scholarly journals Recovery of gene haplotypes from a metagenome

2017 ◽  
Author(s):  
Samuel M. Nicholls ◽  
Wayne Aubrey ◽  
Arwyn Edwards ◽  
Kurt de Grave ◽  
Sharon Huws ◽  
...  
Keyword(s):  
Population Level ◽  
Gene Families ◽  
Accessory Gene ◽  
Complete Understanding ◽  
Rumen Microbiome ◽  
Significant Difference ◽  
Illumina Data ◽  
Long Read ◽  
Significant Step ◽  
Gene Isoform

AbstractElucidation of population-level diversity of microbiomes is a significant step towards a complete understanding of the evolutionary, ecological and functional importance of microbial communities. Characterizing this diversity requires the recovery of the exact DNA sequence (haplotype) of each gene isoform from every individual present in the community. To address this, we present Hansel and Gretel: a freely-available data structure and algorithm, providing a software package that reconstructs the most likely haplotypes from metagenomes. We demonstrate recovery of haplotypes from short-read Illumina data for a bovine rumen microbiome, and verify our predictions are 100% accurate with long-read PacBio CCS sequencing. We show that Gretel’s haplotypes can be analyzed to determine a significant difference in mutation rates between core and accessory gene families in an ovine rumen microbiome. All tools, documentation and data for evaluation are open source and available via our repository: https://github.com/samstudio8/gretel

Cranial crassicaudiasis in two coastal dolphin species from South Africa is predominantly a disease of immature individuals

2020 ◽  
Vol 139 ◽  
pp. 93-102 ◽  
Author(s):  
MF Van Bressem ◽  
P Duignan ◽  
JA Raga ◽  
K Van Waerebeek ◽  
N Fraijia-Fernández ◽  
...  
Keyword(s):  
South Africa ◽  
Bone Development ◽  
Bottlenose Dolphins ◽  
Fatal Outcome ◽  
Population Level ◽  
Cape Coast ◽  
Osteolytic Lesions ◽  
Immune Mediated ◽  
Significant Difference ◽  
The Difference

Crassicauda spp. (Nematoda) infest the cranial sinuses of several odontocetes, causing diagnostic trabecular osteolytic lesions. We examined skulls of 77 Indian Ocean humpback dolphins Sousa plumbea and 69 Indo-Pacific bottlenose dolphins Tursiops aduncus, caught in bather-protecting nets off KwaZulu-Natal (KZN) from 1970-2017, and skulls of 6 S. plumbea stranded along the southern Cape coast in South Africa from 1963-2002. Prevalence of cranial crassicaudiasis was evaluated according to sex and cranial maturity. Overall, prevalence in S. plumbea and T. aduncus taken off KZN was 13 and 31.9%, respectively. Parasitosis variably affected 1 or more cranial bones (frontal, pterygoid, maxillary and sphenoid). No significant difference was found by gender for either species, allowing sexes to be pooled. However, there was a significant difference in lesion prevalence by age, with immature T. aduncus 4.6 times more likely affected than adults, while for S. plumbea, the difference was 6.5-fold. As severe osteolytic lesions are unlikely to heal without trace, we propose that infection is more likely to have a fatal outcome for immature dolphins, possibly because of incomplete bone development, lower immune competence in clearing parasites or an over-exuberant inflammatory response in concert with parasitic enzymatic erosion. Cranial osteolysis was not observed in mature males (18 S. plumbea, 21 T. aduncus), suggesting potential cohort-linked immune-mediated resistance to infestation. Crassicauda spp. may play a role in the natural mortality of S. plumbea and T. aduncus, but the pathogenesis and population level impact remain unknown.

