scholarly journals Variants in RNA-Seq data show a continued mutation rate during strain preservation of Schizophyllum commune

2017 ◽  
Author(s):  
Thies Gehrmann ◽  
Jordi F. Pelkmans ◽  
Luis G. Lugones ◽  
Han A.B. Wösten ◽  
Thomas Abeel ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Schizophyllum Commune ◽  
Agar Plate ◽  
Protein Domain ◽  
Laboratory Model ◽  
Rna Seq ◽  
Spontaneous Mutations ◽  
Growth And Survival ◽  
In The Wild ◽  
The Impact

AbstractBackgroundTypical microorganism studies link genetic markers to physiological observations, like growth and survival. Experiments are carefully designed, comparing wildtype strains with knockout strains, and replications are conducted to capture biological variation. To maintain monoclonal strains, strain preservation systems are used to keep the number of generations between the primary stock and the experimental measurement low, to decrease the influence of spontaneous mutations on the experimental outcome. The impact of spontaneous mutations during the minimal number of growth cycles for the experimental design is, however, poorly studied.ResultsWe set out to characterize the mutation landscape using a transcriptomic dataset of Schizophyllum commune, a laboratory model for mushroom formation. We designed a methodology to detect SNPs from the RNA-seq data, and found a mutation rate of 1.923 10−8 per haploid genome per base per generation, highly similar to the previously described mutation rate of S. commune in the wild. Our results imply that approximately 300 mutations are generated during growth of a colony on an agar plate, of which 5 would introduce stop codons. Knock-outs did not incur an increase of mutations and chromosomal recombination occurring at mating type loci was frequent. We found that missense and nonsense SNPs were selected against throughout the experiment. Also, most mutations show a low variant allele frequency and appear only in a small part of the population. Yet, we found 40 genes that gained a nonsense mutation affecting one of its annotated protein domains, and more than 400 genes having a missense mutation inside an annotated protein domain. Further, we found transcription factors, metabolic genes and cazymes having gained a mutation. Hence, the mutation landscape is wide-spread and has many functional annotations.ConclusionsWe have shown that spontaneous mutations accumulate in typical microorganism experiments, where one usually assumes that these do not happen. As these mutations possibly confound experiments they should be minimized as much as possible, or, at least, be trackable. Therefore, we recommend labs to ensure that biological replicates originate from different parental plates, as much as possible.

scholarly journals Spontaneous mutations in diploid Saccharomyces cerevisiae: another thousand cell generations

2008 ◽  
Vol 90 (3) ◽  
pp. 229-241 ◽  
Author(s):  
DAVID W. HALL ◽  
ROD MAHMOUDIZAD ◽  
ANDREW W. HURD ◽  
SARAH B. JOSEPH
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mutation Rate ◽  
Sampling Error ◽  
Cell Generation ◽  
Haploid Genome ◽  
Spontaneous Mutations ◽  
Beneficial Mutations ◽  
Absolute Value ◽  
Genome Wide ◽  
The Impact

SummaryPreviously we performed a 1012-generation mutation accumulation (MA) study in yeast and found that a surprisingly large proportion of fitness-altering mutations were beneficial. To verify this result and assess the impact of sampling error in our previous study, we have continued the MA experiment for an additional 1050 cell generations and re-estimated mutation parameters. After correcting for biases due to selection, we estimate that 13% of the mutations accumulated during this study are beneficial. We conclude that the high proportions of beneficial mutations observed in this and our previous study cannot be explained by sampling error. We also estimate the genome-wide mutation rate to be 13·7×10−5 mutations per haploid genome per cell generation and the absolute value of the average heterozygous effect of a mutation to be 7·3%.

