and to estimate the number of expressed genes in a single cell and in a population of cells. A random "basal" transcription mechanism for protein-coding genes in all or almost all eukaryotic cell types is predicted. This fundamental mechanism might enhance the expression of rarely expressed genes and, thus, provide a basic level of phenotypic diversity, adaptability, and random monoallelic expression in cell populations. PMID:12136033

The changes of gene expression profiling between segmental vitiligo, generalized vitiligo and healthy individual.

PubMed

Wang, Ping; Li, Yong; Nie, Huiqiong; Zhang, Xiaoyan; Shao, Qiongyan; Hou, Xiuli; Xu, Wen; Hong, Weisong; Xu, Aie

2016-10-01

Vitiligo is a common acquired depigmentation skin disease characterized by loss or dysfunction of melanocytes within the skin lesion, but its pathologenesis is far from lucid. The gene expression profiling of segmental vitiligo (SV) and generalized vitiligo (GV) need further investigation. To better understanding the common and distinct factors, especially in the view of gene expression profile, which were involved in the diseases development and maintenance of segmental vitiligo (SV) and generalized vitiligo (GV). Peripheral bloods were collected from SV, GV and healthy individual (HI), followed by leukocytes separation and total RNA extraction. The high-throughput whole genome expression microarrays were used to assay the gene expression profiles between HI, SV and GV. Bioinformatics tools were employed to annotated the biological function of differently expressed genes. Quantitative PCR assay was used to validate the gene expression of array. Compared to HI, 239 over-expressed genes and 175 down-expressed genes detected in SV, 688 over-expressed genes and 560 down-expressed genes were found in GV, following the criteria of log2 (fold change)≥0.585 and P value<0.05. In these differently expressed genes, 60 over-expressed genes and 60 down-expressed genes had similar tendency in SV and GV. Compared to SV, 223 genes were up regulated and 129 genes were down regulated in GV. In the SV with HI as control, the differently expressed genes were mainly involved in the adaptive immune response, cytokine-cytokine receptor interaction, chemokine signaling, focal adhesion and sphingolipid metabolism. The differently expressed genes between GV and HI were mainly involved in the innate immune, autophagy, apoptosis, melanocyte biology, ubiquitin mediated proteolysis and tyrosine metabolism, which was different from SV. While the differently expressed genes between SV and GV were mainly involved in the metabolism pathway of purine, pyrimidine, glycolysis and sphingolipid. Above results suggested that they not only shared part bio-process and signal pathway, but more important, they utilized different biological mechanism in their pathogenesis and maintenance. Our results provide a comprehensive view on the gene expression profiling change between SV and GV especially in the side of leukocytes, and may facilitate the future study on their molecular mechanism and theraputic targets. Copyright © 2016 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights reserved.

Identification of reference genes in human myelomonocytic cells for gene expression studies in altered gravity.

PubMed

Thiel, Cora S; Hauschild, Swantje; Tauber, Svantje; Paulsen, Katrin; Raig, Christiane; Raem, Arnold; Biskup, Josefine; Gutewort, Annett; Hürlimann, Eva; Unverdorben, Felix; Buttron, Isabell; Lauber, Beatrice; Philpot, Claudia; Lier, Hartwin; Engelmann, Frank; Layer, Liliana E; Ullrich, Oliver

2015-01-01

Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes ("housekeeping genes") are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity.

Adaptation of Musca domestica L. Field Population to Laboratory Breeding Causes Transcriptional Alterations

PubMed Central

Højland, Dorte H.; Jensen, Karl-Martin Vagn; Kristensen, Michael

2014-01-01

Background The housefly, Musca domestica, has developed resistance to most insecticides applied for its control. Expression of genes coding for detoxification enzymes play a role in the response of the housefly when encountered by a xenobiotic. The highest level of constitutive gene expression of nine P450 genes was previously found in a newly-collected susceptible field population in comparison to three insecticide-resistant laboratory strains and a laboratory reference strain. Results We compared gene expression of five P450s by qPCR as well as global gene expression by RNAseq in the newly-acquired field population (845b) in generation F1, F13 and F29 to test how gene expression changes following laboratory adaption. Four (CYP6A1, CYP6A36, CYP6D3, CYP6G4) of five investigated P450 genes adapted to breeding by decreasing expression. CYP6D1 showed higher female expression in F29 than in F1. For males, about half of the genes accessed in the global gene expression were up-regulated in F13 and F29 in comparison with the F1 population. In females, 60% of the genes were up-regulated in F13 in comparison with F1, while 33% were up-regulated in F29. Forty potential P450 genes were identified. In most cases, P450 gene expression was decreased in F13 flies in comparison with F1. Gene expression then increased from F13 to F29 in males and decreased further in females. Conclusion The global gene expression changes massively during adaptation to laboratory breeding. In general, global expression decreased as a result of laboratory adaption in males, while female expression was not unidirectional. Expression of P450 genes was in general down-regulated as a result of laboratory adaption. Expression of hexamerin, coding for a storage protein was increased, while gene expression of genes coding for amylases decreased. This suggests a major impact of the surrounding environment on gene response to xenobiotics and genetic composition of housefly strains. PMID:24489682

Sapwood area as an estimator of leaf area and foliar weight in cherrybark oak and green ash

Treesearch

James S. Meadows; John D. Hodges

2002-01-01

The relationships between foliar weight/leaf area and four stem dimensions (d.b.h., total stem cross-sectional area, total sapwood area, and current sapwood area at breast height) were investigated in two important bottomland tree species of the Southern United States, cherrybark oak (Quercus falcata var. pagodifolia ...

Response of sapling stands to cultural treatments

Treesearch

H. Clay Smith

1989-01-01

The main reasons for precommercial cultural practices in sapling stands (trees less than 5 inches d.b.h.) are to increase growth of residual trees, increase stand value, and improve or maintain species composition. On good sites (northern red oak site index 70 and above), treating sapling stands may be justified by increased diameter growth of high value species. On...

Comparisons of two methods of harvesting biomass for energy

Treesearch

W.F. Watson; B.J. Stokes; I.W. Savelle

1986-01-01

Two harvesting methods for utilization of understory biomass were tested against a conventional harvesting method to determine relative costs. The conventional harvesting method tested removed all pine 6 inches diameter at breast height (DBH) and larger and hardwood sawlogs as tree length logs. The two intensive harvesting methods were a one-pass and a two-pass method...

Comparisons of modeled height predictions to ocular height estimates

Treesearch

W.A. Bechtold; S.J. Zarnoch; W.G. Burkman

1998-01-01

Equations used by USDA Forest Service Forest Inventory and Analysis projects to predict individual tree heights on the basis of species and d.b.h. were improved by the addition of mean overstory height. However, ocular estimates of total height by field crews were more accurate than the statistically improved models, especially for hardwood species. Height predictions...

Populus tremuloides mortality near the southwestern edge of its range

Treesearch

Thomas J. Zegler; Margaret M. Moore; Mary L. Fairweather; Kathryn B. Ireland; Peter Z. Fule

2012-01-01

Mortality and crown dieback of quaking aspen (Populus tremuloides) were extensive on the Williams Ranger District, Kaibab National Forest in northern Arizona. We collected data from a random sample of 48 aspen sites to determine the relationship of predisposing site and stand factors and contributing agents to ramet mortality. Mortality of overstory (P10.1 cm DBH)...

Response of timber growth and avian communities to quality vegetation management in mid-rotation crp pine plantations

Treesearch

Brandon G. Sladek; Ian A. Munn; L. Wes Burder; Scott D. Roberts

2006-01-01

Provisions of the 2002 Farm Bill gave Conservation Reserve Program (CRP) participants greater flexibility to implement mid-contract management activities that encourage wildlife habitat improvement and timber production. Quality Vegetation Management (QVM) is one such technique that utilizes the selective herbicide Imazapyr and prescribed burning. Timber growth (d.b.h...

Age structure and growth of California black oak (Quercus kelloggii) in the central Sierra Nevada, California

Treesearch

Barrett A. Garrison; Christopher D. otahal; Matthew L. Triggs

2002-01-01

Age structure and growth of California black oak (Quercus kelloggii) was determined from tagged trees at four 26.1-acre study stands in Placer County, California. Stands were dominated by large diameter (>20 inch dbh) California black oak and ponderosa pine (Pinus ponderosa). Randomly selected trees were tagged in June-August...

Effects of seed source origin on bark thickness of Douglas-fir (Pseudotsuga menziesii) growing in southwestern Germany

Treesearch

Ulrich Kohnle; Sebastian Hein; Frank C. Sorensen; Aaron R. Weiskittel

2012-01-01

Provenance-specific variation in bark thickness in Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) is important for accurate volume calculations and might carry ecological implications as well. To investigate variation, diameter at breast height (dbh) and double bark thickness (dbt) were measured in 10 experiments in southwestern Germany (16...

The longevity of large pine snags in eastern Texas

Treesearch

Richard N. Conner; Daniel Saenz

2005-01-01

Habitat for cavity-nesting wildlife is closely tied to the availability of standing dead trees (snags). Large snags (>40 cm dbh) are particularly important because they provide cavity- excavation substrate for both large and small cavity excavators. Historically in the southern United States, common belief has been that the utility of pine (Pinus spp.) snags for...

Thinning stagnated ponderosa and Jeffrey pine stands in northeastern California: 30-year effects

Treesearch

Robert J. Lilieholm; Dennis E. Teeguarden; Donald T. Gordon

1989-01-01

Response to precommercial thinning in stagnated 55-year-old ponderosa (Pinus ponderosa Dougl. ex Laws.) and Jeffrey pine (P. jeffreyi Grev. and Balf.) stands in northeastern alifornia was rapid and long-lasting. During the first 5 years after thinning, average annual diameter at breast height (d.b.h.) and height growth of trees on...

Remnant Bottomland Forests near the Terminus of the Mississippi River in Southeastern Louisiana

Treesearch

David A. White; Stephanie A. Skojac

2002-01-01

The woody communities of seven of the most intact bottomland hardwood forests of southeastern Louisiana are described. The seven forests are on old levee ridges associated with past distributaries of the Mississippi River. The communities were divided by diameter size class into overstory (>10.0 cm dbh) and understory (3.0 cm >...

Differences in Computed Individual-Tree Volumes Caused by Differences in Field Measurements

Treesearch

James A. Westfall

2008-01-01

Individual-tree volumes are primarily predicted using volume equations that rely on measured tree attributes. In the northeastern United States, the Forest Inventory and Analysis program determines tree volume using dbh, bole height, proportion of cull, and species information. These measurements are subject to variability due to a host of factors. The sensitivity of...

Bark thermal properties of selected central hardwood species

Treesearch

Gretel E. Hengst; Jeffery O. Dawson

1993-01-01

Some physical, thermal, and chemical properties of bark of eleven tree species native to the central hardwood region were measured to determine their potential to protect the vascular cambium from damage by fire. The relationship between dbh and bark thickness for each of sixteen species was determined. For purposes of monitoring seasonal trends, two species (Quercus...

The Roots of Plantation Cottonwood: Their Characteristics and Properties

Treesearch

John K. Francis

1985-01-01

The root biomass and its distribution and the growth rate of roots of pulpwood-size cottonwood (Popolus deltoides) in plantations were estimated by excavation and sampling. About 27 percent of the total biomass was in root tissue. Equations for predicting stump-taproot dry weight from d.b.h. and top dry weight were derived. Lateral roots in two...

Estimating Slash Quantity from Standing Loblolly Pine

Treesearch

Dale D. Wade

1969-01-01

No significant difference were found between variances of two prediction equations for estimating loblolly pine crown weight from diameter breast height (d.b.h). One equation was developed from trees on the Georgia Piedmont and the other from tress on the South Carolina Coastal Plain. An equation and table are presented for estimating loblolly pine slash weights from...

Use of three-point taper systems in timber cruising

Treesearch

James W. Flewelling; Richard L. Ernst; Lawrence M. Raynes

2000-01-01

Tree volumes and profiles are often estimated as functions of total height and DBH. Alternative estimators include form-class methods, importance sampling, the centroid method, and multi-point profile (taper) estimation systems; all of these require some measurement or estimate of upper stem diameters. The multi-point profile system discussed here allows for upper stem...

Sugar maple provenance study: West Virginia outplanting - 10-year results

Treesearch

G. W. Wendel; W. J. Gabriel

1980-01-01

After 10 years, survival of sugar maple (Acer saccharum Marsh.) provenances outplanted in West Virginia did not differ significantly. Total height, height growth and dbh measurements were significantly different among provenances. Fifty percent of the trees had major forks below 9.0 feet. Thirty-eight percent of the trees had no forks but 71 percent...

Bark Thickness of 17-Year-Old Loblolly Pine Planted at Different Spacings

Treesearch

Donald P. Feduccia; William F. Mann

1975-01-01

Diameter at breast height was the only variable affecting double bark thickness at d.b.h. and midpoint of the merchantable stem for young loblolly pine planted at five initial spacings on plots with site indices of 77 to 111 feet. Bark thickness at the 4-inch top was not correlated with breast-height diameter.

An individual-tree dbh-total height model with random plot effects for shortleaf pine

Treesearch

Chakra B. Budhathoki; Thomas B. Lynch; James M. Guldin

2007-01-01

Individual tree measurements were available from over 200 permanent plots established during 1985-1987 and later remeasured in naturally regenerated stands of shortleaf pine (Pinus echinata Mill.) in western Arkansas and eastern Oklahoma. The objective of this study was to model shortleaf pine growth in natural stands for the region. As a major...

Releasing 75- to 80-year-old Appalachian hardwood sawtimber trees--5-year d.b.h. response

Treesearch

H.C. Smith; G.W. Miller

1991-01-01

Generally, mature trees on good growing sites are seldom thinned or released. Instead, at maturity the trees are harvested. Data were summarized from north-central West Virginia study areas (northern red oak site index 70 feet and above) where mature trees were released on all sides of the crown (full release).

Thinning sprout clumps

Treesearch

Richard M. Godman

1992-01-01

How do you deal with stump sprouts in second-growth hardwood stands? Although thinning them takes special effort to avoid causing decay, stump sprouts are the only way to regenerate certain species such as basswood. Generally, you should thin them early and preferably when potential crop stems are 3 inches d.b.h. or less. But if you delay thinning until they are pole-...

Sustained mahogany (Swietenia macrophylla) plantation heartwood increment.

Treesearch

Frank H. Wadsworth; Edgardo. Gonzalez

2008-01-01

In a search for an increment-based rotation for plantation mahogany(Swietenia macrophylla King), heartwood volume per tree was regressed on DBH (trunk diameter outside bark at 1.4 m above the ground) and merchantable height measurements. We updated a previous study [Wadsworth, F.H., González González, E., Figuera Colón, J.C., Lugo P...

Effects of alternative treatments on canopy fuel characteristics in five conifer stands

Treesearch

Joe H. Scott; Elizabeth D. Reinhardt

2007-01-01

A detailed study of canopy fuel characteristics in five different forest types provided a unique dataset for simulating the effects of various stand manipulation treatments on canopy fuels. Low thinning, low thinning with commercial dbh limit, and crown thinning had similar effects on canopy bulk density (CBD) and canopy fuel load (CFL...

Validation of SILVAH for tolerant hardwoods in Ontario

Treesearch

Jacek Bankowski; Daniel C. Dey; Rice Jim; Eric Boysen; Roj Miller

1995-01-01

SILVAH, a stand growth simulator commonly used in the northeastern United States, has been evaluated by comparing predicted and actual growth of tolerant hardwoods in southern Ontario. The data came from 139 stands, unmanaged or managed (thinned), even-aged or uneven-aged. The data were used to test the accuracy of diameter distribution, basal area, mean quadratic DBH...

Silvicultural treatments in sapling stands

Treesearch

Neil I. Lamson

1989-01-01

Sapling stands are those in which codominant trees average less than 5 inches d.b.h. Silvicultural treatments in sapling stands can be summed up in two words: CROP TREES. Any silvicultural treatment must help crop trees if the investment in sapling stands is going to pay off. Just cutting "bad" or "undesirable" trees does not insure that crop trees...

An RNA-Seq based gene expression atlas of the common bean.

PubMed

O'Rourke, Jamie A; Iniguez, Luis P; Fu, Fengli; Bucciarelli, Bruna; Miller, Susan S; Jackson, Scott A; McClean, Philip E; Li, Jun; Dai, Xinbin; Zhao, Patrick X; Hernandez, Georgina; Vance, Carroll P

2014-10-06

Common bean (Phaseolus vulgaris) is grown throughout the world and comprises roughly 50% of the grain legumes consumed worldwide. Despite this, genetic resources for common beans have been lacking. Next generation sequencing, has facilitated our investigation of the gene expression profiles associated with biologically important traits in common bean. An increased understanding of gene expression in common bean will improve our understanding of gene expression patterns in other legume species. Combining recently developed genomic resources for Phaseolus vulgaris, including predicted gene calls, with RNA-Seq technology, we measured the gene expression patterns from 24 samples collected from seven tissues at developmentally important stages and from three nitrogen treatments. Gene expression patterns throughout the plant were analyzed to better understand changes due to nodulation, seed development, and nitrogen utilization. We have identified 11,010 genes differentially expressed with a fold change ≥ 2 and a P-value < 0.05 between different tissues at the same time point, 15,752 genes differentially expressed within a tissue due to changes in development, and 2,315 genes expressed only in a single tissue. These analyses identified 2,970 genes with expression patterns that appear to be directly dependent on the source of available nitrogen. Finally, we have assembled this data in a publicly available database, The Phaseolus vulgaris Gene Expression Atlas (Pv GEA), http://plantgrn.noble.org/PvGEA/ . Using the website, researchers can query gene expression profiles of their gene of interest, search for genes expressed in different tissues, or download the dataset in a tabular form. These data provide the basis for a gene expression atlas, which will facilitate functional genomic studies in common bean. Analysis of this dataset has identified genes important in regulating seed composition and has increased our understanding of nodulation and impact of the nitrogen source on assimilation and distribution throughout the plant.

Analysis of bHLH coding genes using gene co-expression network approach.

PubMed

Srivastava, Swati; Sanchita; Singh, Garima; Singh, Noopur; Srivastava, Gaurava; Sharma, Ashok

2016-07-01

Network analysis provides a powerful framework for the interpretation of data. It uses novel reference network-based metrices for module evolution. These could be used to identify module of highly connected genes showing variation in co-expression network. In this study, a co-expression network-based approach was used for analyzing the genes from microarray data. Our approach consists of a simple but robust rank-based network construction. The publicly available gene expression data of Solanum tuberosum under cold and heat stresses were considered to create and analyze a gene co-expression network. The analysis provide highly co-expressed module of bHLH coding genes based on correlation values. Our approach was to analyze the variation of genes expression, according to the time period of stress through co-expression network approach. As the result, the seed genes were identified showing multiple connections with other genes in the same cluster. Seed genes were found to be vary in different time periods of stress. These analyzed seed genes may be utilized further as marker genes for developing the stress tolerant plant species.

Validating internal controls for quantitative plant gene expression studies

PubMed Central

Brunner, Amy M; Yakovlev, Igor A; Strauss, Steven H

2004-01-01

Background Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression levels for reference genes are adequately consistent among the samples used, nor compare alternative genes to assess which are most reliable for the experimental conditions analyzed. Results Using real-time RT-PCR to study the expression of 10 poplar (genus Populus) housekeeping genes, we demonstrate a simple method for determining the degree of stability of gene expression over a set of experimental conditions. Based on a traditional method for analyzing the stability of varieties in plant breeding, it defines measures of gene expression stability from analysis of variance (ANOVA) and linear regression. We found that the potential internal control genes differed widely in their expression stability over the different tissues, developmental stages and environmental conditions studied. Conclusion Our results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression. The method we demonstrated facilitates statistical and graphical evaluation of gene expression stability. Selection of the best reference gene for a given set of experimental conditions should enable detection of biologically significant changes in gene expression that are too small to be revealed by less precise methods, or when highly variable reference genes are unknowingly used in real-time RT-PCR experiments. PMID:15317655

Characterization of basal gene expression trends over a diurnal cycle in Xiphophorus maculatus skin, brain and liver.

PubMed

Lu, Yuan; Reyes, Jose; Walter, Sean; Gonzalez, Trevor; Medrano, Geraldo; Boswell, Mikki; Boswell, William; Savage, Markita; Walter, Ronald

2018-06-01

Evolutionarily conserved diurnal circadian mechanisms maintain oscillating patterns of gene expression based on the day-night cycle. Xiphophorus fish have been used to evaluate transcriptional responses after exposure to various light sources and it was determined that each source incites distinct genetic responses in skin tissue. However, basal expression levels of genes that show oscillating expression patterns in day-night cycle, may affect the outcomes of such experiments, since basal gene expression levels at each point in the circadian path may influence the profile of identified light responsive genes. Lack of knowledge regarding diurnal fluctuations in basal gene expression patterns may confound the understanding of genetic responses to external stimuli (e.g., light) since the dynamic nature of gene expression implies animals subjected to stimuli at different times may be at very different stages within the continuum of genetic homeostasis. We assessed basal gene expression changes over a 24-hour period in 200 select Xiphophorus gene targets known to transcriptionally respond to various types of light exposure. We identified 22 genes in skin, 36 genes in brain and 28 genes in liver that exhibit basal oscillation of expression patterns. These genes, including known circadian regulators, produced the expected expression patterns over a 24-hour cycle when compared to circadian regulatory genes identified in other species, especially human and other vertebrate animal models. Our results suggest the regulatory network governing diurnal oscillating gene expression is similar between Xiphophorus and other vertebrates for the three Xiphophorus organs tested. In addition, we were able to categorize light responsive gene sets in Xiphophorus that do, and do not, exhibit circadian based oscillating expression patterns. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification of Reference Genes in Human Myelomonocytic Cells for Gene Expression Studies in Altered Gravity

PubMed Central

Thiel, Cora S.; Hauschild, Swantje; Tauber, Svantje; Paulsen, Katrin; Raig, Christiane; Raem, Arnold; Biskup, Josefine; Gutewort, Annett; Hürlimann, Eva; Philpot, Claudia; Lier, Hartwin; Engelmann, Frank; Layer, Liliana E.

2015-01-01

Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes (“housekeeping genes”) are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity. PMID:25654098

Life-cycle and growth-phase-dependent regulation of the ubiquitin genes of Trypanosoma cruzi.

PubMed

Manning-Cela, Rebeca; Jaishankar, Sobha; Swindle, John

2006-07-01

Trypanosoma cruzi, the causative agent of Chagas disease, exhibits a complex life cycle that is accompanied by the stage-specific gene expression. At the molecular level, very little is known about gene regulation in trypanosomes. Complex gene organizations coupled with polycistronic transcription units make the analysis of regulated gene expression difficult in trypanosomes. The ubiquitin genes of T. cruzi are a good example of this complexity. They are organized as a single cluster containing five ubiquitin fusion (FUS) and five polyubiquitin (PUB) genes that are polycistronically transcribed but expressed differently in response to developmental and environmental changes. Gene replacements were used to study FUS and PUB gene expression at different stages of growth and at different points in the life cycle of T. cruzi. Based on the levels of reporter gene expression, it was determined that FUS1 expression was downregulated as the parasites approached stationary phase, whereas PUB12.5 polyubiquitin gene expression increased. Conversely, FUS1 expression increases when epimastigotes and amastigotes differentiate into trypomastigotes, whereas the expression of PUB12.5 decreases when epimastigotes differentiate into amastigotes and trypomastigotes. Although the level of CAT activity in logarithmic growing epimastigotes is six- to seven-fold higher when the gene was expressed from the FUS1 locus than when expressed from the PUB12.5 locus, the rate of transcription from the two loci was the same implying that post-transcriptional mechanisms play a dominant role in the regulation of gene expression.

Gene expression changes with age in skin, adipose tissue, blood and brain.

PubMed

Glass, Daniel; Viñuela, Ana; Davies, Matthew N; Ramasamy, Adaikalavan; Parts, Leopold; Knowles, David; Brown, Andrew A; Hedman, Asa K; Small, Kerrin S; Buil, Alfonso; Grundberg, Elin; Nica, Alexandra C; Di Meglio, Paola; Nestle, Frank O; Ryten, Mina; Durbin, Richard; McCarthy, Mark I; Deloukas, Panagiotis; Dermitzakis, Emmanouil T; Weale, Michael E; Bataille, Veronique; Spector, Tim D

2013-07-26

Previous studies have demonstrated that gene expression levels change with age. These changes are hypothesized to influence the aging rate of an individual. We analyzed gene expression changes with age in abdominal skin, subcutaneous adipose tissue and lymphoblastoid cell lines in 856 female twins in the age range of 39-85 years. Additionally, we investigated genotypic variants involved in genotype-by-age interactions to understand how the genomic regulation of gene expression alters with age. Using a linear mixed model, differential expression with age was identified in 1,672 genes in skin and 188 genes in adipose tissue. Only two genes expressed in lymphoblastoid cell lines showed significant changes with age. Genes significantly regulated by age were compared with expression profiles in 10 brain regions from 100 postmortem brains aged 16 to 83 years. We identified only one age-related gene common to the three tissues. There were 12 genes that showed differential expression with age in both skin and brain tissue and three common to adipose and brain tissues. Skin showed the most age-related gene expression changes of all the tissues investigated, with many of the genes being previously implicated in fatty acid metabolism, mitochondrial activity, cancer and splicing. A significant proportion of age-related changes in gene expression appear to be tissue-specific with only a few genes sharing an age effect in expression across tissues. More research is needed to improve our understanding of the genetic influences on aging and the relationship with age-related diseases.

Differential expression profiles and pathways of genes in sugarcane leaf at elongation stage in response to drought stress

PubMed Central

Li, Changning; Nong, Qian; Solanki, Manoj Kumar; Liang, Qiang; Xie, Jinlan; Liu, Xiaoyan; Li, Yijie; Wang, Weizan; Yang, Litao; Li, Yangrui

2016-01-01

Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, a pot experiment was performed with the sugarcane variety GT21 at three water-deficit levels (mild, moderate, and severe) during the elongation stage and gene expression was analyzed using microarray technology. Physiological parameters of sugarcane showed significant alterations in response to drought stress. Based on the expression profile of 15,593 sugarcane genes, 1,501 (9.6%) genes were differentially expressed under different water-level treatments; 821 genes were upregulated and 680 genes were downregulated. A gene similarity analysis showed that approximately 62.6% of the differentially expressed genes shared homology with functional proteins. In a Gene Ontology (GO) analysis, 901 differentially expressed genes were assigned to 36 GO categories. Moreover, 325 differentially expressed genes were classified into 101 pathway categories involved in various processes, such as the biosynthesis of secondary metabolites, ribosomes, carbon metabolism, etc. In addition, some unannotated genes were detected; these may provide a basis for studies of water-deficit tolerance. The reliability of the observed expression patterns was confirmed by RT-PCR. The results of this study may help identify useful genes for improving drought tolerance in sugarcane. PMID:27170459

GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

PubMed

Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

2018-01-01

When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

Circular RNA and gene expression profiles in gastric cancer based on microarray chip technology.

PubMed

Sui, Weiguo; Shi, Zhoufang; Xue, Wen; Ou, Minglin; Zhu, Ying; Chen, Jiejing; Lin, Hua; Liu, Fuhua; Dai, Yong

2017-03-01

The aim of the present study was to screen gastric cancer (GC) tissue and adjacent tissue for differences in mRNA and circular (circRNA) expression, to analyze the differences in circRNA and mRNA expression, and to investigate the circRNA expression in gastric carcinoma and its mechanism. circRNA and mRNA differential expression profiles generated using Agilent microarray technology were analyzed in the GC tissues and adjacent tissues. qRT-PCR was used to verify the differential expression of circRNAs and mRNAs according to the interactions between circRNAs and miRNAs as well as the possible existence of miRNA and mRNA interactions. We found that: i) the circRNA expression profile revealed 1,285 significant differences in circRNA expression, with circRNA expression downregulated in 594 samples and upregulated in 691 samples via interactions with miRNAs. The qRT-PCR validation experiments showed that hsa_circRNA_400071, hsa_circRNA_000543 and hsa_circRNA_001959 expression was consistent with the microarray analysis results. ii) 29,112 genes were found in the GC tissues and adjacent tissues, including 5,460 differentially expressed genes. Among them, 2,390 differentially expressed genes were upregulated and 3,070 genes were downregulated. Gene Ontology (GO) analysis of the differentially expressed genes revealed these genes involved in biological process classification, cellular component classification and molecular function classification. Pathway analysis of the differentially expressed genes identified 83 significantly enriched genes, including 28 upregulated genes and 55 downregulated genes. iii) 69 differentially expressed circRNAs were found that might adsorb specific miRNAs to regulate the expression of their target gene mRNAs. The conclusions are: i) differentially expressed circRNAs had corresponding miRNA binding sites. These circRNAs regulated the expression of target genes through interactions with miRNAs and might become new molecular biomarkers for GC in the future. ii) Differentially expressed genes may be involved in the occurrence of GC via a variety of mechanisms. iii) CD44, CXXC5, MYH9, MALAT1 and other genes may have important implications for the occurrence and development of GC through the regulation, interaction, and mutual influence of circRNA-miRNA-mRNA via different mechanisms.

A P-Norm Robust Feature Extraction Method for Identifying Differentially Expressed Genes

PubMed Central

Liu, Jian; Liu, Jin-Xing; Gao, Ying-Lian; Kong, Xiang-Zhen; Wang, Xue-Song; Wang, Dong

2015-01-01

In current molecular biology, it becomes more and more important to identify differentially expressed genes closely correlated with a key biological process from gene expression data. In this paper, based on the Schatten p-norm and Lp-norm, a novel p-norm robust feature extraction method is proposed to identify the differentially expressed genes. In our method, the Schatten p-norm is used as the regularization function to obtain a low-rank matrix and the Lp-norm is taken as the error function to improve the robustness to outliers in the gene expression data. The results on simulation data show that our method can obtain higher identification accuracies than the competitive methods. Numerous experiments on real gene expression data sets demonstrate that our method can identify more differentially expressed genes than the others. Moreover, we confirmed that the identified genes are closely correlated with the corresponding gene expression data. PMID:26201006

A P-Norm Robust Feature Extraction Method for Identifying Differentially Expressed Genes.

PubMed

Liu, Jian; Liu, Jin-Xing; Gao, Ying-Lian; Kong, Xiang-Zhen; Wang, Xue-Song; Wang, Dong

2015-01-01

In current molecular biology, it becomes more and more important to identify differentially expressed genes closely correlated with a key biological process from gene expression data. In this paper, based on the Schatten p-norm and Lp-norm, a novel p-norm robust feature extraction method is proposed to identify the differentially expressed genes. In our method, the Schatten p-norm is used as the regularization function to obtain a low-rank matrix and the Lp-norm is taken as the error function to improve the robustness to outliers in the gene expression data. The results on simulation data show that our method can obtain higher identification accuracies than the competitive methods. Numerous experiments on real gene expression data sets demonstrate that our method can identify more differentially expressed genes than the others. Moreover, we confirmed that the identified genes are closely correlated with the corresponding gene expression data.

Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti

PubMed Central

Wang, Xu; Werren, John H.; Clark, Andrew G.

2015-01-01

There is extraordinary diversity in sexual dimorphism (SD) among animals, but little is known about its epigenetic basis. To study the epigenetic architecture of SD in a haplodiploid system, we performed RNA-seq and whole-genome bisulfite sequencing of adult females and males from two closely related parasitoid wasps, Nasonia vitripennis and Nasonia giraulti. More than 75% of expressed genes displayed significantly sex-biased expression. As a consequence, expression profiles are more similar between species within each sex than between sexes within each species. Furthermore, extremely male- and female-biased genes are enriched for totally different functional categories: male-biased genes for key enzymes in sex-pheromone synthesis and female-biased genes for genes involved in epigenetic regulation of gene expression. Remarkably, just 70 highly expressed, extremely male-biased genes account for 10% of all transcripts in adult males. Unlike expression profiles, DNA methylomes are highly similar between sexes within species, with no consistent sex differences in methylation found. Therefore, methylation changes cannot explain the extensive level of sex-biased gene expression observed. Female-biased genes have smaller sequence divergence between species, higher conservation to other hymenopterans, and a broader expression range across development. Overall, female-biased genes have been recruited from genes with more conserved and broadly expressing “house-keeping” functions, whereas male-biased genes are more recently evolved and are predominately testis specific. In summary, Nasonia accomplish a striking degree of sex-biased expression without sex chromosomes or epigenetic differences in methylation. We propose that methylation provides a general signal for constitutive gene expression, whereas other sex-specific signals cause sex-biased gene expression. PMID:26100871

Extent and character of circadian gene expression in Drosophila melanogaster: identification of twenty oscillating mRNAs in the fly head.

