Genome annotation and evolution of chemosensory receptors in spider mites

Understanding the evolution of species and speciation, the mechanism producing the diversity of life on Earth, has always fascinated scientists. In recent years, advances in next generation sequencing techniques, together with the development of data analyzing software tools, allow us to sequence and analyze genomes of many species and reconstruct their evolutionary history. We can detect the evolutionary changes of a group of species or of different populations of a single species. In this thesis, we perform studies on three spider mite genomes, Tetranychus urticae, Tetranychus evansi and Tetranychus lintearius. The spider mites belong to the Chelicerata, the second largest group of arthropods after insects. While many insect genomes were sequenced and analyzed already, Tetranychus urticae represents the first complete chelicerate genome. This thesis has been organized into five chapters. The introductory Chapter 1 provides an overview of the explosion of genome sequences in times of the fast development of next generation sequencing techniques, describes genome annotation information, methods and pipelines to give biological meaning to these genomes, and explains the importance of genome based research for the evolution of arthropod-plant interactions. In addition, a short overview of the chemosensory receptors is provided since in the thesis we have particularly studied the annotation and evolution of this gene family in three different spider mites. Chapter 2 provides the results of annotation and analysis of the Tetranychus urticae genome (London strain). T. urticae represents one of the most polyphagous arthropod herbivores, feeding on more than 1,100 plant species including species known to produce toxic compounds. We have annotated the T. urticae genome with support of RNA-seq data and made it publicly available to the research community. The T. urticae genome sequence reveals herbivorous pest adaptations with strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Moreover, how this pest responds to a changing host environment is shown by deep transcriptome analysis of T. urticae feeding on different plants. Thus, the T. urticae genome sequence opens up new avenues for understanding the evolution of arthropods as well as the fundamentals of plant–herbivore interactions. The next two chapters (Chapter 3 and Chapter 4) present studies on the annotation and evolution of chemosensory receptors (CRs) in three different spider mites. Chemosensory receptors help animals to detect certain chemical components in their environment to find food, to locate shelter, mates and offspring, and to avoid danger. In Chapter 3, starting from Daphnia and insect chemosensory receptors, we describe mining the T. urticae genome for putative chemosensory receptors, including the ones related to insect gustatory receptors (GRs), the ionotropic receptors (IRs) and the epithelial Na+ channels (ENaCs). T. urticae has a huge repertoire of GRs, many more than the total number of GRs and odorant receptors (ORs) found to date in any other arthropod. Similar to Daphnia pulex, we observed the complete lack of ORs in T. urticae. This is consistent with the hypothesis that ORs are an insect-specific class of GR-related chemosensory receptors. Futhermore, we compare chemosensory receptor genes among three strains (London, Montpellier, and EtoxR). We find that GR genes that are intact in some T. urticae populations appeared to be inactived in other populations. Next, in Chapter 4, we describe the annotation of GR genes in T. evansi and T. lintearius, and the evolutionary analysis of this gene family in the three spider mites. We identify many GR gene expansions in the polyphagous T. urticae, a few gene expansions and many gene losses in the oligophagous T. evansi, and no gene expansion but also many gene losses in the monophagous T. lintearius. Finally, general remarks are discussed in the Chapter 5

Isolation and selection of bacteria against shrimp pathogenic Vibrio parahaemolyticus from shrimp pond water on Duyen Hai district, Tra Vinh province

Antibiotic has frequently been used in the shrimp-farming process in Vietnam. This leads to the status that antibiotic-resistant bacteria and products do not receive in the market. Bacteria had the resistant ability to pathogenic bacteria in water, and they have an important role in sustainable aquaculture. This study aimed to isolate and select good bacterial strains against Vibrio parahaemolyticus, pathogenic bacteria, on shrimp from 8 samples of shrimp pond water at 3 villages Ngu Lac, Phuoc An and Long Toan of Duyen Hai district, Tra Vinh province on NB agar medium. As a result, fifty-nine bacterial isolates were isolated and 10/59 isolates (16.95%) were identified as resistant to Vibrio parahaemolyticus by the well diffusion method. In 10 isolates, there were 7 isolates had good resistance to select for PCR technique and sequencing. The result indicated that these seven strains, including DH1m, DH2f, DH4d, DH8i, DH8m, DH8n, belonged to Bacilli and DH1n strain belonged to Streptomyces sp

Treatment of landfill leachate through struvite precipitation and nitrogen removal bacteria and poly-phosphate bacteria (in-pots experiment)

Abstract— Landfill leacheate is a type of wastewater which contains large amounts of nitrogen and phosphorus, therefore it needed to be treated before releasing to directly to the environment. The combination between struvite precipitation and nitrogen removal and poly-P bacteria into wastewater for landfill leachate treatment has been found to be a cost-effective practive, a viable technology in terms of environmental protection and sustainability, especially in the developing-countries. For optimum struvite crystallization from landfill leachate, the Mg:PO4 molar ratio as (1.2:1) was used, the pH of reaction was adjusted to 9 and the sample was stirred continously during 40 minutes. The supernatant sample was then added 1% nitrogen removal bacteria (Pseudomonas stutzeri D3b strain) and 1% poly-P bacteria (Kurthia sp. TGT1013L strain), 5 g glucose/L and aeration 12/24h during 3 days, ammonium concentration reduced significantly from 1076 mg/L to 1.5 mg/L and orthophosphate concentration decreased noticeably from 24.91 mg/L to 7.6 mg/L

