scholarly journals Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase

2021 ◽  
Vol 9 (4) ◽  
pp. 749
Author(s):  
Gülbahar Abaramak ◽  
Jaime Ricardo Porras-Domínguez ◽  
Henry Christopher Janse van Rensburg ◽  
Eveline Lescrinier ◽  
Ebru Toksoy Öner ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Halophilic Archaea ◽  
Maximum Activity ◽  
Physiological Relevance ◽  
Health Related ◽  
Specific Alternative ◽  
Binding Groove ◽  
Native Host

Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.

scholarly journals Molecular Characterization of PGC-1β (PPAR Gamma Coactivator 1β) and its Roles in Mitochondrial Biogenesis in Blunt Snout Bream (Megalobrama amblycephala)

2020 ◽  
Vol 21 (6) ◽  
pp. 1935 ◽  
Author(s):  
Kangle Lu ◽  
Tomas Policar ◽  
Xiaojun Song ◽  
Samad Rahimnejad
Keyword(s):  
Molecular Characterization ◽  
Mitochondrial Biogenesis ◽  
Phylogenetic Analyses ◽  
Ppar Gamma ◽  
Megalobrama Amblycephala ◽  
Fat Intake ◽  
High Fat ◽  
Blunt Snout Bream ◽  
Mitochondria Biogenesis

This study aimed at achieving the molecular characterization of peroxisome proliferator-activated receptor-gamma coactivator 1β (PGC-1β) and exploring its modulatory roles in mitochondria biogenesis in blunt snout bream (Megalobrama amblycephala). A full-length cDNA of PGC-1β was cloned from liver which covered 3110 bp encoding 859 amino acids. The conserved motifs of PGC-1β family proteins were gained by MEME software, and the phylogenetic analyses showed motif loss and rearrangement of PGC-1β in fish. The function of PGC-1β was evaluated through overexpression and knockdown of PGC-1β in primary hepatocytes of blunt snout bream. We observed overexpression of PGC-1β along with enhanced mitochondrial transcription factor A (TFAM) expression and mtDNA copies in hepatocytes, and its knockdown led to slightly reduced NRF1 expression. However, knockdown of PGC-1β did not significantly influence TFAM expression or mtDNA copies. The alterations in mitochondria biogenesis were assessed following high-fat intake, and the results showed that it induces downregulation of PGC-1β. Furthermore, significant decreases in mitochondrial respiratory chain activities and mitochondria biogenesis were observed by high-fat intake. Our findings demonstrated that overexpression of PGC-1β induces the enhancement of TFAM expression and mtDNA amount but not NRF-1. Therefore, it could be concluded that PGC-1β is involved in mitochondrial biogenesis in blunt snout bream but not through PGC-1β/NRF-1 pathway.

Molecular and phylogenetic analyses of the liver amphistome Explanatum explanatum (Creplin, 1847) Fukui, 1929 in ruminants from Bangladesh and Nepal based on nuclear ribosomal ITS2 and mitochondrial nad1 sequences

2016 ◽  
Vol 91 (4) ◽  
pp. 497-503 ◽  
Author(s):  
U.K. Mohanta ◽  
H.B. Rana ◽  
B. Devkota ◽  
T. Itagaki
Keyword(s):  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Economic Loss ◽  
Fixation Index ◽  
Its2 Region ◽  
Group I ◽  
Severe Liver Damage ◽  
Second Internal Transcribed Spacer ◽  
First Time

AbstractExplanatum explanatum flukes, liver amphistomes of ruminants, cause significant economic loss in the livestock industry by inducing severe liver damage. A total of 66 flukes from 26 buffaloes and 7 cattle in four different geographic areas of Bangladesh and 20 flukes from 10 buffaloes in the Chitwan district of Nepal were subjected for analysis. The sequences (442 bp) of the second internal transcribed spacer (ITS2) of ribosomal DNA and the variable fragments (657 bp) of mitochondrial nicotinamide dehydrogenase subunit 1 (nad1) of E. explanatum flukes from Bangladesh and Nepal were analysed. The aim of this study was molecular characterization of the flukes and to elucidate their origin and biogeography. In the ITS2 region, two genotypes were detected among the flukes from Bangladesh, while flukes from Nepal were of only one genotype. Phylogenetic analyses inferred from the nad1 gene revealed that at least four divergent populations (groups I–IV) are distributed in Bangladesh, whereas two divergent populations were found to be distributed in Nepal. Fst values (pairwise fixation index) suggest that Bangladeshi and Nepalese populations of group I to IV are significantly different from each other; but within groups III and IV, the populations from Bangladesh and Nepal were genetically close. This divergence in the nad1 gene indicates that each lineage of E. explanatum from diverse geography was co-adapted during the multiple domestication events of ruminants. This study, for the first time, provides molecular characterization of E. explanatum in Bangladesh and Nepal, and may provide useful information for elucidating its origin and dispersal route in Asia.