PubMed

Van Gelder, R N; Bae, H; Palazzolo, M J; Krasnow, M A

1995-12-01

Although mRNAs expressed with a circadian rhythm have been isolated from many species, the extent and character of circadianly regulated gene expression is unknown for any animal. In Drosophila melanogaster, only the period (per) gene, an essential component of the circadian pacemaker, is known to show rhythmic mRNA expression. Recent work suggests that the encoded Per protein controls its own transcription by an autoregulatory feedback loop. Per might also control the rhythmic expression of other genes to generate circadian behavior and physiology. The goals of this work were to evaluate the extent and character of circadian control of gene expression in Drosophila, and to identify genes dependent on per for circadian expression. A large collection of anonymous, independent cDNA clones was used to screen for transcripts that are rhythmically expressed in the fly head. 20 of the 261 clones tested detected mRNAs with a greater than two-fold daily change in abundance. Three mRNAs were maximally expressed in the morning, whereas 17 mRNAs were most abundant in the evening--when per mRNA is also maximally expressed (but when the flies are inactive). Further analysis of the three 'morning' cDNAs showed that each has a unique dependence on the presence of a light-dark cycle, on timed feeding, and on the function of the per gene for its oscillation. These dependencies were different from those determined for per and for a novel 'evening' gene. Sequence analysis indicated that all but one of the 20 cDNAs identified previously uncloned genes. Diurnal control of gene expression is a significant but limited phenomenon in the fly head, which involves many uncharacterized genes. Diurnal control is mediated by multiple endogenous and exogenous mechanisms, even at the level of individual genes. A subset of circadianly expressed genes are predominantly or exclusively dependent on per for their rhythmic expression. The per gene can therefore influence the expression of genes other than itself, but for many rhythmically expressed genes, per functions in conjunction with external inputs to control their daily expression patterns.

Polycistronic gene expression in Aspergillus niger.

PubMed

Schuetze, Tabea; Meyer, Vera

2017-09-25

Genome mining approaches predict dozens of biosynthetic gene clusters in each of the filamentous fungal genomes sequenced so far. However, the majority of these gene clusters still remain cryptic because they are not expressed in their natural host. Simultaneous expression of all genes belonging to a biosynthetic pathway in a heterologous host is one approach to activate biosynthetic gene clusters and to screen the metabolites produced for bioactivities. Polycistronic expression of all pathway genes under control of a single and tunable promoter would be the method of choice, as this does not only simplify cloning procedures, but also offers control on timing and strength of expression. However, polycistronic gene expression is a feature not commonly found in eukaryotic host systems, such as Aspergillus niger. In this study, we tested the suitability of the viral P2A peptide for co-expression of three genes in A. niger. Two genes descend from Fusarium oxysporum and are essential to produce the secondary metabolite enniatin (esyn1, ekivR). The third gene (luc) encodes the reporter luciferase which was included to study position effects. Expression of the polycistronic gene cassette was put under control of the Tet-On system to ensure tunable gene expression in A. niger. In total, three polycistronic expression cassettes which differed in the position of luc were constructed and targeted to the pyrG locus in A. niger. This allowed direct comparison of the luciferase activity based on the position of the luciferase gene. Doxycycline-mediated induction of the Tet-On expression cassettes resulted in the production of one long polycistronic mRNA as proven by Northern analyses, and ensured comparable production of enniatin in all three strains. Notably, gene position within the polycistronic expression cassette matters, as, luciferase activity was lowest at position one and had a comparable activity at positions two and three. The P2A peptide can be used to express at least three genes polycistronically in A. niger. This approach can now be applied to heterologously express entire secondary metabolite gene clusters polycistronically or to co-express any genes of interest in equimolar amounts.

Intracellular high cholesterol content disorders the clock genes, apoptosis-related genes and fibrinolytic-related genes rhythmic expressions in human plaque-derived vascular smooth muscle cells.

PubMed

Lin, Changpo; Tang, Xiao; Xu, Lirong; Qian, Ruizhe; Shi, Zhenyu; Wang, Lixin; Cai, Tingting; Yan, Dong; Fu, Weiguo; Guo, Daqiao

2017-07-10

The clock genes are involved in regulating cardiovascular functions, and their expression disorders would lead to circadian rhythm disruptions of clock-controlled genes (CCGs), resulting in atherosclerotic plaque formation and rupture. Our previous study revealed the rhythmic expression of clock genes were attenuated in human plaque-derived vascular smooth muscle cells (PVSMCs), but failed to detect the downstream CCGs expressions and the underlying molecular mechanism. In this study, we examined the difference of CCGs rhythmic expression between human normal carotid VSMCs (NVSMCs) and PVSMCs. Furthermore, we compared the cholesterol and triglycerides levels between two groups and the link to clock genes and CCGs expressions. Seven health donors' normal carotids and 19 carotid plaques yielded viable cultured NVSMCs and PVSMCs. The expression levels of target genes were measured by quantitative real-time PCR and Western-blot. The intracellular cholesterol and triglycerides levels were measured by kits. The circadian expressions of apoptosis-related genes and fibrinolytic-related genes were disordered. Besides, the cholesterol levels were significant higher in PVSMCs. After treated with cholesterol or oxidized low density lipoprotein (ox-LDL), the expressions of clock genes were inhibited; and the rhythmic expressions of clock genes, apoptosis-related genes and fibrinolytic-related genes were disturbed in NVSMCs, which were similar to PVSMCs. The results suggested that intracellular high cholesterol content of PVSMCs would lead to the disorders of clock genes and CCGs rhythmic expressions. And further studies should be conducted to demonstrate the specific molecular mechanisms involved.

Double-filter identification of vascular-expressed genes using Arabidopsis plants with vascular hypertrophy and hypotrophy.

PubMed

Ckurshumova, Wenzislava; Scarpella, Enrico; Goldstein, Rochelle S; Berleth, Thomas

2011-08-01

Genes expressed in vascular tissues have been identified by several strategies, usually with a focus on mature vascular cells. In this study, we explored the possibility of using two opposite types of altered tissue compositions in combination with a double-filter selection to identify genes with a high probability of vascular expression in early organ primordia. Specifically, we generated full-transcriptome microarray profiles of plants with (a) genetically strongly reduced and (b) pharmacologically vastly increased vascular tissues and identified a reproducible cohort of 158 transcripts that fulfilled the dual requirement of being underrepresented in (a) and overrepresented in (b). In order to assess the predictive value of our identification scheme for vascular gene expression, we determined the expression patterns of genes in two unbiased subsamples. First, we assessed the expression patterns of all twenty annotated transcription factor genes from the cohort of 158 genes and found that seventeen of the twenty genes were preferentially expressed in leaf vascular cells. Remarkably, fifteen of these seventeen vascular genes were clearly expressed already very early in leaf vein development. Twelve genes with published leaf expression patterns served as a second subsample to monitor the representation of vascular genes in our cohort. Of those twelve genes, eleven were preferentially expressed in leaf vascular tissues. Based on these results we propose that our compendium of 158 genes represents a sample that is highly enriched for genes expressed in vascular tissues and that our approach is particularly suited to detect genes expressed in vascular cell lineages at early stages of their inception. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Increased gene expression noise in human cancers is correlated with low p53 and immune activities as well as late stage cancer.

PubMed

Han, Rongfei; Huang, Guanqun; Wang, Yejun; Xu, Yafei; Hu, Yueming; Jiang, Wenqi; Wang, Tianfu; Xiao, Tian; Zheng, Duo

2016-11-01

Gene expression in metazoans is delicately organized. As genetic information transmits from DNA to RNA and protein, expression noise is inevitably generated. Recent studies begin to unveil the mechanisms of gene expression noise control, but the changes of gene expression precision in pathologic conditions like cancers are unknown. Here we analyzed the transcriptomic data of human breast, liver, lung and colon cancers, and found that the expression noise of more than 74.9% genes was increased in cancer tissues as compared to adjacent normal tissues. This suggested that gene expression precision controlling collapsed during cancer development. A set of 269 genes with noise increased more than 2-fold were identified across different cancer types. These genes were involved in cell adhesion, catalytic and metabolic functions, implying the vulnerability of deregulation of these processes in cancers. We also observed a tendency of increased expression noise in patients with low p53 and immune activity in breast, liver and lung caners but not in colon cancers, which indicated the contributions of p53 signaling and host immune surveillance to gene expression noise in cancers. Moreover, more than 53.7% genes had increased noise in patients with late stage than early stage cancers, suggesting that gene expression precision was associated with cancer outcome. Together, these results provided genomic scale explorations of gene expression noise control in human cancers.

[Differential expression genes of bone tissues surrounding implants in diabetic rats by gene chip].

PubMed

Wang, Xin-xin; Ma, Yue; Li, Qing; Jiang, Bao-qi; Lan, Jing

2012-10-01

To compare mRNA expression profiles of bone tissues surrounding implants between normal rats and rats with diabetes using microarray technology. Six Wistar rats were randomly selected and divided into normal model group and diabetic group. Diabetic model condition was established by injecting Streptozotocin into peritoneal space. Titanium implants were implanted into the epiphyseal end of the rats' tibia. Bone tissues surrounding implant were harvested and sampled after 3 months to perform comprehensive RNA gene expression profiling, including 17983 for genome-wide association study.GO analysis was used to compare different gene expression and real-time PCR was used to confirm the results on core samples. The results indicated that there were 1084 differential gene expression. In the diabetic model, there were 352 enhanced expression genes, 732 suppressed expression genes. GO analysis involved 1154 different functional type. Osteoblast related gene expressions in bone tissue samples of diabetic rats were decreased, and lipid metabolism pathway related gene expression was increased.

Gene Architectures that Minimize Cost of Gene Expression.

PubMed

Frumkin, Idan; Schirman, Dvir; Rotman, Aviv; Li, Fangfei; Zahavi, Liron; Mordret, Ernest; Asraf, Omer; Wu, Song; Levy, Sasha F; Pilpel, Yitzhak

2017-01-05

Gene expression burdens cells by consuming resources and energy. While numerous studies have investigated regulation of expression level, little is known about gene design elements that govern expression costs. Here, we ask how cells minimize production costs while maintaining a given protein expression level and whether there are gene architectures that optimize this process. We measured fitness of ∼14,000 E. coli strains, each expressing a reporter gene with a unique 5' architecture. By comparing cost-effective and ineffective architectures, we found that cost per protein molecule could be minimized by lowering transcription levels, regulating translation speeds, and utilizing amino acids that are cheap to synthesize and that are less hydrophobic. We then examined natural E. coli genes and found that highly expressed genes have evolved more forcefully to minimize costs associated with their expression. Our study thus elucidates gene design elements that improve the economy of protein expression in natural and heterologous systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Pituitary adenylyl cyclase-activating polypeptide (PACAP) and its receptor (PAC1-R) are positioned to modulate afferent signaling in the cochlea.

PubMed

Drescher, M J; Drescher, D G; Khan, K M; Hatfield, J S; Ramakrishnan, N A; Abu-Hamdan, M D; Lemonnier, L A

2006-09-29

Pituitary adenylyl cyclase-activating polypeptide (PACAP), via its specific receptor pituitary adenylyl cyclase-activating polypeptide receptor 1 (PAC1-R), is known to have roles in neuromodulation and neuroprotection associated with glutamatergic and cholinergic neurotransmission, which, respectively, are believed to form the primary basis for afferent and efferent signaling in the organ of Corti. Previously, we identified transcripts for PACAP preprotein and multiple splice variants of its receptor, PAC1-R, in microdissected cochlear subfractions. In the present work, neural localizations of PACAP and PAC1-R within the organ of Corti and spiral ganglion were examined, defining sites of PACAP action. Immunolocalization of PACAP and PAC1-R in the organ of Corti and spiral ganglion was compared with immunolocalization of choline acetyltransferase (ChAT) and synaptophysin as efferent neuronal markers, and glutamate receptor 2/3 (GluR2/3) and neurofilament 200 as afferent neuronal markers, for each of the three cochlear turns. Brightfield microscopy giving morphological detail for individual immunolocalizations was followed by immunofluorescence detection of co-localizations. PACAP was found to be co-localized with ChAT in nerve fibers of the intraganglionic spiral bundle and beneath the inner and outer hair cells within the organ of Corti. Further, evidence was obtained that PACAP is expressed in type I afferent axons leaving the spiral ganglion en route to the auditory nerve, potentially serving as a neuromodulator in axonal terminals. In contrast to the efferent localization of PACAP within the organ of Corti, PAC1-R immunoreactivity was co-localized with afferent dendritic neuronal marker GluR2/3 in nerve fibers passing beneath and lateral to the inner hair cell and in fibers at supranuclear and basal sites on outer hair cells. Given the known association of PACAP with catecholaminergic neurotransmission in sympathoadrenal function, we also re-examined the issue of whether the organ of Corti receives adrenergic innervation. We now demonstrate the existence of nerve fibers within the organ of Corti which are immunoreactive for the adrenergic marker dopamine beta-hydroxylase (DBH). DBH immunoreactivity was particularly prominent in nerve fibers both at the base and near the cuticular plate of outer hair cells of the apical turn, extending to the non-sensory Hensen's cell region. Evidence was obtained for limited co-localization of DBH with PAC1-R and PACAP. In the process of this investigation, we obtained evidence that efferent and afferent nerve fibers, in addition to adrenergic nerve fibers, are present at supranuclear sites on outer hair cells and distributed within the non-sensory epithelium of the apical cochlear turn for rat, based upon immunoreactivity for the corresponding neuronal markers. Overall, PACAP is hypothesized to act within the organ of Corti as an efferent neuromodulator of afferent signaling via PAC1-R that is present on type I afferent dendrites, in position to afford protection from excitotoxicity. Additionally, PACAP/PAC1-R may modulate secretion of catecholamines from adrenergic terminals within the organ of Corti.

Alpha2-adrenoceptor blockade accelerates the neurogenic, neurotrophic, and behavioral effects of chronic antidepressant treatment.

PubMed

Yanpallewar, Sudhirkumar U; Fernandes, Kimberly; Marathe, Swananda V; Vadodaria, Krishna C; Jhaveri, Dhanisha; Rommelfanger, Karen; Ladiwala, Uma; Jha, Shanker; Muthig, Verena; Hein, Lutz; Bartlett, Perry; Weinshenker, David; Vaidya, Vidita A

2010-01-20

Slow-onset adaptive changes that arise from sustained antidepressant treatment, such as enhanced adult hippocampal neurogenesis and increased trophic factor expression, play a key role in the behavioral effects of antidepressants. alpha(2)-Adrenoceptors contribute to the modulation of mood and are potential targets for the development of faster acting antidepressants. We investigated the influence of alpha(2)-adrenoceptors on adult hippocampal neurogenesis. Our results indicate that alpha(2)-adrenoceptor agonists, clonidine and guanabenz, decrease adult hippocampal neurogenesis through a selective effect on the proliferation, but not the survival or differentiation, of progenitors. These effects persist in dopamine beta-hydroxylase knock-out (Dbh(-/-)) mice lacking norepinephrine, supporting a role for alpha(2)-heteroceptors on progenitor cells, rather than alpha(2)-autoreceptors on noradrenergic neurons that inhibit norepinephrine release. Adult hippocampal progenitors in vitro express all the alpha(2)-adrenoceptor subtypes, and decreased neurosphere frequency and BrdU incorporation indicate direct effects of alpha(2)-adrenoceptor stimulation on progenitors. Furthermore, coadministration of the alpha(2)-adrenoceptor antagonist yohimbine with the antidepressant imipramine significantly accelerates effects on hippocampal progenitor proliferation, the morphological maturation of newborn neurons, and the increase in expression of brain derived neurotrophic factor and vascular endothelial growth factor implicated in the neurogenic and behavioral effects of antidepressants. Finally, short-duration (7 d) yohimbine and imipramine treatment results in robust behavioral responses in the novelty suppressed feeding test, which normally requires 3 weeks of treatment with classical antidepressants. Our results demonstrate that alpha(2)-adrenoceptors, expressed by progenitor cells, decrease adult hippocampal neurogenesis, while their blockade speeds up antidepressant action, highlighting their importance as targets for faster acting antidepressants.

α2-adrenoceptor blockade accelerates the neurogenic, neurotrophic, and behavioral effects of chronic antidepressant treatment

PubMed Central

Yanpallewar, Sudhirkumar U.; Fernandes, Kimberly; Marathe, Swananda V.; Vadodaria, Krishna C.; Jhaveri, Dhanisha; Rommelfanger, Karen; Ladiwala, Uma; Jha, Shanker; Muthig, Verena; Hein, Lutz; Bartlett, Perry; Weinshenker, David; Vaidya, Vidita A.

2010-01-01

Slow-onset adaptive changes that arise from sustained antidepressant treatment, such as enhanced adult hippocampal neurogenesis and increased trophic factor expression, play a key role in the behavioral effects of antidepressants. α2-adrenoceptors contribute to the modulation of mood and are potential targets for the development of faster acting antidepressants. We investigated the influence of α2-adrenoceptors on adult hippocampal neurogenesis. Our results indicate that α2-adrenoceptor agonists, clonidine and guanabenz, decrease adult hippocampal neurogenesis through a selective effect on the proliferation, but not the survival or differentiation, of progenitors. These effects persist in dopamine β-hydroxylase knockout (Dbh −/−) mice lacking norepinephrine, supporting a role for α2-heteroceptors on progenitor cells, rather than α2-autoreceptors on noradrenergic neurons that inhibit norepinephrine release. Adult hippocampal progenitors in vitro express all the α2-adrenoceptor subtypes, and decreased neurosphere frequency and BrdU incorporation indicate direct effects of α2-adrenoceptor stimulation on progenitors. Further, co-administration of the α2-adrenoceptor antagonist yohimbine with the antidepressant imipramine significantly accelerates effects on hippocampal progenitor proliferation, the morphological maturation of newborn neurons, and the increase in expression of brain derived neurotrophic factor and vascular endothelial growth factor implicated in the neurogenic and behavioral effects of antidepressants. Finally, short duration (7 day) yohimbine and imipramine treatment results in robust behavioral responses in the novelty suppressed feeding test, which normally requires 3 weeks of treatment with classical antidepressants. Our results demonstrate that α2-adrenoceptors, expressed by progenitor cells, decrease adult hippocampal neurogenesis, while their blockade speeds up antidepressant action, highlighting their importance as targets for faster acting antidepressants. PMID:20089918

Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection

PubMed Central

2012-01-01

Background Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection. Results We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Several genes showed differential expression between control and stress conditions. Gene ontology (GO) enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs) were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with differential gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks). The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5) apoptosis and cell death categories were enriched. Of the 287 positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments. Conclusions Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study. PMID:22853646

Functional clustering of time series gene expression data by Granger causality

PubMed Central

2012-01-01

Background A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes. Results In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its consequence. Conclusions This kind of analysis can be used as a complementary approach for functional clustering, wherein genes would be clustered not solely based on their expression similarity but on their topological proximity built according to the intensity of Granger causality among them. PMID:23107425

Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression

PubMed Central

Richter, Karin; Wirta, Valtteri; Dahl, Lina; Bruce, Sara; Lundeberg, Joakim; Carlsson, Leif; Williams, Cecilia

2006-01-01

Background Expression of the LIM-homeobox gene Lhx2 in murine hematopoietic cells allows for the generation of hematopoietic stem cell (HSC)-like cell lines. To address the molecular basis of Lhx2 function, we generated HSC-like cell lines where Lhx2 expression is regulated by a tet-on system and hence dependent on the presence of doxycyclin (dox). These cell lines efficiently down-regulate Lhx2 expression upon dox withdrawal leading to a rapid differentiation into various myeloid cell types. Results Global gene expression of these cell lines cultured in dox was compared to different time points after dox withdrawal using microarray technology. We identified 267 differentially expressed genes. The majority of the genes overlapping with HSC-specific databases were those down-regulated after turning off Lhx2 expression and a majority of the genes overlapping with those defined as late progenitor-specific genes were the up-regulated genes, suggesting that these cell lines represent a relevant model system for normal HSCs also at the level of global gene expression. Moreover, in situ hybridisations of several genes down-regulated after dox withdrawal showed overlapping expression patterns with Lhx2 in various tissues during embryonic development. Conclusion Global gene expression analysis of HSC-like cell lines with inducible Lhx2 expression has identified genes putatively linked to self-renewal / differentiation of HSCs, and function of Lhx2 in organ development and stem / progenitor cells of non-hematopoietic origin. PMID:16600034

Integrated analysis of gene expression and methylation profiles of 48 candidate genes in breast cancer patients.

PubMed

Li, Zibo; Heng, Jianfu; Yan, Jinhua; Guo, Xinwu; Tang, Lili; Chen, Ming; Peng, Limin; Wu, Yepeng; Wang, Shouman; Xiao, Zhi; Deng, Zhongping; Dai, Lizhong; Wang, Jun

2016-11-01

Gene-specific methylation and expression have shown biological and clinical importance for breast cancer diagnosis and prognosis. Integrated analysis of gene methylation and gene expression may identify genes associated with biology mechanism and clinical outcome of breast cancer and aid in clinical management. Using high-throughput microfluidic quantitative PCR, we analyzed the expression profiles of 48 candidate genes in 96 Chinese breast cancer patients and investigated their correlation with gene methylation and associations with breast cancer clinical parameters. Breast cancer-specific gene expression alternation was found in 25 genes with significant expression difference between paired tumor and normal tissues. A total of 9 genes (CCND2, EGFR, GSTP1, PGR, PTGS2, RECK, SOX17, TNFRSF10D, and WIF1) showed significant negative correlation between methylation and gene expression, which were validated in the TCGA database. Total 23 genes (ACADL, APC, BRCA2, CADM1, CAV1, CCND2, CST6, EGFR, ESR2, GSTP1, ICAM5, NPY, PGR, PTGS2, RECK, RUNX3, SFRP1, SOX17, SYK, TGFBR2, TNFRSF10D, WIF1, and WRN) annotated with potential TFBSs in the promoter regions showed negative correlation between methylation and expression. In logistics regression analysis, 31 of the 48 genes showed improved performance in disease prediction with combination of methylation and expression coefficient. Our results demonstrated the complex correlation and the possible regulatory mechanisms between DNA methylation and gene expression. Integration analysis of methylation and expression of candidate genes could improve performance in breast cancer prediction. These findings would contribute to molecular characterization and identification of biomarkers for potential clinical applications.

Genome-wide profiling identifies a subset of methamphetamine (METH)-induced genes associated with METH-induced increased H4K5Ac binding in the rat striatum

PubMed Central

2013-01-01

Background METH is an illicit drug of abuse that influences gene expression in the rat striatum. Histone modifications regulate gene transcription. Methods We therefore used microarray analysis and genome-scale approaches to examine potential relationships between the effects of METH on gene expression and on DNA binding of histone H4 acetylated at lysine 4 (H4K5Ac) in the rat dorsal striatum of METH-naïve and METH-pretreated rats. Results Acute and chronic METH administration caused differential changes in striatal gene expression. METH also increased H4K5Ac binding around the transcriptional start sites (TSSs) of genes in the rat striatum. In order to relate gene expression to histone acetylation, we binned genes of similar expression into groups of 100 genes and proceeded to relate gene expression to H4K5Ac binding. We found a positive correlation between gene expression and H4K5Ac binding in the striatum of control rats. Similar correlations were observed in METH-treated rats. Genes that showed acute METH-induced increased expression in saline-pretreated rats also showed METH-induced increased H4K5Ac binding. The acute METH injection caused similar increases in H4K5Ac binding in METH-pretreated rats, without affecting gene expression to the same degree. Finally, genes that showed METH-induced decreased expression exhibited either decreases or no changes in H4K5Ac binding. Conclusion Acute METH injections caused increased gene expression of genes that showed increased H4K5Ac binding near their transcription start sites. PMID:23937714

Genome-wide profiling identifies a subset of methamphetamine (METH)-induced genes associated with METH-induced increased H4K5Ac binding in the rat striatum.

PubMed

Cadet, Jean Lud; Jayanthi, Subramaniam; McCoy, Michael T; Ladenheim, Bruce; Saint-Preux, Fabienne; Lehrmann, Elin; De, Supriyo; Becker, Kevin G; Brannock, Christie

2013-08-12

METH is an illicit drug of abuse that influences gene expression in the rat striatum. Histone modifications regulate gene transcription. We therefore used microarray analysis and genome-scale approaches to examine potential relationships between the effects of METH on gene expression and on DNA binding of histone H4 acetylated at lysine 4 (H4K5Ac) in the rat dorsal striatum of METH-naïve and METH-pretreated rats. Acute and chronic METH administration caused differential changes in striatal gene expression. METH also increased H4K5Ac binding around the transcriptional start sites (TSSs) of genes in the rat striatum. In order to relate gene expression to histone acetylation, we binned genes of similar expression into groups of 100 genes and proceeded to relate gene expression to H4K5Ac binding. We found a positive correlation between gene expression and H4K5Ac binding in the striatum of control rats. Similar correlations were observed in METH-treated rats. Genes that showed acute METH-induced increased expression in saline-pretreated rats also showed METH-induced increased H4K5Ac binding. The acute METH injection caused similar increases in H4K5Ac binding in METH-pretreated rats, without affecting gene expression to the same degree. Finally, genes that showed METH-induced decreased expression exhibited either decreases or no changes in H4K5Ac binding. Acute METH injections caused increased gene expression of genes that showed increased H4K5Ac binding near their transcription start sites.

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data.

PubMed

Tintle, Nathan L; Sitarik, Alexandra; Boerema, Benjamin; Young, Kylie; Best, Aaron A; Dejongh, Matthew

2012-08-08

Statistical analyses of whole genome expression data require functional information about genes in order to yield meaningful biological conclusions. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) are common sources of functionally grouped gene sets. For bacteria, the SEED and MicrobesOnline provide alternative, complementary sources of gene sets. To date, no comprehensive evaluation of the data obtained from these resources has been performed. We define a series of gene set consistency metrics directly related to the most common classes of statistical analyses for gene expression data, and then perform a comprehensive analysis of 3581 Affymetrix® gene expression arrays across 17 diverse bacteria. We find that gene sets obtained from GO and KEGG demonstrate lower consistency than those obtained from the SEED and MicrobesOnline, regardless of gene set size. Despite the widespread use of GO and KEGG gene sets in bacterial gene expression data analysis, the SEED and MicrobesOnline provide more consistent sets for a wide variety of statistical analyses. Increased use of the SEED and MicrobesOnline gene sets in the analysis of bacterial gene expression data may improve statistical power and utility of expression data.

Validation of housekeeping genes as an internal control for gene expression studies in Giardia lamblia using quantitative real-time PCR.

PubMed

Marcial-Quino, Jaime; Fierro, Francisco; De la Mora-De la Mora, Ignacio; Enríquez-Flores, Sergio; Gómez-Manzo, Saúl; Vanoye-Carlo, America; Garcia-Torres, Itzhel; Sierra-Palacios, Edgar; Reyes-Vivas, Horacio

2016-04-25

The analysis of transcript levels of specific genes is important for understanding transcriptional regulation and for the characterization of gene function. Real-time quantitative reverse transcriptase PCR (RT-qPCR) has become a powerful tool to quantify gene expression. The objective of this study was to identify reliable housekeeping genes in Giardia lamblia. Twelve genes were selected for this purpose, and their expression was analyzed in the wild type WB strain and in two strains with resistance to nitazoxanide (NTZ) and metronidazole (MTZ), respectively. RefFinder software analysis showed that the expression of the genes is different in the three strains. The integrated data from the four analyses showed that the NADH oxidase (NADH) and aldolase (ALD) genes were the most steadily expressed genes, whereas the glyceraldehyde-3-phosphate dehydrogenase gene was the most unstable. Additionally, the relative expression of seven genes were quantified in the NTZ- and MTZ-resistant strains by RT-qPCR, using the aldolase gene as the internal control, and the results showed a consistent differential pattern of expression in both strains. The housekeeping genes found in this work will facilitate the analysis of mRNA expression levels of other genes of interest in G. lamblia. Copyright © 2016 Elsevier B.V. All rights reserved.

Targeting gene expression selectively in cancer cells by using the progression-elevated gene-3 promoter.

PubMed

Su, Zhao-Zhong; Sarkar, Devanand; Emdad, Luni; Duigou, Gregory J; Young, Charles S H; Ware, Joy; Randolph, Aaron; Valerie, Kristoffer; Fisher, Paul B

2005-01-25

One impediment to effective cancer-specific gene therapy is the rarity of regulatory sequences targeting gene expression selectively in tumor cells. Although many tissue-specific promoters are recognized, few cancer-selective gene promoters are available. Progression-elevated gene-3 (PEG-3) is a rodent gene identified by subtraction hybridization that displays elevated expression as a function of transformation by diversely acting oncogenes, DNA damage, and cancer cell progression. The promoter of PEG-3, PEG-Prom, displays robust expression in a broad spectrum of human cancer cell lines with marginal expression in normal cellular counterparts. Whereas GFP expression, when under the control of a CMV promoter, is detected in both normal and cancer cells, when GFP is expressed under the control of the PEG-Prom, cancer-selective expression is evident. Mutational analysis identifies the AP-1 and PEA-3 transcription factors as primary mediators of selective, cancer-specific expression of the PEG-Prom. Synthesis of apoptosis-inducing genes, under the control of the CMV promoter, inhibits the growth of both normal and cancer cells, whereas PEG-Prom-mediated expression of these genes kills only cancer cells and spares normal cells. The efficacy of the PEG-Prom as part of a cancer gene therapeutic regimen is further documented by in vivo experiments in which PEG-Prom-controlled expression of an apoptosis-inducing gene completely inhibited prostate cancer xenograft growth in nude mice. These compelling observations indicate that the PEG-Prom, with its cancer-specific expression, provides a means of selectively delivering genes to cancer cells, thereby providing a crucial component in developing effective cancer gene therapies.

Evaluation of Allelic Expression of Imprinted Genes in Adult Human Blood

PubMed Central

Frost, Jennifer M.; Monk, Dave; Stojilkovic-Mikic, Taita; Woodfine, Kathryn; Chitty, Lyn S.; Murrell, Adele; Stanier, Philip; Moore, Gudrun E.

2010-01-01

Background Imprinted genes are expressed from only one allele in a parent-of-origin dependent manner. Loss of imprinted (LOI) expression can result in a variety of human disorders and is frequently reported in cancer. Biallelic expression of imprinted genes in adult blood has been suggested as a useful biomarker and is currently being investigated in colorectal cancer. In general, the expression profiles of imprinted genes are well characterised during human and mouse fetal development, but not in human adults. Methodology/Principal Findings We investigated quantitative expression of 36 imprinted genes in adult human peripheral blood leukocytes obtained from healthy individuals. Allelic expression was also investigated in B and T lymphocytes and myeloid cells. We found that 21 genes were essentially undetectable in adult blood. Only six genes were demonstrably monoallelic, and most importantly, we found that nine genes were either biallelic or showed variable expression in different individuals. Separated leukocyte populations showed the same expression patterns as whole blood. Differential methylation at each of the imprinting control loci analysed was maintained, including regions that contained biallelically expressed genes. This suggests in some cases methylation has become uncoupled from its role in regulating gene expression. Conclusions/Significance We conclude that only a limited set of imprinted genes, including IGF2 and SNRPN, may be useful for LOI cancer biomarker studies. In addition, blood is not a good tissue to use for the discovery of new imprinted genes. Finally, lymphocyte DNA methylation status in the adult may not always be a reliable indicator of monoallelic gene expression. PMID:21042416

Evaluation and selection of reliable reference genes for gene expression under abiotic stress in cotton (Gossypium hirsutum L.).

