scholarly journals The Genetic Basis of a Craniofacial Disease Provides Insight into COPII Coat Assembly

2007 ◽  
Vol 13 (5) ◽  
pp. 623-634 ◽  
Author(s):  
J. Christopher Fromme ◽  
Mariella Ravazzola ◽  
Susan Hamamoto ◽  
Mohammed Al-Balwi ◽  
Wafaa Eyaid ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Insight Into

scholarly journals QTL analysis of self-selected macronutrient diet intake: fat, carbohydrate, and total kilocalories

2002 ◽  
Vol 11 (3) ◽  
pp. 205-217 ◽  
Author(s):  
Brenda K. Smith Richards ◽  
Brenda N. Belton ◽  
Angela C. Poole ◽  
James J. Mancuso ◽  
Gary A. Churchill ◽  
...  
Keyword(s):  
Body Weight ◽  
Qtl Analysis ◽  
Genetic Basis ◽  
Body Weight Gain ◽  
Macronutrient Intake ◽  
Naturally Occurring ◽  
Trait Locus ◽  
Diet Intake ◽  
Insight Into ◽  
Protein Quantitative Trait Locus

The present study investigated the inheritance of dietary fat, carbohydrate, and kilocalorie intake traits in an F2 population derived from an intercross between C57BL/6J (fat-preferring) and CAST/EiJ (carbohydrate-preferring) mice. Mice were phenotyped for self-selected food intake in a paradigm which provided for 10 days a choice between two macronutrient diets containing 78/22% of energy as a composite of either fat/protein or carbohydrate/protein. Quantitative trait locus (QTL) analysis identified six significant loci for macronutrient intake: three for fat intake on chromosomes (Chrs) 8 ( Mnif1), 18 ( Mnif2), and X ( Mnif3), and three for carbohydrate intake on Chrs 17 ( Mnic1), 6 ( Mnic2), and X ( Mnic3). An absence of interactions among these QTL suggests the existence of separate mechanisms controlling the intake of fat and carbohydrate. Two significant QTL for cumulative kilocalorie intake, adjusted for baseline body weight, were found on Chrs 17 ( Kcal1) and 18 ( Kcal2). Without body weight adjustment, another significant kcal locus appeared on distal Chr 2 ( Kcal3). These macronutrient and kilocalorie QTL, with the exception of loci on Chrs 8 and X, encompassed chromosomal regions influencing body weight gain and adiposity in this F2 population. These results provide new insight into the genetic basis of naturally occurring variation in nutrient intake phenotypes.

scholarly journals First approach to pod dehiscence in faba bean: genetic and histological analyses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
David Aguilar-Benitez ◽  
Inés Casimiro-Soriguer ◽  
Ana M. Torres
Keyword(s):  
Faba Bean ◽  
Linkage Mapping ◽  
Genetic Basis ◽  
Genomic Analysis ◽  
Fiber Layer ◽  
Dehiscence Zone ◽  
Molecular Bases ◽  
Insight Into ◽  
Pod Dehiscence ◽  
Comprehensive Study

Abstract Pod dehiscence causes important yield losses in cultivated crops and therefore has been a key trait strongly selected against in crop domestication. In spite of the growing knowledge on the genetic basis of dehiscence in different crops, no information is available so far for faba bean. Here we conduct the first comprehensive study for faba bean pod dehiscence by combining, linkage mapping, comparative genomics, QTL analysis and histological examination of mature pods. Mapping of dehiscence-related genes revealed conservation of syntenic blocks among different legumes. Three QTLs were identified in faba bean chromosomes II, IV and VI, although none of them was stable across years. Histological analysis supports the convergent phenotypic evolution previously reported in cereals and related legume species but revealed a more complex pattern in faba bean. Contrary to common bean and soybean, the faba bean dehiscence zone appears to show functional equivalence to that described in crucifers. The lignified wall fiber layer, which is absent in the paucijuga primitive line Vf27, or less lignified and vacuolated in other dehiscent lines, appears to act as the major force triggering pod dehiscence in this species. While our findings, provide new insight into the mechanisms underlying faba bean dehiscence, full understanding of the molecular bases will require further studies combining precise phenotyping with genomic analysis.

