GLORIA

GEOMAR Library Ocean Research Information Access

X

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Online Resource
    Online Resource
    HV1 mtDNA Reveals the High Genetic Diversity and the Ancient Origin of Vietnamese Dogs
    MDPI AG ; 2023
    In:  Animals Vol. 13, No. 6 ( 2023-03-12), p. 1036-
    Details
    In: Animals, MDPI AG, Vol. 13, No. 6 ( 2023-03-12), p. 1036-
    Abstract: In this study, samples from 429 dog individuals across three main regions of Vietnam (Southern Vietnam (SVN), Central Vietnam (CVN), and Northern Vietnam (NVN)) were collected to analyze the 582 bp region mtDNA HVI, so as to study the genetic diversity and to screen the rare haplotype E in the Vietnamese village dog population. Nine new haplotypes A, two new haplotypes B, and three haplotypes C were unique to Vietnam dogs, in which the new haplotypes An3, An7, Cn1, and Cn3 concerned mutations at new polymorphism sites (15,517, 15,505, 15,479, and 15,933, respectively) which have not been previously reported. The detection of haplotypes A9 and A29, and the appearance of haplotype A200 in the two individual dogs sampled support that the Southeast Asian dog is the ancestor of today’s Australian dingo and Polynesian dog. The two rare haplotypes E (E1 and E4) were reconfirmed in Vietnamese dogs and discussed. This study also contributes to strengthening the theory of domestication of dogs to the south of the Yangtze River and the Southeast Asian origin of the dingo.
    Type of Medium: Online Resource
    ISSN: 2076-2615
    URL: Article
    DOI: 10.3390/ani13061036
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2606558-7
    SSG: 23
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 2
    Online Resource
    Online Resource
    Investigating the impact of spike protein mutations on SARS-CoV-2 virulence in benin using network centrality and molecular docking approaches
    Publishing House for Science and Technology, Vietnam Academy of Science and Technology (Publications) ; 2023
    In:  Vietnam Journal of Biotechnology ( 2023-06-30)
    Details
    In: Vietnam Journal of Biotechnology, Publishing House for Science and Technology, Vietnam Academy of Science and Technology (Publications), ( 2023-06-30)
    Abstract: The COVID-19 pandemic is ongoing and spreading around the world, which means a continuous increase in the number of infections and death. SARS-CoV-2 constantly rapidly stored mutation in the Spike gene to adapt with the host cell. The Spike gene encoded spike protein directly interacts with hACE2 on the human cell surface. Herein, using the network centrality and molecular docking approaches, we detected key mutations that positively affect spike protein. Based on network centrality, we demonstrate that the A23403G (D614G) mutation in the Spike gene is the center of a network which means this mutation has a positive effect on the virus. In addition, analyzing the interaction of spike protein with hACE2, we highlighted that the mutation appeared in the RBD region by changing the electrostatic energy of the complex. Remarkably, mutations N440K, L452R, T478K, E484K, Q493R, and Q498R increased binding free energy of Spike-hACE2 complex due to the change of the side chain into a positive charge. The Eta, Delta, and Omicron variants existed in one or more of these mutations resulting in higher binding free energy and binding affinity than the Wuhan variant indicating sounder interaction with hACE2. In general, mutations appearing on the spike protein tended to cause the surface to become positively charged in order to interact easily with the negative surface of the hACE2 receptor.
