scholarly journals A glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast

2021 ◽  
Author(s):  
Margarida Silva ◽  
Ana Pontes ◽  
Ricardo Franco-Duarte ◽  
Pedro Soares ◽  
Jose Paulo Sampaio ◽  
...  
Keyword(s):  
Dairy Products ◽  
Early Stage ◽  
Gene Content ◽  
Bread Dough ◽  
Structure Variation ◽  
Torulaspora Delbrueckii ◽  
A Genome ◽  
Maltose Utilization ◽  
Gal Genes ◽  
Mal Genes

The yeast Torulaspora delbrueckii is gaining importance for biotechnology due to its ability to increase wine sensorial complexity and for enhancing pre-frozen bread dough leavening. However, little is known about its population structure, variation in gene content, or possible domestication routes. Here, we address these issues and update the delimitation of T. delbrueckii along five major clades. Among the three European clades, a basal lineage is associated with the wild arboreal niche, while the two other lineages are linked with anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix- Anthropic clade). Using 62 genomes we identified 5629 genes in the pangenome of T. delbrueckii and 270 genes in the cloud genome. A pangenome tree analysis showed that wine strains have a genome composition more similar to European wild arboreal strains than to those of the Mix Anthropic clade, in contradiction with the phylogenetic analysis. An association of gene content and ecology gave further support to the hypothesis that the Mix - Anthropic clade has the most specialized genome content and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. Contrary to S. cerevisiae, domestication in T. delbrueckii is not primed by alcoholic fermentation and appears to be a recent event.

scholarly journals Characterization of the early response of Arabidopsis thaliana to Dickeya dadantii infection using expression profiling

2018 ◽  
Author(s):  
Frédérique Van Gijsegem ◽  
Frédérique Bitton ◽  
Anne-Laure Laborie ◽  
Yvan Kraepiel ◽  
Jacques Pédron
Keyword(s):  
Arabidopsis Thaliana ◽  
Early Stage ◽  
Plant Defence ◽  
Plant Responses ◽  
Type I ◽  
In Planta ◽  
Secretion Systems ◽  
Dickeya Dadantii ◽  
A Genome

AbstractTo draw a global view of plant responses to interactions with the phytopathogenic enterobacterale Dickeya dadantii, a causal agent of soft rot diseases on many plant species, we analysed the early Arabidopsis responses to D. dadantii infection. We performed a genome-wide analysis of the Arabidopsis thaliana transcriptome during D. dadantii infection and conducted a genetic study of identified responses.A limited set of genes related to plant defence or interactions with the environment were induced at an early stage of infection, with an over-representation of genes involved in both the metabolism of indole glucosinolates (IGs) and the jasmonate (JA) defence pathway. Bacterial type I and type II secretion systems are required to trigger the induction of IG and JA-related genes while the type III secretion system appears to partially inhibit these defence pathways. Using Arabidopsis mutants impaired in JA biosynthesis or perception, we showed that induction of some IG metabolism genes was COI1-dependent but, surprisingly, JA-independent. Moreover, characterisation of D. dadantii disease progression in Arabidopsis mutants impaired in JA or IG pathways showed that JA triggers an efficient plant defence response that does not involve IGs.The induction of the IG pathway by bacterial pathogens has been reported several times in vitro. This study shows for the first time, that this induction does indeed occur in planta, but also that this line of defence is ineffective against D. dadantii infection, in contrast to its role to counteract herbivorous or fungal pathogen attacks.

scholarly journals Dietary changes in early-stage breast cancer patients from pre-surgery and over the 12 months post-surgery

2020 ◽  
Vol 125 (2) ◽  
pp. 172-182
Author(s):  
Sonja H. Brunvoll ◽  
Inger Thune ◽  
Gro F. Bertheussen ◽  
Frøydis Fjeldheim ◽  
Vidar G. Flote ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Dairy Products ◽  
Early Stage ◽  
Processed Meat ◽  
Breast Cancer Patients ◽  
Food Diary ◽  
Dietary Changes ◽  
Post Surgery ◽  
Over Time

