scholarly journals Hybrid and Environmental Effects on Gene Expression in Poplar Clones in Pure and Mixed with Black Locust Stands

Forests ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1075
Author(s):  
Oleksandra Kuchma ◽  
Dennis Janz ◽  
Ludger Leinemann ◽  
Andrea Polle ◽  
Konstantin V. Krutovsky ◽  
...  
Keyword(s):  
Gene Expression ◽  
Environmental Conditions ◽  
Black Locust ◽  
Early Stage ◽  
Robinia Pseudoacacia ◽  
Mixed Stands ◽  
Important Indicator ◽  
Poplar Clones ◽  
Mixed Cultivation ◽  
Study Sites

Mixed cropping might be seen as an alternative to monocultures by better protecting biodiversity and improving ecosystem services and resources. In the presented study, we tested the genetic and ecological effects of pure and mixed propagation of different poplar hybrids planted together with black locust trees. Poplar (Populus) hybrids are widely used for bioenergy in monoculture systems due to their rapid and high biomass production. Black locust (Robinia pseudoacacia L.) is a species with the ability to fix nitrogen and seen as a promising candidate for mixed cultivation. Eight different poplar hybrids and black locust trees from three provenances planted in two study sites with different environmental conditions were tested in varying combinations in pure and mixed stands to observe effects of the different hybrids and genotypes, site conditions and the mixed growing on the performance of poplar and its gene expression. Transcriptome analyses of leaves from four poplar clones selected according to their divergent growth performance were conducted to study differential gene expression that can be an important indicator of differences in growing conditions and success. Differences in gene expression were most pronounced among hybrids and different genotypes of the same hybrid, followed by the study site influence, and were least pronounced between mixed and pure stands. The genotypes of the same hybrid were clearly separated from each other. Clear separation between the study sites for all clones was also observed. Only a few genes were differently expressed in pure vs. mixed stand comparisons for each clone, but there were no common genes that were differently expressed in pure vs. mixed stands in all clones. In total, 199 genes showed differential expression between the study sites regardless of poplar clone or type of stands. The analysis suggested that plant genotypes and environmental conditions were more important at the early stage of stand development than pure or mixed cultivation.

Site Quality in Relation to Damage by Locust Borer, Megacyllene robiniae Forster in Black Locust

1998 ◽  
Vol 33 (1) ◽  
pp. 106-112 ◽  
Author(s):  
Victor D. Echaves ◽  
Dan M. Harman ◽  
Amy L. Harman
Keyword(s):  
Sea Level ◽  
Black Locust ◽  
Robinia Pseudoacacia ◽  
Site Index ◽  
Site Quality ◽  
Soil Factors ◽  
Herbaceous Biomass ◽  
Study Sites ◽  
Robinia Pseudoacacia L ◽  
Attack Intensity

Forty-three study sites within eight counties in Maryland were utilized in an investigation of Site Index in relation to attack by the locust borer, Megacyllene robiniae (Forster), on the black locus tree, Robinia pseudoacacia L. In addition, several other factors related to borer attack intensity were tested for relationship with Site Index of black locust. Site Index was found to be negatively correlated with borer tunnels per tree, i.e., sites with higher Site Indices had statistically fewer borer attacks per tree. Positive correlation was also inferred between Site Index, borer attacks, and (1) scarring from previous year's borer attacks, (2) herbaceous biomass within-site, (3) elevation above sea level, (4) soil factors, including pH, %sand, silt, and clay.

scholarly journals Mortality of Different Populus Genotypes in Recently Established Mixed Short Rotation Coppice with Robinia pseudoacacia L.

Forests ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 410 ◽  
Author(s):  
Jessica Rebola-Lichtenberg ◽  
Peter Schall ◽  
Peter Annighöfer ◽  
Christian Ammer ◽  
Ludger Leinemann ◽  
...  
Keyword(s):  
Tree Species ◽  
Black Locust ◽  
Robinia Pseudoacacia ◽  
Mortality Rates ◽  
Short Rotation Coppice ◽  
Mixed Stands ◽  
Fast Growing ◽  
Short Rotation ◽  
Robinia Pseudoacacia L ◽  
Biomass For Energy

Short rotation coppices play an increasing role in providing wooden biomass for energy. Mixing fast-growing tree species in short rotation coppices may result in complementary effects and increased yield. The aim of this study was to analyze the effect on mortality of eight different poplar genotypes (Populus sp.) in mixed short rotation coppices with three different provenances of the N-fixing tree species black locust (Robinia pseudoacacia L.). Pure and mixed stands were established at two sites of contrasting fertility. Survival of poplar was assessed for each tree two times a year, for a period of three years. In the first two years, high variation in mortality was observed between the genotypes, but no significant differences between pure and mixed stands were identified. However, three years after planting, higher mortality rates were observed in the mixtures across all poplar genotypes in comparison to pure stands. The expected advantage on growth of combining an N-fixing tree with an N-demanding tree species, such as poplar, was overshadowed by the Robinia’s dominance and competitiveness.