Household and Population-Level Behavioural Changes Due to COVID-19 Pandemic: A Smart Thermostat Based Comparative Data Analysis

2021 ◽  
Vol 10 (1) ◽  
pp. 1-6
Author(s):  
Kirti Sundar Sahu ◽  
Arlene Oetomo ◽  
Niloofar Jalali ◽  
Plinio P. Morita
Keyword(s):  
Data Analysis ◽  
Population Level ◽  
World Health ◽  
Motion Sensors ◽  
Household Level ◽  
Work From Home ◽  
Significant Difference ◽  
Health Organization ◽  
Smart Thermostat ◽  
The Impact

The World Health Organization declared the coronavirus outbreak as a pandemic on March 11, 2020. To inhibit the spread of COVID-19, governments around the globe, including Canada, have implemented physical distancing and lockdown measures, including a work-from-home policy. Canada in 2020 has developed a 24-Hour Movement Guideline for all ages laying guidance on the ideal amount of physical activity, sedentary behaviour, and sleep (PASS) for an individual in a day. The purpose of this study was to investigate changes on the household and population-level in lifestyle behaviours (PASS) and time spent indoors at the household level, following the implementation of physical distancing protocols and stay-at-home guidelines. For this study, we used 2019 and 2020 data from ecobee, a Canadian smart Wi-Fi thermostat company, through the Donate Your Data (DYD) program. Using motion sensors data, we quantified the amount of sleep by using the absence of movement, and similarly, increased sensor activation to show a longer duration of household occupancy. The key findings of this study were; during the COVID-19 pandemic, overall household-level activity increased significantly compared to pre-pandemic times, there was no significant difference between household-level behaviours between weekdays and weekends during the pandemic, average sleep duration has not changed, but the pattern of sleep behaviour significantly changed, specifically, bedtime and wake up time delayed, indoor time spent has been increased and outdoor time significantly reduced. Our data analysis shows the feasibility of using big data to monitor the impact of the COVID-19 pandemic on the household and population-level behaviours and patterns of change.

scholarly journals Amynthas corticis genome reveals molecular mechanisms behind global distribution

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xing Wang ◽  
Yi Zhang ◽  
Yufeng Zhang ◽  
Mingming Kang ◽  
Yuanbo Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
The Body ◽  
Gene Family Evolution ◽  
Complex Environments ◽  
Protein Coding ◽  
Itraq Analysis ◽  
Rdna Sequencing ◽  
Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

scholarly journals Health state of the citizens of Nothern Kosovska Mitrovica

2010 ◽  
Vol 138 (11-12) ◽  
pp. 746-751
Author(s):  
Momcilo Mirkovic ◽  
Snezana Simic ◽  
Jelena Marinkovic ◽  
Sladjana Djuric
Keyword(s):  
Health Survey ◽  
Health Assessment ◽  
Population Level ◽  
Cross Sectional Study ◽  
Health Condition ◽  
Health State ◽  
Cross Sectional ◽  
Significance Level ◽  
Self Rated Health ◽  
Significant Difference

Introduction. For health assessment, beside the data of routine health statistics, it is necessary to include and data obtained by a health survey of the citizens. Objective. The aim of this study was to establish how northern Kosovska Mitrovica adults assess their health and which diseases are most common among the population, as well as to investigate differences in relation to demographic and socioeconomic characteristics, the characteristics of social interaction and health behavior and habits. Methods. The research was conducted as a cross-sectional study conducted on the representative sample of adult citizens in northern Kosovska Mitrovica in 2006. Two hundred-eighteen respondents were included in the survey. In the research we used a questionnaire identical to the Health Survey conducted in Serbia in 2006. The significance of differences in responses about self-rated health and chronic diseases in relation to the characteristics of respondents? responses were determined by X2-test with the significance level of 0.05. Results. Over half of the respondents (54.7%) assessed their health condition as good or very good. There was a significant difference in self-rated health in relation to the respondents? age (?2=202.036; p=0.000), education (?2=72.412; p=0.000), social support (?2=12.416; p=0.015), smoking (?2=11.675; p=0.020) and physical activity (?2=61.842; p=0.000). The leading health problems among the respondents were high blood pressure, rheumatologic diseases of joints, ulcer of the duodenal or gastric ulcer, gall bladder disease and high blood fat. Conclusion. Adult residents of northern Kosovska Mitrovica assessed their health as better than the residents of Serbia without Kosovo and Metohia. The diseases in which stress plays the major role among etiological factors are in the leading position. The obtained data on the population level of specific areas represent the basis in the planning of health education and health promotion activities.