AbstractThe time after a breast cancer diagnosis is a potential period for making positive dietary changes, but previous results are conflicting. The main aim of the present study was to study breast cancer patients’ dietary changes during the 12 months post-surgery and from 12 months pre-surgery to 12 months post-surgery with repeated administration of a 7-d pre-coded food diary and an FFQ, respectively. Women (n 506), mean age 55·3 years diagnosed with invasive breast cancer (stages I and II), were included. The dietary intake was quite stable over time, but the intake was lower for energy (0·3 and 0·4 MJ/d), alcohol (1·9 and 1·5 g/d) and vegetables (17 and 22 g/d) at 6 months than 3 weeks post-surgery (food diary) and at 12 months post-surgery than pre-surgery (FFQ), respectively. Furthermore, energy percentage (E%) from carbohydrates increased between 0·8 and 1·2 E% and E% from fat decreased between 0·6 and 0·8 E% over time, measured by both dietary assessment methods. We observed a higher intake of dairy products (11 g/d) at 6 months post-surgery (food diary), and a lower intake of dairy products (34 g/d) and red and processed meat (7·2 g/d) at 12 months post-surgery (FFQ). Moreover, 24 % of the patients claimed they made dietary changes, but mostly they did not change their diet differently compared with those patients who claimed no changes. In conclusion, breast cancer patients reported only minor dietary changes from 12 months pre-surgery and during the 12 months post-surgery.

scholarly journals Detection of Colorectal Cancer in Circulating Cell-Free DNA by Methylated CpG Tandem Amplification and Sequencing

2019 ◽  
Vol 65 (7) ◽  
pp. 916-926 ◽  
Author(s):  
Jingyi Li ◽  
Xin Zhou ◽  
Xiaomeng Liu ◽  
Jie Ren ◽  
Jilian Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Early Stage ◽  
Plasma Samples ◽  
Dna Hypermethylation ◽  
Cell Free Dna ◽  
Noncancerous Tissue ◽  
Clinical Sensitivity ◽  
Free Dna ◽  
A Genome ◽  
Circulating Cell Free Dna

Abstract BACKGROUND Aberrant DNA hypermethylation of CpG islands occurs frequently throughout the genome in human colorectal cancer (CRC). A genome-wide DNA hypermethylation analysis technique using circulating cell-free DNA (cfDNA) is attractive for the noninvasive early detection of CRC and discrimination between CRC and other cancer types. METHODS We applied the methylated CpG tandem amplification and sequencing (MCTA-Seq) method, with a fully methylated molecules algorithm, to plasma samples from patients with CRC (n = 147) and controls (n = 136), as well as cancer and adjacent noncancerous tissue samples (n = 66). We also comparatively analyzed plasma samples from patients with hepatocellular carcinoma (HCC; n = 36). RESULTS Dozens of DNA hypermethylation markers including known (e.g., SEPT9 and IKZF1) and novel (e.g., EMBP1, KCNQ5, CHST11, APBB1IP, and TJP2) genes were identified for effectively detecting CRC in cfDNA. A panel of 80 markers discriminated early-stage CRC patients and controls with a clinical sensitivity of 74% and clinical specificity of 90%. Patients with early-stage CRC and HCC could be discriminated at clinical sensitivities of approximately 70% by another panel of 128 markers. CONCLUSIONS MCTA-Seq is a promising method for the noninvasive detection of CRC.

scholarly journals A Genome-Wide CRISPR Activation Screen Identifies Genes Involved in Protection from Zika Virus Infection

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 149
Author(s):  
Anna Dukhovny ◽  
Kevin Lamkiewicz ◽  
Qian Chen ◽  
Markus Fricke ◽  
Nabila Jabrane-Ferrat ◽  
...  
Keyword(s):  
Cell Death ◽  
Zika Virus ◽  
Early Stage ◽  
Specific Treatment ◽  
Febrile Illness ◽  
Neurological Complications ◽  
Host Factors ◽  
Zikv Infection ◽  
A Genome ◽  
Crispr Activation

Zika virus (ZIKV) is an arthropod-borne emerging pathogen causing febrile illness. ZIKV is associated with the Guillain–Barré syndrome and other neurological complications. The vertical transmission of ZIKV can cause fetus demise, stillbirths or severe congenital abnormalities and neurological complications. There is still no vaccine or specific treatment for ZIKV infection. To identify the host factors that can rescue cells from ZIKV infection, we used a genome-scale CRISPR activation screen. Our highly ranking hits included a short list of interferon-stimulated genes (ISGs) previously reported to have antiviral activity. Validation of the screen results highlighted interferon lambda 2 (IFN-lamda2) and interferon alpha-inducible protein 6 (IFI6) as genes providing high levels of protection from ZIKV infection. The activation of these genes had an effect at an early stage in the viral infection. In addition, infected cells expressing single guide RNAs (sgRNAs) for both of these genes displayed lower levels of cell death than did the controls. Furthermore, the identified genes were significantly induced in ZIKV-infected placenta explants. These results highlighted a set of ISGs directly relevant for rescuing cells from ZIKV infection or its associated cell death, thus substantiating CRISPR activation screens as a valid tool for identifying host factors impeding pathogen infection.

