scholarly journals Interlinks between Wildlife and Domestic Cycles of Echinococcus spp. in Kenya

2020 ◽  
Author(s):  
Dorothy Kagendo ◽  
Eric Muchiri ◽  
Peter Gitonga ◽  
Esther Muthoni
Keyword(s):  
Domestic Dogs ◽  
Local Alignment ◽  
Mixed Infections ◽  
Surveillance Systems ◽  
Taenia Hydatigena ◽  
Fecal Samples ◽  
Wild Carnivores ◽  
Search Tool ◽  
Taenia Species ◽  
Echinococcus Spp

Effective conservation and management of wildlife in the current changing world, call for incorporation of infectious zoonotic diseases surveillance systems, among other interventions. One of such diseases is echinococcosis, a zoonotic disease caused by Echinococcus species. This disease exists in two distinct life cycle patterns, the domestic and wildlife cycles. To investigate possible inter-links between these cycles in Kenya, 729 fecal samples from wild carnivores and 406 from domestic dogs (Canis lupus familiaris) collected from Maasai Mara and Samburu National Reserves were analyzed. Taeniid eggs were isolated by zinc chloride sieving-flotation method and subjected to polymerase chain reaction of nicotinamide adenine dehydrogenase subunit 1 (NAD1). Subsequent amplicons were sequenced, edited and analyzed with GENtle VI.94 program. The samples were further subjected to molecular identification of specific host species origin. All sequences obtained were compared with those in Gene-bank using Basic Local Alignment Search Tool (BLAST). The study found that there were 74 taeniid positive samples, 53 from wild carnivores and 21 from domestic dogs. In wildlife, mixed infections with Echinococcus and Taenia species were identified and these included E. granulosus sensu stricto, E. felidis, T. canadensis G6/7, Taenia hydatigena, T. multiceps, and T. saginata. Domestic dogs harbored Echinococcus and Taenia species similar to wild carnivores including E. granulosus G1–3, E. felidis, T. multiceps, T. hydatigena, and T. madoquae. Taenia species of nine taeniid eggs were not identified. Majority of genotypes were found in hyena (Crocuta crocuta) fecal samples. Distribution of Echinococcus and Taenia spp. varied with hosts. Mixed infections of Echinococcus spp, T. multiceps and T. hydatigena in a single animal were common. There seemed to be existence of interactions between the two cycles, although public health consequences are unknown. The presence of T. saginata in hyena suggests scavenging of human fecal matter by the animal. In addition, presence of T. multiceps, T hydatigena, T madoquae and T. saginata in the two cycles suggested possible human exposure to these parasites. The results are important in drawing up of strategies and policies towards prevention and control of Echinococcosis and other Taenia related parasitic infections, especially in endemic areas given their potential risk to public and socio- economic livelihood.

The Influence of Memory-Aware Computation on Distributed BLAST

2019 ◽  
Vol 14 (2) ◽  
pp. 157-163
Author(s):  
Majid Hajibaba ◽  
Mohsen Sharifi ◽  
Saeid Gorgin
Keyword(s):  
Search Time ◽  
Genomic Research ◽  
Local Alignment ◽  
Negative Effects ◽  
Sequencing Technologies ◽  
Percent Improvement ◽  
Fast Processing ◽  
Search Tool ◽  
Memory Awareness ◽  
Generation Sequencing

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

scholarly journals Kelch 13-propeller polymorphisms in Plasmodium falciparum from Jazan region, southwest Saudi Arabia

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Ommer Mohammed Dafalla ◽  
Mohammed Alzahrani ◽  
Ahmed Sahli ◽  
Mohammed Abdulla Al Helal ◽  
Mohammad Mohammad Alhazmi ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Saudi Arabia ◽  
Parasite Clearance ◽  
Sub Saharan Africa ◽  
Local Alignment ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Synonymous Mutations ◽  
Search Tool ◽  
Sub Saharan

