scholarly journals Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars

2021 ◽  
Author(s):  
Álvaro Montesinos ◽  
Chris Dardick ◽  
María José Rubio-Cabetas ◽  
Jérôme Grimplet
Keyword(s):  
Gene Expression ◽  
Critical Role ◽  
Gene Families ◽  
Fruit Trees ◽  
Hormonal Responses ◽  
Breeding Programs ◽  
Branch Angle ◽  
Conserved Domain ◽  
Family Gene ◽  
High Degree

Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a share conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1 , LAZY2 , TAC1 , DRO1 , DRO2 , IGT-like . After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1 , LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation was established between the expression profile of these genes and the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that unlike many species, IGT family genes do not play a critical role in the control of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.

scholarly journals Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0252001
Author(s):  
Álvaro Montesinos ◽  
Chris Dardick ◽  
María José Rubio-Cabetas ◽  
Jérôme Grimplet
Keyword(s):  
Gene Expression ◽  
Growth Habit ◽  
Gene Families ◽  
Fruit Trees ◽  
Light Perception ◽  
Hormonal Responses ◽  
Breeding Programs ◽  
Branch Angle ◽  
Conserved Domain ◽  
High Degree

Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a shared conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1, LAZY2, TAC1, DRO1, DRO2, IGT-like. After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. To our knowledge, this is the first effort to analyze the diversity of IGT family proteins in members of the same tree species. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1, LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation could be established between the expression profile of these genes and the variability observed in the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that neither the expression nor the genetic polymorphism of IGT family genes are correlated to diversity of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.

scholarly journals S-Genotype Profiles of Turkish Apricot Germplasm

2016 ◽  
Vol 44 (1) ◽  
pp. 67-71 ◽  
Author(s):  
Kadir Ugurtan YILMAZ ◽  
Busra BASBUG ◽  
Kahraman GURCAN ◽  
Hasan PINAR ◽  
Julia HALASZ ◽  
...  
Keyword(s):  
Fruit Trees ◽  
Flowering Plants ◽  
Single Locus ◽  
Self Incompatibility ◽  
Breeding Programs ◽  
Allelic Variants ◽  
Self Fertilization ◽  
High Degree ◽  
Research Institute

In flowering plants, gametophytic self-incompatibility, controlled by a single locus with several allelic variants, is one of the major problems preventing self-fertilization. Among fruit trees, apricots show to a high degree self-incompatibility, especially in Middle-Asian and Iranian-Caucasian eco-geographical groups. In the present study, self-(in)compatibility characteristics of a total of 236 apricot genotypes (218 Turkish and 18 foreign) found within the National Apricot Germplasms of Apricot Research Institute in Malatya, Turkey was studied. Analyses were carried out by using four primer pairs (SRc-F and SRc-R, EM-PC2consFD and EM-PC3consRD, AprSC8-R and PaConsI-F, AprFBC8-F and AprFBC8-R). A total of 11 S-RNase alleles (S2, S3, S6, S7, S8, S9, S11, S12, S13, S20 and Sc) were determined in the 236 apricot genotypes. As Turkish and foreign apricot genotypes are determined mostly self-incompatible, the data obtained hereby might be of good use for apricot breeding programs and more practically, for apricot new plantations; thus pollinator cultivars should be considered when self-incompatible apricot cultivars are being used.

Hilar cholangiocarcinoma

2018 ◽  
Vol 1 (3) ◽  
pp. 28-30
Author(s):  
Tanita Suttichaimongkol
Keyword(s):  
Magnetic Resonance ◽  
Hilar Cholangiocarcinoma ◽  
Critical Role ◽  
Magnetic Resonance Cholangiopancreatography ◽  
Resonance Imaging ◽  
Extrahepatic Cholangiocarcinoma ◽  
Case Presentation ◽  
Duct Epithelium ◽  
Bile Duct Epithelium ◽  
High Degree

Cholangiocarcinoma is a primary biliary tract tumor arising from the bile duct epithelium. Classically, these tumors have been categorized according to their anatomic location as intrahepatic and extrahepatic. Hilar cholangiocarcinoma is the most common type of extrahepatic cholangiocarcinoma. It is the most difficult cancer to diagnose and therefore carries a poor prognosis with a 5-year survivalrate of less than 10%. Diagnostic imaging, coupled with a high degree of clinical suspicion, play a critical role in timely diagnosis, staging, and evaluation for surgical resectability. The most common imagingmodalities used for diagnosis and staging of hilar cholangiocarcinoma include ultrasound (US), computed tomography (CT), magnetic resonance imaging/magnetic resonance cholangiopancreatography(MRI/MRCP). This article showed a case presentation and reviewed the imaging appearance of hilar cholangiocarcinoma.   Figure 1  Greyscale sonography at the level of hepatic hilum revealed an ill-defined hilar mass (asterisk)resulting in upstream dilatation of right (arrow) and left (arrow head) main intrahepatic duct.  