LOCUST BORER (COLEOPTERA: CERAMBYCIDAE) ATTACK IN RELATION TO PULSED ELECTRIC CURRENT IN BLACK LOCUST TREES

1989 ◽  
Vol 24 (1) ◽  
pp. 124-132
Author(s):  
Dan M. Harman ◽  
Anne Bourne ◽  
Amy L. Harman
Keyword(s):  
Electric Current ◽  
Black Locust ◽  
Robinia Pseudoacacia ◽  
Current Season ◽  
Pulsed Electric Current ◽  
Cambium Layer ◽  
Study Sites ◽  
Robinia Pseudoacacia L

Resistance to pulsed electric current (ER) applied to the cambium layer was studied in black locust trees, Robinia pseudoacacia L., in relation to tree thrift indices, and particularly to intensity of current-season attacks by the locust borer Megacyllene robinia. A total of 415 borer attacks were sustained by 241 trees, with a maximum of 20 attacks per tree. Although variation in the data was high both within and among study sites, ER was positively correlated with borer mines per tree and with increased degrees of tree suppression, represented by dominance classes. ER ranged from 2 to 32 kohms per tree, with roughly 95% of the trees reading less than 25 kohms. Borer mines per tree were also correlated with tree dominance class, with more attacks incurred by increasingly suppressed trees.

An Integrated Feature Selection Algorithm for Cancer Classification using Gene Expression Data

2019 ◽  
Vol 21 (9) ◽  
pp. 631-645 ◽  
Author(s):  
Saeed Ahmed ◽  
Muhammad Kabir ◽  
Zakir Ali ◽  
Muhammad Arif ◽  
Farman Ali ◽  
...  
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Expression Data ◽  
Classification Accuracy ◽  
Early Stage ◽  
Small Sample Size ◽  
Feature Selection Method ◽  
Small Sample ◽  
Expression Data ◽  
Base Function

Aim and Objective: Cancer is a dangerous disease worldwide, caused by somatic mutations in the genome. Diagnosis of this deadly disease at an early stage is exceptionally new clinical application of microarray data. In DNA microarray technology, gene expression data have a high dimension with small sample size. Therefore, the development of efficient and robust feature selection methods is indispensable that identify a small set of genes to achieve better classification performance. Materials and Methods: In this study, we developed a hybrid feature selection method that integrates correlation-based feature selection (CFS) and Multi-Objective Evolutionary Algorithm (MOEA) approaches which select the highly informative genes. The hybrid model with Redial base function neural network (RBFNN) classifier has been evaluated on 11 benchmark gene expression datasets by employing a 10-fold cross-validation test. Results: The experimental results are compared with seven conventional-based feature selection and other methods in the literature, which shows that our approach owned the obvious merits in the aspect of classification accuracy ratio and some genes selected by extensive comparing with other methods. Conclusion: Our proposed CFS-MOEA algorithm attained up to 100% classification accuracy for six out of eleven datasets with a minimal sized predictive gene subset.

scholarly journals Genes associated with inflammation and bone remodeling are highly expressed in the bone of patients with the early-stage cam-type femoroacetabular impingement

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Guanying Gao ◽  
Ruiqi Wu ◽  
Rongge Liu ◽  
Jianquan Wang ◽  
Yingfang Ao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Tissue ◽  
Bone Remodeling ◽  
Femoroacetabular Impingement ◽  
Early Stage ◽  
Control Group ◽  
Tissue Samples ◽  
Expression Levels ◽  
Normal Bone ◽  
Impingement Zone

Abstract Background Recent studies have shown high expression levels of certain inflammatory, anabolic, and catabolic genes in the articular cartilage from the impingement zone of the hips with femoroacetabular impingement (FAI), representing an increased metabolic state. Nevertheless, little is known about the molecular properties of bone tissue from the impingement zone of hips with FAI. Methods Bone tissue samples from patients with early-stage cam-type FAI were collected during hip arthroscopy for treatment of cam-type FAI. Control bone tissue samples were collected from six patients who underwent total hip replacement because of a femoral neck fracture. Quantitative real-time polymerase chain reaction (PCR) was performed to determine the gene expression associated with inflammation and bone remodeling. The differences in the gene expression in bone tissues from the patients with early-stage cam-type FAI were also evaluated based on clinical parameters. Results In all, 12 patients with early-stage cam-type FAI and six patients in the control group were included in this study. Compared to the control samples, the bone tissue samples from patients with FAI showed higher expression levels of interleukin-6 (IL-6), alkaline phosphatase (ALP), receptor activator of nuclear factor-kB ligand (RANKL), and osteoprotegerin (OPG) (P < 0.05). IL-1 expression was detected only in the control group. On the other hand, there was no significant difference in IL-8 expression between the patients with FAI and the control group. The patients with FAI having a body mass index (BMI) of >24 kg/m2 showed higher ALP expression (P < 0.05). Further, the expression of IL-6 and ALP was higher in the patients with FAI in whom the lateral center-edge angle was >30° (P < 0.05). Conclusions Our results indicated the metabolic condition of bone tissues in patients with early-stage cam-type FAI differed from that of normal bone in the femoral head-neck junction. The expression levels of the genes associated with inflammation and bone remodeling were higher in the bone tissue of patients with early-stage cam-type FAI than in the patients with normal bone tissue.

scholarly journals Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Melanie Lindner ◽  
Irene Verhagen ◽  
Heidi M. Viitaniemi ◽  
Veronika N. Laine ◽  
Marcel E. Visser ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Environmental Conditions ◽  
Brain Regions ◽  
Temporal Changes ◽  
Egg Laying ◽  
Gene Body ◽  
Cpg Site ◽  
Repeated Sampling ◽  
Over Time

Abstract Background DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n = 6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled. Results We simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10 kb up- and downstream regions adjacent to the gene body. Conclusion Temporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.

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