Multilevel Evolution: The Fate of Duplicated Genes

2002 ◽  
Vol 216 (1) ◽  
Author(s):  
Paulien Hogeweg
Keyword(s):  
Information Integration ◽  
Large Scale ◽  
Evolutionary Dynamics ◽  
Single Point ◽  
Gene Content ◽  
Minor Role ◽  
Single Point Mutation ◽  
Duplicated Genes ◽  
A Genome ◽  
Multilevel Evolution

Biological evolution is a multilevel process and should be studied as such. A first, important step in studying evolution in this way has been the work of Peter Schuster and co-workers on RNA evolution. For RNA the genotype-phenotype mapping can be calculated explicitly. The resulting evolutionary dynamics is dominated by neutral paths, and the potential of major change by a single point mutation.Examining whole genomes, of which about 60 are now available, we see that gene content of genomes is changing relatively rapidly: gene duplication, gene loss and gene generation is ubiquitous. In fact, it seems that point-mutations play a relatively minor role, relative to changes in gene regulation and gene content in adaptive evolution.Large scale micro-array studies, in which the expression of every gene can be measured simultaneously, give a first glimpse of the `division of labor´ between duplicated genes. A preliminary analysis suggests that differential expression is often the primary event which allows duplicated genes to be maintained in a genome, but alternate routes also exist, most notably on the one hand the mere need of a lot of product, and on the other hand differentiation within multi-protein complexes consisting of homologous genes.I will discuss these results in terms of multilevel evolution. in particular in terms of information integration and the alternatives of `individual based´

scholarly journals Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum Genes

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Hiromi Nishida ◽  
Choong-Soo Yun
Keyword(s):  
Content Analysis ◽  
Gene Silencing ◽  
Early Stage ◽  
Gc Content ◽  
Dna Fragments ◽  
Bacterial Group ◽  
A Genome ◽  
Transposable Genetic Elements ◽  
Similar Gene ◽  
Gc Contents

Although the bacterium Symbiobacterium thermophilum has a genome with a high guanine-cytosine (GC) content (69%), it belongs to a low GC content bacterial group. We detected only 18 low GC content regions with 5 or more consecutive genes whose GC contents were below 65% in the genome of this organism. S. thermophilum has 66 transposase genes, which are markers of transposable genetic elements, and 38 (58%) of them were located in the low GC content regions, suggesting that Symbiobacterium has a similar gene silencing system as Salmonella. The top hit (best match) analyses for each Symbiobacterium protein showed that putative horizontally transferred genes and vertically inherited genes are scattered across the genome. Approximately 25% of the 3338 Symbiobacterium proteins have the highest similarity with the protein of a phylogenetically distant organism. The putative horizontally transferred genes also have a high GC content, suggesting that Symbiobacterium has gained many DNA fragments from phylogenetically distant organisms during the early stage of Firmicutes evolution. After acquiring genes, Symbiobacterium increased the GC content of the horizontally transferred genes and thereby maintained a genome with a high GC content.

scholarly journals Mitochondria and hydrogenosomes are two forms of the same fundamental organelle

2003 ◽  
Vol 358 (1429) ◽  
pp. 191-203 ◽  
Author(s):  
Martin Embley ◽  
Mark van der Giezen ◽  
David S. Horner ◽  
Patricia L. Dyal ◽  
Peter Foster
Keyword(s):  
Early Stage ◽  
Phylogenetic Analyses ◽  
Eukaryotic Cell ◽  
Published Data ◽  
Ferredoxin Oxidoreductase ◽  
Cell Compartments ◽  
Microbial Eukaryotes ◽  
A Genome ◽  
Different Types ◽  
Pyruvate Ferredoxin Oxidoreductase

Published data suggest that hydrogenosomes, organelles found in diverse anaerobic eukaryotes that make energy and hydrogen, were once mitochondria. As hydrogenosomes generally lack a genome, the conversion is probably one way. The sources of the key hydrogenosomal enzymes, pyruvate : ferredoxin oxidoreductase (PFO) and hydrogenase, are not resolved by current phylogenetic analyses, but it is likely that both were present at an early stage of eukaryotic evolution. Once thought to be restricted to a few unusual anaerobic eukaryotes, the proteins are intimately integrated into the fabric of diverse eukaryotic cells, where they are targeted to different cell compartments, and not just hydrogenosomes. There is no evidence supporting the view that PFO and hydrogenase originated from the mitochondrial endosymbiont, as posited by the hydrogen hypothesis for eukaryogenesis. Other organelles derived from mitochondria have now been described in anaerobic and parasitic microbial eukaryotes, including species that were once thought to have diverged before the mitochondrial symbiosis. It thus seems possible that all eukaryotes may eventually be shown to contain an organelle of mitochondrial ancestry, to which different types of biochemistry can be targeted. It remains to be seen if, despite their obvious differences, this family of organelles shares a common function of importance for the eukaryotic cell, other than energy production, that might provide the underlying selection pressure for organelle retention.