    Type of Medium: Online Resource
    ISSN: 2815-5912 , 2815-5955
    URL: Article
    DOI: 10.15625/1811-4989/18276
    Language: Unknown
    Publisher: Publishing House for Science and Technology, Vietnam Academy of Science and Technology (Publications)
    Publication Date: 2023
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 3
    Online Resource
    Online Resource
    mtDNA haplotype network analysis: Exploring genetic relationships and diversity in dog haplogroups
    GSC Online Press ; 2023
    In:  GSC Biological and Pharmaceutical Sciences Vol. 24, No. 1 ( 2023-7-30), p. 224-232
    Details
    In: GSC Biological and Pharmaceutical Sciences, GSC Online Press, Vol. 24, No. 1 ( 2023-7-30), p. 224-232
    Abstract: The genetic diversity and relationships of dog haplogroups were studied by analyzing the HV1 region of mitochondrial DNA. Previous studies have found six distinct haplogroups (A, B, C, D, E, and F) in dogs. Haplogroups A, B, and C were widely distributed, while haplogroups D, E, F were rare and distributed in restricted regions. In this study, HV1 sequences from global dog populations were collected, categorized into haplotypes, and used to construct haplotype networks. The results showed that haplogroup A was the most prevalent, comprising approximately 72.34% of dogs worldwide. Haplogroups A, B, and C together accounted for around 97.40% of the global dog population. Haplogroups D, E, and F were rare, constituting less than 3% of the dog population. Haplogroups E and F made up only about 1-2%. Number of haplotypes in haplogroups D, E, and F were little, sgesting that these haplotypes were introduced into the canine population more recently with limited time for significant mutations. Analysis of haplotype networks showed that haplotypes A were introduced into the dog populations in the early stage of dog domestication. Haplotype Eharbouring dogs were genetically close to wolves, suggesting a recent introduction of haplogroup E. Similarly, haplogroup F exhibited a narrow distribution primarily in Japanese dogs, with haplotype F3 identified as the founder haplotype likely introduced from a few wolves carrying the F3 haplotype.Through the analysis of the haplotype network and assessment of the betweenness value, this study has identified important haplotypes contributing significantly to the dog population. These analyses offer valuable insights into the identification of founder haplotypes involved in the formation of dog breeds worldwide, serving as a valuable reference for breed development and genetic studies.
    Type of Medium: Online Resource
    ISSN: 2581-3250
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.30574/gscbps.2023.24.1
    DOI: 10.30574/gscbps
    DOI: 10.30574/gscbps.2023.24.1.0284
    Language: Unknown
    Publisher: GSC Online Press
    Publication Date: 2023
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 4
    Online Resource
    Online Resource
    The Lactamase Engineering Database: a critical survey of TEM sequences in public databases
    Springer Science and Business Media LLC ; 2009
    In:  BMC Genomics Vol. 10, No. 1 ( 2009-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2009-12)
    Abstract: TEM β-lactamases are the main cause for resistance against β-lactam antibiotics. Sequence information about TEM β-lactamases is mainly found in the NCBI peptide database and TEM mutation table at http://www.lahey.org/Studies/temtable.asp . While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometimes inconsistent. Therefore, the Lactamase Engineering Database has been developed to collect the TEM β-lactamase sequences from the NCBI peptide database and the TEM mutation table, systematically compare sequence information and naming, identify inconsistencies, and thus provide a versatile tool for reconciliation of data and for an investigation of the sequence-function relationship. Description The LacED currently provides 2399 sequence entries and 37 structure entries. Sequence information on 150 different TEM β-lactamases was derived from the TEM mutation table which provides a unique number to each protein classified as TEM β-lactamase. 293 TEM-like proteins were found in the NCBI protein database, but only 113 TEM β-lactamase were common to both data sets. The 180 TEM β-lactamases from the NCBI protein database which have not yet been assigned to a TEM number fall in three classes: (1) 89 proteins from microbial organisms and 35 proteins from cloning or expression vectors had a new mutation profile; (2) 55 proteins had inconsistent annotation in terms of TEM assignment or reported mutation profile; (3) 39 proteins are fragments. The LacED is web accessible at http://www.LacED.uni-stuttgart.de and contains multisequence alignments, structure information and reconciled annotation of TEM β-lactamases. The LacED is weekly updated and supplies all data for download. Conclusion The Lactamase Engineering Database enables a systematic analysis of TEM β-lactamase sequence and annotation data from different data sources, and thus provides a valuable tool to identify inconsistencies in sequences from the NCBI peptide database, to detect TEM β-lactamases with a novel mutation profile, and to identify new amino acid positions at which mutations can occur.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/1471-2164-10-390