PubMed

Wang, Min; Wang, Qinglian; Zhang, Baohong

2013-11-01

Reference genes are critical for normalization of the gene expression level of target genes. The widely used housekeeping genes may change their expression levels at different tissue under different treatment or stress conditions. Therefore, systematical evaluation on the housekeeping genes is required for gene expression analysis. Up to date, no work was performed to evaluate the housekeeping genes in cotton under stress treatment. In this study, we chose 10 housekeeping genes to systematically assess their expression levels at two different tissues (leaves and roots) under two different abiotic stresses (salt and drought) with three different concentrations. Our results show that there is no best reference gene for all tissues at all stress conditions. The reliable reference gene should be selected based on a specific condition. For example, under salt stress, UBQ7, GAPDH and EF1A8 are better reference genes in leaves; TUA10, UBQ7, CYP1, GAPDH and EF1A8 were better in roots. Under drought stress, UBQ7, EF1A8, TUA10, and GAPDH showed less variety of expression level in leaves and roots. Thus, it is better to identify reliable reference genes first before performing any gene expression analysis. However, using a combination of housekeeping genes as reference gene may provide a new strategy for normalization of gene expression. In this study, we found that combination of four housekeeping genes worked well as reference genes under all the stress conditions. © 2013.

The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes.

PubMed

Gautier, Aude; Le Gac, Florence; Lareyre, Jean-Jacques

2011-02-01

The gonadal soma-derived factor (GSDF) belongs to the transforming growth factor-β superfamily and is conserved in teleostean fish species. Gsdf is specifically expressed in the gonads, and gene expression is restricted to the granulosa and Sertoli cells in trout and medaka. The gsdf gene expression is correlated to early testis differentiation in medaka and was shown to stimulate primordial germ cell and spermatogonia proliferation in trout. In the present study, we show that the gsdf gene localizes to a syntenic chromosomal fragment conserved among vertebrates although no gsdf-related gene is detected on the corresponding genomic region in tetrapods. We demonstrate using quantitative RT-PCR that most of the genes localized in the synteny are specifically expressed in medaka gonads. Gsdf is the only gene of the synteny with a much higher expression in the testis compared to the ovary. In contrast, gene expression pattern analysis of the gsdf surrounding genes (nup54, aff1, klhl8, sdad1, and ptpn13) indicates that these genes are preferentially expressed in the female gonads. The tissue distribution of these genes is highly similar in medaka and zebrafish, two teleostean species that have diverged more than 110 million years ago. The cellular localization of these genes was determined in medaka gonads using the whole-mount in situ hybridization technique. We confirm that gsdf gene expression is restricted to Sertoli and granulosa cells in contact with the premeiotic and meiotic cells. The nup54 gene is expressed in spermatocytes and previtellogenic oocytes. Transcripts corresponding to the ovary-specific genes (aff1, klhl8, and sdad1) are detected only in previtellogenic oocytes. No expression was detected in the gonocytes in 10 dpf embryos. In conclusion, we show that the gsdf gene localizes to a syntenic chromosomal fragment harboring evolutionary conserved genes in vertebrates. These genes are preferentially expressed in previtelloogenic oocytes, and thus, they display a different cellular localization compared to that of the gsdf gene indicating that the later gene is not co-regulated. Interestingly, our study identifies new clustered genes that are specifically expressed in previtellogenic oocytes (nup54, aff1, klhl8, sdad1). Copyright © 2010 Elsevier B.V. All rights reserved.

Single cell transcriptome analysis of MCF-7 reveals consistently and inconsistently expressed gene groups each associated with distinct cellular localization and functions

PubMed Central

Chen, Tzu-Han; Shiau, Hsin-Chieh

2018-01-01

Single cell transcriptome (SCT) analysis provides superior resolution to illustrate tumor cell heterogeneity for clinical implications. We characterized four SCTs of MCF-7 using 143 housekeeping genes (HKGs) as control, of which lactate dehydrogenase B (LDHB) expression is silenced. These SCT libraries mapped to 11,423, 11,486, 10,380, and 11,306 RefSeq genes (UCSC), respectively. High consistency in HKG expression levels across all four SCTs, along with transcriptional silencing of LDHB, was observed, suggesting a high sensitivity and reproducibility of the SCT analysis. Cross-library comparison on expression levels by scatter plotting revealed a linear correlation and an 83–94% overlap in transcript isoforms and expressed genes were also observed. To gain insight of transcriptional diversity among the SCTs, expressed genes were split into consistently expressed (CE) (expressed in all SCTs) and inconsistently expressed (IE) (expressed in some but not all SCTs) genes for further characterization, along with the 142 expressed HKGs as a reference. Distinct transcriptional strengths were found among these groups, with averages of 1,612.0, 88.0 and 1.2 FPKM for HKGs, CE and IE, respectively. Comparison between CE and IE groups further indicated that expressions of CE genes vary more significantly than that of IE genes. Gene Ontology analysis indicated that proteins encoded by CE genes are mainly involved in fundamental intracellular activities, while proteins encoded by IE genes are mainly for extracellular activities, especially acting as receptors or ion channels. The diversified gene expressions, especially for those encoded by IE genes, may contribute to cancer drug resistance. PMID:29920548

Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants.

PubMed

Kudo, Toru; Sasaki, Yohei; Terashima, Shin; Matsuda-Imai, Noriko; Takano, Tomoyuki; Saito, Misa; Kanno, Maasa; Ozaki, Soichi; Suwabe, Keita; Suzuki, Go; Watanabe, Masao; Matsuoka, Makoto; Takayama, Seiji; Yano, Kentaro

2016-10-13

In quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes. Recently emerging RNA sequencing (RNA-seq) provides an ideal resource for comprehensive exploration of reference genes since this method is capable of detecting all expressed genes, in principle including even unknown genes. We report the results of a comprehensive exploration of reference genes using public RNA-seq data from plants such as Arabidopsis thaliana (Arabidopsis), Glycine max (soybean), Solanum lycopersicum (tomato) and Oryza sativa (rice). To select reference genes suitable for the broadest experimental conditions possible, candidates were surveyed by the following four steps: (1) evaluation of the basal expression level of each gene in each experiment; (2) evaluation of the expression stability of each gene in each experiment; (3) evaluation of the expression stability of each gene across the experiments; and (4) selection of top-ranked genes, after ranking according to the number of experiments in which the gene was expressed stably. Employing this procedure, 13, 10, 12 and 21 top candidates for reference genes were proposed in Arabidopsis, soybean, tomato and rice, respectively. Microarray expression data confirmed that the expression of the proposed reference genes under broad experimental conditions was more stable than that of commonly used reference genes. These novel reference genes will be useful for analyzing gene expression profiles across experiments carried out under various experimental conditions.

Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling.

PubMed

Hinchliffe, Doug J; Meredith, William R; Yeater, Kathleen M; Kim, Hee Jin; Woodward, Andrew W; Chen, Z Jeffrey; Triplett, Barbara A

2010-05-01

Gene expression profiles of developing cotton (Gossypium hirsutum L.) fibers from two near-isogenic lines (NILs) that differ in fiber-bundle strength, short-fiber content, and in fewer than two genetic loci were compared using an oligonucleotide microarray. Fiber gene expression was compared at five time points spanning fiber elongation and secondary cell wall (SCW) biosynthesis. Fiber samples were collected from field plots in a randomized, complete block design, with three spatially distinct biological replications for each NIL at each time point. Microarray hybridizations were performed in a loop experimental design that allowed comparisons of fiber gene expression profiles as a function of time between the two NILs. Overall, developmental expression patterns revealed by the microarray experiment agreed with previously reported cotton fiber gene expression patterns for specific genes. Additionally, genes expressed coordinately with the onset of SCW biosynthesis in cotton fiber correlated with gene expression patterns of other SCW-producing plant tissues. Functional classification and enrichment analysis of differentially expressed genes between the two NILs revealed that genes associated with SCW biosynthesis were significantly up-regulated in fibers of the high-fiber quality line at the transition stage of cotton fiber development. For independent corroboration of the microarray results, 15 genes were selected for quantitative reverse transcription PCR analysis of fiber gene expression. These analyses, conducted over multiple field years, confirmed the temporal difference in fiber gene expression between the two NILs. We hypothesize that the loci conferring temporal differences in fiber gene expression between the NILs are important regulatory sequences that offer the potential for more targeted manipulation of cotton fiber quality.

Evolutionary conservation of vertebrate notochord genes in the ascidian Ciona intestinalis.

PubMed

Kugler, Jamie E; Passamaneck, Yale J; Feldman, Taya G; Beh, Jeni; Regnier, Todd W; Di Gregorio, Anna

2008-11-01

To reconstruct a minimum complement of notochord genes evolutionarily conserved across chordates, we scanned the Ciona intestinalis genome using the sequences of 182 genes reported to be expressed in the notochord of different vertebrates and identified 139 candidate notochord genes. For 66 of these Ciona genes expression data were already available, hence we analyzed the expression of the remaining 73 genes and found notochord expression for 20. The predicted products of the newly identified notochord genes range from the transcription factors Ci-XBPa and Ci-miER1 to extracellular matrix proteins. We examined the expression of the newly identified notochord genes in embryos ectopically expressing Ciona Brachyury (Ci-Bra) and in embryos expressing a repressor form of this transcription factor in the notochord, and we found that while a subset of the genes examined are clearly responsive to Ci-Bra, other genes are not affected by alterations in its levels. We provide a first description of notochord genes that are not evidently influenced by the ectopic expression of Ci-Bra and we propose alternative regulatory mechanisms that might control their transcription. Copyright 2008 Wiley-Liss, Inc.

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions.

PubMed

Versluis, Dennis; D'Andrea, Marco Maria; Ramiro Garcia, Javier; Leimena, Milkha M; Hugenholtz, Floor; Zhang, Jing; Öztürk, Başak; Nylund, Lotta; Sipkema, Detmer; van Schaik, Willem; de Vos, Willem M; Kleerebezem, Michiel; Smidt, Hauke; van Passel, Mark W J

2015-07-08

Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance.

Clustering cancer gene expression data by projective clustering ensemble

PubMed Central

Yu, Xianxue; Yu, Guoxian

2017-01-01

Gene expression data analysis has paramount implications for gene treatments, cancer diagnosis and other domains. Clustering is an important and promising tool to analyze gene expression data. Gene expression data is often characterized by a large amount of genes but with limited samples, thus various projective clustering techniques and ensemble techniques have been suggested to combat with these challenges. However, it is rather challenging to synergy these two kinds of techniques together to avoid the curse of dimensionality problem and to boost the performance of gene expression data clustering. In this paper, we employ a projective clustering ensemble (PCE) to integrate the advantages of projective clustering and ensemble clustering, and to avoid the dilemma of combining multiple projective clusterings. Our experimental results on publicly available cancer gene expression data show PCE can improve the quality of clustering gene expression data by at least 4.5% (on average) than other related techniques, including dimensionality reduction based single clustering and ensemble approaches. The empirical study demonstrates that, to further boost the performance of clustering cancer gene expression data, it is necessary and promising to synergy projective clustering with ensemble clustering. PCE can serve as an effective alternative technique for clustering gene expression data. PMID:28234920

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

NASA Astrophysics Data System (ADS)

Versluis, Dennis; D'Andrea, Marco Maria; Ramiro Garcia, Javier; Leimena, Milkha M.; Hugenholtz, Floor; Zhang, Jing; Öztürk, Başak; Nylund, Lotta; Sipkema, Detmer; Schaik, Willem Van; de Vos, Willem M.; Kleerebezem, Michiel; Smidt, Hauke; Passel, Mark W. J. Van

2015-07-01

Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance.

Involvement of Resveratrol and ω-3 Polyunsaturated Fatty Acids on Sirtuin 1 Gene Expression in THP1 Cells.

PubMed

Tsuchiya, Takafumi; Endo, Ayano; Tsujikado, Kyoko; Inukai, Toshihiko

2017-10-01

Resveratrol, a kind of polyphenol, has the potential to activate the longevity gene in several cells, in the same manner as calorie restriction. We investigated the effect of resveratrol and ω-3-line polyunsaturated fatty acid on surtuin 1 (SIRT1) gene expression in human monocytes (THP1) cells. We examined the gene expression of THP1 cells using real-time polymerase chain reaction and Western blotting analysis. Resveratol, eicosapentaenoic acid (EPA) and docosahexaeanoic acid (DHA) as n-3 polyunsaturated fatty acid were added on THP1 cells. We observed the changes in the SIRT1 gene expression in those cells, under various doses of agents and in time courses. Then, we examined the interaction of glucose and mannitol on those agents׳ effect of the gene expression. The concentration range of glucose and mannitol was from 5-20mM, respectively. The SIRT1 gene expression could be defined in 24 and 48 hours both in real-time polymerase chain reaction analysis and in Western blotting. Resveratrol showed SIRT1 gene expression in a dose-dependent manner in the range of 0-20μM in both analyses. Although EPA at 10μM showed marked increase in SIRT1 gene expression compared to control condition in Western blotting, this phenomenon was not in dose-dependent manner. DHA did not exhibit any augmentation of SIRT1 gene expression in a dose-dependent manner in the range of 0-20μM in both analyses. We refined the dose-dependent inhibition of the SIRT1 gene expression within 20mM glucose medium. Although 20mM did not exhibit any inhibition, 10μM resveratrol induced the gene expression compared to control medium. Both 5 and 15mM mannitol medium did not significantly alter basic gene expression and 10μM resveratrol-induced gene expression. The present results suggest that resveratrol and EPA, but not DHA, markedly activated the SIRT1 gene expression in THP1 cells, and that high glucose medium could inhibit the basic gene expression, but not powerful resveratrol-induced gene expression, in those cells. Copyright © 2017 Southern Society for Clinical Investigation. Published by Elsevier Inc. All rights reserved.

Influence of Genetic Variations in Selenoprotein Genes on the Pattern of Gene Expression after Supplementation with Brazil Nuts

PubMed Central

Rogero, Marcelo M.; Hesketh, John

2017-01-01

Selenium (Se) is an essential micronutrient for human health. Its beneficial effects are exerted by selenoproteins, which can be quantified in blood and used as molecular biomarkers of Se status. We hypothesize that the presence of genetic polymorphisms in selenoprotein genes may: (1) influence the gene expression of specific selenoproteins and (2) influence the pattern of global gene expression after Brazil nut supplementation. The study was conducted with 130 healthy volunteers in Sao Paulo, Brazil, who consumed one Brazil nut (300 μg/Se) a day for eight weeks. Gene expression of GPX1 and SELENOP and genotyping were measured by real-time PCR using TaqMan Assays. Global gene expression was assessed by microarray using Illumina HumanHT-12 v4 BeadChips. Brazil nut supplementation significantly increased GPX1 mRNA expression only in subjects with CC genotype at rs1050450 (p < 0.05). SELENOP mRNA expression was significantly higher in A-carriers at rs7579 either before or after supplementation (p < 0.05). Genotype for rs713041 in GPX4 affected the pattern of blood cell global gene expression. Genetic variations in selenoprotein genes modulated both GPX1 and SELENOP selenoprotein gene expression and global gene expression in response to Brazil nut supplementation. PMID:28696394

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction.

PubMed

Yu, Yao; Tu, Kang; Zheng, Siyuan; Li, Yun; Ding, Guohui; Ping, Jie; Hao, Pei; Li, Yixue

2009-08-25

In the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing and analyzing in scientific researches. In our work, we integrated gene expression information from Gene Expression Omnibus (GEO), biomedical ontology from Medical Subject Headings (MeSH) and signaling pathway knowledge from sigPathway entries to develop a context mining tool for gene expression analysis - GEOGLE. GEOGLE offers a rapid and convenient way for searching relevant experimental datasets, pathways and biological terms according to multiple types of queries: including biomedical vocabularies, GDS IDs, gene IDs, pathway names and signature list. Moreover, GEOGLE summarizes the signature genes from a subset of GDSes and estimates the correlation between gene expression and the phenotypic distinction with an integrated p value. This approach performing global searching of expression data may expand the traditional way of collecting heterogeneous gene expression experiment data. GEOGLE is a novel tool that provides researchers a quantitative way to understand the correlation between gene expression and phenotypic distinction through meta-analysis of gene expression datasets from different experiments, as well as the biological meaning behind. The web site and user guide of GEOGLE are available at: http://omics.biosino.org:14000/kweb/workflow.jsp?id=00020.

Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.)

PubMed Central

2010-01-01

Background Perennial ryegrass (Lolium perenne L.) is an important pasture and turf crop. Biotechniques such as gene expression studies are being employed to improve traits in this temperate grass. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is among the best methods available for determining changes in gene expression. Before analysis of target gene expression, it is essential to select an appropriate normalisation strategy to control for non-specific variation between samples. Reference genes that have stable expression at different biological and physiological states can be effectively used for normalisation; however, their expression stability must be validated before use. Results Existing Serial Analysis of Gene Expression data were queried to identify six moderately expressed genes that had relatively stable gene expression throughout the year. These six candidate reference genes (eukaryotic elongation factor 1 alpha, eEF1A; TAT-binding protein homolog 1, TBP-1; eukaryotic translation initiation factor 4 alpha, eIF4A; YT521-B-like protein family protein, YT521-B; histone 3, H3; ubiquitin-conjugating enzyme, E2) were validated for qRT-PCR normalisation in 442 diverse perennial ryegrass (Lolium perenne L.) samples sourced from field- and laboratory-grown plants under a wide range of experimental conditions. Eukaryotic EF1A is encoded by members of a multigene family exhibiting differential expression and necessitated the expression analysis of different eEF1A encoding genes; a highly expressed eEF1A (h), a moderately, but stably expressed eEF1A (s), and combined expression of multigene eEF1A (m). NormFinder identified eEF1A (s) and YT521-B as the best combination of two genes for normalisation of gene expression data in perennial ryegrass following different defoliation management in the field. Conclusions This study is unique in the magnitude of samples tested with the inclusion of numerous field-grown samples, helping pave the way to conduct gene expression studies in perennial biomass crops under field-conditions. From our study several stably expressed reference genes have been validated. This provides useful candidates for reference gene selection in perennial ryegrass under conditions other than those tested here. PMID:20089196

DNMT3B modulates the expression of cancer-related genes and downregulates the expression of the gene VAV3 via methylation

PubMed Central

Peralta-Arrieta, Irlanda; Hernández-Sotelo, Daniel; Castro-Coronel, Yaneth; Leyva-Vázquez, Marco Antonio; Illades-Aguiar, Berenice

2017-01-01

Altered promoter DNA methylation is one of the most important epigenetic abnormalities in human cancer. DNMT3B, de novo methyltransferase, is clearly related to abnormal methylation of tumour suppressor genes, DNA repair genes and its overexpression contributes to oncogenic processes and tumorigenesis in vivo. The purpose of this study was to assess the effect of the overexpression of DNMT3B in HaCaT cells on global gene expression and on the methylation of selected genes to the identification of genes that can be target of DNMT3B. We found that the overexpression of DNMT3B in HaCaT cells, modulate the expression of genes related to cancer, downregulated the expression of 151 genes with CpG islands and downregulated the expression of the VAV3 gene via methylation of its promoter. These results highlight the importance of DNMT3B in gene expression and human cancer. PMID:28123849

DNMT3B modulates the expression of cancer-related genes and downregulates the expression of the gene VAV3 via methylation.

PubMed

Peralta-Arrieta, Irlanda; Hernández-Sotelo, Daniel; Castro-Coronel, Yaneth; Leyva-Vázquez, Marco Antonio; Illades-Aguiar, Berenice

2017-01-01

Altered promoter DNA methylation is one of the most important epigenetic abnormalities in human cancer. DNMT3B, de novo methyltransferase, is clearly related to abnormal methylation of tumour suppressor genes, DNA repair genes and its overexpression contributes to oncogenic processes and tumorigenesis in vivo . The purpose of this study was to assess the effect of the overexpression of DNMT3B in HaCaT cells on global gene expression and on the methylation of selected genes to the identification of genes that can be target of DNMT3B. We found that the overexpression of DNMT3B in HaCaT cells, modulate the expression of genes related to cancer, downregulated the expression of 151 genes with CpG islands and downregulated the expression of the VAV3 gene via methylation of its promoter. These results highlight the importance of DNMT3B in gene expression and human cancer.

Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks.

PubMed

Yeung, Enoch; Dy, Aaron J; Martin, Kyle B; Ng, Andrew H; Del Vecchio, Domitilla; Beck, James L; Collins, James J; Murray, Richard M

2017-07-26

Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks. We compare expression of induced genes arranged in convergent, divergent, or tandem orientations. Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem-oriented genes. Orientation affects gene expression whether one or both genes are induced. We postulate that transcriptional interference in divergent and tandem genes, mediated by supercoiling, can explain differences in expression and validate this hypothesis through modeling and in vitro supercoiling relaxation experiments. Treatment with gyrase abrogated intergenic context effects, bringing expression levels within 30% of each other. We rebuilt the toggle switch with convergent genes, taking advantage of supercoiling effects to improve threshold detection and switch stability. Copyright © 2017 Elsevier Inc. All rights reserved.

Differential gene expression in queen–worker caste determination in bumble-bees

PubMed Central

Pereboom, Jeffrey J. M; Jordan, William C; Sumner, Seirian; Hammond, Robert L; Bourke, Andrew F. G

2005-01-01

Investigating how differential gene expression underlies caste determination in the social Hymenoptera is central to understanding how variation in gene expression underlies adaptive phenotypic diversity. We investigated for the first time the association between differential gene expression and queen–worker caste determination in the bumble-bee Bombus terrestris. Using suppression subtractive hybridization we isolated 12 genes that were differentially expressed in queen- and worker-destined larvae. We found that the sets of genes underlying caste differences in larvae and adults failed to overlap greatly. We also found that B. terrestris shares some of the genes whose differential expression is associated with caste determination in the honeybee, Apis mellifera, but their expression patterns were not identical. Instead, we found B. terrestris to exhibit a novel pattern, whereby most genes upregulated (i.e. showing relatively higher levels of expression) in queen-destined larvae early in development were upregulated in worker-destined larvae late in development. Overall, our results suggest that caste determination in B. terrestris involves a difference not so much in the identity of genes expressed by queen- and worker-destined larvae, but primarily in the relative timing of their expression. This conclusion is of potential importance in the further study of phenotypic diversification via differential gene expression. PMID:16024376

Regulatory systems for hypoxia-inducible gene expression in ischemic heart disease gene therapy.

PubMed

Kim, Hyun Ah; Rhim, Taiyoun; Lee, Minhyung

2011-07-18

Ischemic heart diseases are caused by narrowed coronary arteries that decrease the blood supply to the myocardium. In the ischemic myocardium, hypoxia-responsive genes are up-regulated by hypoxia-inducible factor-1 (HIF-1). Gene therapy for ischemic heart diseases uses genes encoding angiogenic growth factors and anti-apoptotic proteins as therapeutic genes. These genes increase blood supply into the myocardium by angiogenesis and protect cardiomyocytes from cell death. However, non-specific expression of these genes in normal tissues may be harmful, since growth factors and anti-apoptotic proteins may induce tumor growth. Therefore, tight gene regulation is required to limit gene expression to ischemic tissues, to avoid unwanted side effects. For this purpose, various gene expression strategies have been developed for ischemic-specific gene expression. Transcriptional, post-transcriptional, and post-translational regulatory strategies have been developed and evaluated in ischemic heart disease animal models. The regulatory systems can limit therapeutic gene expression to ischemic tissues and increase the efficiency of gene therapy. In this review, recent progresses in ischemic-specific gene expression systems are presented, and their applications to ischemic heart diseases are discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

Expression patterns of WRKY genes in di-haploid Populus simonii × P. nigra in response to salinity stress revealed by quantitative real-time PCR and RNA sequencing.

PubMed

Wang, Shengji; Wang, Jiying; Yao, Wenjing; Zhou, Boru; Li, Renhua; Jiang, Tingbo

2014-10-01

Spatio-temporal expression patterns of 13 out of 119 poplar WRKY genes indicated dynamic and tissue-specific roles of WRKY family proteins in salinity stress tolerance. To understand the expression patterns of poplar WRKY genes under salinity stress, 51 of the 119 WRKY genes were selected from di-haploid Populus simonii × P. nigra by quantitative real-time PCR (qRT-PCR). We used qRT-PCR to profile the expression of the top 13 genes under salinity stress across seven time points, and employed RNA-Seq platforms to cross-validate it. Results demonstrated that all the 13 WRKY genes were expressed in root, stem, and leaf tissues, but their expression levels and overall patterns varied notably in these tissues. Regarding overall gene expression in roots, the 13 genes were significantly highly expressed at all six time points after the treatment, reaching the plateau of expression at hour 9. In leaves, the 13 genes were similarly up-regulated from 3 to 12 h in response to NaCl treatment. In stems, however, expression levels of the 13 genes did not show significant changes after the NaCl treatment. Regarding individual gene expression across the time points and the three tissues, the 13 genes can be classified into three clusters: the lowly expressed Cluster 1 containing PthWRKY28, 45 and 105; intermediately expressed Clusters 2 including PthWRKY56, 88 and 116; and highly expressed Cluster 3 consisting of PthWRKY41, 44, 51, 61, 62, 75 and 106. In general, genes in Cluster 2 and 3 displayed a dynamic pattern of "induced amplification-recovering", suggesting that these WRKY genes and corresponding pathways may play a critical role in mediating salt response and tolerance in a dynamic and tissue-specific manner.

Hox gene expression during postlarval development of the polychaete Alitta virens.

PubMed

Bakalenko, Nadezhda I; Novikova, Elena L; Nesterenko, Alexander Y; Kulakova, Milana A

2013-05-01

Hox genes are the family of transcription factors that play a key role in the patterning of the anterior-posterior axis of all bilaterian animals. These genes display clustered organization and colinear expression. Expression boundaries of individual Hox genes usually correspond with morphological boundaries of the body. Previously, we studied Hox gene expression during larval development of the polychaete Alitta virens (formerly Nereis virens) and discovered that Hox genes are expressed in nereid larva according to the spatial colinearity principle. Adult Alitta virens consist of multiple morphologically similar segments, which are formed sequentially in the growth zone. Since the worm grows for most of its life, postlarval segments constantly change their position along the anterior-posterior axis. We studied the expression dynamics of the Hox cluster during postlarval development of the nereid Alitta virens and found that 8 out of 11 Hox genes are transcribed as wide gene-specific gradients in the ventral nerve cord, ectoderm, and mesoderm. The expression domains constantly shift in accordance with the changing proportions of the growing worm, so expression domains of most Hox genes do not have stable anterior or/and posterior boundaries.In the course of our study, we revealed long antisense RNA (asRNA) for some Hox genes. Expression patterns of two of these genes were analyzed using whole-mount in-situ hybridization. This is the first discovery of antisense RNA for Hox genes in Lophotrochozoa. Hox gene expression in juvenile A. virens differs significantly from Hox gene expression patterns both in A. virens larva and in other Bilateria.We suppose that the postlarval function of the Hox genes in this polychaete is to establish and maintain positional coordinates in a constantly growing body, as opposed to creating morphological difference between segments.

Per tree estimates with n-tree distance sampling: an application to increment core data

Treesearch

Thomas B. Lynch; Robert F. Wittwer

2002-01-01

Per tree estimates using the n trees nearest a point can be obtained by using a ratio of per unit area estimates from n-tree distance sampling. This ratio was used to estimate average age by d.b.h. classes for cottonwood trees (Populus deltoides Bartr. ex Marsh.) on the Cimarron National Grassland. Increment...

A form of two-phase sampling utilizing regression analysis

Treesearch

Michael A. Fiery; John R. Brooks

2007-01-01

A two-phase sampling technique was introduced and tested on several horizontal point sampling inventories of hardwood tracts located in northern West Virginia and western Maryland. In this sampling procedure species and dbh are recorded for all “in-trees” on all sample points. Sawlog merchantable height was recorded on a subsample of intensively measured (second phase...

Estimates of live-tree carbon stores in the Pacific Northwest are sensitive to model selection

Treesearch

Susanna L. Melson; Mark E. Harmon; Jeremy S. Fried; James B. Domingo

2011-01-01

Estimates of live-tree carbon stores are influenced by numerous uncertainties. One of them is model-selection uncertainty: one has to choose among multiple empirical equations and conversion factors that can be plausibly justified as locally applicable to calculate the carbon store from inventory measurements such as tree height and diameter at breast height (DBH)....

Establishment of white spruce growth trial in an aspen understory

Treesearch

Chris Maundrell; C. Hawkins

2001-01-01

A conifer release trial was established in a 45-year-old aspen overstory stand in Northeast British Columbia, Canada. Thinning occurred from 0 to 100% in increments of approximately 10% to yield a total of ten units. Treatment consisted of physically cutting aspen stems at the root collar or girdling at breast height (d.b.h.) for trees 10 cm d...

D.B.H. and Survival Analysis: A New Methodology for Assessing Forest Inventory Mortality

Treesearch

Christopher W. Woodall; Patricia L. Grambsch; William Thomas

2005-01-01

Tree mortality has typically been assessed in Forest Inventory and Analysis (FIA) studies through summaries of mortality by location, species, and causal agents. Although these methods have historically been used for most of FIA's tree mortality analyses, they are inadequate for robust assessment of mortality trends and dynamics. To offer a new method of analyzing...

Indiana Bat, Myotis Sodalis, Maternity Roosts in the Southern United States

Treesearch

Eric R. Britzke; Michael J. Harvey; Susan C. Loeb

2003-01-01

We characterized Indiana bat (Myotis sodalis) roosting habitat at three maternity colony sites in western North Carolina and easter Tennessee. Using radio telemetry, we tracked six bats a total of 40 bat days (range 4-9 days/bat). In 1999, we located a primary roost in an eastern hemlock (Tsuga canadensis) snag (109 cm DBH) in the...

Silvicultural potential for pre-comercial treatment in northern forest type

Treesearch

H. W.,Jr Hocker

1977-01-01

It is proposed that pre-commercial thinning of young northern hardwood, oak, white pine and spruce-fir stands be carried out using appropriate stocking guides to regulate stand density. Thinning should be carried out when stands are-between 1" and 2" dbh. Pruning of eastern white pine is recommended, while pruning of spruce and yellow birch seems feasible,...

Controlling beech root and stump sprouts using the cut-stump treatment

Treesearch

Jeffery D. Kochenderfer; James N. Kochenderfer; Gary W. Miller

2006-01-01

Application costs and efficacy were determined for cut-stump treatments applied to American beech (Fagus grandifolia Ehrh.) to control root and stump sprouts in central West Virginia. Glyphosate as Glypro (53.8%) was applied to the outer 2 in. of beech stumps from trees >6.0-in. dbh within 1 hour after cutting. In addition to treatment plots,...

Merchantable Volume Table for Ucar in Puerto Rico

Treesearch

John K. Francis

1988-01-01

Ucar (Bucida buceras L.) is a timber tree of the dry forests of islands in and lands surrounding the Caribbean. The wood is attractive and strong but very heavy and hard. Little information and no volume tables were available for the species, however. Fifty trees from forests in Puerto Rico were measured for d.b.h., merchantable height, and diameter...

Reproduction 12 years after seed-tree harvest cutting in Appalachian hardwoods

Treesearch

H. Clay Smith; Robert L. Rosier; K. P. Hammack

1976-01-01

Woody reproduction 12 years after a seed-tree harvest cutting was evaluated for three central Appalachian hardwood sites in West Virginia, including species composition; size, number, and distribution; stem quality; effects of early cultural treatments; and influence of grapevines. Reproduction ranged from 1,250 to 1,700 stems per acre in the 1.0 to 4.9 inch dbh size...

Six-year beechnut production in New Hampshire

Treesearch

William B. Leak; Raymond E. Graber; Raymond E. Graber

1993-01-01

Beechnut production and losses were studied over a 6-year period in 41 northern hardwood stands ranging in age from 10 to 140 years in the White Mountains of New Hampshire. Beechnut production increased consistently with stand age or d.b.h. of dominant trees and percentage of basal area composed of beech. Losses to insects, rodents, and birds before the seed reached...

New Models for Predicting Diameter at Breast Height from Stump Dimensions

Treesearch

James A. Westfall

2010-01-01

Models to predict dbh from stump dimensions are presented for 18 species groups. Data used to fit the models were collected across thirteen states in the northeastern United States. Primarily because of the presence of multiple measurements from each tree, a mixed-effects modeling approach was used to account for the lack of independence among observations. The...

Handbook for predicting slash weight of trees in the Northeast.

Treesearch

Duane R. Freeman; Robert M. Loomis; Peter J. Roussopoulos

1982-01-01

Tables are provided for estimating tree crown weights based on species and diameters (d.b.h.) for 10 conifer and 9 hardwood species or species groups of the North Central and Northeastern United States. Procedures are given for predicting slash weights resulting from: cutting timber, trampling during logging activities, and defect and breakage left on the site after...