scholarly journals The molecular characterization of 16 new sequence variants of Hop stunt viroid reveals the existence of invariable regions and a conserved hammerhead-like structure on the viroid molecule

2001 ◽  
Vol 82 (4) ◽  
pp. 953-962 ◽  
Author(s):  
Khalid Amari ◽  
Gustavo Gomez ◽  
Arben Myrta ◽  
Biagio Di Terlizzi ◽  
Vicente Pallás
Keyword(s):  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Sequence Variants ◽  
Molecular Variability ◽  
Stunt Viroid ◽  
Cruciform Structure ◽  
Mediterranean Countries ◽  
Hop Stunt Viroid ◽  
Variable Domains

At present isolates of Hop stunt viroid (HSVd) are divided into five groups: three major groups (plum-type, hop-type and citrus-type) each containing isolates from only a limited number of isolation hosts and two minor groups that were presumed to derive from recombination events between members of the main groups. In this work we present the characterization of 16 new sequence variants of HSVd obtained from four Mediterranean countries (Cyprus, Greece, Morocco and Turkey) where this viroid had not previously been described. Molecular variability comparisons considering the totality of the sequence variants characterized so far revealed that most of the variability is found in the pathogenic and variable domains of the viroid molecule whereas both the terminal right (TR) and left (TL) domains are regions of low or no variability, respectively, suggesting the existence of constraints limiting the heterogeneity of the sequence variants. Phylogenetic analyses revealed that sequence variants belonging to the two minor recombinant subgroups are more frequent than previously thought. When the cruciform structure alternative to the typical rod-like conformation was considered it was observed that the upper part of this structure (hairpin I) was strictly conserved whereas in the lower part a reduced variability was found. The existence of a covariation in this lower part was notable. Interestingly, a hammerhead-like sequence was found within the TR domain of HSVd and it was strictly conserved in all the sequence variants. The evolutionary implications of the presence of this motif on the HSVd are discussed.

scholarly journals Epidemiological investigation and phylogenetic analyses of contagious ecthyma virus from goat in Bangladesh

2017 ◽  
Vol 2 (4) ◽  
pp. 555-561 ◽  
Author(s):  
Md Thoufic Anam Azad ◽  
Sukumar Saha ◽  
Md Shahin Alam ◽  
Papia Monoura ◽  
Md Giasuddin ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Virus Detection ◽  
Case Fatality ◽  
High Morbidity ◽  
Contagious Ecthyma ◽  
Age Group ◽  
Proliferative Lesion ◽  
Epidemiologic Characteristics

The aim of this study was to know the epidemiologic characteristics of contagious ecthyma and molecular characterization of the contagious ecthyma virus or ORF virus (ORFV). Sixty four households having 293 goats in Chuadanga district of Bangladesh were surveyed and 30 scab materials were collected from ORF affected goat. Virus detection by PCR was attempted. Sequencing was done for characterization. Goats (n=70) in 15 out of 64 (23.44%) households were found to be infected with ORF. The overall morbidity, mortality and case fatality was 23.89 (70/293), 1.02 (3/293) and 4.29% (3/70), respectively. A proliferative lesion in mouth, lips and gum was found in 100.00% affected goats. Besides, proliferative lesions were also found in legs (19.00%), body (13.00%), and ears (10.00%) of goats. Highest morbidity (29.00%) was found in goats of 7 months-1years aged group and lowest (2.05%) in goats of 2-3 years or more. About 79.00% goats were affected during January-March, 2011 and 21.00% during October–December, 2010. About 93.33% (28/30) scab samples were found positive by PCR. For molecular characterization PCR amplified viral interlukin-10 (vIL10) gene of 5 different ORFV were sequenced. One virus obtained from sheep and four from goat. Goat isolates were found very closely related (97.20-98.60%) to each other while sheep virus has 95.20-97.20% homology with goat viruses and clustered separately. Our isolates were closely related to Norwegian sheep isolates. It is concluded that ORFV is circulating in Bangladesh with high morbidity but low mortality and all age group of goats are susceptible to this disease. Circulating viruses are closely related to each other.Asian J. Med. Biol. Res. December 2016, 2(4): 555-561

scholarly journals Molecular Characterization of Imported and Autochthonous Dengue in Northeastern Spain