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2009
    detail.hit.zdb_id: 2041499-7
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 5
    Online Resource
    Online Resource
    Effect of time and temperature on the survival rate of mouse sperm (Mus musculus var. Albino) in short-term preservation without cryoprotectant agents
    Belgorod National Research University ; 2014
    In:  Research Result. SERIES PHYSIOLOGY Vol. 1, No. 2 ( 2014)
    Details
    In: Research Result. SERIES PHYSIOLOGY, Belgorod National Research University, Vol. 1, No. 2 ( 2014)
    Type of Medium: Online Resource
    ISSN: 2409-0298
    Uniform Title: Effect of time and temperature on the survival rate of mouse sperm (Mus musculus var. Albino) in short-term preservation without cryoprotectant agents
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.18413/2409-0298-2014-2
    DOI: 10.18413/2409-0298
    DOI: 10.18413/2409-0298-2014-1-2-4-10
    Language: Unknown
    Publisher: Belgorod National Research University
    Publication Date: 2014
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 6
    Online Resource
    Online Resource
    Characterization of Omicron XBB subvariants in Vietnam
    GSC Online Press ; 2023
    In:  GSC Biological and Pharmaceutical Sciences Vol. 24, No. 3 ( 2023-9-30), p. 337-343
    Details
    In: GSC Biological and Pharmaceutical Sciences, GSC Online Press, Vol. 24, No. 3 ( 2023-9-30), p. 337-343
    Abstract: SARS-CoV-2, an RNA virus that causes COVID-19, is known for its high mutation rate. Its latest variant, Omicron, has raised concerns due to several amino acid substitutions in the spike protein that could increase its transmissibility and virulence. Omicron has also produced subvariants with specific nucleotide mutations to evade antibodies and enhance infectivity. One of these subvariants, XBB, has become prevalent in Vietnam. Therefore, it is essential to accurately assess the genetic diversity of this emerging variant. This study analyzed the April 15th, 2023 updated data and identified nine XBB and subvariants in Vietnam, with XBB.1.5 being the most common. Phylogenetic analysis revealed that the original XBB variant was related to BA.2.75, and XBB.1.5 had a close relationship with XBB.1.2. A crucial mutation, G22317T (G252V), played an essential role in the emergence of the XBB subvariant, and XBB.1.5 split from XBB.1.2 with an A22405T (E281D) mutation, as shown by the mutation network.
    Type of Medium: Online Resource
    ISSN: 2581-3250
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.30574/gscbps.2023.24.3
    DOI: 10.30574/gscbps
    DOI: 10.30574/gscbps.2023.24.3.0400
    Language: Unknown
    Publisher: GSC Online Press
    Publication Date: 2023
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 7
    Online Resource
    Online Resource
    Emerging XBB variants in Vietnam show high affinity for hACE2
    GSC Online Press ; 2023
    In:  GSC Biological and Pharmaceutical Sciences Vol. 23, No. 3 ( 2023-6-30), p. 231-236
    Details
    In: GSC Biological and Pharmaceutical Sciences, GSC Online Press, Vol. 23, No. 3 ( 2023-6-30), p. 231-236
    Abstract: Since the beginning of 2022, the Omicron variant of the SARS-CoV-2 virus responsible for the COVID-19 pandemic has been the dominant variant. Numerous subvariants of Omicron have been identified, including BA.2.75, BA.4, and BA.5, which are classified as Variants of Concern (VOCs) due to their potential to cause severe illness. Additionally, an emerging variant called XBB has recently caused outbreaks and is believed to be highly lethal. To better understand the XBB variant, we compared the variation in the S protein to that of the other variants. Our initial findings indicate that the XBB variant has spread in Vietnam and carries unique nucleotide changes in the S gene. Specifically, we observed two mutations, G22317T (G252V) and C23123T (P521S), that have resulted in a new subvariant called XBB.1 on the phylogenetic tree. Our analysis also suggests that the XBB variant has a high affinity for hACE2, as indicated by an increase in the interface's number of residues and van der Waals energy. We found that XBB has conserved mutations in RBD that enhance its binding affinity for hACE2. In this report, we noted the mutation V83A, H146Q, and G252V in the NTD increased the binding free energy of the XBB spike protein in the complex with hACE2.