Spathodea campanulata Beauv

Treesearch

Kristina F. Connor; John K. Francis

2008-01-01

The African tuliptree - Spathodea campanulata Beauv. - is a medium-sized tree that commonly reaches a height of 21 m but may reach 30 m in some parts of West Africa. In Puerto Rico, the largest African tuliptree measures 35 m tall and 1.75 m in dbh; heart and butt rots are common in trees older than 20 to 25 years that have suffered mechanical or...

Root-Crown Relations of Young Sugar Maple and Yellow Birch

Treesearch

Carl H. Tubbs

1977-01-01

Young forest-grown sugar maple and yellow birch (1 to 6 inches d.b.h.) crowns were mapped and roots excavated. Crown dimensions were compared. Sugar maple roots usually terminated within a few feet of the crown perimeter. Yellow birch roots frequently terminated well outside crown perimeters and roots of birch were more irregularly distributed than those of maple....

Survival, growth, and juvenile-mature correlations in a West Virginia sugar maple provenance test 25 years after establishment

Treesearch

Thomas M. Schuler

1994-01-01

Survival, total height, diameter at breast height (d.b.h.), and stem quality of sugar maple trees of different provenances were compared 25 years after establishment in north-central West Virginia. Provenances were from Michigan, Minnesota, West Virginia, Massachusetts, New Hampshire, Vermont, Maine, and Quebec, Canada. There were significant differences between...

Fire regimes for pine-grassland communities in the southeastern United States

Treesearch

Thomas A. Waldrop; David L. White; Steven M. Jones

1992-01-01

Abstract - Four combinations of season and frequency of burning were applied in Coastal Plain loblolly pine stands over a 43-year period. Overstory species composition and growth were unaffected by treatment. Above-ground portions of small hardwoods Qess than 12.5 cm d.b.h.1 were hilled and replaced by numerous sprouts under periodic summer, periodic winter, and annual...

Red maple development in mixed hardwood stands in West Virginia

Treesearch

Brian Tift

1997-01-01

Recent evidence has shown that red maple (Acer rubrum) may become a more prominent species in eastern mixed hardwood stands. This study will examine the strategies used by red maple to reach dominant and codominant canopy positions on two different stands (one mesic and one drier). Stand level data such as dbh, height, crown class, height class, and...

Underplanting northern red oak in Missouri without herbicides.

Treesearch

Paul S. Johnson

1992-01-01

Describes a provisional assessment of the effectiveness of applying herbicides to woody competitors between 0.5- and 1.5- inches d.b.h. before underplanting northern red oak. Results suggest that no weed control, i.e., not using herbicides, would require only modest increases in the numbers or initial size of nursery stock needed to obtain a given future stocking goal...

The urban forests of Philadelphia

Treesearch

David J. Nowak; Allison R. Bodine; Robert Hoehn; Alexis Ellis; Sarah C. Low; Lara A. Roman; Jason G. Henning; Emily Stephan; Tom Taggert; Ted Endreny

2016-01-01

An analysis of the urban forest in Philadelphia, Pennsylvania, reveals that this city has an estimated 2.9 million trees (encompassing all woody plants greater than 1 inch diameter at breast height [d.b.h]) with tree canopy that covers 20 percent of the city. The most common tree species are spicebush, black cherry, ash, tree-of-heaven, and boxelder, but the most...

Feasibility of utilizing small diameter southern pine for biomass in the Virginia Coastal Plain

Treesearch

Nathan C. Hanzelka; M. Chad Bolding; Scott M. Barrett; Jay Sullivan

2016-01-01

New or retrofitted wood-fired energy plants have increased demand for woody biomass in the stateof Virginia. Loblolly pine (Pinus taeda) commonly serves as a feedstock for these energy plants. Pulpwood conventionally requires a minimum diameter of 4 inches diameter at breast height (DBH) for merchantability, whereas a minimum merchantable diameter...

Tree Growth in Several Tropical Forests of Puerto Rico

Treesearch

Peter L. Weaver

1979-01-01

About 2400 individual stems > 4.1 cm d.b.h., and representing about 100 species, from six plots in three Life Zones, some with edaphic variationand/orsilviculturaltreatment, scattered throughout Puerto Rico, were studied for varying periods, usually ranging from 24 through 30 years but in one instance for only 2 years. Also, more than 11,000 mangrove stems > 1 cm...

Performance of Species-Reciprocal Hybrids Between Slash and Shortleaf Pines

Treesearch

O.O. Wells

1978-01-01

Hybrids between shortleaf and slash pine were made by controlled pollination with each species used alternatively as the female parent. Hybrids with shortleaf as the female parent survived planting better than those with slash as the female parent. In all other respects-height, d.b.h., and resistance to diseases and insects-the species used as female parent did not...

Height and diameter variation in twelve white ash provenance/progeny tests in eastern United States

Treesearch

G. Rink; F.H. Kung

1991-01-01

Results from 12- and 13-year old rangewide provenance/progeny tests of white ash (Fraxinus americana L.) planted at 12 locations throughout the eastern United States are reported. Although heritability of white ash tree height and dbh is high at both the provenance and family levels, the trend in variance components is for increasing provenance and...

A Height–Diameter Curve for Longleaf Pine Plantations in the Gulf Coastal Plain

Treesearch

Daniel Leduc; Jeffery Goelz

2009-01-01

Tree height is a critical component of a complete growth-and-yield model because it is one of the primary components used in volume calculation. To develop an equation to predict total height from dbh for longleaf pine (Pinus palustris Mill.) plantations in the West Gulf region, many different sigmoidal curve forms, weighting functions, and ways of...

Variation among northern red oak provenances in bark thickness:dbh ratios

Treesearch

Matthew S. Russell; Jeffrey O. Dawson

1995-01-01

Differences in bark thickness in relation to diameter at breast height were observed in a 30-32 year old Illinois planting of 32 provenances of northern red oak (Quercus rubra) from throughout its natural range. Bark thickness by itself is often a good indication of relative cambial insulation from fire. Fire resistance in trees can largely be...

Approximation of the breast height diameter distribution of two-cohort stands by mixture models I Parameter estimation

Treesearch

Rafal Podlaski; Francis A. Roesch

2013-01-01

Study assessed the usefulness of various methods for choosing the initial values for the numerical procedures for estimating the parameters of mixture distributions and analysed variety of mixture models to approximate empirical diameter at breast height (dbh) distributions. Two-component mixtures of either the Weibull distribution or the gamma distribution were...

Stand basal-area and tree-diameter growth in red spruce-fir forests in Maine, 1960-80

Treesearch

S.J. Zarnoch; D.A. Gansner; D.S. Powell; T.A. Birch; T.A. Birch

1990-01-01

Stand basal-area change and individual surviving red spruce d.b.h. growth from 1960 to 1980 were analyzed for red spruce-fir stands in Maine. Regression modeling was used to relate these measures of growth to stand and tree conditions and to compare growth throughout the period. Results indicate a decline in growth.

Local and general above-stump biomass functions for loblolly pine and slash pine trees

Treesearch

Carlos A. Gonzalez-Beneke; Salvador Gezan; Tmothy J. Albaugh; H. Lee Allen; Harold E. Burkhart; Thomas R. Fox; Eric J. Jokela; Christopher Maier; Timothy A. Martin; Rafael A. Rubilar; Lisa J. Samuelson

2014-01-01

There is an increasing interest in estimating biomass for loblolly pine (Pinus taeda L.) and slash pine (Pinus elliottii Engelm. var. elliottii), two of the most ecologically and commercially important tree species in North America. The majority of the available individual-tree allometric models are local, relying on stem diameter outside bark at breast height (dbh)...

Individual Tree Biomass Models for Plantation Grown American Sycamore

Treesearch

Regan B. Willson; Bryce E. Schlaegel; Harvey E. Kennedy

1982-01-01

Individual tree volume and green and dry weight equations are derived for American sycamore from a 5-year-old plantation in southeast Arkansas. Two trees have been destructively sampled each year from each of 20 plots. Observations from 168 trees are used to predict tree weight and volume as a function of dbh, total height, age, and initial number of trees. Separate...

Liberation: Acceptable production of tropical forest timber.

Treesearch

Frank H. Wadsworth; Johan Zweede

2006-01-01

Reduced impact logging in an eastern Amazonian terra firme forest left more than half of the next crop trees growing at a rate corresponding to a rotation of more than a century to attain 60-cm dbh. Two years after the logging, in 20 ha of the logged forest, tree competitors around crop trees were eliminated. Competitors were defined as trees whose crowns overtopped...

Effects of Fertilization on the Vegetation Dynamics of Yougn Loblolly Pine Plantations

Treesearch

Ryan McKnight; Eric Heitzman

2004-01-01

We examined growth of loblolly pine (Pinus taeda L.) and non-pine vegetation in three 4- to 6-year-old plantations in Arkansas, Mississippi, and Louisiana that were fertilized with varying rates of N and P. Two years after treatment, pine d.b.h. growth had generally increased with fertilization rate, with significant differences in Arkansas and...

A mixed-effects model for the dbh-height relationship of shortleaf pine (Pinus echinata Mill.)

Treesearch

Chakra B. Budhathoki; Thomas B. Lynch; James M. Guldin

2008-01-01

Individual tree measurements were available from over 200 permanent plots established during 1985-1987 and later remeasured in naturally regenerated even-aged stands of shortleaf pine (Pinus echinata Mill.) in western Arkansas and eastern Oklahoma. The objective of this study was to model shortleaf pine growth in natural stands for the region. As a...

Growth Comparisons of Planted Sweetgum and Sycamore

Treesearch

R. M. Krinard

1988-01-01

From age 18 through age 23, average annual growth of planted sweetgum (Liquidambar styraciflua L.) on Commerce silt loam exceeded growth of sweetgum on Sharkey clay by about 45 percent in diameter at breast height (d.b.h.) and height, 75 percent in basal area, and more than three times in cubic volume. At age 18 on the Commerce soil, sycamore (

Stem quality of oak in 15-year-old stands: influence of species within harvesting treatment and fencing

Treesearch

Kurt W. Gottschalk

1997-01-01

The effect of harvesting treatment, fencing, and species on the stem quality of oak (Quercus spp.) was evaluated in mixed-hardwood stands on the Allegheny Plateau in central Pennsylvania. The regeneration harvests included commercial clearcut that removed most stems ≥ 15 cm dbh and a clearcut with timber stand improvement (TSI) that removed...

Incidence of twolined chestnut borer and Hypoxylon atropunctatum on dead oaks along an acidic deposition gradient from Arkansas to Ohio

Treesearch

R.A. Haack; R.W. Blank

1991-01-01

The incidence of twolined chestnut borer (TLCB), Agrilus bilineatus (Weber), and the canker fungus Hypoxylon atropunctatum (Schw. ex Fr.) Cke. was recoreded on dead oak (Quercus) trees !Y7 cm diameter at breast height (DBH) along an acidic deposition gradient from Arkansas to Ohio in 1989 and 1990. Approximately...

Effects of soil water table regime on tree community species richness and structure of alluvial forest fragments in Southeast Brazil.

PubMed

Silva, A C; Higuchi, P; van den Berg, E

2010-08-01

In order to determine the influence of soil water table fluctuation on tree species richness and structure of alluvial forest fragments, 24 plots were allocated in a point bar forest and 30 plots in five forest fragments located in a floodplain, in the municipality of São Sebastião da Bela Vista, Southeast Brazil, totalizing 54, 10 X 20 m, plots. The information recorded in each plot were the soil water table level, diameter at breast height (dbh), total height and botanical identity off all trees with dbh > 5 cm. The water table fluctuation was assessed through 1 m deep observation wells in each plot. Correlations analysis indicated that sites with shallower water table in the flooding plains had a low number of tree species and high tree density. Although the water table in the point bar remained below the wells during the study period, low tree species richness was observed. There are other events taking place within the point bar forest that assume a high ecological importance, such as the intensive water velocity during flooding and sedimentation processes.

[Vertical distribution of fuels in Pinus yunnanensis forest and related affecting factors].

PubMed

Wang, San; Niu, Shu-Kui; Li, De; Wang, Jing-Hua; Chen, Feng; Sun, Wu

2013-02-01

In order to understand the effects of fuel loadings spatial distribution on forest fire kinds and behaviors, the canopy fuels and floor fuels of Pinus yunnanensis forests with different canopy density, diameter at breast height (DBH), tree height, and stand age and at different altitude, slope grade, position, and aspect in Southwest China were taken as test objects, with the fuel loadings and their spatial distribution characteristics at different vertical layers compared and the fire behaviors in different stands analyzed. The relationships between the fuel loadings and the environmental factors were also analyzed by canonical correspondence analysis (CCA). In different stands, there existed significant differences in the vertical distribution of fuels. Pinus yunnanensis-Qak-Syzygium aromaticum, Pinus yunnanensis-oak, and Pinus yunnanensis forests were likely to occur floor fire but not crown fire, while Pinus yunnanensis-Platycladus orientalis, Pinus yunnanensis-Keteleeria fortune, and Keteleeria fortune-Pinus yunnanensis were not only inclined to occur floor fire, but also, the floor fire could be easily transformed into crown fire. The crown fuels were mainly affected by the stand age, altitude, DBH, and tree height, while the floor fuels were mainly by the canopy density, slope grade, altitude, and stand age.

Improving Lidar-based Aboveground Biomass Estimation with Site Productivity for Central Hardwood Forests, USA

NASA Astrophysics Data System (ADS)

Shao, G.; Gallion, J.; Fei, S.

2016-12-01

Sound forest aboveground biomass estimation is required to monitor diverse forest ecosystems and their impacts on the changing climate. Lidar-based regression models provided promised biomass estimations in most forest ecosystems. However, considerable uncertainties of biomass estimations have been reported in the temperate hardwood and hardwood-dominated mixed forests. Varied site productivities in temperate hardwood forests largely diversified height and diameter growth rates, which significantly reduced the correlation between tree height and diameter at breast height (DBH) in mature and complex forests. It is, therefore, difficult to utilize height-based lidar metrics to predict DBH-based field-measured biomass through a simple regression model regardless the variation of site productivity. In this study, we established a multi-dimension nonlinear regression model incorporating lidar metrics and site productivity classes derived from soil features. In the regression model, lidar metrics provided horizontal and vertical structural information and productivity classes differentiated good and poor forest sites. The selection and combination of lidar metrics were discussed. Multiple regression models were employed and compared. Uncertainty analysis was applied to the best fit model. The effects of site productivity on the lidar-based biomass model were addressed.

[Quantitative relationships of intra- and interspecific competition in Cryptocarya concinna].

PubMed

Zhang, Chi; Huang, Zhongliang; Li, Jiong; Shi, Junhui; Li, Lin

2006-01-01

The monsoon evergreen broad-leaved forest (MEBF) in Dinghushan Nature Reserve (DNR) has been considered as a zonal vegetation in lower subtropical China, with a history of more than 400 years. In this paper, the intra- and interspecific competition intensity in Cryptocarya concinna, one of the constructive species in MEBF in DNR was quantitatively analyzed by Hegyi single-tree competition index model. The results showed that the intraspecific competition intensity in C. concinna decreased gradually with increasing tree diameter. For C. concinna, its intraspecific competition was weaker than its interspecific competition with Aporosa yunnanensis. The competition intensity of interspecific competition with C. concinna followed the order of A. yunnanensis > Schima superba > Gironniera subaequalis > Acmena acuminatissima > Castanopsis chinensis > Syzygium rehderianum > Pygeum topengii > Blastus cochinchinensis > Sarcosperma laurinum > Pterospermum lanceaefolium > Cryptocarya chinensis. The relationship of the DBH of objective tree and the competition intensity between competitive tree and objective tree in the whole forest and C. concinna population nearly conformed to power function, while that between other competitive tree and the objective C. concinna tree conformed to logarithm function. There was a significantly negative correlation between the competition intensity and the DBH of objective tree.

Genomic DNA-based absolute quantification of gene expression in Vitis

USDA-ARS?s Scientific Manuscript database

Many studies in which gene expression is quantified by polymerase chain reaction represent the expression of a gene of interest (GOI) relative to that of a reference gene (RG). Relative expression is founded on the assumptions that RG expression is stable across samples, treatments, organs, etc., an...

Co-regulation of the atrial natriuretic factor and cardiac myosin light chain-2 genes during alpha-adrenergic stimulation of neonatal rat ventricular cells. Identification of cis sequences within an embryonic and a constitutive contractile protein gene which mediate inducible expression.

PubMed

Knowlton, K U; Baracchini, E; Ross, R S; Harris, A N; Henderson, S A; Evans, S M; Glembotski, C C; Chien, K R

1991-04-25

To study the mechanisms which mediate the transcriptional activation of cardiac genes during alpha adrenergic stimulation, the present study examined the regulated expression of three cardiac genes, a ventricular embryonic gene (atrial natriuretic factor, ANF), a constitutively expressed contractile protein gene (cardiac MLC-2), and a cardiac sodium channel gene. alpha 1-Adrenergic stimulation activates the expression and release of ANF from neonatal ventricular cells. As assessed by RNase protection analyses, treatment with alpha-adrenergic agonists increases the steady-state levels of ANF mRNA by greater than 15-fold. However, a rat cardiac sodium channel gene mRNA is not induced, indicating that alpha-adrenergic stimulation does not lead to an increase in the expression of all cardiac genes. Studies employing a series of rat ANF luciferase and rat MLC-2 luciferase fusion genes identify 315- and 92-base pair cis regulatory sequences within an embryonic gene (ANF) and a constitutively expressed contractile protein gene (MLC-2), respectively, which mediate alpha-adrenergic-inducible gene expression. Transfection of various ANF luciferase reporters into neonatal rat ventricular cells demonstrated that upstream sequences which mediate tissue-specific expression (-3003 to -638) can be segregated from those responsible for inducibility. The lack of inducibility of a cardiac Na+ channel gene, and the segregation of ANF gene sequences which mediate cardiac specific from those which mediate inducible expression, provides further insight into the relationship between muscle-specific and inducible expression during cardiac myocyte hypertrophy. Based on these results, a testable model is proposed for the induction of embryonic cardiac genes and constitutively expressed contractile protein genes and the noninducibility of a subset of cardiac genes during alpha-adrenergic stimulation of neonatal rat ventricular cells.

A framework for analyzing the relationship between gene expression and morphological, topological, and dynamical patterns in neuronal networks.

PubMed

de Arruda, Henrique Ferraz; Comin, Cesar Henrique; Miazaki, Mauro; Viana, Matheus Palhares; Costa, Luciano da Fontoura

2015-04-30

A key point in developmental biology is to understand how gene expression influences the morphological and dynamical patterns that are observed in living beings. In this work we propose a methodology capable of addressing this problem that is based on estimating the mutual information and Pearson correlation between the intensity of gene expression and measurements of several morphological properties of the cells. A similar approach is applied in order to identify effects of gene expression over the system dynamics. Neuronal networks were artificially grown over a lattice by considering a reference model used to generate artificial neurons. The input parameters of the artificial neurons were determined according to two distinct patterns of gene expression and the dynamical response was assessed by considering the integrate-and-fire model. As far as single gene dependence is concerned, we found that the interaction between the gene expression and the network topology, as well as between the former and the dynamics response, is strongly affected by the gene expression pattern. In addition, we observed a high correlation between the gene expression and some topological measurements of the neuronal network for particular patterns of gene expression. To our best understanding, there are no similar analyses to compare with. A proper understanding of gene expression influence requires jointly studying the morphology, topology, and dynamics of neurons. The proposed framework represents a first step towards predicting gene expression patterns from morphology and connectivity. Copyright © 2015. Published by Elsevier B.V.

HOX gene expression in phenotypic and genotypic subgroups and low HOXA gene expression as an adverse prognostic factor in pediatric ALL.

PubMed

Starkova, Julia; Zamostna, Blanka; Mejstrikova, Ester; Krejci, Roman; Drabkin, Harry A; Trka, Jan

2010-12-01

HOX genes play an important role in both normal lymphopoiesis and leukemogenesis. However, HOX expression patterns in leukemia cells compared to normal lymphoid progenitors have not been systematically studied in acute lymphoblastic leukemia (ALL) subtypes. The RNA expression levels of HOXA, HOXB, and CDX1/2 genes were analyzed by qRT-PCR in a cohort of 61 diagnostic pediatric ALL samples and FACS-sorted subpopulations of normal lymphoid progenitors. The RNA expression of HOXA7-10, HOXA13, and HOXB2-4 genes was exclusively detected in leukemic cells and immature progenitors. The RNA expression of HOXB6 and CDX2 genes was exclusively detected in leukemic cells but not in B-lineage cells at any of the studied developmental stages. HOXA3-4, HOXA7, and HOXB3-4 genes were differentially expressed between BCP-ALL and T-ALL subgroups, and among genotypically defined MLL/AF4, TEL/AML1, BCR/ABL, hyperdiploid and normal karyotype subgroups. However, this differential expression did not define specific clusters in hierarchical cluster analysis. HOXA7 gene was low expressed at the RNA level in patients with hyperdiploid leukemia, whereas HOXB7 and CDX2 genes were low expressed in TEL/AML1-positive and BCR/ABL-positive cases, respectively. In contrast to previous findings in acute myeloid leukemia, high HOXA RNA expression was associated with an excellent prognosis in Cox's regression model (P = 0.03). In MLL/AF4-positive ALL, lower HOXA RNA expression correlated with the methylation status of their promoters. HOX gene RNA expression cannot discriminate leukemia subgroups or relative maturity of leukemic cells. However, HOXA RNA expression correlates with prognosis, and particular HOX genes are expressed in specific genotypically characterized subgroups.

Evolution of AGL6-like MADS Box Genes in Grasses (Poaceae): Ovule Expression Is Ancient and Palea Expression Is New[W][OA

PubMed Central

Reinheimer, Renata; Kellogg, Elizabeth A.

2009-01-01

AGAMOUS-like6 (AGL6) genes encode MIKC-type MADS box transcription factors and are closely related to SEPALLATA and AP1/FUL-like genes. Here, we focus on the molecular evolution and expression of the AGL6-like genes in grasses. We have found that AGL6-like genes are expressed in ovules, lodicules (second whorl floral organs), paleas (putative first whorl floral organs), and floral meristems. Each of these expression domains was acquired at a different time in evolution, indicating that each represents a distinct function of the gene product and that the AGL6-like genes are pleiotropic. Expression in the inner integument of the ovule appears to be an ancient expression pattern corresponding to the expression of the gene in the megasporangium and integument in gymnosperms. Expression in floral meristems appears to have been acquired in the angiosperms and expression in second whorl organs in monocots. Early in grass evolution, AGL6-like orthologs acquired a new expression domain in the palea. Stamen expression is variable. Most grasses have a single AGL6-like gene (orthologous to the rice [Oryza sativa] gene MADS6). However, rice and other species of Oryza have a second copy (orthologous to rice MADS17) that appears to be the result of an ancient duplication. PMID:19749151

Untangling the Contributions of Sex-Specific Gene Regulation and X-Chromosome Dosage to Sex-Biased Gene Expression in Caenorhabditis elegans

PubMed Central

Kramer, Maxwell; Rao, Prashant; Ercan, Sevinc

2016-01-01

Dosage compensation mechanisms equalize the level of X chromosome expression between sexes. Yet the X chromosome is often enriched for genes exhibiting sex-biased, i.e., imbalanced expression. The relationship between X chromosome dosage compensation and sex-biased gene expression remains largely unexplored. Most studies determine sex-biased gene expression without distinguishing between contributions from X chromosome copy number (dose) and the animal’s sex. Here, we uncoupled X chromosome dose from sex-specific gene regulation in Caenorhabditis elegans to determine the effect of each on X expression. In early embryogenesis, when dosage compensation is not yet fully active, X chromosome dose drives the hermaphrodite-biased expression of many X-linked genes, including several genes that were shown to be responsible for hermaphrodite fate. A similar effect is seen in the C. elegans germline, where X chromosome dose contributes to higher hermaphrodite X expression, suggesting that lack of dosage compensation in the germline may have a role in supporting higher expression of X chromosomal genes with female-biased functions in the gonad. In the soma, dosage compensation effectively balances X expression between the sexes. As a result, somatic sex-biased expression is almost entirely due to sex-specific gene regulation. These results suggest that lack of dosage compensation in different tissues and developmental stages allow X chromosome copy number to contribute to sex-biased gene expression and function. PMID:27356611

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs.

PubMed

Gálvez, José Héctor; Tai, Helen H; Lagüe, Martin; Zebarth, Bernie J; Strömvik, Martina V

2016-05-19

Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha(-1) was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency.

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs

PubMed Central

Gálvez, José Héctor; Tai, Helen H.; Lagüe, Martin; Zebarth, Bernie J.; Strömvik, Martina V.

2016-01-01

Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha−1 was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency. PMID:27193058

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations

PubMed Central

Peng, Cheng; Shiu, Shin-Han

2016-01-01

Gene co-expression has been widely used to hypothesize gene function through guilt-by association. However, it is not clear to what degree co-expression is informative, whether it can be applied to genes involved in different biological processes, and how the type of dataset impacts inferences about gene functions. Here our goal is to assess the utility and limitations of using co-expression as a criterion to recover functional associations between genes. By determining the percentage of gene pairs in a metabolic pathway with significant expression correlation, we found that many genes in the same pathway do not have similar transcript profiles and the choice of dataset, annotation quality, gene function, expression similarity measure, and clustering approach significantly impacts the ability to recover functional associations between genes using Arabidopsis thaliana as an example. Some datasets are more informative in capturing coordinated expression profiles and larger data sets are not always better. In addition, to recover the maximum number of known pathways and identify candidate genes with similar functions, it is important to explore rather exhaustively multiple dataset combinations, similarity measures, clustering algorithms and parameters. Finally, we validated the biological relevance of co-expression cluster memberships with an independent phenomics dataset and found that genes that consistently cluster with leucine degradation genes tend to have similar leucine levels in mutants. This study provides a framework for obtaining gene functional associations by maximizing the information that can be obtained from gene expression datasets. PMID:27935950

Skin transcriptome profiles associated with coat color in sheep

PubMed Central

2013-01-01

Background Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color. Results There were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category. Conclusion The white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep. PMID:23758853

GEsture: an online hand-drawing tool for gene expression pattern search.

PubMed

Wang, Chunyan; Xu, Yiqing; Wang, Xuelin; Zhang, Li; Wei, Suyun; Ye, Qiaolin; Zhu, Youxiang; Yin, Hengfu; Nainwal, Manoj; Tanon-Reyes, Luis; Cheng, Feng; Yin, Tongming; Ye, Ning

2018-01-01

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a 'desirable' or 'user-defined' pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users' requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.

Juxtaposed genes in 7q21-22 amplicon contribute for two major gastric cancer sub-Types by mutual exclusive expression.

PubMed

Tamilzhalagan, Sembulingam; Muthuswami, Muthulakshmi; Ganesan, Kumaresan

2017-04-01

Genomic Copy Number Variations (CNV) and the associated gene signatures are useful for cancer prognosis, diagnosis, and targeted therapeutics. Earlier, 7q21-22 region was reported for frequent amplification in gastric cancer and potential candidate genes were identified. An analysis of the expression pattern of the 159 genes located in this amplicon revealed the consistent elevated expression of 21 genes in gastric tumors. These genes are closely arranged within the 20 Mb region, and they showed a bimodal expression pattern. SHFM1 and 14 other genes are expressed in intestinal type gastric tumors. COL1A2 and PCOLCE genes of this region are expressed in diffuse type gastric tumors. Similarly, genome-wide expression neighbors of SHFM1 and COL1A2 also showed mutually exclusive expression pattern, and stratify intestinal and diffuse type gastric tumors. The expression of COL1A2 gene-set is associated with poor prognosis, whereas the SHFM1 gene-set is associated with better prognosis among the gastric cancer patients. Despite being physical neighbors, the SHFM1 and COL1A2 genes express differentially in the two major clinical sub-types of gastric cancer in a mutually exclusive manner. The tight gene regulations operating between these juxtaposed genes deserve investigation to understand the molecular regulatory switch defining the determinants of the gastric cancer sub-types. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

[Application of dhfr gene negative Chinese hamster ovary cell line to express hepatitis B virus surface antigen].

PubMed

Yi, Y; Zhang, M; Liu, C

2001-06-01

To set up an efficient expressing system for recombinant hepatitis B virus surface antigen (HBsAg) in dhfr gene negative CHO cell line. HBsAg gene expressing plasmid pCI-dhfr-S was constructed by integrating HBsAg gene into plasmid pCI which carries dhfr gene. The HBsAg expressing cell line was set up by transfection of plasmid pCI-dhfr-S into dhfr gene negative CHO cell line in the way of lipofectin. Under the selective pressure of MTX, 18 of 28 clonized cell lines expressed HBsAg, 4 of them reached a high titer of 1:32 and protein content 1-3 micrograms/ml. In this study, the high level expression of HBsAg demonstrated that the dhfr negative mammalian cell line when recombined with plasmid harboring the corresponding deleted gene can efficiently express the foreign gene. The further steps toward building optimum conditions of the expressing system and the increase of expressed product are under study.

Gene expression inference with deep learning.

PubMed

Chen, Yifei; Li, Yi; Narayan, Rajiv; Subramanian, Aravind; Xie, Xiaohui

2016-06-15

Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes. We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes. D-GEX is available at https://github.com/uci-cbcl/D-GEX CONTACT: xhx@ics.uci.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Gene expression inference with deep learning

PubMed Central

Chen, Yifei; Li, Yi; Narayan, Rajiv; Subramanian, Aravind; Xie, Xiaohui

2016-01-01

Motivation: Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes. Results: We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes. Availability and implementation: D-GEX is available at https://github.com/uci-cbcl/D-GEX. Contact: xhx@ics.uci.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26873929

An atlas of gene expression and gene co-regulation in the human retina.

PubMed

Pinelli, Michele; Carissimo, Annamaria; Cutillo, Luisa; Lai, Ching-Hung; Mutarelli, Margherita; Moretti, Maria Nicoletta; Singh, Marwah Veer; Karali, Marianthi; Carrella, Diego; Pizzo, Mariateresa; Russo, Francesco; Ferrari, Stefano; Ponzin, Diego; Angelini, Claudia; Banfi, Sandro; di Bernardo, Diego

2016-07-08

The human retina is a specialized tissue involved in light stimulus transduction. Despite its unique biology, an accurate reference transcriptome is still missing. Here, we performed gene expression analysis (RNA-seq) of 50 retinal samples from non-visually impaired post-mortem donors. We identified novel transcripts with high confidence (Observed Transcriptome (ObsT)) and quantified the expression level of known transcripts (Reference Transcriptome (RefT)). The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. The RefT included 13 792 genes across 94 521 known transcripts. Mitochondrial genes were among the most highly expressed, accounting for about 10% of the reads. Of all the protein-coding genes in Gencode, 65% are expressed in the retina. We exploited inter-individual variability in gene expression to infer a gene co-expression network and to identify genes specifically expressed in photoreceptor cells. We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. RNA-seq data and the gene co-expression network are available online (http://retina.tigem.it). © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Selection and validation of reference genes for gene expression analysis in apomictic and sexual Cenchrus ciliaris

PubMed Central

2013-01-01

Background Apomixis is a naturally occurring asexual mode of seed reproduction resulting in offspring genetically identical to the maternal plant. Identifying differential gene expression patterns between apomictic and sexual plants is valuable to help deconstruct the trait. Quantitative RT-PCR (qRT-PCR) is a popular method for analyzing gene expression. Normalizing gene expression data using proper reference genes which show stable expression under investigated conditions is critical in qRT-PCR analysis. We used qRT-PCR to validate expression and stability of six potential reference genes (EF1alpha, EIF4A, UBCE, GAPDH, ACT2 and TUBA) in vegetative and reproductive tissues of B-2S and B-12-9 accessions of C. ciliaris. Findings Among tissue types evaluated, EF1alpha showed the highest level of expression while TUBA showed the lowest. When all tissue types were evaluated and compared between genotypes, EIF4A was the most stable reference gene. Gene expression stability for specific ovary stages of B-2S and B-12-9 was also determined. Except for TUBA, all other tested reference genes could be used for any stage-specific ovary tissue normalization, irrespective of the mode of reproduction. Conclusion Our gene expression stability assay using six reference genes, in sexual and apomictic accessions of C. ciliaris, suggests that EIF4A is the most stable gene across all tissue types analyzed. All other tested reference genes, with the exception of TUBA, could be used for gene expression comparison studies between sexual and apomictic ovaries over multiple developmental stages. This reference gene validation data in C. ciliaris will serve as an important base for future apomixis-related transcriptome data validation. PMID:24083672

Object-location training elicits an overlapping but temporally distinct transcriptional profile from contextual fear conditioning.