scholarly journals Medical Sciences’ Students Responses During the Late Phase of the COVID-19 Pandemic in Iran: A Comprehensive Investigation of the Risk Perception and Information Exposure

2021 ◽  
Author(s):  
Mahan Shafie ◽  
Mahsa Mayeli ◽  
Hamed Hosseini ◽  
Mahnaz Ashoorkhani
Keyword(s):  
Risk Perception ◽  
Perceived Risk ◽  
Late Phase ◽  
Population Level ◽  
Sources Of Information ◽  
Medical Sciences ◽  
Online Questionnaire ◽  
Significant Difference ◽  
Information Exposure ◽  
Risk Patients

COVID-19 pandemic obligated applying population-level behavioral modifications to effectively prevent the spread of the disease. This necessitated investigating those measures that determine population behavior. Herein we have studied risk perception and information exposure that are among those determinants in Iran. 402 cases from medical sciences students were enrolled during the last week of September 2020. Using an online questionnaire, risk perception and sources of information about COVID-19 were investigated. Although most students considered COVID-19 preventable, merely a few considered the disease curable. A higher risk was perceived concerning the families compared to themselves. Moreover, most of them believed the prognosis good even in high-risk patients. Social media was the most informative source used; however, health professionals were considered the most reliable. The risk perception was equal between those diagnosed with COVID-19 or had a family member diagnosed compared to those without such exposure in most questions. Also, no significant difference was observed in risk perception between those students with serious underlying medical conditions and those without one regarding most items. Lastly, major and grade were the most significant demographic contributors to the risk perception. Moderate risk was perceived overall among the cases in which major and grade were the only remarkable demographic contributors. Unexpectedly, underlying medical history was not significantly correlated with the perceived risk. Lastly, previous COVID-19 exposure merely altered the curability and preventability perception.

scholarly journals Antennal transcriptome analyses and olfactory protein identification in an important wood-boring moth pest, Streltzoviella insularis (Lepidoptera: Cossidae)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yuchao Yang ◽  
Wenbo Li ◽  
Jing Tao ◽  
Shixiang Zong
Keyword(s):  
Protein Identification ◽  
Molecular Mechanisms ◽  
Control Strategies ◽  
Phylogenetic Analyses ◽  
Insect Pest ◽  
Expression Patterns ◽  
Urban Forestry ◽  
Gene Families ◽  
Specific Expression ◽  
Significant Difference

AbstractOlfaction plays key roles in insect survival and reproduction, such as feeding, courtship, mating, and oviposition. The olfactory-based control strategies have been developed an important means for pest management. Streltzoviella insularis is a destructive insect pest of many street tree species, and characterization of its olfactory proteins could provide targets for the disruption of their odour recognition processes and for urban forestry protection. In this study, we assembled the antennal transcriptome of S. insularis by next-generation sequencing and annotated the main olfactory multi-gene families, including 28 odorant-binding proteins (OBPs), 12 chemosensory proteins (CSPs), 56 odorant receptors (ORs), 11 ionotropic receptors (IRs), two sensory neuron membrane proteins (SNMPs), and 101 odorant-degrading enzymes (ODEs). Sequence and phylogenetic analyses confirmed the characteristics of these proteins. We further detected tissue- and sex-specific expression patterns of OBPs, CSPs and SNMPs by quantitative real time-PCR. Most OBPs were highly and differentially expressed in the antennae of both sexes. SinsCSP10 was expressed more highly in male antennae than in other tissues. Two SNMPs were highly expressed in the antennae, with no significant difference in expression between the sexes. Our results lay a solid foundation for understanding the precise molecular mechanisms underlying S. insularis odour recognition.