Environmental factors affecting growth and survival of juvenile western rock lobsters Panulirus longipes (Milne-Edwards)

1975 ◽  
Vol 26 (2) ◽  
pp. 177 ◽  
Author(s):  
RG Chittleborough
Keyword(s):  
Growth Rate ◽  
Food Supply ◽  
Growth Increment ◽  
Dominant Factor ◽  
Feeding Rates ◽  
Continuous Darkness ◽  
Growth And Survival ◽  
Factors Affecting ◽  
In The Wild ◽  
The Impact

The effects of temperature, photoperiod, oxygen, food supply, crowding, and autotomy of limbs have been measured under controlled conditions in aquaria. Growth rate increased with temperature to a maximum 26� C above which both growth rate and survival declined. Varying the length of photoperiod did not affect growth rate or survival, except that the growth rate was depressed significantly in continuous darkness. A mild deficiency of oxygen (60-67 % saturation) resulted in a smaller size increment at a moult; depression to 47-55 % saturation caused deaths at ecdysis. Daily feeding was necessary to maintain maximum rate of growth. The fist response to decreased food supply was a reduction in frequency of moulting. More severe shortage of food also depressed growth increment per moult. Feeding rates and conversion ratios have been measured. Frequency of moulting (and hence growth rate) was depressed markedly when juveniles were held in isolation. At a moult replacing two lost limbs, the growth rate was not affected; replacement of four limbs reduced that moult increment. Single loss of up to four limbs did not result in an earlier moult, but repetitive loss of two or more limbs at or immediately after each ecdysis led to precocious moulting. The impact of these and other components of the environment (shelter, salinity, turbidity, competitors and predators) upon juveniles during the 4 years spent on shallow coastal reefs is discussed. Food supply is emerging as the dominant factor determining growth and survival in the wild population.

scholarly journals The environmental and ecological determinants of elevated Ross River Virus exposure in koalas residing in urban coastal landscapes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Brian J. Johnson ◽  
Amy Robbins ◽  
Narayan Gyawali ◽  
Oselyne Ong ◽  
Joanne Loader ◽  
...  
Keyword(s):  
Animal Movement ◽  
Ross River Virus ◽  
Mosquito Vector ◽  
Large Numbers ◽  
Culex Annulirostris ◽  
Coastal Landscapes ◽  
In The Wild ◽  
Virus Exposure ◽  
Elevated Exposure ◽  
The Impact

AbstractKoala populations in many areas of Australia have declined sharply in response to habitat loss, disease and the effects of climate change. Koalas may face further morbidity from endemic mosquito-borne viruses, but the impact of such viruses is currently unknown. Few seroprevalence studies in the wild exist and little is known of the determinants of exposure. Here, we exploited a large, spatially and temporally explicit koala survey to define the intensity of Ross River Virus (RRV) exposure in koalas residing in urban coastal environments in southeast Queensland, Australia. We demonstrate that RRV exposure in koalas is much higher (> 80%) than reported in other sero-surveys and that exposure is uniform across the urban coastal landscape. Uniformity in exposure is related to the presence of the major RRV mosquito vector, Culex annulirostris, and similarities in animal movement, tree use, and age-dependent increases in exposure risk. Elevated exposure ultimately appears to result from the confinement of remaining coastal koala habitat to the edges of permanent wetlands unsuitable for urban development and which produce large numbers of competent mosquito vectors. The results further illustrate that koalas and other RRV-susceptible vertebrates may serve as useful sentinels of human urban exposure in endemic areas.

scholarly journals Combining tissue and circulating tumor DNA increases the detection rate of a CTNNB1 mutation in hepatocellular carcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Stine Karlsen Oversoe ◽  
Michelle Simone Clement ◽  
Britta Weber ◽  
Henning Grønbæk ◽  
Stephen Jacques Hamilton-Dutoit ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Mutation Rate ◽  
Detection Rate ◽  
Tumor Tissue ◽  
Circulating Tumor Dna ◽  
Treatment Modalities ◽  
Advanced Hepatocellular Carcinoma ◽  
Tissue Samples ◽  
The Impact ◽  
Tumor Dna