PubMed

Poplawski, Shane G; Schoch, Hannah; Wimmer, Mathieu; Hawk, Joshua D; Walsh, Jennifer L; Giese, Karl P; Abel, Ted

2014-12-01

Hippocampus-dependent learning is known to induce changes in gene expression, but information on gene expression differences between different learning paradigms that require the hippocampus is limited. The bulk of studies investigating RNA expression after learning use the contextual fear conditioning task, which couples a novel environment with a footshock. Although contextual fear conditioning has been useful in discovering gene targets, gene expression after spatial memory tasks has received less attention. In this study, we used the object-location memory task and studied gene expression at two time points after learning in a high-throughput manner using a microfluidic qPCR approach. We found that expression of the classic immediate-early genes changes after object-location training in a fashion similar to that observed after contextual fear conditioning. However, the temporal dynamics of gene expression are different between the two tasks, with object-location memory producing gene expression changes that last at least 2 hours. Our findings indicate that different training paradigms may give rise to distinct temporal dynamics of gene expression after learning. Copyright © 2014 Elsevier Inc. All rights reserved.

Object-Location Training Elicits an Overlapping but Temporally Distinct Transcriptional Profile from Contextual Fear Conditioning

PubMed Central

Wimmer, Mathieu; Hawk, Joshua D.; Walsh, Jennifer L.; Giese, Karl P.; Abel, Ted

2014-01-01

Hippocampus-dependent learning is known to induce changes in gene expression, but information on gene expression differences between different learning paradigms that require the hippocampus is limited. The bulk of studies investigating RNA expression after learning use the contextual fear conditioning task, which couples a novel environment with a footshock. Although contextual fear conditioning has been useful in discovering gene targets, gene expression after spatial memory tasks has received less attention. In this study, we used the object-location memory task and studied gene expression at two time points after learning in a high-throughput manner using a microfluidic qPCR approach. We found that expression of the classic immediate-early genes changes after object-location training in a fashion similar to that observed after contextual fear conditioning. However, the temporal dynamics of gene expression are different between the two tasks, with object-location memory producing gene expression changes that last at least 2 hours. Our findings indicate that different training paradigms may give rise to distinct temporal dynamics of gene expression after learning. PMID:25242102

Using RNA-seq data to select reference genes for normalizing gene expression in apple roots.

PubMed

Zhou, Zhe; Cong, Peihua; Tian, Yi; Zhu, Yanmin

2017-01-01

Gene expression in apple roots in response to various stress conditions is a less-explored research subject. Reliable reference genes for normalizing quantitative gene expression data have not been carefully investigated. In this study, the suitability of a set of 15 apple genes were evaluated for their potential use as reliable reference genes. These genes were selected based on their low variance of gene expression in apple root tissues from a recent RNA-seq data set, and a few previously reported apple reference genes for other tissue types. Four methods, Delta Ct, geNorm, NormFinder and BestKeeper, were used to evaluate their stability in apple root tissues of various genotypes and under different experimental conditions. A small panel of stably expressed genes, MDP0000095375, MDP0000147424, MDP0000233640, MDP0000326399 and MDP0000173025 were recommended for normalizing quantitative gene expression data in apple roots under various abiotic or biotic stresses. When the most stable and least stable reference genes were used for data normalization, significant differences were observed on the expression patterns of two target genes, MdLecRLK5 (MDP0000228426, a gene encoding a lectin receptor like kinase) and MdMAPK3 (MDP0000187103, a gene encoding a mitogen-activated protein kinase). Our data also indicated that for those carefully validated reference genes, a single reference gene is sufficient for reliable normalization of the quantitative gene expression. Depending on the experimental conditions, the most suitable reference genes can be specific to the sample of interest for more reliable RT-qPCR data normalization.

Using RNA-seq data to select reference genes for normalizing gene expression in apple roots

PubMed Central

Zhou, Zhe; Cong, Peihua; Tian, Yi

2017-01-01

Gene expression in apple roots in response to various stress conditions is a less-explored research subject. Reliable reference genes for normalizing quantitative gene expression data have not been carefully investigated. In this study, the suitability of a set of 15 apple genes were evaluated for their potential use as reliable reference genes. These genes were selected based on their low variance of gene expression in apple root tissues from a recent RNA-seq data set, and a few previously reported apple reference genes for other tissue types. Four methods, Delta Ct, geNorm, NormFinder and BestKeeper, were used to evaluate their stability in apple root tissues of various genotypes and under different experimental conditions. A small panel of stably expressed genes, MDP0000095375, MDP0000147424, MDP0000233640, MDP0000326399 and MDP0000173025 were recommended for normalizing quantitative gene expression data in apple roots under various abiotic or biotic stresses. When the most stable and least stable reference genes were used for data normalization, significant differences were observed on the expression patterns of two target genes, MdLecRLK5 (MDP0000228426, a gene encoding a lectin receptor like kinase) and MdMAPK3 (MDP0000187103, a gene encoding a mitogen-activated protein kinase). Our data also indicated that for those carefully validated reference genes, a single reference gene is sufficient for reliable normalization of the quantitative gene expression. Depending on the experimental conditions, the most suitable reference genes can be specific to the sample of interest for more reliable RT-qPCR data normalization. PMID:28934340

Stepwise evolution of corolla symmetry in CYCLOIDEA2-like and RADIALIS-like gene expression patterns in Lamiales.

PubMed

Zhong, Jinshun; Kellogg, Elizabeth A

2015-08-01

• CYCLOIDEA2 (CYC2)-like and RADIALIS (RAD)-like genes are needed for the normal development of corolla bilateral symmetry in Antirrhinum majus L. (snapdragon, Plantaginaceae, Lamiales). However, if and how changes in expression of CYC2-like and RAD-like genes correlate with the origin of corolla bilateral symmetry early in Lamiales remains largely unknown. The asymmetrical expression of CYC2-like and/or RAD-like genes during floral meristem development could be ancestral or derived in Plantaginaceae.• We used in situ RNA localization to examine the expression of CYC2-like and RAD-like genes in two early-diverging Lamiales.• CYC2-like and RAD-like genes are expressed broadly in the floral meristems in early-diverging Lamiales with radially symmetrical corollas, in contrast to their restricted expression in adaxial/lateral regions in core Lamiales. The expression pattern of CYC2-like genes has evolved in stepwise fashion, in that CYC2-like genes are likely expressed briefly in the floral meristem during flower development in sampled Oleaceae; prolonged expression of CYC2-like genes in petals originated in the common ancestor of Tetrachondraceae and core Lamiales, and asymmetrical expression in adaxial/lateral petals appeared later, in the common ancestor of the core Lamiales. Likewise, expression of RAD-like genes in petals appeared in early-diverging Lamiales or earlier; asymmetrical expression in adaxial/lateral petals then appeared in core Lamiales.• These data plus published reports of CYC2-like and RAD-like genes show that asymmetrical expression of these two genes is likely derived and correlates with the origins of corolla bilateral symmetry. © 2015 Botanical Society of America, Inc.

Transient, Inducible, Placenta-Specific Gene Expression in Mice

PubMed Central

Fan, Xiujun; Petitt, Matthew; Gamboa, Matthew; Huang, Mei; Dhal, Sabita; Druzin, Maurice L.; Wu, Joseph C.

2012-01-01

Molecular understanding of placental functions and pregnancy disorders is limited by the absence of methods for placenta-specific gene manipulation. Although persistent placenta-specific gene expression has been achieved by lentivirus-based gene delivery methods, developmentally and physiologically important placental genes have highly stage-specific functions, requiring controllable, transient expression systems for functional analysis. Here, we describe an inducible, placenta-specific gene expression system that enables high-level, transient transgene expression and monitoring of gene expression by live bioluminescence imaging in mouse placenta at different stages of pregnancy. We used the third generation tetracycline-responsive tranactivator protein Tet-On 3G, with 10- to 100-fold increased sensitivity to doxycycline (Dox) compared with previous versions, enabling unusually sensitive on-off control of gene expression in vivo. Transgenic mice expressing Tet-On 3G were created using a new integrase-based, site-specific approach, yielding high-level transgene expression driven by a ubiquitous promoter. Blastocysts from these mice were transduced with the Tet-On 3G-response element promoter-driving firefly luciferase using lentivirus-mediated placenta-specific gene delivery and transferred into wild-type pseudopregnant recipients for placenta-specific, Dox-inducible gene expression. Systemic Dox administration at various time points during pregnancy led to transient, placenta-specific firefly luciferase expression as early as d 5 of pregnancy in a Dox dose-dependent manner. This system enables, for the first time, reliable pregnancy stage-specific induction of gene expression in the placenta and live monitoring of gene expression during pregnancy. It will be widely applicable to studies of both placental development and pregnancy, and the site-specific Tet-On G3 mouse will be valuable for studies in a broad range of tissues. PMID:23011919

Analyzing gene expression time-courses based on multi-resolution shape mixture model.

PubMed

Li, Ying; He, Ye; Zhang, Yu

2016-11-01

Biological processes actually are a dynamic molecular process over time. Time course gene expression experiments provide opportunities to explore patterns of gene expression change over a time and understand the dynamic behavior of gene expression, which is crucial for study on development and progression of biology and disease. Analysis of the gene expression time-course profiles has not been fully exploited so far. It is still a challenge problem. We propose a novel shape-based mixture model clustering method for gene expression time-course profiles to explore the significant gene groups. Based on multi-resolution fractal features and mixture clustering model, we proposed a multi-resolution shape mixture model algorithm. Multi-resolution fractal features is computed by wavelet decomposition, which explore patterns of change over time of gene expression at different resolution. Our proposed multi-resolution shape mixture model algorithm is a probabilistic framework which offers a more natural and robust way of clustering time-course gene expression. We assessed the performance of our proposed algorithm using yeast time-course gene expression profiles compared with several popular clustering methods for gene expression profiles. The grouped genes identified by different methods are evaluated by enrichment analysis of biological pathways and known protein-protein interactions from experiment evidence. The grouped genes identified by our proposed algorithm have more strong biological significance. A novel multi-resolution shape mixture model algorithm based on multi-resolution fractal features is proposed. Our proposed model provides a novel horizons and an alternative tool for visualization and analysis of time-course gene expression profiles. The R and Matlab program is available upon the request. Copyright © 2016 Elsevier Inc. All rights reserved.

Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution

PubMed Central

Moretti, Stefano; van Leeuwen, Danitsja; Gmuender, Hans; Bonassi, Stefano; van Delft, Joost; Kleinjans, Jos; Patrone, Fioravante; Merlo, Domenico Franco

2008-01-01

Background In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, game theory has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions. Results In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called Comparative Analysis of Shapley value (shortly, CASh), is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability. Conclusion CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a synergistic effect between coalitional games and statistics that resulted in a selection of genes with a potential impact in the regulation of complex pathways. PMID:18764936

Variation-preserving normalization unveils blind spots in gene expression profiling

PubMed Central

Roca, Carlos P.; Gomes, Susana I. L.; Amorim, Mónica J. B.; Scott-Fordsmand, Janeck J.

2017-01-01

RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much larger than currently believed, and that it can be measured with available assays. Our results also explain, at least partially, the reproducibility problems encountered in transcriptomics studies. We expect that this improvement in detection will help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression. PMID:28276435

Wheat differential gene expression induced by different races of Puccinia triticina.

PubMed

Neugebauer, Kerri A; Bruce, Myron; Todd, Tim; Trick, Harold N; Fellers, John P

2018-01-01

Puccinia triticina, the causal agent of wheat leaf rust, causes significant losses in wheat yield and quality each year worldwide. During leaf rust infection, the host plant recognizes numerous molecules, some of which trigger host defenses. Although P. triticina reproduces clonally, there is still variation within the population due to a high mutation frequency, host specificity, and environmental adaptation. This study explores how wheat responds on a gene expression level to different P. triticina races. Six P. triticina races were inoculated onto a susceptible wheat variety and samples were taken at six days post inoculation, just prior to pustule eruption. RNA sequence data identified 63 wheat genes differentially expressed between the six races. A time course, conducted over the first seven days post inoculation, was used to examine the expression pattern of 63 genes during infection. Forty-seven wheat genes were verified to have differential expression. Three common expression patterns were identified. In addition, two genes were associated with race specific gene expression. Differential expression of an ER molecular chaperone gene was associated with races from two different P. triticina lineages. Also, differential expression in an alanine glyoxylate aminotransferase gene was associated with races with virulence shifts for leaf rust resistance genes.

Genome-Wide Identification, Characterization and Expression Analysis of the Solute Carrier 6 Gene Family in Silkworm (Bombyx mori)

PubMed Central

Tang, Xin; Liu, Huawei; Chen, Quanmei; Wang, Xin; Xiong, Ying; Zhao, Ping

2016-01-01

The solute carrier 6 (SLC6) gene family, initially known as the neurotransmitter transporters, plays vital roles in the regulation of neurotransmitter signaling, nutrient absorption and motor behavior. In this study, a total of 16 candidate genes were identified as SLC6 family gene homologs in the silkworm (Bombyx mori) genome. Spatio-temporal expression patterns of silkworm SLC6 gene transcripts indicated that these genes were highly and specifically expressed in midgut, brain and gonads; moreover, these genes were expressed primarily at the feeding stage or adult stage. Levels of expression for most midgut-specific and midgut-enriched gene transcripts were down-regulated after starvation but up-regulated after re-feeding. In addition, we observed that expression levels of these genes except for BmSLC6-15 and BmGT1 were markedly up-regulated by a juvenile hormone analog. Moreover, brain-enriched genes showed differential expression patterns during wandering and mating processes, suggesting that these genes may be involved in modulating wandering and mating behaviors. Our results improve our understanding of the expression patterns and potential physiological functions of the SLC6 gene family, and provide valuable information for the comprehensive functional analysis of the SLC6 gene family. PMID:27706106

Identification of Reference Genes for Normalizing Quantitative Real-Time PCR in Urechis unicinctus

NASA Astrophysics Data System (ADS)

Bai, Yajiao; Zhou, Di; Wei, Maokai; Xie, Yueyang; Gao, Beibei; Qin, Zhenkui; Zhang, Zhifeng

2018-06-01

The reverse transcription quantitative real-time PCR (RT-qPCR) has become one of the most important techniques of studying gene expression. A set of valid reference genes are essential for the accurate normalization of data. In this study, five candidate genes were analyzed with geNorm, NormFinder, BestKeeper and ΔCt methods to identify the genes stably expressed in echiuran Urechis unicinctus, an important commercial marine benthic worm, under abiotic (sulfide stress) and normal (adult tissues, embryos and larvae at different development stages) conditions. The comprehensive results indicated that the expression of TBP was the most stable at sulfide stress and in developmental process, while the expression of EF- 1- α was the most stable at sulfide stress and in various tissues. TBP and EF- 1- α were recommended as a suitable reference gene combination to accurately normalize the expression of target genes at sulfide stress; and EF- 1- α, TBP and TUB were considered as a potential reference gene combination for normalizing the expression of target genes in different tissues. No suitable gene combination was obtained among these five candidate genes for normalizing the expression of target genes for developmental process of U. unicinctus. Our results provided a valuable support for quantifying gene expression using RT-qPCR in U. unicinctus.

Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).

PubMed

Xu, Yuantao; Wu, Guizhi; Hao, Baohai; Chen, Lingling; Deng, Xiuxin; Xu, Qiang

2015-11-23

With the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play important roles in biological evolution and functions. Two set of citrus LSGs, 296 citrus-specific genes (CSGs) and 1039 orphan genes specific to sweet orange, were identified by comparative analysis between the sweet orange genome sequences and 41 genomes and 273 transcriptomes. With the two sets of genes, gene structure and gene expression pattern were investigated. On average, both the CSGs and orphan genes have fewer exons, shorter gene length and higher GC content when compared with those evolutionarily conserved genes (ECs). Expression profiling indicated that most of the LSGs expressed in various tissues of sweet orange and some of them exhibited distinct temporal and spatial expression patterns. Particularly, the orphan genes were preferentially expressed in callus, which is an important pluripotent tissue of citrus. Besides, part of the CSGs and orphan genes expressed responsive to abiotic stress, indicating their potential functions during interaction with environment. This study identified and characterized two sets of LSGs in citrus, dissected their sequence features and expression patterns, and provided valuable clues for future functional analysis of the LSGs in sweet orange.

Genome-Wide Identification, Characterization and Expression Analysis of the Solute Carrier 6 Gene Family in Silkworm (Bombyx mori).

PubMed

Tang, Xin; Liu, Huawei; Chen, Quanmei; Wang, Xin; Xiong, Ying; Zhao, Ping

2016-10-03

The solute carrier 6 (SLC6) gene family, initially known as the neurotransmitter transporters, plays vital roles in the regulation of neurotransmitter signaling, nutrient absorption and motor behavior. In this study, a total of 16 candidate genes were identified as SLC6 family gene homologs in the silkworm (Bombyx mori) genome. Spatio-temporal expression patterns of silkworm SLC6 gene transcripts indicated that these genes were highly and specifically expressed in midgut, brain and gonads; moreover, these genes were expressed primarily at the feeding stage or adult stage. Levels of expression for most midgut-specific and midgut-enriched gene transcripts were down-regulated after starvation but up-regulated after re-feeding. In addition, we observed that expression levels of these genes except for BmSLC6-15 and BmGT1 were markedly up-regulated by a juvenile hormone analog. Moreover, brain-enriched genes showed differential expression patterns during wandering and mating processes, suggesting that these genes may be involved in modulating wandering and mating behaviors. Our results improve our understanding of the expression patterns and potential physiological functions of the SLC6 gene family, and provide valuable information for the comprehensive functional analysis of the SLC6 gene family.

Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates

PubMed Central

Matsui, Toshiaki; Yamamoto, Toshiyuki; Wyder, Stefan; Zdobnov, Evgeny M; Kadowaki, Tatsuhiko

2009-01-01

Background Large-scale comparison of metazoan genomes has revealed that a significant fraction of genes of the last common ancestor of Bilateria (Urbilateria) is lost in each animal lineage. This event could be one of the underlying mechanisms involved in generating metazoan diversity. However, the present functions of these ancient genes have not been addressed extensively. To understand the functions and evolutionary mechanisms of such ancient Urbilaterian genes, we carried out comprehensive expression profile analysis of genes shared between vertebrates and honey bees but not with the other sequenced ecdysozoan genomes (honey bee-vertebrate specific, HVS genes) as a model. Results We identified 30 honey bee and 55 mouse HVS genes. Many HVS genes exhibited tissue-selective expression patterns; intriguingly, the expression of 60% of honey bee HVS genes was found to be brain enriched, and 24% of mouse HVS genes were highly expressed in either or both the brain and testis. Moreover, a minimum of 38% of mouse HVS genes demonstrated neuron-enriched expression patterns, and 62% of them exhibited expression in selective brain areas, particularly the forebrain and cerebellum. Furthermore, gene ontology (GO) analysis of HVS genes predicted that 35% of genes are associated with DNA transcription and RNA processing. Conclusion These results suggest that HVS genes include genes that are biased towards expression in the brain and gonads. They also demonstrate that at least some of Urbilaterian genes retained in the specific animal lineage may be selectively maintained to support the species-specific phenotypes. PMID:19138430

Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates.

PubMed

Matsui, Toshiaki; Yamamoto, Toshiyuki; Wyder, Stefan; Zdobnov, Evgeny M; Kadowaki, Tatsuhiko

2009-01-12

Large-scale comparison of metazoan genomes has revealed that a significant fraction of genes of the last common ancestor of Bilateria (Urbilateria) is lost in each animal lineage. This event could be one of the underlying mechanisms involved in generating metazoan diversity. However, the present functions of these ancient genes have not been addressed extensively. To understand the functions and evolutionary mechanisms of such ancient Urbilaterian genes, we carried out comprehensive expression profile analysis of genes shared between vertebrates and honey bees but not with the other sequenced ecdysozoan genomes (honey bee-vertebrate specific, HVS genes) as a model. We identified 30 honey bee and 55 mouse HVS genes. Many HVS genes exhibited tissue-selective expression patterns; intriguingly, the expression of 60% of honey bee HVS genes was found to be brain enriched, and 24% of mouse HVS genes were highly expressed in either or both the brain and testis. Moreover, a minimum of 38% of mouse HVS genes demonstrated neuron-enriched expression patterns, and 62% of them exhibited expression in selective brain areas, particularly the forebrain and cerebellum. Furthermore, gene ontology (GO) analysis of HVS genes predicted that 35% of genes are associated with DNA transcription and RNA processing. These results suggest that HVS genes include genes that are biased towards expression in the brain and gonads. They also demonstrate that at least some of Urbilaterian genes retained in the specific animal lineage may be selectively maintained to support the species-specific phenotypes.

Comprehensive analysis of pathway or functionally related gene expression in the National Cancer Institute's anticancer screen.

PubMed

Huang, Ruili; Wallqvist, Anders; Covell, David G

2006-03-01

We have analyzed the level of gene coregulation, using gene expression patterns measured across the National Cancer Institute's 60 tumor cell panels (NCI(60)), in the context of predefined pathways or functional categories annotated by KEGG (Kyoto Encyclopedia of Genes and Genomes), BioCarta, and GO (Gene Ontology). Statistical methods were used to evaluate the level of gene expression coherence (coordinated expression) by comparing intra- and interpathway gene-gene correlations. Our results show that gene expression in pathways, or groups of functionally related genes, has a significantly higher level of coherence than that of a randomly selected set of genes. Transcriptional-level gene regulation appears to be on a "need to be" basis, such that pathways comprising genes encoding closely interacting proteins and pathways responsible for vital cellular processes or processes that are related to growth or proliferation, specifically in cancer cells, such as those engaged in genetic information processing, cell cycle, energy metabolism, and nucleotide metabolism, tend to be more modular (lower degree of gene sharing) and to have genes significantly more coherently expressed than most signaling and regular metabolic pathways. Hierarchical clustering of pathways based on their differential gene expression in the NCI(60) further revealed interesting interpathway communications or interactions indicative of a higher level of pathway regulation. The knowledge of the nature of gene expression regulation and biological pathways can be applied to understanding the mechanism by which small drug molecules interfere with biological systems.

Tightly Regulated Expression of Autographa californica Multicapsid Nucleopolyhedrovirus Immediate Early Genes Emerges from Their Interactions and Possible Collective Behaviors

PubMed Central

Taka, Hitomi; Asano, Shin-ichiro; Matsuura, Yoshiharu; Bando, Hisanori

2015-01-01

To infect their hosts, DNA viruses must successfully initiate the expression of viral genes that control subsequent viral gene expression and manipulate the host environment. Viral genes that are immediately expressed upon infection play critical roles in the early infection process. In this study, we investigated the expression and regulation of five canonical regulatory immediate-early (IE) genes of Autographa californica multicapsid nucleopolyhedrovirus: ie0, ie1, ie2, me53, and pe38. A systematic transient gene-expression analysis revealed that these IE genes are generally transactivators, suggesting the existence of a highly interactive regulatory network. A genetic analysis using gene knockout viruses demonstrated that the expression of these IE genes was tolerant to the single deletions of activator IE genes in the early stage of infection. A network graph analysis on the regulatory relationships observed in the transient expression analysis suggested that the robustness of IE gene expression is due to the organization of the IE gene regulatory network and how each IE gene is activated. However, some regulatory relationships detected by the genetic analysis were contradictory to those observed in the transient expression analysis, especially for IE0-mediated regulation. Statistical modeling, combined with genetic analysis using knockout alleles for ie0 and ie1, showed that the repressor function of ie0 was due to the interaction between ie0 and ie1, not ie0 itself. Taken together, these systematic approaches provided insight into the topology and nature of the IE gene regulatory network. PMID:25816136

Unstable Expression of Commonly Used Reference Genes in Rat Pancreatic Islets Early after Isolation Affects Results of Gene Expression Studies.

PubMed

Kosinová, Lucie; Cahová, Monika; Fábryová, Eva; Týcová, Irena; Koblas, Tomáš; Leontovyč, Ivan; Saudek, František; Kříž, Jan

2016-01-01

The use of RT-qPCR provides a powerful tool for gene expression studies; however, the proper interpretation of the obtained data is crucially dependent on accurate normalization based on stable reference genes. Recently, strong evidence has been shown indicating that the expression of many commonly used reference genes may vary significantly due to diverse experimental conditions. The isolation of pancreatic islets is a complicated procedure which creates severe mechanical and metabolic stress leading possibly to cellular damage and alteration of gene expression. Despite of this, freshly isolated islets frequently serve as a control in various gene expression and intervention studies. The aim of our study was to determine expression of 16 candidate reference genes and one gene of interest (F3) in isolated rat pancreatic islets during short-term cultivation in order to find a suitable endogenous control for gene expression studies. We compared the expression stability of the most commonly used reference genes and evaluated the reliability of relative and absolute quantification using RT-qPCR during 0-120 hrs after isolation. In freshly isolated islets, the expression of all tested genes was markedly depressed and it increased several times throughout the first 48 hrs of cultivation. We observed significant variability among samples at 0 and 24 hrs but substantial stabilization from 48 hrs onwards. During the first 48 hrs, relative quantification failed to reflect the real changes in respective mRNA concentrations while in the interval 48-120 hrs, the relative expression generally paralleled the results determined by absolute quantification. Thus, our data call into question the suitability of relative quantification for gene expression analysis in pancreatic islets during the first 48 hrs of cultivation, as the results may be significantly affected by unstable expression of reference genes. However, this method could provide reliable information from 48 hrs onwards.

Over-expression of brain-derived neurotrophic factor in mesenchymal stem cells transfected with recombinant lentivirus BDNF gene.

PubMed

Zhang, X; Zhu, J; Zhang, K; Liu, T; Zhang, Z

2016-12-30

This study was aimed at investigating the expression of brain-derived neurotrophic factor (BDNF) in mesenchymal stem cells (MSCs) modified with recombinant lentivirus bearing BDNF gene. Lentivirus vectors bearing BDNF gene were constructed. MSCs were isolated from rats and cultured. The lentiviral vectors containing BDNF gene were transfected into the MSCs, and BDNF gene and protein expressions were monitored with enhanced green fluorescent protein (EGFP). RT-PCR and Western blot were used to measure gene and protein expressions, respectibvely in MSCs, MSCs-EGFP and MSCs-EGFP-BDNF groups. Green fluorescence assay confirmed successful transfection of BDNF gene recombinant lentivirus into MSCs. RT-PCR and Western blot revealed that BDNF gene and protein expressions in the MSCs-EGFP-BDNF group were significantly higher than that in MSCs group and MSCs-EGFP group. There were no statistically significant differences in gene expression between MSCs and MSCs-EGFP groups. MSCs can over-express BDNF when transfected with recombinant lentivirus bearing BDNF gene.

Accelerated recruitment of new brain development genes into the human genome.

PubMed

Zhang, Yong E; Landback, Patrick; Vibranovski, Maria D; Long, Manyuan

2011-10-01

How the human brain evolved has attracted tremendous interests for decades. Motivated by case studies of primate-specific genes implicated in brain function, we examined whether or not the young genes, those emerging genome-wide in the lineages specific to the primates or rodents, showed distinct spatial and temporal patterns of transcription compared to old genes, which had existed before primate and rodent split. We found consistent patterns across different sources of expression data: there is a significantly larger proportion of young genes expressed in the fetal or infant brain of humans than in mouse, and more young genes in humans have expression biased toward early developing brains than old genes. Most of these young genes are expressed in the evolutionarily newest part of human brain, the neocortex. Remarkably, we also identified a number of human-specific genes which are expressed in the prefrontal cortex, which is implicated in complex cognitive behaviors. The young genes upregulated in the early developing human brain play diverse functional roles, with a significant enrichment of transcription factors. Genes originating from different mechanisms show a similar expression bias in the developing brain. Moreover, we found that the young genes upregulated in early brain development showed rapid protein evolution compared to old genes also expressed in the fetal brain. Strikingly, genes expressed in the neocortex arose soon after its morphological origin. These four lines of evidence suggest that positive selection for brain function may have contributed to the origination of young genes expressed in the developing brain. These data demonstrate a striking recruitment of new genes into the early development of the human brain.

Selection of reference genes for gene expression studies related to intramuscular fat deposition in Capra hircus skeletal muscle.

PubMed

Zhu, Wuzheng; Lin, Yaqiu; Liao, Honghai; Wang, Yong

2015-01-01

The identification of suitable reference genes is critical for obtaining reliable results from gene expression studies using quantitative real-time PCR (qPCR) because the expression of reference genes may vary considerably under different experimental conditions. In most cases, however, commonly used reference genes are employed in data normalization without proper validation, which may lead to incorrect data interpretation. Here, we aim to select a set of optimal reference genes for the accurate normalization of gene expression associated with intramuscular fat (IMF) deposition during development. In the present study, eight reference genes (PPIB, HMBS, RPLP0, B2M, YWHAZ, 18S, GAPDH and ACTB) were evaluated by three different algorithms (geNorm, NormFinder and BestKeeper) in two types of muscle tissues (longissimus dorsi muscle and biceps femoris muscle) across different developmental stages. All three algorithms gave similar results. PPIB and HMBS were identified as the most stable reference genes, while the commonly used reference genes 18S and GAPDH were the most variably expressed, with expression varying dramatically across different developmental stages. Furthermore, to reveal the crucial role of appropriate reference genes in obtaining a reliable result, analysis of PPARG expression was performed by normalization to the most and the least stable reference genes. The relative expression levels of PPARG normalized to the most stable reference genes greatly differed from those normalized to the least stable one. Therefore, evaluation of reference genes must be performed for a given experimental condition before the reference genes are used. PPIB and HMBS are the optimal reference genes for analysis of gene expression associated with IMF deposition in skeletal muscle during development.

Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia

PubMed Central

Cheaib, Miriam; Dehghani Amirabad, Azim; Nordström, Karl J. V.; Schulz, Marcel H.; Simon, Martin

2015-01-01

Phenotypic variation of a single genotype is achieved by alterations in gene expression patterns. Regulation of such alterations depends on their time scale, where short-time adaptations differ from permanently established gene expression patterns maintained by epigenetic mechanisms. In the ciliate Paramecium, serotypes were described for an epigenetically controlled gene expression pattern of an individual multigene family. Paradoxically, individual serotypes can be triggered in Paramecium by alternating environments but are then stabilized by epigenetic mechanisms, thus raising the question to which extend their expression follows environmental stimuli. To characterize environmental adaptation in the context of epigenetically controlled serotype expression, we used RNA-seq to characterize transcriptomes of serotype pure cultures. The resulting vegetative transcriptome resource is first analysed for genes involved in the adaptive response to the altered environment. Secondly, we identified groups of genes that do not follow the adaptive response but show co-regulation with the epigenetically controlled serotype system, suggesting that their gene expression pattern becomes manifested by similar mechanisms. In our experimental set-up, serotype expression and the entire group of co-regulated genes were stable among environmental changes and only heat-shock genes altered expression of these gene groups. The data suggest that the maintenance of these gene expression patterns in a lineage represents epigenetically controlled robustness counteracting short-time adaptation processes. PMID:26231545

Integrating Genomic Analysis with the Genetic Basis of Gene Expression: Preliminary Evidence of the Identification of Causal Genes for Cardiovascular and Metabolic Traits Related to Nutrition in Mexicans123

PubMed Central

Bastarrachea, Raúl A.; Gallegos-Cabriales, Esther C.; Nava-González, Edna J.; Haack, Karin; Voruganti, V. Saroja; Charlesworth, Jac; Laviada-Molina, Hugo A.; Veloz-Garza, Rosa A.; Cardenas-Villarreal, Velia Margarita; Valdovinos-Chavez, Salvador B.; Gomez-Aguilar, Patricia; Meléndez, Guillermo; López-Alvarenga, Juan Carlos; Göring, Harald H. H.; Cole, Shelley A.; Blangero, John; Comuzzie, Anthony G.; Kent, Jack W.