PRE-ENGINEERED (PACKAGE/AND OR ON-SITE) WASTEWATER TREATMENT PLANTS

Joint Research on Environmental Science and Technology for the Eart

Complex evolutionary dynamics of massively expanded chemosensory receptor families in an extreme generalist chelicerate herbivore

While mechanisms to detoxify plant produced, anti-herbivore compounds have been associated with plant host use by herbivores, less is known about the role of chemosensory perception in their life histories. This is especially true for generalists, including chelicerate herbivores that evolved herbivory independently from the more studied insect lineages. To shed light on chemosensory perception in a generalist herbivore, we characterized the chemosensory receptors (CRs) of the chelicerate two-spotted spider mite, Tetranychus urticae, an extreme generalist. Strikingly, T. urticae has more CRs than reported in any other arthropod to date. Including pseudogenes, 689 gustatory receptors were identified, as were 136 degenerin/Epithelial Na+ Channels (ENaCs) that have also been implicated as CRs in insects. The genomic distribution of T. urticae gustatory receptors indicates recurring bursts of lineage-specific proliferations, with the extent of receptor clusters reminiscent of those observed in the CR-rich genomes of vertebrates or C. elegans. Although pseudogenization of many gustatory receptors within clusters suggests relaxed selection, a subset of receptors is expressed. Consistent with functions as CRs, the genomic distribution and expression of ENaCs in lineage-specific T. urticae expansions mirrors that observed for gustatory receptors. The expansion of ENaCs in T. urticae to > 3-fold that reported in other animals was unexpected, raising the possibility that ENaCs in T. urticae have been co-opted to fulfill a major role performed by unrelated CRs in other animals. More broadly, our findings suggest an elaborate role for chemosensory perception in generalist herbivores that are of key ecological and agricultural importance

Growth and quality of hydroponic cultivated spinach (Spinacia oleracea L.) affected by the light intensity of red and blue LEDs

This study aimed to evaluate the effect of four light intensities (90, 140, 190 and 240 μmol m-2 s-1) provided by red-blue LED light (spectrum ratio: R660/B450 = 4/1) on the growth and quality of hydroponic cultivated spinach. The results showed that when the light intensity increased, plant height, leaf number, root length, leaf width, shoot fresh weight, shoot dry weight, root fresh weight and root dry weight were increased but specific leaf weight and shoot-to-root ratio did not increase. The highest values of growth parameters were observed under 190 μmol m-2 s-1 treatment, while the lowest values were observed under 90 μmol m-2 s-1 treatment. At higher light intensities, K+, oxalic acid and nitrate contents tended to decrease but not Ca2+ content. Meanwhile, the highest values of Fe2+, crude fiber, soluble-solids, total polyphenol and vitamin C contents were observed under 190 μmol m-2 s-1 treatment, but 190 μmol m-2 s-1 treatment showed the lowest organic acid content. Our results indicated that among all experimental lighting treatments, 190 μmol m-2 s-1 light intensity showed the best effect on the growth and quality of hydroponic cultivated spinach

Elevated Levels of Cell-Free Circulating DNA in Patients with Acute Dengue Virus Infection

BACKGROUND: Apoptosis is thought to play a role in the pathogenesis of severe dengue and the release of cell-free DNA into the circulatory system in several medical conditions. Therefore, we investigated circulating DNA as a potential biomarker for severe dengue. METHODS AND FINDINGS: A direct fluorometric degradation assay using PicoGreen was performed to quantify cell-free DNA from patient plasma. Circulating DNA levels were significantly higher in patients with dengue virus infection than with other febrile illnesses and healthy controls. Remarkably, the increase of DNA levels correlated with the severity of dengue. Additionally, multivariate logistic regression analysis showed that circulating DNA levels independently correlated with dengue shock syndrome. CONCLUSIONS: Circulating DNA levels were increased in dengue patients and correlated with dengue severity. Additional studies are required to show the benefits of this biomarker in early dengue diagnosis and for the prognosis of shock complication

Depression, anxiety and stress among healthcare workers in the context of the COVID-19 pandemic: a cross-sectional study in a tertiary hospital in Northern Vietnam

IntroductionThe outbreak of coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) had significant effects on the mental well-being in general, particularly for healthcare professionals. This study examined the prevalence of depression, anxiety, and stress, and identified the associated risk factors amongst healthcare workers during the COVID-19 outbreak in a tertiary hospital located in Vietnam.MethodsWe conducted a cross-sectional study at a tertiary-level hospital, where the Depression Anxiety and Stress Scale 21 (DASS-21) web-based questionnaire was employed. We analyzed the determinant factors by employing multivariate logistic models.ResultsThe prevalence of depression, anxiety, and stress symptoms were 19.2%, 24.7%, and 13.9%, respectively. Factors such as engaging in shift work during the pandemic, taking care of patients with COVID-19, and staff’s health status were associated with mental health issues among health professionals. In addition, having alternate rest periods was likely to reduce the risk of stress.ConclusionThe prevalence of mental health problems in healthcare workers during the COVID-19 pandemic was relatively high. Having resting periods could potentially mitigate the development of stress among health professionals. Our findings could be taken into account for improving mental health of the health professional population