Abstract Background Artemisinin-based combination therapy (ACT) is recommended at the initial phase for treatment of Plasmodium falciparum, to reduce morbidity and mortality in all countries where malaria is endemic. Polymorphism in portions of P. falciparum gene encoding kelch (K13)-propeller domains is associated with delayed parasite clearance after ACT. Of about 124 different non-synonymous mutations, 46 have been identified in Southeast Asia (SEA), 62 in sub-Saharan Africa (SSA) and 16 in both the regions. This is the first study designed to analyse the prevalence of polymorphism in the P. falciparum k13-propeller domain in the Jazan region of southwest Saudi Arabia, where malaria is endemic. Methods One-hundred and forty P. falciparum samples were collected from Jazan region of southwest Saudi Arabia at three different times: 20 samples in 2011, 40 samples in 2016 and 80 samples in 2020 after the implementation of ACT. Plasmodium falciparum kelch13 (k13) gene DNA was extracted, amplified, sequenced, and analysed using a basic local alignment search tool (BLAST). Results This study obtained 51 non-synonymous (NS) mutations in three time groups, divided as follows: 6 single nucleotide polymorphisms (SNPs) ‘11.8%’ in samples collected in 2011 only, 3 (5.9%) in 2011and 2016, 5 (9.8%) in 2011 and 2020, 5 (9.8%) in 2016 only, 8 (15.7%) in 2016 and 2020, 14 (27.5%) in 2020 and 10 (19.6%) in all the groups. The BLAST revealed that the 2011 isolates were genetically closer to African isolates (53.3%) than Asian ones (46.7%). Interestingly, this proportion changed completely in 2020, to become closer to Asian isolates (81.6%) than to African ones (18.4%). Conclusions Despite the diversity of the identified mutations in the k13-propeller gene, these data did not report widespread artemisinin-resistant polymorphisms in the Jazan region where these samples were collected. Such a process would be expected to increase frequencies of mutations associated with the resistance of ACT.

scholarly journals First occurrence of Amblyomma ovale in the State of Rio Grande do Norte, Brazil

2013 ◽  
Vol 22 (1) ◽  
pp. 167-170 ◽  
Author(s):  
Caroline Gracielle Torres Ferreira ◽  
Ana Carla Diógenes Suassuna Bezerra ◽  
Otávio Valério de Carvalho ◽  
Márcia Rogéria de Almeida ◽  
Claudio Mafra
Keyword(s):  
Tick Species ◽  
Rio Grande ◽  
The State ◽  
Boophilus Microplus ◽  
Domestic Dogs ◽  
Wild Animals ◽  
Emerging Pathogens ◽  
Wild Carnivores ◽  
Amblyomma Ovale ◽  
First Occurrence

This study aims to report the occurrence of parasitism byAmblyomma ovale (Koch, 1844) in dogs in the municipality of Apodi, Rio Grande do Norte, Brazil. Specimens were identified as being one female and two males of A. ovale, besides; the animal was infested by five females of Rhipicephalus(Boophilus) microplus and seven females and three males of R. sanguineus. The finding ofA. ovale confirms results in the literature that these ticks, reported in several species of wild carnivores, can also infect dogs in Brazil. The distribution of this tick species in several Brazilian states has already been confirmed, but this is the first report in the State of Rio Grande do Norte. This finding highlights the risk of the carrying of emerging and re-emerging pathogens to peridomestic hosts are as, either because of the frequency of these ticks in wild environments or the presence of infected wild animals near peridomestic environments, exposing domestic dogs to parasitism byA. ovale ticks and, therefore, to agents potentially carried by this ectoparasite.

scholarly journals Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

2021 ◽  
Vol 322 ◽  
pp. 01038
Author(s):  
Tuah N. M. Wulandari
Keyword(s):  
Phylogenetic Tree ◽  
Coi Gene ◽  
Local Alignment ◽  
Mtdna Sequences ◽  
Mitochondrial Coi ◽  
Search Tool ◽  
Very High ◽  
I Gene

The mtDNA sequences revealed that several of the fish studied were Hampala macrolepidota and Barbonymus gonionotus. The objective of this research was to learn the pattern of COI gene in mtDNA and establish a phylogenetic tree. Basic Local Alignment Search Tool-nucleotide (BLASTn) confirmed that Barbonymus gonionotus froma the Ranau Lake, South Sumatera has 100% matching ranges to the species from Memberamo River (Indonesia), India, Bangladesh, Thailand (Mae Khlong), Indo-Myanmar, and Malaysia_1. The lowest closeness (98.76%) is related to species from Thailand (Lower Ing). The Blast investigation appears us that the level of familiarity was very high, it is coming to 98-100% in Barbonymus gonionotus. Hampala macrolepidota had 100% matching ranges to the species from Indonesia (SouthaSumatera_1) and Vietnam. They had 99.05%-99.84% closeness from Malaysia_1,2&3, Indonesia (South Sumatera_2&3, Java and Bali_1,2&3).

scholarly journals A Case Report on Genetic Analysis of Exon2 of Thyroid Transcription Factor 2 Gene in Congenital Hypothyroidism Patient