2012-01-01

Whole-transcriptome expression profiling provides novel phenotypes for analysis of complex traits. Gene expression measurements reflect quantitative variation in transcript-specific messenger RNA levels and represent phenotypes lying close to the action of genes. Understanding the genetic basis of gene expression will provide insight into the processes that connect genotype to clinically significant traits representing a central tenet of system biology. Synchronous in vivo expression profiles of lymphocytes, muscle, and subcutaneous fat were obtained from healthy Mexican men. Most genes were expressed at detectable levels in multiple tissues, and RNA levels were correlated between tissue types. A subset of transcripts with high reliability of expression across tissues (estimated by intraclass correlation coefficients) was enriched for cis-regulated genes, suggesting that proximal sequence variants may influence expression similarly in different cellular environments. This integrative global gene expression profiling approach is proving extremely useful for identifying genes and pathways that contribute to complex clinical traits. Clearly, the coincidence of clinical trait quantitative trait loci and expression quantitative trait loci can help in the prioritization of positional candidate genes. Such data will be crucial for the formal integration of positional and transcriptomic information characterized as genetical genomics. PMID:22797999

Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance.

PubMed

Das, Shibsankar; Roymondal, Uttam; Sahoo, Satyabrata

2009-08-15

Based on the hypothesis that highly expressed genes are often characterized by strong compositional bias in terms of codon usage, there are a number of measures currently in use that quantify codon usage bias in genes, and hence provide numerical indices to predict the expression levels of genes. With the recent advent of expression measure from the score of the relative codon usage bias (RCBS), we have explicitly tested the performance of this numerical measure to predict the gene expression level and illustrate this with an analysis of Yeast genomes. In contradiction with previous other studies, we observe a weak correlations between GC content and RCBS, but a selective pressure on the codon preferences in highly expressed genes. The assertion that the expression of a given gene depends on the score of relative codon usage bias (RCBS) is supported by the data. We further observe a strong correlation between RCBS and protein length indicating natural selection in favour of shorter genes to be expressed at higher level. We also attempt a statistical analysis to assess the strength of relative codon bias in genes as a guide to their likely expression level, suggesting a decrease of the informational entropy in the highly expressed genes.

ATNT: an enhanced system for expression of polycistronic secondary metabolite gene clusters in Aspergillus niger.

PubMed

Geib, Elena; Brock, Matthias

2017-01-01

Fungi are treasure chests for yet unexplored natural products. However, exploitation of their real potential remains difficult as a significant proportion of biosynthetic gene clusters appears silent under standard laboratory conditions. Therefore, elucidation of novel products requires gene activation or heterologous expression. For heterologous gene expression, we previously developed an expression platform in Aspergillus niger that is based on the transcriptional regulator TerR and its target promoter P terA . In this study, we extended this system by regulating expression of terR  by the doxycycline inducible Tet-on system. Reporter genes cloned under the control of the target promoter P terA remained silent in the absence of doxycycline, but were strongly expressed when doxycycline was added. Reporter quantification revealed that the coupled system results in about five times higher expression rates compared to gene expression under direct control of the Tet-on system. As production of secondary metabolites generally requires the expression of several biosynthetic genes, the suitability of the self-cleaving viral peptide sequence P2A was tested in this optimised expression system. P2A allowed polycistronic expression of genes required for Asp-melanin formation in combination with the gene coding for the red fluorescent protein tdTomato. Gene expression and Asp-melanin formation was prevented in the absence of doxycycline and strongly induced by addition of doxycycline. Fluorescence studies confirmed the correct subcellular localisation of the respective enzymes. This tightly regulated but strongly inducible expression system enables high level production of secondary metabolites most likely even those with toxic potential. Furthermore, this system is compatible with polycistronic gene expression and, thus, suitable for the discovery of novel natural products.

Faster-X Evolution of Gene Expression in Drosophila

PubMed Central

Meisel, Richard P.; Malone, John H.; Clark, Andrew G.

2012-01-01

DNA sequences on X chromosomes often have a faster rate of evolution when compared to similar loci on the autosomes, and well articulated models provide reasons why the X-linked mode of inheritance may be responsible for the faster evolution of X-linked genes. We analyzed microarray and RNA–seq data collected from females and males of six Drosophila species and found that the expression levels of X-linked genes also diverge faster than autosomal gene expression, similar to the “faster-X” effect often observed in DNA sequence evolution. Faster-X evolution of gene expression was recently described in mammals, but it was limited to the evolutionary lineages shortly following the creation of the therian X chromosome. In contrast, we detect a faster-X effect along both deep lineages and those on the tips of the Drosophila phylogeny. In Drosophila males, the dosage compensation complex (DCC) binds the X chromosome, creating a unique chromatin environment that promotes the hyper-expression of X-linked genes. We find that DCC binding, chromatin environment, and breadth of expression are all predictive of the rate of gene expression evolution. In addition, estimates of the intraspecific genetic polymorphism underlying gene expression variation suggest that X-linked expression levels are not under relaxed selective constraints. We therefore hypothesize that the faster-X evolution of gene expression is the result of the adaptive fixation of beneficial mutations at X-linked loci that change expression level in cis. This adaptive faster-X evolution of gene expression is limited to genes that are narrowly expressed in a single tissue, suggesting that relaxed pleiotropic constraints permit a faster response to selection. Finally, we present a conceptional framework to explain faster-X expression evolution, and we use this framework to examine differences in the faster-X effect between Drosophila and mammals. PMID:23071459

The Rice B-Box Zinc Finger Gene Family: Genomic Identification, Characterization, Expression Profiling and Diurnal Analysis

PubMed Central

Huang, Jianyan; Zhao, Xiaobo; Weng, Xiaoyu; Wang, Lei; Xie, Weibo

2012-01-01

Background The B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now. Methodology/Principal Findings In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern. Conclusions/Significance The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes. PMID:23118960

A Glycine Riboswitch in Streptococcus pyogenes Controls Expression of a Sodium:Alanine Symporter Family Protein Gene.

PubMed

Khani, Afsaneh; Popp, Nicole; Kreikemeyer, Bernd; Patenge, Nadja

2018-01-01

Regulatory RNAs play important roles in the control of bacterial gene expression. In this study, we investigated gene expression regulation by a putative glycine riboswitch located in the 5'-untranslated region of a sodium:alanine symporter family (SAF) protein gene in the group A Streptococcus pyogenes serotype M49 strain 591. Glycine-dependent gene expression mediated by riboswitch activity was studied using a luciferase reporter gene system. Maximal reporter gene expression was observed in the absence of glycine and in the presence of low glycine concentrations. Differences in glycine-dependent gene expression were not based on differential promoter activity. Expression of the SAF protein gene and the downstream putative cation efflux protein gene was investigated in wild-type bacteria by RT-qPCR transcript analyses. During growth in the presence of glycine (≥1 mM), expression of the genes were downregulated. Northern blot analyses revealed premature transcription termination in the presence of high glycine concentrations. Growth in the presence of 0.1 mM glycine led to the production of a full-length transcript. Furthermore, stability of the SAF protein gene transcript was drastically reduced in the presence of glycine. We conclude that the putative glycine riboswitch in S. pyogenes serotype M49 strain 591 represses expression of the SAF protein gene and the downstream putative cation efflux protein gene in the presence of high glycine concentrations. Sequence and secondary structure comparisons indicated that the streptococcal riboswitch belongs to the class of tandem aptamer glycine riboswitches.

Array-based comparative genomic hybridization-guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs.

PubMed

Tsai, Pei-Chien; Breen, Matthew

2012-09-01

To identify suitable reference genes for normalization of real-time quantitative PCR (RT-qPCR) assay data for common tumors of dogs. Malignant lymph node (n = 8), appendicular osteosarcoma (9), and histiocytic sarcoma (12) samples and control samples of various nonneoplastic canine tissues. Array-based comparative genomic hybridization (aCGH) data were used to guide selection of 9 candidate reference genes. Expression stability of candidate reference genes and 4 commonly used reference genes was determined for tumor samples with RT-qPCR assays and 3 software programs. LOC611555 was the candidate reference gene with the highest expression stability among the 3 tumor types. Of the commonly used reference genes, expression stability of HPRT was high in histiocytic sarcoma samples, and expression stability of Ubi and RPL32 was high in osteosarcoma samples. Some of the candidate reference genes had higher expression stability than did the commonly used reference genes. Data for constitutively expressed genes with high expression stability are required for normalization of RT-qPCR assay results. Without such data, accurate quantification of gene expression in tumor tissue samples is difficult. Results of the present study indicated LOC611555 may be a useful RT-qPCR assay reference gene for multiple tissue types. Some commonly used reference genes may be suitable for normalization of gene expression data for tumors of dogs, such as lymphomas, osteosarcomas, or histiocytic sarcomas.

Daytime soybean transcriptome fluctuations during water deficit stress.

PubMed

Rodrigues, Fabiana Aparecida; Fuganti-Pagliarini, Renata; Marcolino-Gomes, Juliana; Nakayama, Thiago Jonas; Molinari, Hugo Bruno Correa; Lobo, Francisco Pereira; Harmon, Frank G; Nepomuceno, Alexandre Lima

2015-07-07

Since drought can seriously affect plant growth and development and little is known about how the oscillations of gene expression during the drought stress-acclimation response in soybean is affected, we applied Illumina technology to sequence 36 cDNA libraries synthesized from control and drought-stressed soybean plants to verify the dynamic changes in gene expression during a 24-h time course. Cycling variables were measured from the expression data to determine the putative circadian rhythm regulation of gene expression. We identified 4866 genes differentially expressed in soybean plants in response to water deficit. Of these genes, 3715 were differentially expressed during the light period, from which approximately 9.55% were observed in both light and darkness. We found 887 genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes, 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Such differences in plants under stress were primarily observed in ZT0 (early morning) to ZT8 (late day) and also from ZT4 to ZT12. Stress-related pathways were triggered in response to water deficit primarily during midday, when more genes were up-regulated compared to early morning. Additionally, genes known to be involved in secondary metabolism and hormone signaling were also expressed in the dark period. Gene expression networks can be dynamically shaped to acclimate plant metabolism under environmental stressful conditions. We have identified putative cycling genes that are expressed in soybean leaves under normal developmental conditions and genes whose expression oscillates under conditions of water deficit. These results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

PubMed Central

Versluis, Dennis; D’Andrea, Marco Maria; Ramiro Garcia, Javier; Leimena, Milkha M.; Hugenholtz, Floor; Zhang, Jing; Öztürk, Başak; Nylund, Lotta; Sipkema, Detmer; Schaik, Willem van; de Vos, Willem M.; Kleerebezem, Michiel; Smidt, Hauke; Passel, Mark W.J. van

2015-01-01

Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance. PMID:26153129

Selection of reliable reference genes for gene expression studies in Trichoderma afroharzianum LTR-2 under oxalic acid stress.

PubMed

Lyu, Yuping; Wu, Xiaoqing; Ren, He; Zhou, Fangyuan; Zhou, Hongzi; Zhang, Xinjian; Yang, Hetong

2017-10-01

An appropriate reference gene is required to get reliable results from gene expression analysis by quantitative real-time reverse transcription PCR (qRT-PCR). In order to identify stable and reliable reference genes in Trichoderma afroharzianum under oxalic acid (OA) stress, six commonly used housekeeping genes, i.e., elongation factor 1, ubiquitin, ubiquitin-conjugating enzyme, glyceraldehyde-3-phosphate dehydrogenase, α-tubulin, actin, from the effective biocontrol isolate T. afroharzianum strain LTR-2 were tested for their expression during growth in liquid culture amended with OA. Four in silico programs (comparative ΔCt, NormFinder, geNorm and BestKeeper) were used to evaluate the expression stabilities of six candidate reference genes. The elongation factor 1 gene EF-1 was identified as the most stably expressed reference gene, and was used as the normalizer to quantify the expression level of the oxalate decarboxylase coding gene OXDC in T. afroharzianum strain LTR-2 under OA stress. The result showed that the expression of OXDC was significantly up-regulated as expected. This study provides an effective method to quantify expression changes of target genes in T. afroharzianum under OA stress. Copyright © 2017 Elsevier B.V. All rights reserved.

Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

NASA Astrophysics Data System (ADS)

Vize, Peter D.; Gerth, Victor E.

2007-01-01

Analysis of gene expression patterns within an organism plays a critical role in associating genes with biological processes in both health and disease. During embryonic development the analysis and comparison of different gene expression patterns allows biologists to identify candidate genes that may regulate the formation of normal tissues and organs and to search for genes associated with congenital diseases. No two individual embryos, or organs, are exactly the same shape or size so comparing spatial gene expression in one embryo to that in another is difficult. We will present our efforts in comparing gene expression data collected using both volumetric and projection approaches. Volumetric data is highly accurate but difficult to process and compare. Projection methods use UV mapping to align texture maps to standardized spatial frameworks. This approach is less accurate but is very rapid and requires very little processing. We have built a database of over 180 3D models depicting gene expression patterns mapped onto the surface of spline based embryo models. Gene expression data in different models can easily be compared to determine common regions of activity. Visualization software, both Java and OpenGL optimized for viewing 3D gene expression data will also be demonstrated.

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes.

PubMed

Mazzarelli, Joan M; Brestelli, John; Gorski, Regina K; Liu, Junmin; Manduchi, Elisabetta; Pinney, Deborah F; Schug, Jonathan; White, Peter; Kaestner, Klaus H; Stoeckert, Christian J

2007-01-01

EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth, differentiation of insulin-producing cells, islet or beta-cell injury, and genetic models of impaired beta-cell function. The expression datasets are derived using different microarray platforms, including the BCBC PancChips and Affymetrix gene expression arrays. Other datasets include semi-quantitative RT-PCR and MPSS expression studies. For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site. EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues.

[Study of testicular cancer gene expression in samples of oral leukoplakia and squamous cell carcinoma of the mouth].

PubMed

Skorodumova, L O; Muraev, A A; Zakharova, E S; Shepelev, M V; Korobko, I V; Zaderenko, I A; Ivanov, S Iu; Gnuchev, N V; Georgiev, G P; Larin, S S

2012-01-01

Cancer-testis (CT) antigens are normally expressed mostly in human germ cells, there is also an aberrant expression in some tumor cells. This expression profile makes them potential tumor growth biomarkers and a promising target for tumor immunotherapy. Specificity of CT genes expression in oral malignant and potentially malignant diseases, e.g. oral leukoplakia, is not yet studied. Data on CT genes expression profile in leukoplakia would allow developing new diagnostic methods with potential value for immunotherapy and prophylaxis of leukoplakia malignization. In our study we compared CT genes expression in normal oral mucosa, oral leukoplakia and oral squamous cell carcinoma. We are the first to describe CT genes expression in oral leukoplakia without dysplasia. This findings make impossible differential diagnosis of oral leukoplakia and squamous cell carcinoma on the basis of CT genes expression. The prognostic value of CT genes expression is still unclear, therefore the longitudinal studies are necessary.

Identification and resolution of artifacts in the interpretation of imprinted gene expression.

PubMed

Proudhon, Charlotte; Bourc'his, Déborah

2010-12-01

Genomic imprinting refers to genes that are epigenetically programmed in the germline to express exclusively or preferentially one allele in a parent-of-origin manner. Expression-based genome-wide screening for the identification of imprinted genes has failed to uncover a significant number of new imprinted genes, probably because of the high tissue- and developmental-stage specificity of imprinted gene expression. A very large number of technical and biological artifacts can also lead to the erroneous evidence of imprinted gene expression. In this article, we focus on three common sources of potential confounding effects: (i) random monoallelic expression in monoclonal cell populations, (ii) genetically determined monoallelic expression and (iii) contamination or infiltration of embryonic tissues with maternal material. This last situation specifically applies to genes that occur as maternally expressed in the placenta. Beside the use of reciprocal crosses that are instrumental to confirm the parental specificity of expression, we provide additional methods for the detection and elimination of these situations that can be misinterpreted as cases of imprinted expression.

The chemiluminescence based Ziplex automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip expression profiles.

PubMed

Quinn, Michael C J; Wilson, Daniel J; Young, Fiona; Dempsey, Adam A; Arcand, Suzanna L; Birch, Ashley H; Wojnarowicz, Paulina M; Provencher, Diane; Mes-Masson, Anne-Marie; Englert, David; Tonin, Patricia N

2009-07-06

As gene expression signatures may serve as biomarkers, there is a need to develop technologies based on mRNA expression patterns that are adaptable for translational research. Xceed Molecular has recently developed a Ziplex technology, that can assay for gene expression of a discrete number of genes as a focused array. The present study has evaluated the reproducibility of the Ziplex system as applied to ovarian cancer research of genes shown to exhibit distinct expression profiles initially assessed by Affymetrix GeneChip analyses. The new chemiluminescence-based Ziplex gene expression array technology was evaluated for the expression of 93 genes selected based on their Affymetrix GeneChip profiles as applied to ovarian cancer research. Probe design was based on the Affymetrix target sequence that favors the 3' UTR of transcripts in order to maximize reproducibility across platforms. Gene expression analysis was performed using the Ziplex Automated Workstation. Statistical analyses were performed to evaluate reproducibility of both the magnitude of expression and differences between normal and tumor samples by correlation analyses, fold change differences and statistical significance testing. Expressions of 82 of 93 (88.2%) genes were highly correlated (p < 0.01) in a comparison of the two platforms. Overall, 75 of 93 (80.6%) genes exhibited consistent results in normal versus tumor tissue comparisons for both platforms (p < 0.001). The fold change differences were concordant for 87 of 93 (94%) genes, where there was agreement between the platforms regarding statistical significance for 71 (76%) of 87 genes. There was a strong agreement between the two platforms as shown by comparisons of log2 fold differences of gene expression between tumor versus normal samples (R = 0.93) and by Bland-Altman analysis, where greater than 90% of expression values fell within the 95% limits of agreement. Overall concordance of gene expression patterns based on correlations, statistical significance between tumor and normal ovary data, and fold changes was consistent between the Ziplex and Affymetrix platforms. The reproducibility and ease-of-use of the technology suggests that the Ziplex array is a suitable platform for translational research.

Histone acetylation is associated with differential gene expression in the rapid and robust memory CD8+ T-cell response

PubMed Central

Fann, Monchou; Godlove, Jason M.; Catalfamo, Marta; Wood, William H.; Chrest, Francis J.; Chun, Nicholas; Granger, Larry; Wersto, Robert; Madara, Karen; Becker, Kevin; Henkart, Pierre A.; Weng, Nan-ping

2006-01-01

To understand the molecular basis for the rapid and robust memory T-cell responses, we examined gene expression and chromatin modification by histone H3 lysine 9 (H3K9) acetylation in resting and activated human naive and memory CD8+ T cells. We found that, although overall gene expression patterns were similar, a number of genes are differentially expressed in either memory or naive cells in their resting and activated states. To further elucidate the basis for differential gene expression, we assessed the role of histone H3K9 acetylation in differential gene expression. Strikingly, higher H3K9 acetylation levels were detected in resting memory cells, prior to their activation, for those genes that were differentially expressed following activation, indicating that hyperacetylation of histone H3K9 may play a role in selective and rapid gene expression of memory CD8+ T cells. Consistent with this model, we showed that inducing high levels of H3K9 acetylation resulted in an increased expression in naive cells of those genes that are normally expressed differentially in memory cells. Together, these findings suggest that differential gene expression mediated at least in part by histone H3K9 hyperacetylation may be responsible for the rapid and robust memory CD8+ T-cell response. PMID:16868257

Transcriptome-wide selection of a reliable set of reference genes for gene expression studies in potato cyst nematodes (Globodera spp.).

PubMed

Sabeh, Michael; Duceppe, Marc-Olivier; St-Arnaud, Marc; Mimee, Benjamin

2018-01-01

Relative gene expression analyses by qRT-PCR (quantitative reverse transcription PCR) require an internal control to normalize the expression data of genes of interest and eliminate the unwanted variation introduced by sample preparation. A perfect reference gene should have a constant expression level under all the experimental conditions. However, the same few housekeeping genes selected from the literature or successfully used in previous unrelated experiments are often routinely used in new conditions without proper validation of their stability across treatments. The advent of RNA-Seq and the availability of public datasets for numerous organisms are opening the way to finding better reference genes for expression studies. Globodera rostochiensis is a plant-parasitic nematode that is particularly yield-limiting for potato. The aim of our study was to identify a reliable set of reference genes to study G. rostochiensis gene expression. Gene expression levels from an RNA-Seq database were used to identify putative reference genes and were validated with qRT-PCR analysis. Three genes, GR, PMP-3, and aaRS, were found to be very stable within the experimental conditions of this study and are proposed as reference genes for future work.

Importance of correlation between gene expression levels: application to the type I interferon signature in rheumatoid arthritis.

PubMed

Reynier, Frédéric; Petit, Fabien; Paye, Malick; Turrel-Davin, Fanny; Imbert, Pierre-Emmanuel; Hot, Arnaud; Mougin, Bruno; Miossec, Pierre

2011-01-01

The analysis of gene expression data shows that many genes display similarity in their expression profiles suggesting some co-regulation. Here, we investigated the co-expression patterns in gene expression data and proposed a correlation-based research method to stratify individuals. Using blood from rheumatoid arthritis (RA) patients, we investigated the gene expression profiles from whole blood using Affymetrix microarray technology. Co-expressed genes were analyzed by a biclustering method, followed by gene ontology analysis of the relevant biclusters. Taking the type I interferon (IFN) pathway as an example, a classification algorithm was developed from the 102 RA patients and extended to 10 systemic lupus erythematosus (SLE) patients and 100 healthy volunteers to further characterize individuals. We developed a correlation-based algorithm referred to as Classification Algorithm Based on a Biological Signature (CABS), an alternative to other approaches focused specifically on the expression levels. This algorithm applied to the expression of 35 IFN-related genes showed that the IFN signature presented a heterogeneous expression between RA, SLE and healthy controls which could reflect the level of global IFN signature activation. Moreover, the monitoring of the IFN-related genes during the anti-TNF treatment identified changes in type I IFN gene activity induced in RA patients. In conclusion, we have proposed an original method to analyze genes sharing an expression pattern and a biological function showing that the activation levels of a biological signature could be characterized by its overall state of correlation.

Expression of Fushi tarazu factor 1 homolog and Pit-1 genes in the pituitaries of pre-spawning chum and sockeye salmon.

PubMed

Higa, M; Ando, H; Urano, A

2001-06-01

Fushi tarazu factor-1 (FTZ-F1) and Pit-1 are major pituitary transcription factors, controlling expression of genes coding for gonadotropin (GTH) subunits and growth hormone/prolactin/somatolactin family hormone, respectively. As a first step to investigate physiological factors regulating gene expression of these transcription factors, we determined their mRNA levels in the pituitaries of chum salmon (Oncorhynchus keta) at different stages of sexual maturation. FTZ-F1 gene expression was increased in males at the stage before spermiation, where the levels of GTH alpha and IIbeta subunit mRNAs were elevated. Pit-1 mRNA showed maximum levels at the final stage of sexual maturation in both sexes, when expression of somatolactin gene peaked. To clarify whether gonadotropin-releasing hormone (GnRH) is involved in these increases in FTZ-F1 and Pit-1 gene expression, we examined effects of GnRH analog (GnRHa) administration on their gene expression in maturing sockeye salmon (Oncorhynchus nerka). GnRHa stimulated Pit-1 gene expression in females only, but failed to stimulate FTZ-F1 gene expression in both sexes. The up-regulated expression of FTZ-F1 and Pit-1 genes at the pre-spawning stages suggest that the two transcription factors have roles in sexual maturation of salmonids. Physiological factors regulating gene expression of FTZ-F1 and Pit-1 are discussed in this review.

Identifying potential maternal genes of Bombyx mori using digital gene expression profiling

PubMed Central

Xu, Pingzhen

2018-01-01

Maternal genes present in mature oocytes play a crucial role in the early development of silkworm. Although maternal genes have been widely studied in many other species, there has been limited research in Bombyx mori. High-throughput next generation sequencing provides a practical method for gene discovery on a genome-wide level. Herein, a transcriptome study was used to identify maternal-related genes from silkworm eggs. Unfertilized eggs from five different stages of early development were used to detect the changing situation of gene expression. The expressed genes showed different patterns over time. Seventy-six maternal genes were annotated according to homology analysis with Drosophila melanogaster. More than half of the differentially expressed maternal genes fell into four expression patterns, while the expression patterns showed a downward trend over time. The functional annotation of these material genes was mainly related to transcription factor activity, growth factor activity, nucleic acid binding, RNA binding, ATP binding, and ion binding. Additionally, twenty-two gene clusters including maternal genes were identified from 18 scaffolds. Altogether, we plotted a profile for the maternal genes of Bombyx mori using a digital gene expression profiling method. This will provide the basis for maternal-specific signature research and improve the understanding of the early development of silkworm. PMID:29462160

Dynamic changes in prefrontal cortex gene expression following lysergic acid diethylamide administration.

PubMed

Nichols, Charles D; Garcia, Efrain E; Sanders-Bush, Elaine

2003-03-17

Lysergic acid diethylamide (LSD) is a psychoactive drug that transiently alters human perception, behavior, and mood at extremely low doses. Certain aspects of the behavior elicited by acute doses of LSD closely resemble symptoms of mental disorders such as schizophrenia. Characterizing gene expression profiles after LSD will be important for understanding how it alters behavior, and will lead to novel insights into disorders, such as schizophrenia, whose behavioral symptoms resemble the temporary effects of hallucinogenic drugs. We previously identified a small collection of genes within the rat prefrontal cortex that respond to LSD. Many of the products of these genes are involved in the process of synaptic plasticity. In the current report, we present a detailed analysis of the expression of these genes within the brain using RNase protection analysis. We find that the gene response to LSD is quite dynamic. The expression of some genes increases rapidly and decreases rapidly, while other genes change more gradually. Dose-response studies show two classes of expression; gene expression maximally stimulated at lower doses, versus gene expression that continues to rise at the higher doses. The role of the 5-HT(1A) and 5-HT(2A) receptor in mediating the increases in gene expression was examined in a series of experiments using receptor specific antagonists. Most expression increases were due to activation of the 5-HT(2A) receptor, however expression of two genes had neither a 5-HT(1A) nor a 5-HT(2A) receptor component.

[Differential gene expression profile in ischemic myocardium of Wistar rats with acute myocardial infarction: the study on gene construction, identification and function].

PubMed

Guo, Chun Yu; Yin, Hui Jun; Jiang, Yue Rong; Xue, Mei; Zhang, Lu; Shi, Da Zhuo

2008-06-18

To construct the differential genes expressed profile in the ischemic myocardium tissue reduced from acute myocardial infarction(AMI), and determine the biological functions of target genes. AMI model was generated by ligation of the left anterior descending coronary artery in Wistar rats. Total RNA was extracted from the normal and the ischemic heart tissues under the ligation point 7 days after the operation. Differential gene expression profiles of the two samples were constructed using Long Serial Analysis of Gene Expression(LongSAGE). Real time fluorescence quantitative PCR was used to verify gene expression profile and to identify the expression of 2 functional genes. The activities of enzymes from functional genes were determined by histochemistry. A total of 15,966 tags were screened from the normal and the ischemic LongSAGE maps. The similarities of the sequences were compared using the BLAST algebra in NCBI and 7,665 novel tags were found. In the ischemic tissue 142 genes were significantly changed compared with those in the normal tissue (P<0.05). These differentially expressed genes represented the proteins which might play important roles in the pathways of oxidation and phosphorylation, ATP synthesis and glycolysis. The partial genes identified by LongSAGE were confirmed using real time fluorescence quantitative PCR. Two genes related to energy metabolism, COX5a and ATP5e, were screened and quantified. Expression of two functional genes down-regulated at their mRNA levels and the activities of correlative functional enzymes decreased compared with those in the normal tissue. AMI causes a series of changes in gene expression, in which the abnormal expression of genes related to energy metabolism could be one of the molecular mechanisms of AMI. The intervention of the expressions of COX5a and ATP5e may be a new target for AMI therapy.

Selection and Validation of Reference Genes for Quantitative Real-Time PCR in Buckwheat (Fagopyrum esculentum) Based on Transcriptome Sequence Data

PubMed Central

Demidenko, Natalia V.; Logacheva, Maria D.; Penin, Aleksey A.

2011-01-01

Quantitative reverse transcription PCR (qRT-PCR) is one of the most precise and widely used methods of gene expression analysis. A necessary prerequisite of exact and reliable data is the accurate choice of reference genes. We studied the expression stability of potential reference genes in common buckwheat (Fagopyrum esculentum) in order to find the optimal reference for gene expression analysis in this economically important crop. Recently sequenced buckwheat floral transcriptome was used as source of sequence information. Expression stability of eight candidate reference genes was assessed in different plant structures (leaves and inflorescences at two stages of development and fruits). These genes are the orthologs of Arabidopsis genes identified as stable in a genome-wide survey gene of expression stability and a traditionally used housekeeping gene GAPDH. Three software applications – geNorm, NormFinder and BestKeeper - were used to estimate expression stability and provided congruent results. The orthologs of AT4G33380 (expressed protein of unknown function, Expressed1), AT2G28390 (SAND family protein, SAND) and AT5G46630 (clathrin adapter complex subunit family protein, CACS) are revealed as the most stable. We recommend using the combination of Expressed1, SAND and CACS for the normalization of gene expression data in studies on buckwheat using qRT-PCR. These genes are listed among five the most stably expressed in Arabidopsis that emphasizes utility of the studies on model plants as a framework for other species. PMID:21589908

A comparison of honeybee (Apis mellifera) queen, worker and drone larvae by RNA-Seq.

PubMed

He, Xu-Jiang; Jiang, Wu-Jun; Zhou, Mi; Barron, Andrew B; Zeng, Zhi-Jiang

2017-11-06

Honeybees (Apis mellifera) have haplodiploid sex determination: males develop from unfertilized eggs and females develop from fertilized ones. The differences in larval food also determine the development of females. Here we compared the total somatic gene expression profiles of 2-day and 4-day-old drone, queen and worker larvae by RNA-Seq. The results from a co-expression network analysis on all expressed genes showed that 2-day-old drone and worker larvae were closer in gene expression profiles than 2-day-old queen larvae. This indicated that for young larvae (2-day-old) environmental factors such as larval diet have a greater effect on gene expression profiles than ploidy or sex determination. Drones had the most distinct gene expression profiles at the 4-day larval stage, suggesting that haploidy, or sex dramatically affects the gene expression of honeybee larvae. Drone larvae showed fewer differences in gene expression profiles at the 2-day and 4-day time points than the worker and queen larval comparisons (598 against 1190 and 1181), suggesting a different pattern of gene expression regulation during the larval development of haploid males compared to diploid females. This study indicates that early in development the queen caste has the most distinct gene expression profile, perhaps reflecting the very rapid growth and morphological specialization of this caste compared to workers and drones. Later in development the haploid male drones have the most distinct gene expression profile, perhaps reflecting the influence of ploidy or sex determination on gene expression. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Transcriptomic analysis in the developing zebrafish embryo after compound exposure: Individual gene expression and pathway regulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hermsen, Sanne A.B., E-mail: Sanne.Hermsen@rivm.nl; Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht; Institute for Risk Assessment Sciences

2013-10-01

The zebrafish embryotoxicity test is a promising alternative assay for developmental toxicity. Classically, morphological assessment of the embryos is applied to evaluate the effects of compound exposure. However, by applying differential gene expression analysis the sensitivity and predictability of the test may be increased. For defining gene expression signatures of developmental toxicity, we explored the possibility of using gene expression signatures of compound exposures based on commonly expressed individual genes as well as based on regulated gene pathways. Four developmental toxic compounds were tested in concentration-response design, caffeine, carbamazepine, retinoic acid and valproic acid, and two non-embryotoxic compounds, D-mannitol andmore » saccharin, were included. With transcriptomic analyses we were able to identify commonly expressed genes, which were mostly development related, after exposure to the embryotoxicants. We also identified gene pathways regulated by the embryotoxicants, suggestive of their modes of action. Furthermore, whereas pathways may be regulated by all compounds, individual gene expression within these pathways can differ for each compound. Overall, the present study suggests that the use of individual gene expression signatures as well as pathway regulation may be useful starting points for defining gene biomarkers for predicting embryotoxicity. - Highlights: • The zebrafish embryotoxicity test in combination with transcriptomics was used. • We explored two approaches of defining gene biomarkers for developmental toxicity. • Four compounds in concentration-response design were tested. • We identified commonly expressed individual genes as well as regulated gene pathways. • Both approaches seem suitable starting points for defining gene biomarkers.« less

Genome-wide gene expression profiling reveals aberrant MAPK and Wnt signaling pathways associated with early parthenogenesis.