AyigPmutant strain is a small colony variant ofE. coliand shows pleiotropic antibiotic resistance

2017 ◽  
Vol 63 (12) ◽  
pp. 961-969 ◽  
Author(s):  
Hui Xia ◽  
Qiongwei Tang ◽  
Jie Song ◽  
Jiang Ye ◽  
Haizhen Wu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genetic Basis ◽  
Coenzyme Q ◽  
Small Colony Variant ◽  
E Coli ◽  
Collateral Sensitivity ◽  
Persistent Infections ◽  
Antibiotic Resistance Profile ◽  
Small Colony ◽  
Insight Into

Small colony variants (SCVs) are a commonly observed subpopulation of bacteria that have a small colony size and distinctive biochemical characteristics. SCVs are more resistant than the wild type to some antibiotics and usually cause persistent infections in the clinic. SCV studies have been very active during the past 2 decades, especially Staphylococcus aureus SCVs. However, fewer studies on Escherichia coli SCVs exist, so we studied an E. coli SCV during an experiment involving the deletion of the yigP locus. PCR and DNA sequencing revealed that the SCV was attributable to a defect in the yigP function. Furthermore, we investigated the antibiotic resistance profile of the E. coli SCV and it showed increased erythromycin, kanamycin, and d-cycloserine resistance, but collateral sensitivity to ampicillin, polymyxin, chloramphenicol, tetracycline, rifampin, and nalidixic acid. We tried to determine the association between yigP and the pleiotropic antibiotic resistance of the SCV by analyzing biofilm formation, cellular morphology, and coenzyme Q (Q8) production. Our results indicated that impaired Q8biosynthesis was the primary factor that contributed to the increased resistance and collateral sensitivity of the SCV. This study offers a novel genetic basis for E. coli SCVs and an insight into the development of alternative antimicrobial strategies for clinical therapy.

Mutational Spectrum Analysis of Interesting Correlation and Interrelationship Between RNA Splicing Pathway and Commonly Targeted Genes in Myelodysplastic Syndrome

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 273-273 ◽  
Author(s):  
Yasunobu Nagata ◽  
Masashi Sanada ◽  
Ayana Kon ◽  
Kenichi Yoshida ◽  
Yuichi Shiraishi ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Genetic Basis ◽  
De Novo ◽  
Gene Mutations ◽  
Myeloid Neoplasms ◽  
Disease Subtypes ◽  
The Difference ◽  
De Novo Aml ◽  
Insight Into ◽  
Splicing Machinery

Abstract Abstract 273 Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid neoplasms showing a frequent transition to acute myeloid leukemia. Although they are discriminated from de novo AML by the presence of a preleukemic period and dysplastic cell morphology, the difference in molecular genetics between both neoplasms has not been fully elucidated because of the similar spectrum of gene mutations. In this regards, the recent discovery of frequent pathway mutations (45∼90%) involving the RNA splicing machinery in MDS and related myeloid neoplasm with their rare mutation rate in de novo AML provided a novel insight into the distinct molecular pathogenesis of both neoplasms. Thus far, eight components of the RNA splicing machinery have been identified as the targets of gene mutations, among which U2AF35, SF3B1, SRSF2 and ZRSR2 show the highest mutation rates in MDS and CMML. Meanwhile, the frequency of mutations shows a substantial variation among disease subtypes, although the genetic/biological basis for these differences has not been clarified; SF3B1 mutations explain >90% of the spliceosome gene mutations in RARS and RCMD-RS, while mutations of U2AF35 and ZRSR2 are rare in these categories (< 5%) but common in CMML (16%) and MDS without increased ring sideroblasts (20%). On the other hand, SRSF2 mutations are most frequent in CMML (30%), compared with other subtypes (<10 %) (p<0.001) (Yoshida K, et al, unpublished data). So to obtain an insight into the genetic basis for these difference, we extensively explored spectrums of gene mutations in a set of 161 samples with MDS and related myeloid neoplasms, in which mutations of 10 genes thus far identified as major targets in MDS were examined and their frequencies were compared with regard to the species of mutated components of the splicing machinery. The mutation status of the 161 specimens was determined using the target exon enrichment followed by massively parallel sequencing. In total, 86 mutations were identified in 81(50%) in the 8 components of the splicing machinery. The mutations among 4 genes, U2AF35 (N = 20), SRSF2 (N = 31), SF3B1 (N = 15) and ZRSR2 (N = 10), explained most of the mutations with a much lower mutational rate for SF3A1 (N = 3), PRPF40B (N = 3), U2AF65 (N = 3) and SF1 (N = 1). Conspicuously, higher frequency 4 components of the splicing machinery were mutated in 76 out of the 161 cases (47.2%) in a mutually exclusive manner. On the other hand, 172 mutations of the 10 common targets were identified among 117, including 41 TET2 (25%), 32 RUNX1 (20%), 26 ASXL1 (16%), 24 RAS (NRAS/KRAS) (15%), 22 TP53 (14%), 17 IDH1/2 (10%), 10 CBL (6%) and 10 EZH2 (6%) mutations. We examined the difference between the major spliceosome mutations in terms of the number of the accompanying mutations in the 10 common gene targets. The possible bias from the difference in disease subtypes was compensated by multiple regressions. The SRSF2 mutations are more frequently associated with accompanying gene mutations with a significantly higher number of those mutations (N=29; OR 6.2; 95%CI 1.1–35) compared with that of the U2AF35 mutations (N=14) (p=0.038). Commonly involving the E/A splicing complexes, these splicing pathway mutations lead to compromised 3' splice site recognition. However, individual mutations may still have different impacts on cell functions, which could contribute to the determination of discrete disease phenotypes. It was demonstrated that SRSF2 was involved in the regulation of DNA stability and that depletion of SRSF2 can lead to DNA hypermutability, which may explain the higher number of accompanying gene mutation in SRSF2-mutated cases than cases with other spliceosome gene mutations. In conclusion, it may help to disclosing the genetic basis of MDS and related myeloid neoplasms that highly paralleled resequencing was confirmed SRSF2 mutated case significantly overlapped common mutations. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Searching for Genes Responsible for Patulin Degradation in a Biocontrol Yeast Provides Insight into the Basis for Resistance to This Mycotoxin