Distinctive IgVH Gene Segments Usage and Mutation Status in Chinese Patients with Chronic Lymphocytic Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4708-4708
Author(s):  
Lijuan Chen ◽  
Yaping Zhang ◽  
Wenjuuan Zheng ◽  
Jianyong Li ◽  
Changgeng Ruan
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Gene Family ◽  
Gene Families ◽  
Lymphocytic Leukemia ◽  
Chinese Patients ◽  
Chain Gene ◽  
Mutation Status ◽  
Significant Difference ◽  
Variable Heavy ◽  
Vh Gene

Abstract Chronic lymphocytic leukemia (CLL) is characterized by the relentless accumulation of monoclonal B cells with the appearance of small mature lymphocytes and a characteristic CD5 and CD19 co-expression immunophenotype. The incidence of CLL in Asian countries is lower than that in the Western ones, where CLL is the most common leukemia. To evaluate the frequency and mutation status of immunoglobulin (Ig) variable heavy chain gene (IgVH) expression in Chinese patients with CLL. We investigated IgVH gene segments usage and mutation status by multiplex RT-PCR in 52 CLL patients, and analyzed the relationship between IgVH somatic mutation status and the expression of CD38, ZAP-70 and CLLU1. 38 patients had mutated IgVH, and 14 had unmutated IgVH. The most frequently expressed VH gene family was found to be VH3 (46.2%) followed by VH4 (40.4%), VH1 (5.8%), VH2 (5.8%) and VH7 (1.9%), with no expression of VH5 and VH6 gene families. VH1-69 and VH3-21 which commonly overused in Western CLL weren’t detected in our cohort. The frequency of IgVH gene families indicates significant difference in Chinese CLL patients compared with Western patients, suggesting involvement of ethnic and/or environmental factors in CLL disease initiation. IgVH gene mutation status was significantly associated with the expression of CD38 and CLLU1. The expression of them may be simple and reliable surrogates for the identification of IgVH mutations. VH gene family usage and mutation status VH family n Mutated VH gene Unmutated VH gene VH1 3 3 0 VH2 3 2 1 VH3 24 19 5 VH4 21 16 5 VH5 0 0 0 VH6 0 0 0 VH7 1 0 1

Influence of organic sources of nutrients on vanilla (Vanilla planifolia) as an intercrop in coconut garden

2016 ◽  
Vol 44 (2) ◽  
Author(s):  
H. P. Maheswarappa, V. Krishnakumar, ◽  
Alka Gupta, A. Geetha Kumari
Keyword(s):  
Field Experiments ◽  
Sandy Loam ◽  
Population Level ◽  
Experimental Period ◽  
Fertilizer Application ◽  
Control Treatment ◽  
Cow Dung ◽  
Biogas Slurry ◽  
Significant Difference ◽  
Vigorous Growth