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1910
Author(s):  
Jessica Navero-Castillejos ◽  
Rosa Benitez ◽  
Nuria Torner ◽  
José Muñoz ◽  
Daniel Camprubí-Ferrer ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Genotype I ◽  
Related Case ◽  
Geographical Regions ◽  
Surveillance Programs ◽  
Endemic Areas ◽  
Virus Strains

Dengue is the most significant arbovirus worldwide and a public health threat to non-endemic areas in which Aedes vectors are present. Autochthonous dengue transmission has been reported in several European countries in the last decade. Infected travelers from endemic regions arriving to areas colonized by Aedes albopictus in Europe need to be monitored in surveillance and control programs. We aimed to perform molecular characterization of RT-PCR-positive dengue cases detected in Catalonia, northeastern Spain, from 2013 to 2018. The basic demographic information and the geographical regions of importation were also analyzed. One-hundred four dengue cases were studied (103 imported infections and the first autochthonous case in our region). The dengue virus strains detected were serotyped and genotyped using molecular methods, and phylogenetic analyses were conducted. All four dengue serotypes were detected in travelers, including up to 10 different genotypes, reflecting the global circulation of dengue in endemic areas. The primary travel-related case of the 2018 autochthonous transmission was not identified, but the molecular analysis revealed dengue serotype 1, genotype I of Asian origin. Our results highlight the diversity of imported dengue virus strains and the role of molecular epidemiology in supporting arbovirus surveillance programs.

scholarly journals Biological and Molecular Characterization of an American Sugar Beet-Infecting Beet western yellows virus Isolate

Plant Disease ◽  
2008 ◽  
Vol 92 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Monique Beuve ◽  
Mark Stevens ◽  
Hsing-Yeh Liu ◽  
William M. Wintermantel ◽  
Sébastien Hauser ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Biological Data ◽  
Amino Acid Sequences ◽  
Reading Frame ◽  
Beet Western Yellows Virus ◽  
Turnip Yellows Virus

Three aphid-transmitted viruses belonging to the Polerovirus genus, Beet mild yellowing virus (BMYV), Beet chlorosis virus (BChV), and Beet western yellows virus (BWYV), have been described as pathogens of sugar beet. We present the complete biological, serological, and molecular characterization of an American isolate of Beet western yellows virus (BWYV-USA), collected from yellow beet leaves. The biological data suggested that BWYV-USA displayed a host range similar to that of BMYV, but distinct from those of BChV and the lettuce and rape isolates of Turnip yellows virus. The complete genomic RNA sequence of BWYV-USA showed a genetic organization and expression typical of other Polerovirus members. Comparisons of deduced amino acid sequences showed that P0 and the putative replicase complex (P1-P2) of BWYV-USA are more closely related to Cucurbit aphid-borne yellows virus (CABYV) than to BMYV, whereas alignments of P3, P4, and P5 showed the highest homology with BMYV. Intraspecific and interspecific phylogenetic analyses have suggested that the BWYV-USA genome may be the result of recombination events between a CABYV-like ancestor contributing open reading frame (ORF) 0, ORF 1, and ORF 2, and a beet Polerovirus progenitor providing the 3′ ORFs, with a similar mechanism of speciation occurring for BMYV in Europe. Results demonstrate that BWYV-USA is a distinct species in the Polerovirus genus, clarifying the nomenclature of this important group of viruses.

scholarly journals Biological and Molecular Characterization of Four Botryosphaeria Species Isolated from Pear Plants Showing Stem Wart and Stem Canker in China

Plant Disease ◽  
2014 ◽  
Vol 98 (6) ◽  
pp. 716-726 ◽  
Author(s):  
Lifeng Zhai ◽  
Meixin Zhang ◽  
Gang Lv ◽  
Xiaoren Chen ◽  
Nana Jia ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Stem Canker ◽  
Morphological Characterization ◽  
The Other ◽  
Internal Transcribed Spacer Region ◽  
Pathogenicity Tests ◽  
The Common ◽  
Stem Cankers