2013 ◽  
Vol 79 (9) ◽  
pp. 3101-3115 ◽  
Author(s):  
G. Ianiri ◽  
A. Idnurm ◽  
S. A. I. Wright ◽  
R. Durán-Patrón ◽  
L. Mannina ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Reactive Oxygen Species ◽  
Genetic Basis ◽  
Degradation Process ◽  
Oxygen Species ◽  
Content Type ◽  
Pome Fruits ◽  
Multistep Process ◽  
External Stresses ◽  
Insight Into

ABSTRACTPatulin is a mycotoxin that contaminates pome fruits and derived products worldwide. Basidiomycete yeasts belonging to the subphylumPucciniomycotinahave been identified to have the ability to degrade this molecule efficiently and have been explored through different approaches to understand this degradation process. In this study,Sporobolomycessp. strain IAM 13481 was found to be able to degrade patulin to form two different breakdown products, desoxypatulinic acid and (Z)-ascladiol. To gain insight into the genetic basis of tolerance and degradation of patulin, more than 3,000 transfer DNA (T-DNA) insertional mutants were generated in strain IAM 13481 and screened for the inability to degrade patulin using a bioassay based on the sensitivity ofEscherichia colito patulin. Thirteen mutants showing reduced growth in the presence of patulin were isolated and further characterized. Genes disrupted in patulin-sensitive mutants included homologs ofSaccharomyces cerevisiae YCK2,PAC2,DAL5, andVPS8. The patulin-sensitive mutants also exhibited hypersensitivity to reactive oxygen species as well as genotoxic and cell wall-destabilizing agents, suggesting that the inactivated genes are essential for tolerating and overcoming the initial toxicity of patulin. These results support a model whereby patulin degradation occurs through a multistep process that includes an initial tolerance to patulin that utilizes processes common to other external stresses, followed by two separate pathways for degradation.

scholarly journals Identifying genome level variation in generalist and specialist bacteria and their relationship to abiotic conditions in European freshwater ecosystems

2021 ◽  
Vol 4 ◽  
Author(s):  
Manan Shah ◽  
Till Bornemann ◽  
Julia Nuy ◽  
Alexander Probst ◽  
Daniela Beisser ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Genetic Basis ◽  
Abiotic Factors ◽  
Gc Content ◽  
Nutrient Content ◽  
Freshwater Ecosystems ◽  
Different Types ◽  
Genome Level ◽  
Physical Changes ◽  
Insight Into

