Search results for " sequencing"

Adaptation and ecological speciation in seasonally varying environments at high latitudes: Drosophila virilis group

2022

Living in high latitudes and altitudes sets specific requirements on species’ ability to forecast seasonal changes and to respond to them in an appropriate way. Adaptation into diverse environmental conditions can also lead to ecological speciation through habitat isolation or by inducing changes in traits that influence assortative mating. In this review, we explain how the unique time-measuring systems of Drosophila virilis group species have enabled the species to occupy high latitudes and how the traits involved in species reproduction and survival exhibit strong linkage with latitudinally varying photoperiodic and climatic conditions. We also describe variation in reproductive barriers…

Sequencing, De Novo Assembly and Annotation of the Colorado Potato Beetle, Leptinotarsa decemlineata, Transcriptome

2012

Background. The Colorado potato beetle (Leptinotarsa decemlineata) is a major pest and a serious threat to potato cultivation throughout the northern hemisphere. Despite its high importance for invasion biology, phenology and pest management, little is known about L. decemlineata from a genomic perspective. We subjected European L. decemlineata adult and larval transcriptome samples to 454-FLX massively-parallel DNA sequencing to characterize a basal set of genes from this species. We created a combined assembly of the adult and larval datasets including the publicly available midgut larval Roche 454 reads and provided basic annotation. We were particularly interested in diapause-specific g…

A NEXT GENERATION SEQUENCING APPROACH FOR MOLECULAR DIAGNOSIS OF MONOGENIC DYSLIPIDEMIAS

Molecular tools to assess the diversity and density of denitrifying bacteria in their habitats

2007

Publisher Summary This chapter describes the molecular tools to assess the diversity and density of denitrifying bacteria in their habitats. Genome sequencing and metagenomic projects might even provide new denitrification gene sequences, which could aid in designing more broad range primers. Most information is obtained by cloning and sequencing the polymerase chain reaction (PCR) amplicons, but a more rapid analysis is achieved using fingerprinting techniques. As all PCR-based analyses, the fingerprinting techniques are subjected to well-known biases introduced by, e.g., DNA extraction procedures, primer selection, and PCR conditions. For denitrifiers, the PCR-RFLP (restriction fragment l…

Production of Haploid and Doubled Haploid Lines in Nut Crops: Persian Walnut, Almond, and Hazelnut

2021

This chapter deals with induction of haploidy via parthenogenesis in Persian walnut and via microspore embryogenesis in almond and hazelnut. Haploid induction through in situ parthenogenesis using pollination with irradiated pollen to stimulate the embryogenic development of the egg cell, followed by in vitro culture of the immature haploid embryos. Microspore embryogenesis allows the induction of immature pollen grains (microspores), to move away from the normal gametophytic developmental route in the direction of the sporophytic one, yielding homozygous organisms (embryos in this case). Unlike other fruit crops (such as Citrus), regeneration of entire plants has not yet been obtained in o…

Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia

2020

Introduction Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) occurs approximately 1 in 3.500 live births representing the most common malformation of the upper digestive tract. Only half a century ago, EA/TEF was fatal among affected newborns suggesting that the steady birth prevalence might in parts be due to mutational de novo events in genes involved in foregut development. Methods To identify mutational de novo events in EA/TEF patients, we surveyed the exome of 30 case-parent trios. Identified and confirmed de novo variants were prioritized using in silico prediction tools. To investigate the embryonic role of genes harboring prioritized de novo variants we perfor…

Isolated bladder exstrophy associated with a de novo 0.9 Mb microduplication on chromosome 19p13.12

2012

BACKGROUND: The exstrophy-epispadias complex (BEEC) is a urogenital birth defect of varying severity. The causes of the BEEC are likely to be heterogeneous, with individual environmental or genetic risk factors still being largely unknown. In this study, we aimed to identify de novo causative copy number variations (CNVs) that contribute to the BEEC. METHODS: Array-based molecular karyotyping was performed to screen 110 individuals with BEEC. Promising CNVs were tested for de novo occurrence by investigating parental DNAs. Genes located in regions of rearrangements were prioritized through expression analysis in mice to be sequenced in the complete cohort, to identify high-penetrance mutati…

Insight on bacteria communities in outdoor bronze and marble artefacts in a changing environment

2022

Epilithic bacteria play a fundamental role in the conservation of cultural heritage (CH) materials. On stones, bacterial communities cause both degradation and bioprotection actions. Bronze biocorrosion in non-burial conditions is rarely studied. Only few studies have examined the relationship between bacteria communities and the chemical composi- tion of patinas (surface degradation layers). A better comprehension of bacterial communities growing on our CH is fundamental not only to understand the related decay mechanisms but also to foresee possible shifts in their compo- sition due to climate change. The present study aims at (1) characterizing bacterial communities on bronze andmarble s…

Greenhouse gases from sequential batch membrane bioreactors: A pilot plant case study

2016

Abstract The paper reports the results of nitrous oxide (N 2 O) emissions from aerobic and anoxic tank of a Sequential Batch Membrane Bioreactor (SB-MBR) pilot plant. The influence of salinity variation on N 2 O emission was analyzed by gradually increasing the inlet salt concentration from 0 to 10 g NaCl L −1 . The observed results showed that the N 2 O concentration of the gaseous samples was strongly influenced by the salt concentration. This result was likely related to a worsening of the nitrification activity due to the effect of salinity on autotrophic bacteria. Dissolved oxygen concentration and salinity were found to be the key factors affecting N 2 O concentration in the gaseous s…

Contribution of bacterial biodiversity on the operational performance of a styrene biotrickling filter.

2020

Abstract Long-term operational stability of biotrickling filters (BTFs) degrading volatile organic compounds (VOCs) is dependent on both physicochemical as well as biological properties. Effects of increasingly stressful levels of air pollutants on the microbial structure of biofilms within BTFs are not well understood, especially for VOCs such as styrene. To investigate the relationship between biofilm biodiversity and operational stability, the temporal dynamics of a biofilm from a biotrickling filter subjected to stepwise increasing levels of air polluted with styrene was investigated using 16S rDNA pyrosequencing and PCR-denaturing gradient gel electrophoresis (PCR-DGGE). As styrene con…