2021 ◽  
Vol 3 (2) ◽  
pp. 19-21
Author(s):  
Marjia Khatun ◽  
Laila Anjuman Banu
Keyword(s):  
Transcription Factor ◽  
Pediatric Patient ◽  
Congenital Hypothyroidism ◽  
Sanger Sequencing ◽  
Demographic Data ◽  
Local Alignment ◽  
Cycle Sequencing ◽  
Thyroid Transcription Factor ◽  
Search Tool ◽  
Information Database

A-3-year- old Bangladeshi pediatric patient named Tasin was presented with a diagnosed case of congenital hypothyroidism (CH). This type of hypothyroidism may occur due to the alteration in the nucleotide sequences of the Thyroid transcription factor 2 gene. Few studies are present on the genetic basis of this disease. CH is common in Bangladesh, may be due to geographical variation or other causes. Therefore, this study was conducted to identify whether there was any genetic alteration in the exon2 of Thyroid transcription factor 2 gene. With due procedure and permission from the guardian of the pediatric patient, socio-demographic data was collected. Isolation of DNA, quantitation and qualitation of DNA was ensured, polymerase chain reaction (PCR) was performed, the amplicons that was obtained from PCR; validated visually by gel electrophoresis methods; cycle sequencing was performed by Sanger sequencing. The chromatogram data that was obtained from Sanger sequencing was analyzed and compared with the National Center for Biotechnology Information database by Basic Local Alignment Search Tool search. Sanger sequencing revealed substitution (c.1051G>T) in the Sequence Tagged Site of the exon2 of Thyroid transcription factor 2 gene and this is new variants and not reported in National Center for Biotechnology Information database.

scholarly journals Molecular Characteristics of Carnivore Protoparvovirus 1 With High Sequence Similarity Between Wild and Domestic Carnivores in Taiwan

2021 ◽  
Author(s):  
Ai-Mei Chang ◽  
Chen-Chih Chen
Keyword(s):  
Dna Sequences ◽  
Gastrointestinal Disease ◽  
Sequence Similarity ◽  
Domestic Dogs ◽  
Molecular Characteristics ◽  
High Sequence Similarity ◽  
Vp2 Gene ◽  
Pcr Screening ◽  
Wild Carnivores ◽  
Domestic Carnivores

Carnivore protoparvovirus 1 (CPPV-1) is a DNA virus causing gastrointestinal disease and immunosuppression in various terrestrial carnivores. Domestic dogs and cats are considered the primary CPPV-1 reservoirs. The habitat overlaps of wild carnivores and free-roaming dogs increases the threat of CPPV-1 transmission between them. This study explored the CPPV-1 distribution among wild carnivores through PCR screening and compared the DNA sequences of the partial capsid protein (VP2) between wild and domestic carnivores. In total, 181 samples were screened for the CPPV-1 VP2 gene, including 32 masked palm civets (Paguma larvata), 63 Chinese ferret badgers (Melogale moschata), and 86 crab-eating mongooses (Herpestes urva), from 2015 to 2019 in Taiwan. The average prevalence of CPPV-1 was 17.7% (32/181), with the highest prevalence in masked palm civets (37.5%). In addition, a masked palm civet was coinfected with two CPPV-1 strains. Among the 33 partial VP2 gene sequences, 23 were identical to sequences amplified from domestic dogs and cats in Asia and the remaining 10 were identified for the first time. This study demonstrated that CPPV-1 has circulated between domestic and wild carnivores in rural Taiwan. Therefore, further population control and health management of free-roaming domestic carnivores are recommended.

scholarly journals Dog ownership, dog behaviour and transmission of Echinococcus spp. in the Alay Valley, southern Kyrgyzstan

Parasitology ◽  
2013 ◽  
Vol 140 (13) ◽  
pp. 1674-1684 ◽  
Author(s):  
FREYA VAN KESTEREN ◽  
ALEXANDER MASTIN ◽  
BERMET MYTYNOVA ◽  
ISKENDER ZIADINOV ◽  
BELGEES BOUFANA ◽  
...  
Keyword(s):  
Soviet Union ◽  
Rural Communities ◽  
Environmental Contamination ◽  
Human Infection ◽  
Domestic Dogs ◽  
Dog Ownership ◽  
The Soviet Union ◽  
Almost All ◽  
First Time ◽  
Echinococcus Spp

SUMMARYEchinococcosis is a re-emerging zoonotic disease in Kyrgyzstan, and the incidence of human infection has increased substantially since the collapse of the Soviet Union in 1991. Domestic dogs are hosts of Echinococcus spp. and play an important role in the transmission of these parasites. The demography, ecology and behaviour of dogs are therefore relevant in studying Echinococcus spp. transmission. Dog demographics, roles of dogs, dog movements and faecal environmental contamination were assessed in four rural communities in the Alay Valley, southern Kyrgyzstan. Arecoline purge data revealed for the first time that E. granulosus, E. canadensis and E. multilocularis were present in domestic dogs in the Alay Valley. Surveys revealed that many households had dogs and that dogs played various roles in the communities, as pets, guard dogs or sheep dogs. Almost all dogs were free to roam, and GPS data revealed that many moved outside their communities, thus being able to scavenge offal and consume rodents. Faecal environmental contamination was high, presenting a significant infection risk to the local communities.