Microbial biodiversity is one of the increasingly studied fields, yet we are unable to accurately pinpoint the intricacies of how the biotic landscape changes with its abiotic counterpart. Every organism reacts differently to physical changes in its surrounding(Zeglin (2015)). While there are some generalist microbes that can grow in limited capacity in many different types of environment, there are also some specialists that can flourish in very specific environments(Monard et al. (2016)). We hypothesize that both generalists and specialists have developed advanced strategies that allow them thrive under diverse conditions or in very specific niches, and that these changes should be traceable on the genomic level. We expect to see variations in factors like genome sizes, number of genes, GC content, metabolic pathways that yield growth and replication advantages in nutrient deficient niches and defense mechanisms. We also expect to identify genomic streamlining in organisms that survive in nutrient deficient environments. We are currently studying the genetic basis of why these generalists are so universally present though in smaller numbers, and what allows the specialists to efficiently exploit the abiotic factors of their specific environment in order to flourish. To pursue this, we have sampled and sequenced metagenomes from 47 lakes spread across Europe with strongly diverging environmental conditions such as pH, temperature, organic and nutrient content, elevation, and conductivity. We’ve identified reads from more than 9000 taxonomically unique organisms, of which 700 were identified as generalists and 1200 as specialists, based on niche width permutations. In total we have assembled 313 high quality Metagenome Assembled Genomes (MAGs). Which now allow us to get a more detailed insight into the genetic basis and specific adaptations of these organisms.

scholarly journals Analysis of Draft Genome Sequence of Pseudomonas sp. QTF5 Reveals Its Benzoic Acid Degradation Ability and Heavy Metal Tolerance

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Yang Li ◽  
Yi Ren ◽  
Nan Jiang
Keyword(s):  
Benzoic Acid ◽  
Genetic Basis ◽  
Metal Tolerance ◽  
Draft Genome ◽  
Heavy Metal Tolerance ◽  
Extreme Environment ◽  
Environmental Conservation ◽  
Qiangtang Basin ◽  
Degradation Ability ◽  
Insight Into

Pseudomonas sp. QTF5 was isolated from the continuous permafrost near the bitumen layers in the Qiangtang basin of Qinghai-Tibetan Plateau in China (5,111 m above sea level). It is psychrotolerant and highly and widely tolerant to heavy metals and has the ability to metabolize benzoic acid and salicylic acid. To gain insight into the genetic basis for its adaptation, we performed whole genome sequencing and analyzed the resistant genes and metabolic pathways. Based on 120 published and annotated genomes representing 31 species in the genus Pseudomonas, in silico genomic DNA-DNA hybridization (<54%) and average nucleotide identity calculation (<94%) revealed that QTF5 is closest to Pseudomonas lini and should be classified into a novel species. This study provides the genetic basis to identify the genes linked to its specific mechanisms for adaptation to extreme environment and application of this microorganism in environmental conservation.

scholarly journals Identification and Analysis of Zinc Efficiency-Associated Loci in Maize

2021 ◽  
Vol 12 ◽  
Author(s):  
Jianqin Xu ◽  
Xuejie Wang ◽  
Huaqing Zhu ◽  
Futong Yu
Keyword(s):  
Inbred Line ◽  
Genetic Basis ◽  
Crop Yields ◽  
Zn Deficiency ◽  
Zinc Efficiency ◽  
Physiological Mechanisms ◽  
Zn Uptake ◽  
Trait Locus ◽  
Indole 3 Acetic Acid ◽  
Insight Into

Zinc (Zn) deficiency, a globally predominant micronutrient disorder in crops and humans, reduces crop yields and adversely impacts human health. Despite numerous studies on the physiological mechanisms underlying Zn deficiency tolerance, its genetic basis of molecular mechanism is still poorly understood. Thus, the Zn efficiency of 20 maize inbred lines was evaluated, and a quantitative trait locus (QTL) analysis was performed in the recombination inbred line population derived from the most Zn-efficient (Ye478) and Zn-inefficient inbred line (Wu312) to identify the candidate genes associated with Zn deficiency tolerance. On this basis, we analyzed the expression of ZmZIP1-ZmZIP8. Thirteen QTLs for the traits associated with Zn deficiency tolerance were detected, explaining 7.6–63.5% of the phenotypic variation. The genes responsible for Zn uptake and transport across membranes (ZmZIP3, ZmHMA3, ZmHMA4) were identified, which probably form a sophisticated network to regulate the uptake, translocation, and redistribution of Zn. Additionally, we identified the genes involved in the indole-3-acetic acid (IAA) biosynthesis (ZmIGPS) and auxin-dependent gene regulation (ZmIAA). Notably, a high upregulation of ZmZIP3 was found in the Zn-deficient root of Ye478, but not in that of Wu312. Additionally, ZmZIP4, ZmZIP5, and ZmZIP7 were up-regulated in the Zn-deficient roots of Ye478 and Wu312. Our findings provide a new insight into the genetic basis of Zn deficiency tolerance.

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