    Type of Medium: Online Resource
    ISSN: 2581-3250
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.30574/gscbps.2023.23.3
    DOI: 10.30574/gscbps
    DOI: 10.30574/gscbps.2023.23.3.0256
    Language: Unknown
    Publisher: GSC Online Press
    Publication Date: 2023
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 8
    Online Resource
    Online Resource
    Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database
    Springer Science and Business Media LLC ; 2017
    In:  BMC Genetics Vol. 18, No. 1 ( 2017-12)
    Details
    In: BMC Genetics, Springer Science and Business Media LLC, Vol. 18, No. 1 ( 2017-12)
    Type of Medium: Online Resource
    ISSN: 1471-2156
    URL: Article
    DOI: 10.1186/s12863-017-0528-0
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2041497-3
    detail.hit.zdb_id: 3058779-7
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 9
    Online Resource
    Online Resource
    Examining the effects of lead on the life of larval zebrafish (1-7 days old)
    Belgorod National Research University ; 2014
    In:  Research Result. SERIES PHYSIOLOGY Vol. 1, No. 2 ( 2014)
    Details
    In: Research Result. SERIES PHYSIOLOGY, Belgorod National Research University, Vol. 1, No. 2 ( 2014)
    Type of Medium: Online Resource
    ISSN: 2409-0298
    Uniform Title: Examining the effects of lead on the life of larval zebrafish (1-7 days old)
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.18413/2409-0298-2014-2
    DOI: 10.18413/2409-0298
    DOI: 10.18413/2409-0298-2014-1-2-11-20
    Language: Unknown
    Publisher: Belgorod National Research University
    Publication Date: 2014
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 10
    Online Resource
    Online Resource
    SARS-CoV-2 variants in Vietnam: A comprehensive analysis of nucleotide changes in the spike gene
    GSC Online Press ; 2023
    In:  GSC Biological and Pharmaceutical Sciences Vol. 23, No. 3 ( 2023-6-30), p. 223-230
    Details
    In: GSC Biological and Pharmaceutical Sciences, GSC Online Press, Vol. 23, No. 3 ( 2023-6-30), p. 223-230
    Abstract: SARS-CoV-2, causing the COVID-19 pandemic, has claimed millions of lives worldwide. SARS-CoV-2 has a high mutation rate in its genome, resulting in thousands of variants. The success of SARS-CoV-2 is attributed to a mutation in the S gene, which encodes the spike protein that interacts directly with hACE2. Mutations in this gene are known to increase the transmission rate and the ability to escape the immune system of the virus. This study focused on analyzing the nucleotide changes in the S gene of the SARS-CoV-2 variants that appeared in Vietnam. The results showed that Vietnam recorded many VOC variants, including Alpha, Beta, Delta, and Omicron, with Delta and Omicron being the most prevalent. The S1 region of the S gene had the highest mutation rate, with missense and C to T mutations being the most common. The NTD region contained all deletion and insertion mutations, with the nucleotide at 22198 to 22206 being the hotspot for insertion. The RBD region showed a positive selection during evolution, indicating that it had undergone harsh missense mutation. Overall, this study demonstrates that the S gene in Vietnam has high haplotype and nucleotide diversity. The Omicron variant in Vietnam had the highest nucleotide, haplotype diversity indexes, and average number of mutations in the S gene. These findings provide insights into the genetic diversity of SARS-CoV-2 variants in Vietnam and the impact of the S gene mutations on the evolution of the virus.
    Type of Medium: Online Resource
    ISSN: 2581-3250
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.30574/gscbps.2023.23.3
    DOI: 10.30574/gscbps
    DOI: 10.30574/gscbps.2023.23.3.0251
    Language: Unknown
    Publisher: GSC Online Press
    Publication Date: 2023
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...