A Review on Important Histone Acetyltransferase (HAT) Enzymes as Targets for Cancer Therapy

2019 ◽  
Vol 15 (2) ◽  
pp. 120-130
Author(s):  
Mohammad Ghanbari ◽  
Reza Safaralizadeh ◽  
Kiyanoush Mohammadi
Keyword(s):  
Gene Expression ◽  
Histone Acetyltransferase ◽  
Critical Role ◽  
Cancer Treatments ◽  
Control Of Gene Expression ◽  
Post Translational Modifications ◽  
Therapeutic Drugs ◽  
The Status ◽  
Acetyl Group ◽  
Increase Gene Expression

At the present time, cancer is one of the most lethal diseases worldwide. There are various factors involved in the development of cancer, including genetic factors, lifestyle, nutrition, and so on. Recent studies have shown that epigenetic factors have a critical role in the initiation and development of tumors. The histone post-translational modifications (PTMs) such as acetylation, methylation, phosphorylation, and other PTMs are important mechanisms that regulate the status of chromatin structure and this regulation leads to the control of gene expression. The histone acetylation is conducted by histone acetyltransferase enzymes (HATs), which are involved in transferring an acetyl group to conserved lysine amino acids of histones and consequently increase gene expression. On the basis of similarity in catalytic domains of HATs, these enzymes are divided into different groups such as families of GNAT, MYST, P300/CBP, SRC/P160, and so on. These enzymes have effective roles in apoptosis, signaling pathways, metastasis, cell cycle, DNA repair and other related mechanisms deregulated in cancer. Abnormal activation of HATs leads to uncontrolled amplification of cells and incidence of malignancy signs. This indicates that HAT might be an important target for effective cancer treatments, and hence there would be a need for further studies and designing of therapeutic drugs on this basis. In this study, we have reviewed the important roles of HATs in different human malignancies.

scholarly journals A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom

2021 ◽  
Vol 7 (6) ◽  
pp. 453
Author(s):  
Annie Lebreton ◽  
François Bonnardel ◽  
Yu-Cheng Dai ◽  
Anne Imberty ◽  
Francis M. Martin ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Large Family ◽  
Gene Families ◽  
Carbohydrate Binding ◽  
Sequence Motifs ◽  
Fungal Lectin ◽  
Quaternary Structures ◽  
High Degree ◽  
Carbohydrate Ligand ◽  
Fungal Kingdom

Fungal lectins are a large family of carbohydrate-binding proteins with no enzymatic activity. They play fundamental biological roles in the interactions of fungi with their environment and are found in many different species across the fungal kingdom. In particular, their contribution to defense against feeders has been emphasized, and when secreted, lectins may be involved in the recognition of bacteria, fungal competitors and specific host plants. Carbohydrate specificities and quaternary structures vary widely, but evidence for an evolutionary relationship within the different classes of fungal lectins is supported by a high degree of amino acid sequence identity. The UniLectin3D database contains 194 fungal lectin 3D structures, of which 129 are characterized with a carbohydrate ligand. Using the UniLectin3D lectin classification system, 109 lectin sequence motifs were defined to screen 1223 species deposited in the genomic portal MycoCosm of the Joint Genome Institute. The resulting 33,485 putative lectin sequences are organized in MycoLec, a publicly available and searchable database. These results shed light on the evolution of the lectin gene families in fungi.

scholarly journals Microglial deletion and inhibition alleviate behavior of post-traumatic stress disorder in mice

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Shuoshuo Li ◽  
Yajin Liao ◽  
Yuan Dong ◽  
Xiaoheng Li ◽  
Jun Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Post Traumatic Stress Disorder ◽  
Traumatic Stress ◽  
Microglial Activation ◽  
Stress Disorder ◽  
Critical Role ◽  
Post Traumatic Stress ◽  
Minocycline Treatment ◽  
Post Traumatic ◽  
Shock Exposure