PubMed

Liu, Na; Enkemann, Steven A; Liang, Ping; Hersmus, Remko; Zanazzi, Claudia; Huang, Junjiu; Wu, Chao; Chen, Zhisheng; Looijenga, Leendert H J; Keefe, David L; Liu, Lin

2010-12-01

Mammalian parthenogenesis could not survive but aborted during mid-gestation, presumably because of lack of paternal gene expression. To understand the molecular mechanisms underlying the failure of parthenogenesis at early stages of development, we performed global gene expression profiling and functional analysis of parthenogenetic blastocysts in comparison with those of blastocysts from normally fertilized embryos. Parthenogenetic blastocysts exhibited changes in the expression of 749 genes, of which 214 had lower expression and 535 showed higher expressions than fertilized embryos using a minimal 1.8-fold change as a cutoff. Genes important for placenta development were decreased in their expression in parthenote blastocysts. Some maternally expressed genes were up-regulated and paternal-related genes were down-regulated. Moreover, aberrantly increased Wnt signaling and reduced mitogen-activated protein kinase (MAPK) signaling were associated with early parthenogenesis. The protein level of extracellular signal-regulated kinase 2 (ERK2) was low in parthenogenetic blastocysts compared with that of fertilized blastocysts 120 h after fertilization. 6-Bromoindirubin-3'-oxime, a specific glycogen synthase kinase-3 (GSK-3) inhibitor, significantly decreased embryo hatching. The expression of several imprinted genes was altered in parthenote blastocysts. Gene expression also linked reduced expression of Xist to activation of X chromosome. Our findings suggest that failed X inactivation, aberrant imprinting, decreased ERK/MAPK signaling and possibly elevated Wnt signaling, and reduced expression of genes for placental development collectively may contribute to abnormal placenta formation and failed fetal development in parthenogenetic embryos.

Chamber Specific Gene Expression Landscape of the Zebrafish Heart

PubMed Central

Singh, Angom Ramcharan; Sivadas, Ambily; Sabharwal, Ankit; Vellarikal, Shamsudheen Karuthedath; Jayarajan, Rijith; Verma, Ankit; Kapoor, Shruti; Joshi, Adita; Scaria, Vinod; Sivasubbu, Sridhar

2016-01-01

The organization of structure and function of cardiac chambers in vertebrates is defined by chamber-specific distinct gene expression. This peculiarity and uniqueness of the genetic signatures demonstrates functional resolution attributed to the different chambers of the heart. Altered expression of the cardiac chamber genes can lead to individual chamber related dysfunctions and disease patho-physiologies. Information on transcriptional repertoire of cardiac compartments is important to understand the spectrum of chamber specific anomalies. We have carried out a genome wide transcriptome profiling study of the three cardiac chambers in the zebrafish heart using RNA sequencing. We have captured the gene expression patterns of 13,396 protein coding genes in the three cardiac chambers—atrium, ventricle and bulbus arteriosus. Of these, 7,260 known protein coding genes are highly expressed (≥10 FPKM) in the zebrafish heart. Thus, this study represents nearly an all-inclusive information on the zebrafish cardiac transcriptome. In this study, a total of 96 differentially expressed genes across the three cardiac chambers in zebrafish were identified. The atrium, ventricle and bulbus arteriosus displayed 20, 32 and 44 uniquely expressing genes respectively. We validated the expression of predicted chamber-restricted genes using independent semi-quantitative and qualitative experimental techniques. In addition, we identified 23 putative novel protein coding genes that are specifically restricted to the ventricle and not in the atrium or bulbus arteriosus. In our knowledge, these 23 novel genes have either not been investigated in detail or are sparsely studied. The transcriptome identified in this study includes 68 differentially expressing zebrafish cardiac chamber genes that have a human ortholog. We also carried out spatiotemporal gene expression profiling of the 96 differentially expressed genes throughout the three cardiac chambers in 11 developmental stages and 6 tissue types of zebrafish. We hypothesize that clustering the differentially expressed genes with both known and unknown functions will deliver detailed insights on fundamental gene networks that are important for the development and specification of the cardiac chambers. It is also postulated that this transcriptome atlas will help utilize zebrafish in a better way as a model for studying cardiac development and to explore functional role of gene networks in cardiac disease pathogenesis. PMID:26815362

VH gene expression and regulation in the mutant Alicia rabbit. Rescue of VHa2 allotype expression.

PubMed

Chen, H T; Alexander, C B; Young-Cooper, G O; Mage, R G

1993-04-01

Rabbits of the Alicia strain, derived from rabbits expressing the VHa2 allotype, have a mutation in the H chain locus that has a cis effect upon the expression of VHa2 and VHa- genes. A small deletion at the most J-proximal (3') end of the VH locus leads to low expression of all the genes on the entire chromosome in heterozygous ali mutants and altered relative expression of VH genes in homozygotes. To study VH gene expression and regulation, we used the polymerase chain reaction to amplify the VH genes expressed in spleens of young and adult wild-type and mutant Alicia rabbits. The cDNA from reverse transcription of splenic mRNA was amplified and polymerase chain reaction libraries were constructed and screened with oligonucleotides from framework regions 1 and 3, as well as JH. Thirty-three VH-positive clones were sequenced and analyzed. We found that in mutant Alicia rabbits, products of the first functional VH gene (VH4a2), (or VH4a2-like genes) were expressed in 2- to 8-wk-olds. Expression of both the VHx and VHy types of VHa- genes was also elevated but the relative proportions of VHx and VHy, especially VHx, decreased whereas the relative levels of expression of VH4a2 or VH4a2-like genes increased with age. Our results suggest that the appearance of sequences resembling that of the VH1a2, which is deleted in the mutant ali rabbits, could be caused by alterations of the sequences of the rearranged VH4a2 genes by gene conversions and/or rearrangement of upstream VH1a2-like genes later in development.

Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa.

PubMed

Shi, Rui; Wang, Jack P; Lin, Ying-Chung; Li, Quanzi; Sun, Ying-Hsuan; Chen, Hao; Sederoff, Ronald R; Chiang, Vincent L

2017-05-01

Co-expression networks based on transcriptomes of Populus trichocarpa major tissues and specific cell types suggest redundant control of cell wall component biosynthetic genes by transcription factors in wood formation. We analyzed the transcriptomes of five tissues (xylem, phloem, shoot, leaf, and root) and two wood forming cell types (fiber and vessel) of Populus trichocarpa to assemble gene co-expression subnetworks associated with wood formation. We identified 165 transcription factors (TFs) that showed xylem-, fiber-, and vessel-specific expression. Of these 165 TFs, 101 co-expressed (correlation coefficient, r > 0.7) with the 45 secondary cell wall cellulose, hemicellulose, and lignin biosynthetic genes. Each cell wall component gene co-expressed on average with 34 TFs, suggesting redundant control of the cell wall component gene expression. Co-expression analysis showed that the 101 TFs and the 45 cell wall component genes each has two distinct groups (groups 1 and 2), based on their co-expression patterns. The group 1 TFs (44 members) are predominantly xylem and fiber specific, and are all highly positively co-expressed with the group 1 cell wall component genes (30 members), suggesting their roles as major wood formation regulators. Group 1 TFs include a lateral organ boundary domain gene (LBD) that has the highest number of positively correlated cell wall component genes (36) and TFs (47). The group 2 TFs have 57 members, including 14 vessel-specific TFs, and are generally less correlated with the cell wall component genes. An exception is a vessel-specific basic helix-loop-helix (bHLH) gene that negatively correlates with 20 cell wall component genes, and may function as a key transcriptional suppressor. The co-expression networks revealed here suggest a well-structured transcriptional homeostasis for cell wall component biosynthesis during wood formation.

Influence of white spot syndrome virus infection on hepatopancreas gene expression of `Huanghai No. 2' shrimp ( Fenneropenaeus chinensis)

NASA Astrophysics Data System (ADS)

Meng, Xianhong; Shi, Xiaoli; Kong, Jie; Luan, Sheng; Luo, Kun; Cao, Baoxiang; Liu, Ning; Lu, Xia; Li, Xupeng; Deng, Kangyu; Cao, Jiawang; Zhang, Yingxue; Zhang, Hengheng

2017-10-01

To elucidate the molecular response of shrimp hepatopancreas to white spot syndrome virus (WSSV) infection, microarray was applied to investigate the differentially expressed genes in the hepatopancreas of `Huanghai No. 2' ( Fenneropenaeus chinensis). A total of 59137 unigenes were designed onto a custom-made 60K Agilent chip. After infection, the gene expression profiles in the hepatopancreas of the shrimp with a lower viral load at early (48-96 h), peak (168-192 h) and late (264-288 h) infection phases were analyzed. Of 18704 differentially expressed genes, 6412 were annotated. In total, 5453 differentially expressed genes (1916 annotated) expressed at all three phases, and most of the annotated were either up- or down-regulated continuously. These genes function diversely in, for example, immune response, cytoskeletal system, signal transduction, stress resistance, protein synthesis and processing, metabolism among others. Some of the immune-related genes, including antilipopolysaccharide factor, Kazal-type proteinase inhibitor, C-type lectin and serine protease encoding genes, were up-regulated after WSSV infection. These genes have been reported to be involved in the anti-WSSV responses. The expression of genes related to the cytoskeletal system, including β-actin and myosin but without tubulin genes, were down-regulated after WSSV infection. Astakine was found for the first time in the WSSV-infected F. chinensis. To further confirm the expression of differentially expressed genes, quantitative real-time PCR was performed to test the expression of eight randomly selected genes and verified the reliability and accuracy of the microarray expression analysis. The data will provide valuable information to understanding the immune mechanism of shrimp's response to WSSV.

Inhibition of histone deacetylation and DNA methylation improves gene expression mediated by the adeno-associated virus/phage in cancer cells.

PubMed

Kia, Azadeh; Yata, Teerapong; Hajji, Nabil; Hajitou, Amin

2013-10-22

Bacteriophage (phage), viruses that infect bacteria only, have become promising vectors for targeted systemic delivery of genes to cancer, although, with poor efficiency. We previously designed an improved phage vector by incorporating cis genetic elements of adeno-associated virus (AAV). This novel AAV/phage hybrid (AAVP) specifically targeted systemic delivery of therapeutic genes into tumors. To advance the AAVP vector, we recently introduced the stress-inducible Grp78 tumor specific promoter and found that this dual tumor-targeted AAVP provides persistent gene expression, over time, in cancer cells compared to silenced gene expression from the CMV promoter in the parental AAVP. Herein, we investigated the effect of histone deacetylation and DNA methylation on AAVP-mediated gene expression in cancer cells and explored the effect of cell confluence state on AAVP gene expression efficacy. Using a combination of AAVP expressing the GFP reporter gene, flow cytometry, inhibitors of histone deacetylation, and DNA methylation, we have demonstrated that histone deacetylation and DNA methylation are associated with silencing of gene expression from the CMV promoter in the parental AAVP. Importantly, inhibitors of histone deacetylases boost gene expression in cancer cells from the Grp78 promoter in the dual tumor-targeted AAVP. However, cell confluence had no effect on AAVP-guided gene expression. Our findings prove that combination of histone deacetylase inhibitor drugs with the Grp78 promoter is an effective approach to improve AAVP-mediated gene expression in cancer cells and should be considered for AAVP-based clinical cancer gene therapy.

Hypoxic regulation of the expression of cell proliferation related genes in U87 glioma cells upon inhibition of ire1 signaling enzyme

PubMed

Minchenko, O H; Tsymbal, D O; Minchenko, D O; Riabovol, O O; Ratushna, O O; Karbovskyi, L L

2016-01-01

We have studied the effect of inhibition of IRE1 (inositol requiring enzyme 1), which is a central mediator of endoplasmic reticulum stress and a controller of cell proliferation and tumor growth, on hypoxic regulation of the expression of different proliferation related genes in U87 glioma cells. It was shown that hypoxia leads to up-regulation of the expression of IL13RA2, CD24, ING1, ING2, ENDOG, and POLG genes and to down-regulation – of KRT18, TRAPPC3, TSFM, and MTIF2 genes at the mRNA level in control glioma cells. Changes for ING1 and CD24 genes were more significant. At the same time, inhibition of IRE1 modifies the effect of hypoxia on the expression of all studied genes. In particular, it increases sensitivity to hypoxia of the expression of IL13RA2, TRAPPC3, ENDOG, and PLOG genes and suppresses the effect of hypoxia on the expression of ING1 gene. Additionally, it eliminates hypoxic regulation of KRT18, CD24, ING2, TSFM, and MTIF2 genes expressions and introduces sensitivity to hypoxia of the expression of BET1 gene in glioma cells. The present study demonstrates that hypoxia, which often contributes to tumor growth, affects the expression of almost all studied genes. Additionally, inhibition of IRE1 can both enhance and suppress the hypoxic regulation of these gene expressions in a gene specific manner and thus possibly contributes to slower glioma growth, but several aspects of this regulation must be further clarified.

[Effect of human oviductal embryotrophic factors on gene expression of mouse preimplantation embryos].

PubMed

Yao, Yuan-Qing; Lee, Kai-Fai; Xu, Jia-Seng; Ho, Pak-Chung; Yeung, Shu-Biu

2007-09-01

To investigate the effect of embryotrophic factors (ETF) from human oviductal cells on gene expression of mouse early developmental embryos and discuss the role of fallopian tube in early development of embryos. ETF was isolated from conditioned medium of human oviductal cell line by sequential liquid chromatographic systems. Mouse embryos were treated by ETF in vitro. Using differential display RT-PCR, the gene expression of embryos treated by ETF was compared with embryos without ETF treatment. The differentially expressed genes were separated, re-amplified, cloned and sequenced. Gene expression profiles of embryos with ETF treatment was different from embryos without this treatment. Eight differentially expressed genes were cloned and sequenced. These genes functioned in RNA degradation, synthesis, splicing, protein trafficking, cellular differentiation and embryo development. Embryotrophic factors from human oviductal cells affect gene expression of early developmental embryos. The human oviductal cells play wide roles in early developmental stages of embryos.

Evaluation of Reference Genes for Normalization of Gene Expression Using Quantitative RT-PCR under Aluminum, Cadmium, and Heat Stresses in Soybean.

PubMed

Gao, Mengmeng; Liu, Yaping; Ma, Xiao; Shuai, Qin; Gai, Junyi; Li, Yan

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used to analyze the relative gene expression level, however, the accuracy of qRT-PCR is greatly affected by the stability of reference genes, which is tissue- and environment- dependent. Therefore, choosing the most stable reference gene in a specific tissue and environment is critical to interpret gene expression patterns. Aluminum (Al), cadmium (Cd), and heat stresses are three important abiotic factors limiting soybean (Glycine max) production in southern China. To identify the suitable reference genes for normalizing the expression levels of target genes by qRT-PCR in soybean response to Al, Cd and heat stresses, we studied the expression stability of ten commonly used housekeeping genes in soybean roots and leaves under these three abiotic stresses, using five approaches, BestKeeper, Delta Ct, geNorm, NormFinder and RefFinder. We found TUA4 is the most stable reference gene in soybean root tips under Al stress. Under Cd stress, Fbox and UKN2 are the most stable reference genes in roots and leaves, respectively, while 60S is the most suitable reference gene when analyzing both roots and leaves together. For heat stress, TUA4 and UKN2 are the most stable housekeeping genes in roots and leaves, respectively, and UKN2 is the best reference gene for analysis of roots and leaves together. To validate the reference genes, we quantified the relative expression levels of six target genes that were involved in soybean response to Al, Cd or heat stresses, respectively. The expression patterns of these target genes differed between using the most and least stable reference genes, suggesting the selection of a suitable reference gene is critical for gene expression studies.

The gene expression profile of non-cultured, highly purified human adipose tissue pericytes: Transcriptomic evidence that pericytes are stem cells in human adipose tissue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silva Meirelles, Lindolfo da, E-mail: lindolfomeirelles@gmail.com; Laboratory for Stem Cells and Tissue Engineering, PPGBioSaúde, Lutheran University of Brazil, Av. Farroupilha 8001, 92425-900 Canoas, RS; Deus Wagatsuma, Virgínia Mara de

Pericytes (PCs) are a subset of perivascular cells that can give rise to mesenchymal stromal cells (MSCs) when culture-expanded, and are postulated to give rise to MSC-like cells during tissue repair in vivo. PCs have been suggested to behave as stem cells (SCs) in situ in animal models, although evidence for this role in humans is lacking. Here, we analyzed the transcriptomes of highly purified, non-cultured adipose tissue (AT)-derived PCs (ATPCs) to detect gene expression changes that occur as they acquire MSC characteristics in vitro, and evaluated the hypothesis that human ATPCs exhibit a gene expression profile compatible with anmore » AT SC phenotype. The results showed ATPCs are non-proliferative and express genes characteristic not only of PCs, but also of AT stem/progenitor cells. Additional analyses defined a gene expression signature for ATPCs, and revealed putative novel ATPC markers. Almost all AT stem/progenitor cell genes differentially expressed by ATPCs were not expressed by ATMSCs or culture-expanded ATPCs. Genes expressed by ATMSCs but not by ATPCs were also identified. These findings strengthen the hypothesis that PCs are SCs in vascularized tissues, highlight gene expression changes they undergo as they assume an MSC phenotype, and provide new insights into PC biology. - Highlights: • Non-cultured adipose tissue-derived human pericytes (ncATPCs) exhibit a distinctive gene expression signature. • ncATPCs express key adipose tissue stem cell genes previously described in vivo in mice. • ncATPCs express message for anti-proliferative and antiangiogenic molecules. • Most ncATPC-specific transcripts are absent in culture-expanded pericytes or ATMSCs • Gene expression changes ncATPCs undergo as they acquire a cultured ATMSC phenotype are pointed out.« less

[Construction of rAAV2-GPIIb/IIIa vector and test of its expression and function in vitro].

PubMed

Wang, Kai; Peng, Jian-Qiang; Chen, Fang-Ping; Wu, Xiao-Bin

2006-04-01

This study was aimed to explore the possibility of rAAV2 vector-mediating gene therapy for Glanzmann' s thrombasthenia. The rAAV2-GPIIb/IIIa vector was constructed. The GPIIb/IIIa gene expression in mammal cell were examined by different methods, such as: detection of mRNA expression in BHK-21 cells after 24 hours of infection (MOI = 1 x 10(5) v.g/cell) was performed by RT-PCR; the relation between MOI and quantity of GPII6/IIIa gene expression was detected by FACS after 48 hours of infection; GPIIb/IIIa protein expression in BHK-21 cells after 48 hours of infection (MOI = 10(5) v x g/cell) was assayed by Western blot, GPIIb/IIIa protein expression on cell surface was detected by immunofluorescence, and the biological function of expressing product was determined by PAC-1 conjunct experiments. The results showed that GPIIb/IIIa gene expression in mRNA level could be detected in BHK-21 cells after 24 hours of infection at MOI = 1 x 10(5) v x g/cell and the GPIIb/IIIa gene expression in protein level could be detected in BHK-21 cells after 48 hours of infection at MOI = 1 x 10(5) v x g/cell. In certain range, quantity of GPIIb/IIIa gene expression increased with MOI, but overdose of MOI decreased quantity of GPIIb/IIIa gene expression. Activated product of GPIIb/IIIa gene expression could combined with PAC-I, and possesed normal biological function. In conclusion, rAAV2 vactor can effectively mediate GPIIb and GPIIIa gene expressing in mammal cells, and the products of these genes exhibit biological function. This result may provide a basis for application of rAAV2 vector in Glanzmann's thrombasthenia gene therapy in furture.

Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds

PubMed Central

Dean, Rebecca; Harrison, Peter W.; Wright, Alison E.; Zimmer, Fabian; Mank, Judith E.

2015-01-01

The elevated rate of evolution for genes on sex chromosomes compared with autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex or from nonadaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures; therefore, we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression; however, in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where intersexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection. PMID:26067773

Sex-Biased Gene Expression and Sexual Conflict throughout Development

PubMed Central

Ingleby, Fiona C.; Flis, Ilona; Morrow, Edward H.

2015-01-01

Sex-biased gene expression is likely to account for most sexually dimorphic traits because males and females share much of their genome. When fitness optima differ between sexes for a shared trait, sexual dimorphism can allow each sex to express their optimum trait phenotype, and in this way, the evolution of sex-biased gene expression is one mechanism that could help to resolve intralocus sexual conflict. Genome-wide patterns of sex-biased gene expression have been identified in a number of studies, which we review here. However, very little is known about how sex-biased gene expression relates to sex-specific fitness and about how sex-biased gene expression and conflict vary throughout development or across different genotypes, populations, and environments. We discuss the importance of these neglected areas of research and use data from a small-scale experiment on sex-specific expression of genes throughout development to highlight potentially interesting avenues for future research. PMID:25376837

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies.

PubMed

Caracausi, Maria; Piovesan, Allison; Antonaros, Francesca; Strippoli, Pierluigi; Vitale, Lorenza; Pelleri, Maria Chiara

2017-09-01

The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium‑high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes. Recent advancements in the quality and completeness of human expression microarray data and in their statistical analysis may provide new clues toward the quantitative standardization of human gene expression studies in biology and medicine, both cross‑ and within‑tissue. The systematic approach used by the present study is based on the Transcriptome Mapper tool and exploits the automated reassignment of probes to corresponding genes, intra‑ and inter‑sample normalization, elaboration and representation of gene expression values in linear form within an indexed and searchable database with a graphical interface recording quantitative levels of expression, expression variability and cross‑tissue width of expression for more than 31,000 transcripts. The present study conducted a meta‑analysis of a pool of 646 expression profile data sets from 54 different human tissues and identified actin γ 1 as the HK gene that best fits the combination of all the traditional criteria to be used as a reference gene for general use; two ribosomal protein genes, RPS18 and RPS27, and one aquaporin gene, POM121 transmembrane nucleporin C, were also identified. The present study provided a list of tissue‑ and organ‑specific genes that may be most suited for the following individual tissues/organs: Adipose tissue, bone marrow, brain, heart, kidney, liver, lung, ovary, skeletal muscle and testis; and also provides in these cases a representative, quantitative portrait of the relative, typical gene‑expression profile in the form of searchable database tables.

Automated Discovery of Functional Generality of Human Gene Expression Programs

PubMed Central

Gerber, Georg K; Dowell, Robin D; Jaakkola, Tommi S; Gifford, David K

2007-01-01

An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the characterization of the functional breadth of these programs. The use of human expression data compendia for discovery of such programs presents several challenges including cellular inhomogeneity within samples, genetic and environmental variation across samples, uncertainty in the numbers of programs and sample populations, and temporal behavior. We developed GeneProgram, a new unsupervised computational framework based on Hierarchical Dirichlet Processes that addresses each of the above challenges. GeneProgram uses expression data to simultaneously organize tissues into groups and genes into overlapping programs with consistent temporal behavior, to produce maps of expression programs, which are sorted by generality scores that exploit the automatically learned groupings. Using synthetic and real gene expression data, we showed that GeneProgram outperformed several popular expression analysis methods. We applied GeneProgram to a compendium of 62 short time-series gene expression datasets exploring the responses of human cells to infectious agents and immune-modulating molecules. GeneProgram produced a map of 104 expression programs, a substantial number of which were significantly enriched for genes involved in key signaling pathways and/or bound by NF-κB transcription factors in genome-wide experiments. Further, GeneProgram discovered expression programs that appear to implicate surprising signaling pathways or receptor types in the response to infection, including Wnt signaling and neurotransmitter receptors. We believe the discovered map of expression programs involved in the response to infection will be useful for guiding future biological experiments; genes from programs with low generality scores might serve as new drug targets that exhibit minimal “cross-talk,” and genes from high generality programs may maintain common physiological responses that go awry in disease states. Further, our method is multipurpose, and can be applied readily to novel compendia of biological data. PMID:17696603

Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE

PubMed Central

Wang, Xin; Zhao, Yongjun; Wong, Kim; Ehlers, Peter; Kohara, Yuji; Jones, Steven J; Marra, Marco A; Holt, Robert A; Moerman, Donald G; Hansen, Dave

2009-01-01

Background Germ cells must progress through elaborate developmental stages from an undifferentiated germ cell to a fully differentiated gamete. Some of these stages include exiting mitosis and entering meiosis, progressing through the various stages of meiotic prophase, adopting either a male (sperm) or female (oocyte) fate, and completing meiosis. Additionally, many of the factors needed to drive embryogenesis are synthesized in the germ line. To increase our understanding of the genes that might be necessary for the formation and function of the germ line, we have constructed a SAGE library from hand dissected C. elegans hermaphrodite gonads. Results We found that 4699 genes, roughly 21% of all known C. elegans genes, are expressed in the adult hermaphrodite germ line. Ribosomal genes are highly expressed in the germ line; roughly four fold above their expression levels in the soma. We further found that 1063 of the germline-expressed genes have enriched expression in the germ line as compared to the soma. A comparison of these 1063 germline-enriched genes with a similar list of genes prepared using microarrays revealed an overlap of 460 genes, mutually reinforcing the two lists. Additionally, we identified 603 germline-enriched genes, supported by in situ expression data, which were not previously identified. We also found >4 fold enrichment for RNA binding proteins in the germ line as compared to the soma. Conclusion Using multiple technological platforms provides a more complete picture of global gene expression patterns. Genes involved in RNA metabolism are expressed at a significantly higher level in the germ line than the soma, suggesting a stronger reliance on RNA metabolism for control of the expression of genes in the germ line. Additionally, the number and expression level of germ line expressed genes on the X chromosome is lower than expected based on a random distribution. PMID:19426519

Differential expression of photosynthesis-related genes in pentaploid interspecific hybrid and its decaploid of Fragaria spp.

PubMed

Wang, Tao; Huang, Dongya; Chen, Baoyu; Mao, Nini; Qiao, Yushan; Ji, Muxiang

2018-03-01

Polyploidization always induces a series of changes in genome, transcriptome and epigenetics, of which changes in gene expression are the immediate causes of genotype alterations of polyploid plants. In our previous study on strawberry polyploidization, genes related to photosynthesis were found to undergo changes in gene expression and DNA methylation. Therefore, we chose 11 genes that were closely related to plant photosynthesis and analysed their expression during strawberry hybridization and chromosome doubling. Most genes of pentaploids showed expression levels between parents and were more similar to F. × ananassa. Gene expression levels of decaploids were higher than those of pentaploids and F. × ananassa. Different types of photosynthesis-related genes responded differently to hybridization and chromosome doubling. Chloroplast genes and regulatory genes showed complex responses. Structural genes of the photosynthetic system were expressed at a constant level and displayed a clear dosage effect. The methylation levels of one CG site on SIGE, which regulates expression of chloroplast genes, were negatively correlated with gene expression. In pentaploids and decaploids, more transcripts were from F. × ananassa than from F. viridis. The ratio of transcripts from from F. × ananassa to those from F. viridis was close to the ratio (4:1) of the genome of F. × ananassa to that of F. viridis in pentaploids and decaploids, but there were also some exceptions with obvious deviation.

Reliable reference genes for normalization of gene expression data in tea plants (Camellia sinensis) exposed to metal stresses.

PubMed

Wang, Ming-Le; Li, Qing-Hui; Xin, Hua-Hong; Chen, Xuan; Zhu, Xu-Jun; Li, Xing-Hui

2017-01-01

Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems. In this study, 12 candidate reference genes (i.e., 18S rRNA, Actin, CYP, EF-1α, eIF-4α, GAPDH, MON1, PP2AA3, TBP, TIP41, TUA, and UBC) were cloned from tea plants, and the stability of their expression was examined systematically in 60 samples exposed to diverse heavy metals (i.e., manganese, aluminum, copper, iron, and zinc). Three Excel-based algorithms (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of these genes. PP2AA3 and 18S rRNA were the most stably expressed genes, even though their expression profiles exhibited some variability. Moreover, commonly used reference genes (i.e., GAPDH and TBP) were the least appropriate reference genes for most samples. To further validate the suitability of the analyzed reference genes, the expression level of a phytochelatin synthase gene (i.e., CsPCS1) was determined using the putative reference genes for data normalizations. Our results may be beneficial for future studies involving the quantification of relative gene expression levels in tea plants.

Generation of novel pharmacogenomic candidates in the response to methotrexate in juvenile idiopathic arthritis: correlation between gene expression and genotype

PubMed Central

Moncrieffe, Halima; Hinks, Anne; Ursu, Simona; Kassoumeri, Laura; Etheridge, Angela; Hubank, Mike; Martin, Paul; Weiler, Tracey; Glass, David N; Thompson, Susan D.; Thomson, Wendy; Wedderburn, Lucy R

2010-01-01

Objectives Little is known about mechanisms of efficacy of methotrexate (MTX) in childhood arthritis, or genetic influences upon response to MTX. The aims of this study were to use gene expression profiling to identify novel pathways/genes altered by MTX and then investigate these genes for genotype associations with response to MTX treatment. Methods Gene expression profiling before and after MTX treatment was performed on 11 children with juvenile idiopathic arthritis (JIA) treated with MTX, in whom response at 6 months of treatment was defined. Genes showing the most differential gene expression after treatment were selected for SNP genotyping. Genotype frequencies were compared between non-responders and responders (ACR-Ped70). An independent cohort was available for validation. Results Gene expression profiling before and after MTX treatment revealed 1222 differentially expressed probes sets (fold change >1.7, p< 0.05) and 1065 when restricted to full responder cases only. Six highly differentially expressed genes were analysed for genetic association to response to MTX. Three SNPs in the SLC16A7 gene showed significant association with MTX response. One SNP showed validated association in an independent cohort. Conclusions This study is the first, to our knowledge, to evaluate gene expression profiles in children with JIA before and after MTX, and to analyse genetic variation in differentially expressed genes. We have identified a gene which may contribute to genetic variability in MTX response in JIA, and established as proof of principle that genes which are differentially expressed at mRNA level after drug administration may also be good candidates for genetic analysis. PMID:20827233

Aberrant Gene Expression in Humans

PubMed Central

Yang, Ence; Ji, Guoli; Brinkmeyer-Langford, Candice L.; Cai, James J.