<p>Performance of vanilla, as influenced by organic source of nutrition when grown as intercrop in coconut garden, was studied in sandy loam soil at ICAR-CPCRI, Kasaragod, Kerala for seven years. Field experiments were carried out with different sources of organic manures, recommended NPK fertilizer and no fertilizer treatments. Application of cow dung slurry (6 tonnes ha<sup>-1</sup>) resulted in vigorous growth of vine (vine length of 5.5 m) and higher number of beans per vine (208) and a significantly higher mean fresh yield of bean (1.87 kg vine<sup>-1</sup>). Application of vermicompost (5 kg plant<sup>-1</sup>) + biofertilizers (<em>Bacillus</em> and <em>Azospirillum</em>) and vermiwash were on par and recorded mean fresh yield of 1.47 kg vine<sup>-1</sup> and 1.30 kg vine<sup>-1</sup>, respectively. Control treatment without fertilizer application recorded significantly lower fresh bean yield (0.55 kg vine<sup>-1</sup>) due to lower number of beans per vine (72 nos.).  In the rhizosphere of vanilla, no significant difference for either bacterial or actinomycetes population was noticed among the treatments. The fungal population differed significantly among the treatments and the highest population level was found with application of biogas slurry (62.1x10<sup>3</sup>cfu g<sup>-1</sup> soil), which was on par with application of cow dung slurry (59x10<sup>3</sup> cfu g<sup>-1</sup> soil). Among the function specific microbial communities, the highest population of  P-solubilisers (98x10<sup>3</sup> cfu g<sup>-1</sup> soil) was recorded in the biogas slurry treatment, and it was the lowest in control and vermiwash application treatments. The average coconut yield realized during experimental period(2004-05 to 2009-10) was 136 nuts per palm, recording 53 per cent increase in yield compared to pre-experimental yield (89 nuts per palm). </p>

HEIGHT AS AN INDICATOR OF ECONOMIC STATUS IN THE POLISH TERRITORIES UNDER RUSSIAN RULE AT THE TURN OF THE 19TH TO 20TH CENTURY

2013 ◽  
Vol 46 (5) ◽  
pp. 686-697 ◽  
Author(s):  
ZBIGNIEW CZAPLA ◽  
GRAŻYNA LICZBIŃSKA
Keyword(s):  
20Th Century ◽  
Economic Status ◽  
Population Level ◽  
Multiple Comparisons ◽  
Standard Of Living ◽  
Early 20Th Century ◽  
Economic Factors ◽  
Average Height ◽  
Significant Difference ◽  
Difference Test

SummaryHeight is regarded as one of the indicators of environmental stress at population level, being an excellent barometer of standard of living. The aim of this study was to describe diversity in height among populations living in different regions of the Kingdom of Poland in terms of the economic factors in the second half of the 19th and early 20th century. This study examines the height of adult inhabitants from five guberniyas (provinces) of the Kingdom of Poland (Łomża, Warsaw, Radom, Kalisz and Płock) collected in the years 1897–1914 (N=732 men, N=569 women). Differences in average height of male and female inhabitants across the five guberniyas were examined using ANOVA and the Fisher's LSD (Least Significant Difference) test of multiple comparisons. Statistically significant differences in the height between the guberniyas were observed. Diversity in the economic development in the studied guberniyas of the Kingdom of Poland translated into differences in the height of their inhabitants. Moreover, an increase in mean height over time was noted.

scholarly journals The Arabidopsis thaliana pan-NLRome

2019 ◽  
Author(s):  
Anna-Lena Van de Weyer ◽  
Freddy Monteiro ◽  
Oliver J. Furzer ◽  
Marc T. Nishimura ◽  
Volkan Cevik ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Yield Loss ◽  
Gene Families ◽  
Leucine Rich Repeat ◽  
Dynamic Interactions ◽  
Long Read ◽  
Selective Forces ◽  
Variable Gene ◽  
High Diversity

AbstractDisease is both among the most important selection pressures in nature and among the main causes of yield loss in agriculture. In plants, resistance to disease is often conferred by Nucleotide-binding Leucine-rich Repeat (NLR) proteins. These proteins function as intracellular immune receptors that recognize pathogen proteins and their effects on the plant. Consistent with evolutionarily dynamic interactions between plants and pathogens, NLRs are known to be encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define the majority of the Arabidopsis thaliana species-wide “NLRome”. From NLR sequence enrichment and long-read sequencing of 65 diverse A. thaliana accessions, we infer that the pan-NLRome saturates with approximately 40 accessions. Despite the high diversity of NLRs, half of the pan-NLRome is present in most accessions. We chart the architectural diversity of NLR proteins, identify novel architectures, and quantify the selective forces that act on specific NLRs, domains, and positions. Our study provides a blueprint for defining the pan-NLRome of plant species.

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