CaPSY1 gene plays likely the key role in carotenoid metabolism of pepper (Capsicum annuum) at ripening

2021 ◽  
Vol 48 (2) ◽  
pp. 141
Author(s):  
Xiaochun Wei ◽  
Chunyang Meng ◽  
Yuxiang Yuan ◽  
Ujjal Kumar Nath ◽  
Yanyan Zhao ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Carotenoid Biosynthesis ◽  
Local Alignment ◽  
Fruit Colour ◽  
Virus Induced Gene Silencing ◽  
Carotenoid Metabolism ◽  
Pepper Fruit ◽  
Search Tool ◽  
Pepper Genome ◽  
Aba Content

Phytoene synthase (PSY) is the first committed enzyme in carotenoid biosynthesis, which plays important role in ripen fruit colour. However, the roles of CaPSY genes are not explained detail in ripen pepper fruit colour. In this study, three CaPSY genes (CaPSY1, CaPSY2 and CaPSY3) were identified through basic local alignment search tool (BLAST) in pepper genome. Among them, CaPSY1 was predicted as putative candidate based on relative expression values using five developmental stages of fruit in Zunla-1 cultivar and also in ripen fruits of five contrasting pepper lines. The CaPSY1 was characterised functionally through virus-induced gene silencing (VIGS) in ripen fruits and overexpression in Arabidopsis thaliana (L.) Heynh. Silencing of CaPSY1 gene altered colour with increased lutein and decreased zeaxanthin content in pepper fruits. The transgenic Arabidopsis line CaPSY1 gene showed higher expression of PSY1 gene compared with WT and dwarf phenotype due to reduction of GA3 (gibberellic acid) and higher abscisic acid (ABA) content. Our results confirmed that CaPSY1 gene involved in carotenoid metabolism in ripen pepper fruit and provide clue to develop bright red coloured pepper lines through breeding.

scholarly journals Novel Single Hematophagous Insect RNA Detection Method Supports Its Use as Sentinels to Survey Flaviviruses Circulation

2020 ◽  
Author(s):  
Juliana Sá Teles de Oliveira Molina ◽  
Andreia Moreira dos Santos Carmo ◽  
Gabriel Lopes Pereira ◽  
Leticia Abrantes de Andrade ◽  
Felipe Trovalim Jordão ◽  
...  
Keyword(s):  
Control Strategies ◽  
Phylogenetic Analyses ◽  
Rna Extraction ◽  
Local Alignment ◽  
Rna Detection ◽  
Public Park ◽  
Preventive Control ◽  
Culex Flavivirus ◽  
Search Tool ◽  
Pcr Targeting

Anthropogenic actions, including deforestation, disorganized urbanization, and globalization, contribute to emergence and reemergence of arboviruses worldwide, where Flavivirus is the most prevalent, and its continuous monitoring can help in preventive control strategies. Thus, the aim of this study was to detect flavivirus RNA in single hematophagous insects, which are used as sentinels. Total RNA was extracted from six Aedes aegypti stored since 2003 and from 100 Culicidae and collected through CDC trap in a public park of a Brazilian Northwest city of São Paulo State. Flavivirus was detected through RT/PCR targeting 230–250 bp of the RNA polymerase coding sequence (NS5). PCR amplicons were sequenced by Sanger method, used in comparative analysis over Basic Local Alignment Search Tool (BLAST) in GenBank, and subjected to Neighbor-Joining phylogenetic analyses. Efficiency of Flavivirus diagnosis was confirmed by detection of Dengue virus serotype 2 in Ae. aegypti. From the 100 collected insects, 19 were positive for Culex flavivirus (CxFV). NS5 partial sequence phylogenetic analysis clustered all CxFV in one branch separated from vertebrate flaviviruses, being applicable to the identification of Flavivirus species. The dipteran RNA extraction methodology described in this work supports detection of flaviviruses in single insects maintained in 80% ethanol, which can be used to constant arbovirus surveillance.

Sign in / Sign up

Export Citation Format

Share Document