2015-01-01

Gene expression as an intermediate molecular phenotype has been a focus of research interest. In particular, studies of expression quantitative trait loci (eQTL) have offered promise for understanding gene regulation through the discovery of genetic variants that explain variation in gene expression levels. Existing eQTL methods are designed for assessing the effects of common variants, but not rare variants. Here, we address the problem by establishing a novel analytical framework for evaluating the effects of rare or private variants on gene expression. Our method starts from the identification of outlier individuals that show markedly different gene expression from the majority of a population, and then reveals the contributions of private SNPs to the aberrant gene expression in these outliers. Using population-scale mRNA sequencing data, we identify outlier individuals using a multivariate approach. We find that outlier individuals are more readily detected with respect to gene sets that include genes involved in cellular regulation and signal transduction, and less likely to be detected with respect to the gene sets with genes involved in metabolic pathways and other fundamental molecular functions. Analysis of polymorphic data suggests that private SNPs of outlier individuals are enriched in the enhancer and promoter regions of corresponding aberrantly-expressed genes, suggesting a specific regulatory role of private SNPs, while the commonly-occurring regulatory genetic variants (i.e., eQTL SNPs) show little evidence of involvement. Additional data suggest that non-genetic factors may also underlie aberrant gene expression. Taken together, our findings advance a novel viewpoint relevant to situations wherein common eQTLs fail to predict gene expression when heritable, rare inter-individual variation exists. The analytical framework we describe, taking into consideration the reality of differential phenotypic robustness, may be valuable for investigating complex traits and conditions. PMID:25617623

Reliable reference genes for normalization of gene expression data in tea plants (Camellia sinensis) exposed to metal stresses

PubMed Central

Wang, Ming-Le; Li, Qing-Hui; Xin, Hua-Hong; Chen, Xuan; Zhu, Xu-Jun

2017-01-01

Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems. In this study, 12 candidate reference genes (i.e., 18S rRNA, Actin, CYP, EF-1α, eIF-4α, GAPDH, MON1, PP2AA3, TBP, TIP41, TUA, and UBC) were cloned from tea plants, and the stability of their expression was examined systematically in 60 samples exposed to diverse heavy metals (i.e., manganese, aluminum, copper, iron, and zinc). Three Excel-based algorithms (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of these genes. PP2AA3 and 18S rRNA were the most stably expressed genes, even though their expression profiles exhibited some variability. Moreover, commonly used reference genes (i.e., GAPDH and TBP) were the least appropriate reference genes for most samples. To further validate the suitability of the analyzed reference genes, the expression level of a phytochelatin synthase gene (i.e., CsPCS1) was determined using the putative reference genes for data normalizations. Our results may be beneficial for future studies involving the quantification of relative gene expression levels in tea plants. PMID:28453515

Comprehensive Evaluation of the Contribution of X Chromosome Genes to Platinum Sensitivity

PubMed Central

Gamazon, Eric R.; Im, Hae Kyung; O’Donnell, Peter H.; Ziliak, Dana; Stark, Amy L.; Cox, Nancy J.; Dolan, M. Eileen; Huang, Rong Stephanie

2011-01-01

Utilizing a genome-wide gene expression dataset generated from Affymetrix GeneChip® Human Exon 1.0ST array, we comprehensively surveyed the role of 322 X chromosome gene expression traits on cellular sensitivity to cisplatin and carboplatin. We identified 31 and 17 X chromosome genes whose expression levels are significantly correlated (after multiple testing correction) with sensitivity to carboplatin and cisplatin, respectively, in the combined HapMap CEU and YRI populations (false discovery rate, FDR<0.05). Of those, 14 overlap for both cisplatin and carboplatin. Employing an independent gene expression quantification method, the Illumina Sentrix Human-6 Expression BeadChip, measured on the same HapMap cell lines, we found that 4 and 2 of these genes are significantly associated with carboplatin and cisplatin sensitivity respectively in both analyses. Two genes, CTPS2 and DLG3, were identified by both genome-wide gene expression analyses as correlated with cellular sensitivity to both platinating agents. The expression of DLG3 gene was also found to correlate with cellular sensitivity to platinating agents in NCI60 cancer cell lines. In addition, we evaluated the role of X chromosome gene expression to the observed differences in sensitivity to the platinums between CEU and YRI derived cell lines. Of the 34 distinct genes significantly correlated with either carboplatin or cisplatin sensitivity, 14 are differentially expressed (defined as p<0.05) between CEU and YRI. Thus, sex chromosome genes play a role in cellular sensitivity to platinating agents and differences in the expression level of these genes are an important source of variation that should be included in comprehensive pharmacogenomic studies. PMID:21252287

Dexamethasone Stimulated Gene Expression in Peripheral Blood is a Sensitive Marker for Glucocorticoid Receptor Resistance in Depressed Patients

PubMed Central

Menke, Andreas; Arloth, Janine; Pütz, Benno; Weber, Peter; Klengel, Torsten; Mehta, Divya; Gonik, Mariya; Rex-Haffner, Monika; Rubel, Jennifer; Uhr, Manfred; Lucae, Susanne; Deussing, Jan M; Müller-Myhsok, Bertram; Holsboer, Florian; Binder, Elisabeth B

2012-01-01

Although gene expression profiles in peripheral blood in major depression are not likely to identify genes directly involved in the pathomechanism of affective disorders, they may serve as biomarkers for this disorder. As previous studies using baseline gene expression profiles have provided mixed results, our approach was to use an in vivo dexamethasone challenge test and to compare glucocorticoid receptor (GR)-mediated changes in gene expression between depressed patients and healthy controls. Whole genome gene expression data (baseline and following GR-stimulation with 1.5 mg dexamethasone p.o.) from two independent cohorts were analyzed to identify gene expression pattern that would predict case and control status using a training (N=18 cases/18 controls) and a test cohort (N=11/13). Dexamethasone led to reproducible regulation of 2670 genes in controls and 1151 transcripts in cases. Several genes, including FKBP5 and DUSP1, previously associated with the pathophysiology of major depression, were found to be reliable markers of GR-activation. Using random forest analyses for classification, GR-stimulated gene expression outperformed baseline gene expression as a classifier for case and control status with a correct classification of 79.1 vs 41.6% in the test cohort. GR-stimulated gene expression performed best in dexamethasone non-suppressor patients (88.7% correctly classified with 100% sensitivity), but also correctly classified 77.3% of the suppressor patients (76.7% sensitivity), when using a refined set of 19 genes. Our study suggests that in vivo stimulated gene expression in peripheral blood cells could be a promising molecular marker of altered GR-functioning, an important component of the underlying pathology, in patients suffering from depressive episodes. PMID:22237309

Role of Apoptosis in the Development of Uterine Leiomyoma: Analysis of Expression Patterns of Bcl-2 and Bax in Human Leiomyoma Tissue With Clinical Correlations.

PubMed

Csatlós, Éva; Máté, Szabolcs; Laky, Marcella; Rigó, János; Joó, József Gábor

2015-07-01

To describe gene expression patterns of the apoptotic regulatory genes Bcl and Bax in human uterine leiomyoma tissue. To investigate the relationship between alterations of gene expression patterns and several relevant clinical parameters. We obtained samples from 101 cases undergoing surgery for uterine leiomyoma for gene expression analysis of the Bcl-2 and Bax genes. Gene expression was quantified using RT-PCR technique. In the leiomyoma group, the Bcl-2 gene was significantly overexpressed compared with the control group although there was no such difference in the gene expression of Bax. Gene activity of Bcl-2 positively correlated with the tumor number in individual uterine leiomyoma cases. Although there was no significant correlation between the length of the cumulative lactation period before the development of uterine leiomyoma and Bcl-2 gene expression in the leiomyoma tissue, we observed a trend for a shorter cumulative lactation period to be associated with overexpression of the Bcl-2 gene. Overexpression of the antiapoptotic Bcl-2 gene appeared to be a factor in the development of uterine leiomyoma, whereas gene activity of the proapoptotic Bax gene did not seem to play a role in the process.

Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators.

PubMed

Clarke, Luka A; Botelho, Hugo M; Sousa, Lisete; Falcao, Andre O; Amaral, Margarida D

2015-11-01

A meta-analysis of 13 independent microarray data sets was performed and gene expression profiles from cystic fibrosis (CF), similar disorders (COPD: chronic obstructive pulmonary disease, IPF: idiopathic pulmonary fibrosis, asthma), environmental conditions (smoking, epithelial injury), related cellular processes (epithelial differentiation/regeneration), and non-respiratory "control" conditions (schizophrenia, dieting), were compared. Similarity among differentially expressed (DE) gene lists was assessed using a permutation test, and a clustergram was constructed, identifying common gene markers. Global gene expression values were standardized using a novel approach, revealing that similarities between independent data sets run deeper than shared DE genes. Correlation of gene expression values identified putative gene regulators of the CF transmembrane conductance regulator (CFTR) gene, of potential therapeutic significance. Our study provides a novel perspective on CF epithelial gene expression in the context of other lung disorders and conditions, and highlights the contribution of differentiation/EMT and injury to gene signatures of respiratory disease. Copyright © 2015 Elsevier Inc. All rights reserved.

[Construction and expression of the targeting super-antigen EGF-SEA fusion gene].

PubMed

Xie, Yang; Peng, Shaoping; Liao, Zhiying; Liu, Jiafeng; Liu, Xuemei; Chen, Weifeng

2014-05-01

To construct expression vector for the SEA-EGF fusion gene. Clone the SEA gene and the EGF gene segment with PCR and RT-PCR independently, and connect this two genes by the bridge PCR. Insert the fusion gene EGF-SEA into the expression vector PET-44. Induced the secretion of the fusion protein SEA-EGF by the antileptic. The gene fragment encoding EGF and SEA mature peptide was successfully cloned. The fusion gene EGF-SEA was successfully constructed and was inserted into expression vector. The new recombinant expression vector for fusion gene EGF-SEA is specific for head and neck cancer, laid the foundation for the further study of fusion protein SEA-EGF targeting immune therapy in head and neck tumors.

Extraordinary diversity of visual opsin genes in dragonflies

PubMed Central

Futahashi, Ryo; Kawahara-Miki, Ryouka; Kinoshita, Michiyo; Yoshitake, Kazutoshi; Yajima, Shunsuke; Arikawa, Kentaro; Fukatsu, Takema

2015-01-01

Dragonflies are colorful and large-eyed animals strongly dependent on color vision. Here we report an extraordinary large number of opsin genes in dragonflies and their characteristic spatiotemporal expression patterns. Exhaustive transcriptomic and genomic surveys of three dragonflies of the family Libellulidae consistently identified 20 opsin genes, consisting of 4 nonvisual opsin genes and 16 visual opsin genes of 1 UV, 5 short-wavelength (SW), and 10 long-wavelength (LW) type. Comprehensive transcriptomic survey of the other dragonflies representing an additional 10 families also identified as many as 15–33 opsin genes. Molecular phylogenetic analysis revealed dynamic multiplications and losses of the opsin genes in the course of evolution. In contrast to many SW and LW genes expressed in adults, only one SW gene and several LW genes were expressed in larvae, reflecting less visual dependence and LW-skewed light conditions for their lifestyle under water. In this context, notably, the sand-burrowing or pit-dwelling species tended to lack SW gene expression in larvae. In adult visual organs: (i) many SW genes and a few LW genes were expressed in the dorsal region of compound eyes, presumably for processing SW-skewed light from the sky; (ii) a few SW genes and many LW genes were expressed in the ventral region of compound eyes, probably for perceiving terrestrial objects; and (iii) expression of a specific LW gene was associated with ocelli. Our findings suggest that the stage- and region-specific expressions of the diverse opsin genes underlie the behavior, ecology, and adaptation of dragonflies. PMID:25713365

Regional and temporal differences in gene expression of LH(BETA)T(AG) retinoblastoma tumors.

PubMed

Houston, Samuel K; Pina, Yolanda; Clarke, Jennifer; Koru-Sengul, Tulay; Scott, William K; Nathanson, Lubov; Schefler, Amy C; Murray, Timothy G

2011-07-23

The purpose of this study was to evaluate by microarray the hypothesis that LH(BETA)T(AG) retinoblastoma tumors exhibit regional and temporal variations in gene expression. LH(BETA)T(AG) mice aged 12, 16, and 20 weeks were euthanatized (n = 9). Specimens were taken from five tumor areas (apex, anterior lateral, center, base, and posterior lateral). Samples were hybridized to gene microarrays. The data were preprocessed and analyzed, and genes with a P < 0.01, according to the ANOVA models, and a log(2)-fold change >2.5 were considered to be differentially expressed. Differentially expressed genes were analyzed for overlap with known networks by using pathway analysis tools. There were significant temporal (P < 10(-8)) and regional differences in gene expression for LH(BETA)T(AG) retinoblastoma tumors. At P < 0.01 and log(2)-fold change >2.5, there were significant changes in gene expression of 190 genes apically, 84 genes anterolaterally, 126 genes posteriorly, 56 genes centrally, and 134 genes at the base. Differentially expressed genes overlapped with known networks, with significant involvement in regulation of cellular proliferation and growth, response to oxygen levels and hypoxia, regulation of cellular processes, cellular signaling cascades, and angiogenesis. There are significant temporal and regional variations in the LH(BETA)T(AG) retinoblastoma model. Differentially expressed genes overlap with key pathways that may play pivotal roles in murine retinoblastoma development. These findings suggest the mechanisms involved in tumor growth and progression in murine retinoblastoma tumors and identify pathways for analysis at a functional level, to determine significance in human retinoblastoma. Microarray analysis of LH(BETA)T(AG) retinal tumors showed significant regional and temporal variations in gene expression, including dysregulation of genes involved in hypoxic responses and angiogenesis.

Gene Expression Profiling of Gastric Cancer

PubMed Central

Marimuthu, Arivusudar; Jacob, Harrys K.C.; Jakharia, Aniruddha; Subbannayya, Yashwanth; Keerthikumar, Shivakumar; Kashyap, Manoj Kumar; Goel, Renu; Balakrishnan, Lavanya; Dwivedi, Sutopa; Pathare, Swapnali; Dikshit, Jyoti Bajpai; Maharudraiah, Jagadeesha; Singh, Sujay; Sameer Kumar, Ghantasala S; Vijayakumar, M.; Veerendra Kumar, Kariyanakatte Veeraiah; Premalatha, Chennagiri Shrinivasamurthy; Tata, Pramila; Hariharan, Ramesh; Roa, Juan Carlos; Prasad, T.S.K; Chaerkady, Raghothama; Kumar, Rekha Vijay; Pandey, Akhilesh

2015-01-01

Gastric cancer is the second leading cause of cancer death worldwide, both in men and women. A genomewide gene expression analysis was carried out to identify differentially expressed genes in gastric adenocarcinoma tissues as compared to adjacent normal tissues. We used Agilent’s whole human genome oligonucleotide microarray platform representing ~41,000 genes to carry out gene expression analysis. Two-color microarray analysis was employed to directly compare the expression of genes between tumor and normal tissues. Through this approach, we identified several previously known candidate genes along with a number of novel candidate genes in gastric cancer. Testican-1 (SPOCK1) was one of the novel molecules that was 10-fold upregulated in tumors. Using tissue microarrays, we validated the expression of testican-1 by immunohistochemical staining. It was overexpressed in 56% (160/282) of the cases tested. Pathway analysis led to the identification of several networks in which SPOCK1 was among the topmost networks of interacting genes. By gene enrichment analysis, we identified several genes involved in cell adhesion and cell proliferation to be significantly upregulated while those corresponding to metabolic pathways were significantly downregulated. The differentially expressed genes identified in this study are candidate biomarkers for gastric adenoacarcinoma. PMID:27030788

Evaluation and Validation of Housekeeping Genes as Reference for Gene Expression Studies in Pigeonpea (Cajanus cajan) Under Drought Stress Conditions

PubMed Central

Sinha, Pallavi; Singh, Vikas K.; Suryanarayana, V.; Krishnamurthy, L.; Saxena, Rachit K.; Varshney, Rajeev K.

2015-01-01

Gene expression analysis using quantitative real-time PCR (qRT-PCR) is a very sensitive technique and its sensitivity depends on the stable performance of reference gene(s) used in the study. A number of housekeeping genes have been used in various expression studies in many crops however, their expression were found to be inconsistent under different stress conditions. As a result, species specific housekeeping genes have been recommended for different expression studies in several crop species. However, such specific housekeeping genes have not been reported in the case of pigeonpea (Cajanus cajan) despite the fact that genome sequence has become available for the crop. To identify the stable housekeeping genes in pigeonpea for expression analysis under drought stress conditions, the relative expression variations of 10 commonly used housekeeping genes (EF1α, UBQ10, GAPDH, 18SrRNA, 25SrRNA, TUB6, ACT1, IF4α, UBC and HSP90) were studied on root, stem and leaves tissues of Asha (ICPL 87119). Three statistical algorithms geNorm, NormFinder and BestKeeper were used to define the stability of candidate genes. geNorm analysis identified IF4α and TUB6 as the most stable housekeeping genes however, NormFinder analysis determined IF4α and HSP90 as the most stable housekeeping genes under drought stress conditions. Subsequently validation of the identified candidate genes was undertaken in qRT-PCR based gene expression analysis of uspA gene which plays an important role for drought stress conditions in pigeonpea. The relative quantification of the uspA gene varied according to the internal controls (stable and least stable genes), thus highlighting the importance of the choice of as well as validation of internal controls in such experiments. The identified stable and validated housekeeping genes will facilitate gene expression studies in pigeonpea especially under drought stress conditions. PMID:25849964

Evaluation and validation of housekeeping genes as reference for gene expression studies in pigeonpea (Cajanus cajan) under drought stress conditions.

PubMed

Sinha, Pallavi; Singh, Vikas K; Suryanarayana, V; Krishnamurthy, L; Saxena, Rachit K; Varshney, Rajeev K

2015-01-01

Gene expression analysis using quantitative real-time PCR (qRT-PCR) is a very sensitive technique and its sensitivity depends on the stable performance of reference gene(s) used in the study. A number of housekeeping genes have been used in various expression studies in many crops however, their expression were found to be inconsistent under different stress conditions. As a result, species specific housekeeping genes have been recommended for different expression studies in several crop species. However, such specific housekeeping genes have not been reported in the case of pigeonpea (Cajanus cajan) despite the fact that genome sequence has become available for the crop. To identify the stable housekeeping genes in pigeonpea for expression analysis under drought stress conditions, the relative expression variations of 10 commonly used housekeeping genes (EF1α, UBQ10, GAPDH, 18SrRNA, 25SrRNA, TUB6, ACT1, IF4α, UBC and HSP90) were studied on root, stem and leaves tissues of Asha (ICPL 87119). Three statistical algorithms geNorm, NormFinder and BestKeeper were used to define the stability of candidate genes. geNorm analysis identified IF4α and TUB6 as the most stable housekeeping genes however, NormFinder analysis determined IF4α and HSP90 as the most stable housekeeping genes under drought stress conditions. Subsequently validation of the identified candidate genes was undertaken in qRT-PCR based gene expression analysis of uspA gene which plays an important role for drought stress conditions in pigeonpea. The relative quantification of the uspA gene varied according to the internal controls (stable and least stable genes), thus highlighting the importance of the choice of as well as validation of internal controls in such experiments. The identified stable and validated housekeeping genes will facilitate gene expression studies in pigeonpea especially under drought stress conditions.

Altered gene expression in tree shrew retina and retinal pigment epithelium produced by short periods of minus-lens wear.

PubMed

He, Li; Frost, Michael R; Siegwart, John T; Norton, Thomas T

2018-03-01

Hyperopic refractive error is detected by retinal neurons, which generate GO signals through a direct emmetropization signaling cascade: retinal pigment epithelium (RPE) into choroid and then into sclera, thereby increasing axial elongation. To examine signaling early in this cascade, we measured gene expression in the retina and RPE after short exposure to hyperopia produced by minus-lens wear. Gene expression in each tissue was compared with gene expression in combined retina + RPE. Starting 24 days after normal eye opening, three groups of juvenile tree shrews (n = 7 each) wore a monocular -5 D lens. The untreated fellow eye served as a control. The "6h" group wore the lens for 6 h; the "24h" group wore the lens for 24 h; each group provided separate retina and RPE tissues. Group "24hC" wore the lens for 24 h and provided combined retina + RPE tissue. Quantitative PCR was used to measure the relative differences (treated eye vs. control eye) in mRNA levels for 66 candidate genes. In the retina after 6 h, mRNA levels for seven genes were significantly regulated: EGR1 and FOS (early intermediate genes) were down-regulated in the treated eyes. Genes with secreted protein products, BMP2 and CTGF, were down-regulated, whilst FGF10, IL18, and SST were up-regulated. After 24 h the pattern changed; only one of the seven genes still showed differential expression; BMP2 was still down-regulated. Two new genes with secreted protein products, IGF2 and VIP, were up-regulated. In the RPE, consistent with its role in receiving, processing, and transmitting GO signaling, differential expression was found for genes whose protein products are at the cell surface, intracellular, in the nucleus, and are secreted. After 6 h, mRNA levels for 17 genes were down-regulated in the treated eyes, whilst four genes (GJA1, IGF2R, LRP2, and IL18) were up-regulated. After 24 h the pattern was similar; mRNA levels for 14 of the same genes were still down-regulated; only LRP2 remained up-regulated. mRNA levels for six genes no longer showed differential expression, whilst nine genes, not differentially expressed at 6 h, now showed differential expression. In the combined retina + RPE after 24 h, mRNA levels for only seven genes were differentially regulated despite the differential expression of many genes in the RPE. Four genes showed the same expression in combined tissue as in retina alone, including up-regulation of VIP despite significant VIP down-regulation in RPE. Thus, hyperopia-induced GO signaling, as measured by differential gene expression, differs in the retina and the RPE. Retinal gene expression changed between 6 h and 24 h of treatment, suggesting evolution of the retinal response. Gene expression in the RPE was similar at both time points, suggesting sustained signaling. The combined retina + RPE does not accurately represent gene expression in either retina or, especially, RPE. When gene expression signatures were compared with those in choroid and sclera, GO signaling, as encoded by differential gene expression, differs in each compartment of the direct emmetropization signaling cascade. Copyright © 2018 Elsevier Ltd. All rights reserved.

Gene Expression by Mouse Inner Ear Hair Cells during Development

PubMed Central

Scheffer, Déborah I.; Shen, Jun

2015-01-01

Hair cells of the inner ear are essential for hearing and balance. As a consequence, pathogenic variants in genes specifically expressed in hair cells often cause hereditary deafness. Hair cells are few in number and not easily isolated from the adjacent supporting cells, so the biochemistry and molecular biology of hair cells can be difficult to study. To study gene expression in hair cells, we developed a protocol for hair cell isolation by FACS. With nearly pure hair cells and surrounding cells, from cochlea and utricle and from E16 to P7, we performed a comprehensive cell type-specific RNA-Seq study of gene expression during mouse inner ear development. Expression profiling revealed new hair cell genes with distinct expression patterns: some are specific for vestibular hair cells, others for cochlear hair cells, and some are expressed just before or after maturation of mechanosensitivity. We found that many of the known hereditary deafness genes are much more highly expressed in hair cells than surrounding cells, suggesting that genes preferentially expressed in hair cells are good candidates for unknown deafness genes. PMID:25904789

The effects of laughter on post-prandial glucose levels and gene expression in type 2 diabetic patients.

PubMed

Hayashi, Takashi; Murakami, Kazuo

2009-07-31

This report mainly summarizes the results of our study in which the physiological effects of laughter--as a positive emotional expression--were analyzed with respect to gene expression changes to demonstrate the hypothesis that the mind and genes mutually influence each other. We observed that laughter suppressed 2-h postprandial blood glucose level increase in patients with type 2 diabetes and analyzed gene expression changes. Some genes showed specific changes in their expression. In addition, we revealed that laughter decreased the levels of prorenin in blood; prorenin is involved in the onset of diabetic complications. Further, laughter normalized the expression of the prorenin receptor gene on peripheral blood leukocytes, which had been reduced in diabetic patients; this demonstrated that the inhibitory effects of laughter on the onset/deterioration of diabetic complications at the gene-expression level. In a subsequent study, we demonstrated the effects of laughter by discriminating 14 genes, related to natural killer (NK) cell activity, to exhibit continuous increases in expression as a result of laughter. Our results supported NK cell-mediated improvement in glucose tolerance at the gene-expression level. In this report, we also review other previous studies on laughter.

Correct Hox gene expression established independently of position in Caenorhabditis elegans.

PubMed

Cowing, D; Kenyon, C

1996-07-25

The Hox genes are expressed in a conserved sequence of spatial domains along the anteroposterior (A/P) body axes of many organisms. In Drosophila, position-specific signals located along the A/P axis establish the pattern of Hox gene expression. In the nematode Caenorhabditis elegans, it is not known how the pattern of Hox gene expression is established. C. elegans uses lineal control mechanisms and local cell interactions to specify early blastomere identities. However, many cells expressing the same Hox gene are unrelated by lineage, suggesting that, as in Drosophila, domains of Hox gene expression may be defined by cell-extrinsic A/P positional signals. To test this, we have investigated whether posterior mesodermal and ectodermal cells will express their normal posterior Hox gene when they are mispositioned in the anterior. Surprisingly, we find that correct Hox gene expression does not depend on cell position, but is highly correlated with cell lineage. Thus, although the most striking feature of Hox gene expression is its positional specificity, in C. elegans the pattern is achieved, at least in part, by a lineage-specific control system that operates without regard to A/P position.

Differential gene expression patterns between smokers and non‐smokers: cause or consequence?

PubMed Central

Jansen, Rick; Brooks, Andy; Willemsen, Gonneke; van Grootheest, Gerard; de Geus, Eco; Smit, Jan H.; Penninx, Brenda W.; Boomsma, Dorret I.

2015-01-01

Abstract The molecular mechanisms causing smoking‐induced health decline are largely unknown. To elucidate the molecular pathways involved in cause and consequences of smoking behavior, we conducted a genome‐wide gene expression study in peripheral blood samples targeting 18 238 genes. Data of 743 smokers, 1686 never smokers and 890 ex‐smokers were available from two population‐based cohorts from the Netherlands. In addition, data of 56 monozygotic twin pairs discordant for ever smoking were used. One hundred thirty‐two genes were differentially expressed between current smokers and never smokers (P < 1.2 × 10−6, Bonferroni correction). The most significant genes were G protein‐coupled receptor 15 (P < 1 × 10−150) and leucine‐rich repeat neuronal 3 (P < 1 × 10−44). The smoking‐related genes were enriched for immune system, blood coagulation, natural killer cell and cancer pathways. By taking the data of ex‐smokers into account, expression of these 132 genes was classified into reversible (94 genes), slowly reversible (31 genes), irreversible (6 genes) or inconclusive (1 gene). Expression of 6 of the 132 genes (three reversible and three slowly reversible) was confirmed to be reactive to smoking as they were differentially expressed in monozygotic pairs discordant for smoking. Cis‐expression quantitative trait loci for GPR56 and RARRES3 (downregulated in smokers) were associated with increased number of cigarettes smoked per day in a large genome‐wide association meta‐analysis, suggesting a causative effect of GPR56 and RARRES3 expression on smoking behavior. In conclusion, differential gene expression patterns in smokers are extensive and cluster in several underlying disease pathways. Gene expression differences seem mainly direct consequences of smoking, and largely reversible after smoking cessation. However, we also identified DNA variants that may influence smoking behavior via the mediating gene expression. PMID:26594007

Annotation of gene function in citrus using gene expression information and co-expression networks

PubMed Central

2014-01-01

Background The genus Citrus encompasses major cultivated plants such as sweet orange, mandarin, lemon and grapefruit, among the world’s most economically important fruit crops. With increasing volumes of transcriptomics data available for these species, Gene Co-expression Network (GCN) analysis is a viable option for predicting gene function at a genome-wide scale. GCN analysis is based on a “guilt-by-association” principle whereby genes encoding proteins involved in similar and/or related biological processes may exhibit similar expression patterns across diverse sets of experimental conditions. While bioinformatics resources such as GCN analysis are widely available for efficient gene function prediction in model plant species including Arabidopsis, soybean and rice, in citrus these tools are not yet developed. Results We have constructed a comprehensive GCN for citrus inferred from 297 publicly available Affymetrix Genechip Citrus Genome microarray datasets, providing gene co-expression relationships at a genome-wide scale (33,000 transcripts). The comprehensive citrus GCN consists of a global GCN (condition-independent) and four condition-dependent GCNs that survey the sweet orange species only, all citrus fruit tissues, all citrus leaf tissues, or stress-exposed plants. All of these GCNs are clustered using genome-wide, gene-centric (guide) and graph clustering algorithms for flexibility of gene function prediction. For each putative cluster, gene ontology (GO) enrichment and gene expression specificity analyses were performed to enhance gene function, expression and regulation pattern prediction. The guide-gene approach was used to infer novel roles of genes involved in disease susceptibility and vitamin C metabolism, and graph-clustering approaches were used to investigate isoprenoid/phenylpropanoid metabolism in citrus peel, and citric acid catabolism via the GABA shunt in citrus fruit. Conclusions Integration of citrus gene co-expression networks, functional enrichment analysis and gene expression information provide opportunities to infer gene function in citrus. We present a publicly accessible tool, Network Inference for Citrus Co-Expression (NICCE, http://citrus.adelaide.edu.au/nicce/home.aspx), for the gene co-expression analysis in citrus. PMID:25023870

[Construction, identification and expression of three kinds of shuttle plasmids of adenovirus expression vector of hepatitis C virus structure gene].

PubMed

Cao, Yi-zhan; Hao, Chun-qiu; Feng, Zhi-hua; Zhou, Yong-xing; Li, Jin-ge; Jia, Zhan-sheng; Wang, Ping-zhong

2003-02-01

To construct three recombinant shuttle plasmids of adenovirus expression vector which can express hepatitis C virus(HCV) different structure genes(C, C+E1, C+E1+E2) in order to pack adenovirus expression vectors which can express HCV different structure gene effectively. The different HCV structure genes derived from the plasmid pBRTM/HCV1-3011 by using polymerase chain reaction (PCR) were inserted into the backward position of cytomegalovirus(CMV) immediate early promotor element of shuttle plasmid(pAd.CMV-Link.1) of adenovirus expression vector respectively, then the three recombinant plasmids (pAd.HCV-C, pAd.HCV-CE1, pAd.HCV-S) were obtained. The recombinant plasmids were identified by endonuclease, PCR and sequencing. HCV structure genes were expressed transiently with Lipofectamine 2000 coated in HepG2 cells which were confirmed by immunofluorescence and Western-Blot. Insert DNAs of the three recombinant plasmids' were confirmed to be HCV different structure genes by endonuclease, PCR and sequencing. The three recombinant plasmids can express HCV structure gene (C, C+E1, C+E1+E2) transiently in HepG2 cells which were confirmed by immunofluorescence and Western-Blot. The three recombinant shuttle plasmids of adenovirus expression vector can express HCV structure gene(C, C+E1, C+E1+E2) transiently. This should be useful to pack adenovirus expression vector which can express HCV structure genes.

Microarray identification of novel genes downstream of Six1, a critical factor in cranial placode, somite and kidney development

PubMed Central

Yan, Bo; Neilson, Karen M.; Ranganathan, Ramya; Maynard, Thomas; Streit, Andrea; Moody, Sally A.

2014-01-01

Background Six1 plays an important role in the development of several vertebrate organs, including cranial sensory placodes, somites and kidney. Although Six1 mutations cause one form of Branchio-Otic Syndrome (BOS), the responsible gene in many patients has not been identified; genes that act downstream of Six1 are potential BOS candidates. Results We sought to identify novel genes expressed during placode, somite and kidney development by comparing gene expression between control and Six1-expressing ectodermal explants. The expression patterns of 19 of the significantly up-regulated and 11 of the significantly down-regulated genes were assayed from cleavage to larval stages. 28/30 genes are expressed in the otocyst, a structure that is functionally disrupted in BOS, and 26/30 genes are expressed in the nephric mesoderm, a structure that is functionally disrupted in the related Branchio-Otic-Renal (BOR) syndrome. We also identified the chick homologues of 5 genes and show that they have conserved expression patterns. Conclusions Of the 30 genes selected for expression analyses, all are expressed at many of the developmental times and appropriate tissues to be regulated by Six1. Many have the potential to play a role in the disruption of hearing and kidney function seen in BOS/BOR patients. PMID:25403746

A SHATTERPROOF-like gene controls ripening in non-climacteric strawberries, and auxin and abscisic acid antagonistically affect its expression.

PubMed

Daminato, Margherita; Guzzo, Flavia; Casadoro, Giorgio

2013-09-01

Strawberries (Fragaria×ananassa) are false fruits the ripening of which follows the non-climacteric pathway. The role played by a C-type MADS-box gene [SHATTERPROOF-like (FaSHP)] in the ripening of strawberries has been studied by transiently modifying gene expression through either over-expression or RNA-interference-mediated down-regulation. The altered expression of the FaSHP gene caused a change in the time taken by the over-expressing and the down- regulated fruits to attain the pink stage, which was slightly shorter and much longer, respectively, compared to controls. In parallel with the modified ripening times, the metabolome components and the expression of ripening-related genes also appeared different in the transiently modified fruits. Differences in the response time of the analysed genes suggest that FaSHP can control the expression of ripening genes either directly or indirectly through other transcription factor-encoding genes. Because fleshy strawberries are false fruits these results indicate that C-type MADS-box genes like SHATTERPROOF may act as modulators of ripening in fleshy fruit-like structures independently of their anatomical origin. Treatment of strawberries with either auxin or abscisic acid had antagonistic impacts on both the expression of FaSHP and the expression of ripening-related genes and metabolome components.

Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome

PubMed Central

Roymondal, Uttam; Das, Shibsankar; Sahoo, Satyabrata

2009-01-01

We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest. PMID:19131380

Broad Integration of Expression Maps and Co-Expression Networks Compassing Novel Gene Functions in the Brain

PubMed Central

Okamura-Oho, Yuko; Shimokawa, Kazuro; Nishimura, Masaomi; Takemoto, Satoko; Sato, Akira; Furuichi, Teiichi; Yokota, Hideo

2014-01-01

Using a recently invented technique for gene expression mapping in the whole-anatomy context, termed transcriptome tomography, we have generated a dataset of 36,000 maps of overall gene expression in the adult-mouse brain. Here, using an informatics approach, we identified a broad co-expression network that follows an inverse power law and is rich in functional interaction and gene-ontology terms. Our framework for the integrated analysis of expression maps and graphs of co-expression networks revealed that groups of combinatorially expressed genes, which regulate cell differentiation during development, were present in the adult brain and each of these groups was associated with a discrete cell types. These groups included non-coding genes of unknown function. We found that these genes specifically linked developmentally conserved groups in the network. A previously unrecognized robust expression pattern covering the whole brain was related to the molecular anatomy of key biological processes occurring in particular areas. PMID:25382412