Abstract Background and aims Studies suggest that mutations in the CTNNB1 gene are predictive of response to immunotherapy, an emerging therapy for advanced hepatocellular carcinoma (HCC). Analysis of circulating tumor DNA (ctDNA) offers the possibility of serial non-invasive mutational profiling of tumors. Combining tumor tissue and ctDNA analysis may increase the detection rate of mutations. This study aimed to evaluate the frequency of the CTNNB1 p.T41A mutation in ctDNA and tumor samples from HCC patients and to evaluate the concordance rates between plasma and tissue. We further evaluated changes in ctDNA after various HCC treatment modalities and the impact of the CTNNB1 p.T41A mutation on the clinical course of HCC. Methods We used droplet digital PCR to analyze plasma from 95 patients and the corresponding tumor samples from 37 patients during 3 years follow up. Results In tumor tissue samples, the mutation rate was 8.1% (3/37). In ctDNA from HCC patients, the CTNNB1 mutation rate was 9.5% (9/95) in the pre-treatment samples. Adding results from plasma analysis to the subgroup of patients with available tissue samples, the mutation detection rate increased to 13.5% (5/37). There was no difference in overall survival according to CTNNB1 mutational status. Serial testing of ctDNA suggested a possible clonal evolution of HCC or arising multicentric tumors with separate genetic profiles in individual patients. Conclusion Combining analysis of ctDNA and tumor tissue increased the detection rate of CTNNB1 mutation in HCC patients. A liquid biopsy approach may be useful in a tailored therapy of HCC.

scholarly journals The impact of multifactorial stress combination on plant growth and survival

2021 ◽  
Author(s):  
Sara I. Zandalinas ◽  
Soham Sengupta ◽  
Felix B. Fritschi ◽  
Rajeev K. Azad ◽  
Rachel Nechushtai ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth And Survival ◽  
The Impact

scholarly journals Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Li Tong ◽  
◽  
Po-Yen Wu ◽  
John H. Phan ◽  
Hamid R. Hassazadeh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Data Analysis ◽  
Disease Outcome ◽  
Rna Seq ◽  
Next Generation Sequencing Technology ◽  
Normalization Methods ◽  
The Us ◽  
Sequencing Quality ◽  
Improved Accuracy ◽  
The Impact

Abstract To use next-generation sequencing technology such as RNA-seq for medical and health applications, choosing proper analysis methods for biomarker identification remains a critical challenge for most users. The US Food and Drug Administration (FDA) has led the Sequencing Quality Control (SEQC) project to conduct a comprehensive investigation of 278 representative RNA-seq data analysis pipelines consisting of 13 sequence mapping, three quantification, and seven normalization methods. In this article, we focused on the impact of the joint effects of RNA-seq pipelines on gene expression estimation as well as the downstream prediction of disease outcomes. First, we developed and applied three metrics (i.e., accuracy, precision, and reliability) to quantitatively evaluate each pipeline’s performance on gene expression estimation. We then investigated the correlation between the proposed metrics and the downstream prediction performance using two real-world cancer datasets (i.e., SEQC neuroblastoma dataset and the NIH/NCI TCGA lung adenocarcinoma dataset). We found that RNA-seq pipeline components jointly and significantly impacted the accuracy of gene expression estimation, and its impact was extended to the downstream prediction of these cancer outcomes. Specifically, RNA-seq pipelines that produced more accurate, precise, and reliable gene expression estimation tended to perform better in the prediction of disease outcome. In the end, we provided scenarios as guidelines for users to use these three metrics to select sensible RNA-seq pipelines for the improved accuracy, precision, and reliability of gene expression estimation, which lead to the improved downstream gene expression-based prediction of disease outcome.

scholarly journals Spaceflight Induces Novel Regulatory Responses in Arabidopsis Seedling as Revealed by Combined Proteomic and Transcriptomic Analyses

2020 ◽  
Author(s):  
Colin Peter Singer Kruse ◽  
Alexander D Meyers ◽  
Proma Basu ◽  
Sarahann Hutchinson ◽  
Darron R Luesse ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Membrane Proteins ◽  
Plant Growth ◽  
Gene Transcription ◽  
Space Station ◽  
Growth Efficiency ◽  
Rna Seq ◽  
Plastid Gene ◽  
The Impact