scholarly journals Genetic Effects on Longitudinal Cognitive Decline During the Early Stages of Alzheimer's Disease

2021 ◽  
Author(s):  
Atul Kumar ◽  
Maryam Shoai ◽  
Sebastian Palmqvist ◽  
Erik Stomrud ◽  
John Hardy ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Cognitive Decline ◽  
Genome Wide Association Study ◽  
Early Stage ◽  
Cognitive Change ◽  
Preclinical Ad ◽  
Genome Wide ◽  
A Genome ◽  
Polygenic Scores

Abstract Background Cognitive decline in early-stage Alzheimer’s disease (AD) may depend on genetic variability. Methods In the Swedish BioFINDER study, we used polygenic scores (PGS) (for AD, intelligence and educational attainment), and genetic variants (in a genome-wide association study [GWAS]) to predict longitudinal cognitive change (measured by MMSE) over a mean of 4.2 years. We included 555 β-amyloid (Aβ) negative cognitively unimpaired (CU) individuals, 206 Aβ-positive CU (preclinical AD), 110 Aβ-negative mild cognitive impairment (MCI) patients, and 146 Aβ-positive MCI patients (prodromal AD). Results Polygenic scores for AD (in Aβ-positive individuals) and intelligence (independent of Aβ-status) were associated with cognitive decline. Eight genes were associated with cognitive decline in GWAS (3 independent of Aβ-status). Conclusions AD risk genes may influence cognitive decline in early AD, while genes related to intelligence may modulate cognitive decline irrespective of disease. Therapies targeting the implicated biological pathways may modulate the clinical course of AD.

scholarly journals Genome-wide Association Analysis of Adaptation to Oxygen Stress in Nile Tilapia (Oreochromis Niloticus)

2020 ◽  
Author(s):  
Xiaofei Yu ◽  
Hendrik-Jan Megens ◽  
Samuel B. Mengistu ◽  
John W.M. Bastiaansen ◽  
Han A. Mulder ◽  
...  
Keyword(s):  
Body Weight ◽  
Growth Stage ◽  
Early Stage ◽  
Nervous System Development ◽  
Genome Wide Association ◽  
Environment Interaction ◽  
Genome Wide ◽  
Hypoxic Environment ◽  
A Genome ◽  
Vegf Signalling

Abstract Background: Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish that were raised in either aerated (normoxia) or non-aerated pond (nocturnal hypoxia). During grow out, fish were sampled five times to determine individual body weight (BW) gains. We applied a genome-wide association study to identify SNPs and genes associated with the hypoxic and normoxic environments in the 17th generation of a Genetically Improved Farmed tilapia population. Results: In the hypoxic environment, 36 SNPs associated with at least one of the five body weight measurements (BW1 till BW5), of which six, located between 19.48 Mb and 21.04 Mb on Linkage group (LG) 8, were significant for body weight in the early growth stage (BW1 to BW2). Further significant associations were found for BW in the later growth stage (BW3 to BW5), located on LG1 and LG8. Analysis of genes within the candidate genomic region suggested that MAPK and VEGF signalling were significantly involved in the later growth stage under the hypoxic environment. Well-known hypoxia-regulated genes such as igf1rb, rora, efna3 and aurk were also associated with growth in the later stage in the hypoxic environment. Conversely, 13 linkage groups containing 29 unique significant and suggestive SNPs were found across the whole growth period under the normoxic environment. A meta-analysis showed that 33 SNPs were significantly associated with BW across the two environments, indicating a shared effect independent of hypoxic or normoxic environment. Functional pathways involved in nervous system development and organ growth in the early stage, and oocyte maturation in the later stage.Conclusions: There are clear genotype-growth associations in both normoxic and hypoxic environments, although genome architecture involved changed over the growing period, indicating a transition in metabolism along the way. The involvement of pathways important in hypoxia especially at the later growth stage indicates a genotype-by-environment interaction, in which MAPK and VEGF signalling are important components.

scholarly journals Copy Number Variations Contribute to Intramuscular Fat Content Differences By Affecting The Expression of PELP1 Alternative Splices in Pig

2021 ◽  
Author(s):  
Ligang Wang ◽  
Tian Zhang ◽  
Li Na ◽  
Longchao Zhang ◽  
Xinhua Hou ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
Quality Improvement ◽  
Meat Quality ◽  
Copy Number ◽  
Intramuscular Fat ◽  
Copy Number Variations ◽  
Next Generation Sequencing Data ◽  
Human Beings ◽  
Structure Variation ◽  
A Genome

Abstract Background Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality.ResultsIn this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3’UTR end of the proline, glutamate, and leucine rich protein 1 (PELP1) gene, may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affecting the structure of the PELP1 protein. ConclusionsIn conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and potential treatment of insulin resistance in human beings.

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