Abstract Background Alteration of immune status in the central nervous system (CNS) has been implicated in the development of post-traumatic stress disorder (PTSD). However, the nature of overall changes in brain immunocyte landscape in PTSD condition remains unclear. Methods We constructed a mouse PTSD model by electric foot-shocks followed by contextual reminders and verified the PTSD-related symptoms by behavior test (including contextual freezing test, open-field test, and elevated plus maze test). We examined the immunocyte panorama in the brains of the naïve or PTSD mice by using single-cell mass cytometry. Microglia number and morphological changes in the hippocampus, prefrontal cortex, and amygdala were analyzed by histopathological methods. The gene expression changes of those microglia were detected by quantitative real-time PCR. Genetic/pharmacological depletion of microglia or minocycline treatment before foot-shocks exposure was performed to study the role of microglia in PTSD development and progress. Results We found microglia are the major brain immune cells that respond to PTSD. The number of microglia and ratio of microglia to immunocytes was significantly increased on the fifth day of foot-shock exposure. Furthermore, morphological analysis and gene expression profiling revealed temporal patterns of microglial activation in the hippocampus of the PTSD brains. Importantly, we found that genetic/pharmacological depletion of microglia or minocycline treatment before foot-shock exposure alleviated PTSD-associated anxiety and contextual fear. Conclusion Our results demonstrated a critical role for microglial activation in PTSD development and a potential therapeutic strategy for the clinical treatment of PTSD in the form of microglial inhibition.

scholarly journals Endurance Training Regulates Expression of Some Angiogenesis-Related Genes in Cardiac Tissue of Experimentally Induced Diabetic Rats

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 498
Author(s):  
Mojdeh Khajehlandi ◽  
Lotfali Bolboli ◽  
Marefat Siahkuhian ◽  
Mohammad Rami ◽  
Mohammadreza Tabandeh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Endurance Training ◽  
Molecular Mechanisms ◽  
Cardiac Tissue ◽  
Critical Role ◽  
Diabetic Rats ◽  
Moderate Intensity ◽  
Pcr Analysis ◽  
Cardiac Tissues ◽  
The Impact

Exercise can ameliorate cardiovascular dysfunctions in the diabetes condition, but its precise molecular mechanisms have not been entirely understood. The aim of the present study was to determine the impact of endurance training on expression of angiogenesis-related genes in cardiac tissue of diabetic rats. Thirty adults male Wistar rats were randomly divided into three groups (N = 10) including diabetic training (DT), sedentary diabetes (SD), and sedentary healthy (SH), in which diabetes was induced by a single dose of streptozotocin (50 mg/kg). Endurance training (ET) with moderate-intensity was performed on a motorized treadmill for six weeks. Training duration and treadmill speed were increased during five weeks, but they were kept constant at the final week, and slope was zero at all stages. Real-time polymerase chain reaction (RT-PCR) analysis was used to measure the expression of myocyte enhancer factor-2C (MEF2C), histone deacetylase-4 (HDAC4) and Calmodulin-dependent protein kinase II (CaMKII) in cardiac tissues of the rats. Our results demonstrated that six weeks of ET increased gene expression of MEF2C significantly (p < 0.05), and caused a significant reduction in HDAC4 and CaMKII gene expression in the DT rats compared to the SD rats (p < 0.05). We concluded that moderate-intensity ET could play a critical role in ameliorating cardiovascular dysfunction in a diabetes condition by regulating the expression of some angiogenesis-related genes in cardiac tissues.

scholarly journals Integrating metabolomics and targeted gene expression to uncover potential biomarkers of fungal/oomycetes-associated disease susceptibility in grapevine

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marisa Maia ◽  
António E. N. Ferreira ◽  
Rui Nascimento ◽  
Filipa Monteiro ◽  
Francisco Traquete ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Defence ◽  
Breeding Programs ◽  
Analysis Group ◽  
Expression Of Genes ◽  
Leucoanthocyanidin Reductase ◽  
Defence Responses ◽  
Targeted Gene Expression ◽  
Plant Defence Responses ◽  
First Time

Abstract Vitis vinifera, one of the most cultivated fruit crops, is susceptible to several diseases particularly caused by fungus and oomycete pathogens. In contrast, other Vitis species (American, Asian) display different degrees of tolerance/resistance to these pathogens, being widely used in breeding programs to introgress resistance traits in elite V. vinifera cultivars. Secondary metabolites are important players in plant defence responses. Therefore, the characterization of the metabolic profiles associated with disease resistance and susceptibility traits in grapevine is a promising approach to identify trait-related biomarkers. In this work, the leaf metabolic composition of eleven Vitis genotypes was analysed using an untargeted metabolomics approach. A total of 190 putative metabolites were found to discriminate resistant/partial resistant from susceptible genotypes. The biological relevance of discriminative compounds was assessed by pathway analysis. Several compounds were selected as promising biomarkers and the expression of genes coding for enzymes associated with their metabolic pathways was analysed. Reference genes for these grapevine genotypes were established for normalisation of candidate gene expression. The leucoanthocyanidin reductase 2 gene (LAR2) presented a significant increase of expression in susceptible genotypes, in accordance with catechin accumulation in this analysis group. Up to our knowledge this is the first time that metabolic constitutive biomarkers are proposed, opening new insights into plant selection on breeding programs.

scholarly journals Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 82
Author(s):  
Yunxiao Wei ◽  
Guoliang Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Transcriptional Changes ◽  
Aa Genome ◽  
High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

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