Abstract Background: Understanding of gravity sensing and response is critical to long-term human habitation in space and can provide new advantages for terrestrial agriculture. To this end, the altered gene expression profile induced by microgravity has been repeatedly queried by microarray and RNA-seq experiments to understand gravitropism. However, the quantification of altered protein abundance in space has been minimally investigated. Results: Proteomic (iTRAQ-labelled LC-MS/MS) and transcriptomic (RNA-seq) analyses simultaneously quantified protein and transcript differential expression of three-day old, etiolated Arabidopsis thaliana seedlings grown aboard the International Space Station along with their ground control counterparts. Protein extracts were fractionated to isolate soluble and membrane proteins and analyzed to detect differentially phosphorylated peptides. In total, 968 RNAs, 107 soluble proteins, and 103 membrane proteins were identified as differentially expressed. In addition, the proteomic analyses identified 16 differential phosphorylation events. Proteomic data delivered novel insights and simultaneously provided new context to previously made observations of gene expression in microgravity. There is a sweeping shift in post-transcriptional mechanisms of gene regulation including RNA-decapping protein DCP5, the splicing factors GRP7 and GRP8, and AGO4,. These data also indicate AHA2 and FERONIA as well as CESA1 and SHOU4 as central to the cell wall adaptations seen in spaceflight. Patterns of tubulin-a 1, 3,4 and 6 phosphorylation further reveal an interaction of microtubule and redox homeostasis that mirrors osmotic response signaling elements. The absence of gravity also results in a seemingly wasteful dysregulation of plastid gene transcription. Conclusions: The datasets gathered from Arabidopsis seedlings exposed to microgravity revealed marked impacts on post-transcriptional regulation, cell wall synthesis, redox/microtubule dynamics, and plastid gene transcription. The impact of post-transcriptional regulatory alterations represents an unstudied element of the plant microgravity response with the potential to significantly impact plant growth efficiency and beyond. What’s more, addressing the effects of microgravity on AHA2, CESA1, and alpha tubulins has the potential to enhance cytoskeletal organization and cell wall composition, thereby enhancing biomass production and growth in microgravity. Finally, understanding and manipulating the dysregulation of plastid gene transcription has further potential to address the goal of enhancing plant growth in the stressful conditions of microgravity.

scholarly journals The Rate of Spontaneous Mutation for Life-History Traits in Caenorhabditis elegans

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 119-129 ◽  
Author(s):  
Larissa L Vassilieva ◽  
Michael Lynch
Keyword(s):  
Life History ◽  
Caenorhabditis Elegans ◽  
Mutation Rate ◽  
Life History Traits ◽  
Deleterious Mutation ◽  
Spontaneous Mutation ◽  
Spontaneous Mutations ◽  
Homozygous State ◽  
Mutational Effect ◽  
Biological Differences

Abstract Spontaneous mutations were accumulated in 100 replicate lines of Caenorhabditis elegans over a period of ∼50 generations. Periodic assays of these lines and comparison to a frozen control suggest that the deleterious mutation rate for typical life-history characters in this species is at least 0.05 per diploid genome per generation, with the average mutational effect on the order of 14% or less in the homozygous state and the average mutational heritability ∼0.0034. While the average mutation rate per character and the average mutational heritability for this species are somewhat lower than previous estimates for Drosophila, these differences can be reconciled to a large extent when the biological differences between these species are taken into consideration.

scholarly journals Utilization of Trash Fish for Cultivation of Crablet Mud Crab (Scylla serrata)

2020 ◽  
Vol 25 (3) ◽  
pp. 110-114
Author(s):  
Heppi Iromo ◽  
Dori Rachmawani ◽  
Abdul Jabarsyah ◽  
Zainuddin Zainuddin
Keyword(s):  
Carapace Width ◽  
Survival Rates ◽  
Scylla Serrata ◽  
Mud Crab ◽  
Growth And Survival ◽  
Weight Growth ◽  
Randomized Design ◽  
Trichiurus Lepturus ◽  
Trash Fish ◽  
In The Wild

The high demand for mud crabs in North Kalimantan causes catch to increase in the wild. If it is not balanced with efforts to increase its aquaculture of mud crab, in the future there will be a decline in population. This study aims to determine the growth and survival rate of mud crab seed (crablet, Scylla serrata) in the application method of different types of trash fish. This research used a completely randomized design with 4 treatments and 3 replications. The Crablet used carapace width average 0.07-0.09 cm and weigh average 0.05-0.07 g with total 150 crablets. The treatments applied by trash fish were (A) Tilapia Fish (Oreochromis mossambicus), (B) Longfin Herrings Fish (Ilisha elongata), (C) Sword Fish (Trichiurus lepturus) and (D) Snails (Telescopium telescopium). The results were The best weight growth of crablet occurs in the treatment of T. lepturus (P>0.05) and  the highest of survival rates of crablet were found in treatment T. telescopium (P<0.05)  than the other. The trash fish were used turned out to be able survival of crablet mud crab (Scylla serrata).

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