Pear stem wart and pear stem canker, which have been considered as two different fungal diseases caused by pathogens belonging to Botryosphaeria spp., commonly occur and cause serious damage in the main pear-producing areas in China. To identify the species of this genus infecting pear in China, 131 Botryosphaeria isolates were recovered from pear samples exhibiting symptoms collected from 20 different provinces and areas. Morphological characterization and phylogenetic analyses of the ribosomal DNA internal transcribed spacer region and the β-tubulin and EF1-α genes revealed that Botryosphaeria dothidea, B. rhodina, B. obtusa, and B. parva were associated with different pear stem wart and stem canker symptoms. Remarkably, all isolates of B. dothidea were obtained from the samples showing either stem wart or stem canker lesions; however, the isolates of the other three species were obtained only from the samples showing stem canker. Pathogenicity tests on the pear shoots showed that B. dothidea isolates could induce stem wart or stem canker lesions but all the isolates of the other three species could only induce stem cankers. However, the isolates of B. parva, B. rhodina, and B. obtusa exhibited higher virulence than that of the B. dothidea isolates on the pear fruit. Our results suggest that B. dothidea is the common causal agent for these two diseases (a pear stem wart and a pear-related stem canker), whereas B. parva, B. rhodina, and B. obtusa only cause pear stem canker diseases. To our knowledge, this study represents the first report for biological and molecular characterization of four Botryosphaeria spp. isolated from pear plants showing stem wart and stem canker in China.

scholarly journals First complete genome sequence and molecular characterization of Canine morbillivirus isolated in Central Brazil

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Vivaldo Gomes da Costa ◽  
Marielena Vogel Saivish ◽  
Priscila Gomes de Oliveira ◽  
Abelardo Silva-Júnior ◽  
Marcos Lázaro Moreli ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Canine Distemper Virus ◽  
Phylogenetic Analyses ◽  
Domestic Dogs ◽  
Molecular Characteristics ◽  
Central Brazil ◽  
West Region ◽  
Glycosylation Sites ◽  
Full Length Genome

AbstractThe Brazilian regions are still highly endemic areas for Canine morbillivirus [canine distemper virus (CDV)]. However, little is known regarding the genetic variability of the strain circulating in several Brazilian regions. Here, we report the first full-length genome and molecular characterization of CDV isolated from domestic dogs in the Brazilian Center-West region. Sequence alignment and phylogenetic analyses based on deduced amino acid and nucleotide sequences showed that the isolated strain is characterized as the South America-I/Europe genotype. However, it segregates into a CDV subgenotype branch. Interestingly, both H and F proteins have a gain of a potential N-glycosylation sites compared to the Onderstepoort vaccine strain. Therefore, this study provides a reference to further understand the epidemic and molecular characteristics of the CDV in Brazil.

Molecular characterization of core lipids from halophilic archaea grown under different salinity conditions

2012 ◽  
Vol 48 ◽  
pp. 1-8 ◽  
Author(s):  
Katherine S. Dawson ◽  
Katherine H. Freeman ◽  
Jennifer L. Macalady
Keyword(s):  
Molecular Characterization ◽  
Halophilic Archaea

scholarly journals First Molecular Characterization of Poxviruses in Cattle, Sheep, and Goats in Botswana

2021 ◽  
Author(s):  
Boitumelo Magret Modise ◽  
Tirumala Bharani Kumar Settypalli ◽  
Tebogo Kgotlele ◽  
Dingrong Xue ◽  
Kebonyemodisa Ntesang ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Small Ruminants ◽  
Virus Diseases ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Lumpy Skin Disease ◽  
Multiple Sequence Alignments

Abstract BackgroundPoxviruses within the Capripoxvirus, Orthopoxvirus, and Parapoxvirus genera can infect livestock, with the two former presenting also zoonotic importance. In addition, they induce similar clinical symptoms in common host species, creating a challenge for diagnosis. Although endemic in the country, poxvirus infections of small ruminants and cattle have received little attention in Botswana, and there was no prior attempt of using molecular tools to diagnose the diseases and characterize the pathogens.MethodsA high-resolution melting (HRM) assay was used to detect and differentiate poxviruses in samples from four cattle (from Mahalapye, Kasane, and Molepolole), one sheep (from Jwaneng), and one goat (from Kasane). Molecular characterization of capripoxviruses and parapoxviruses was undertaken by sequence analysis of RPO30 and GPCR genes.ResultsThe HRM assay revealed lumpy skin disease virus (LSDV) in three cattle samples, pseudocowpox virus (PCPV) in one cattle sample, and orf virus (ORFV) in one goat and one sheep sample. The phylogenetic analyses, based on the RPO30 and GPCR, and the inspection of the multiple sequence alignments showed that the LSDV sequences of Botswana were more like those of common LSDV field isolates encountered in Africa, Asia, and Europe. The Botswana PCPV presented unique features and clustered between camel isolates and cattle isolates of the PCPV group. The Botswana ORFV from goat differed from the ORFV collected in sheep.ConclusionsThis study is the first report on the genetic characterization of pox virus diseases circulating in cattle, goats, and sheep in Botswana. It shows the importance of molecular methods to differentially diagnose pox virus diseases of ruminants.

Sign in / Sign up

Export Citation Format

Share Document