scholarly journals Newly identified viral genomes in pangolins with fatal disease

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Wen-Hua Gao ◽  
Xian-Dan Lin ◽  
Yan-Mei Chen ◽  
Chun-Gang Xie ◽  
Zhi-Zhou Tan ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Sampling Site ◽  
Amino Acid Level ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Symptomatic Treatment ◽  
Tick Population ◽  
The Status ◽  
Manis Javanica ◽  
Manis Pentadactyla

Abstract Epizootic pathogens pose a major threat to many wildlife species, particularly in the context of rapidly changing environments. Pangolins (order Pholidota) are highly threatened mammals, in large part due to the trade in illegal wildlife. During July to August 2018 four sick wild pangolins (three Manis javanica and one Manis pentadactyla) exhibiting a variety of clinical symptoms were rescued by the Jinhua Wildlife Protection Station in Zhejiang province, China. Although three of these animals died, fortunately one recovered after 2 weeks of symptomatic treatment. Using meta-transcriptomics combined with reverse transcription polymerase chain reaction (RT-PCR), we identified two novel RNA viruses in two of the dead pangolins. Genomic analysis revealed that these viruses were most closely related to pestiviruses and coltiviruses, although still highly genetically distinct, with more than 48 and 25 per cent sequence divergence at the amino acid level, respectively. We named these Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV) based on the sampling site and hosts. Although coltiviruses (LSPV) are known to be transmitted by ticks, we found no evidence of LSPV in ticks sampled close to where the pangolins were collected. In addition, although DYPV was present in nymph ticks (Amblyomma javanense) collected from a diseased pangolin, they were not found in the local tick population. Epidemiological investigation revealed that both novel viruses might have been imported following the illegal international trade of pangolins. Hence, these data indicate that illegal wildlife trafficking not only threatens the status of pangolin populations, but may also spread epizootic pathogens.

scholarly journals The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases

2021 ◽  
Vol 22 (8) ◽  
pp. 4274
Author(s):  
Dèlia Yubero ◽  
Daniel Natera-de Benito ◽  
Jordi Pijuan ◽  
Judith Armstrong ◽  
Loreto Martorell ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Clinical Symptoms ◽  
Neuromuscular Diseases ◽  
Genomic Analysis ◽  
Molecular Diagnostic ◽  
Diagnostic Process ◽  
Targeted Analysis ◽  
Whole Exome ◽  
Referral Hospitals ◽  
Uncertain Significance

The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives.

scholarly journals Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

2018 ◽  
Vol 19 (12) ◽  
pp. 4039 ◽  
Author(s):  
Mi-Li Liu ◽  
Wei-Bing Fan ◽  
Ning Wang ◽  
Peng-Bin Dong ◽  
Ting-Ting Zhang ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Repeat Sequence ◽  
Biological Research ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Evolutionary Analysis ◽  
Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

scholarly journals Geno-phenotypic characteristics of Ehlers–Danlos syndrome: difficulties of disease type identification and approaches to pathogenetic treatment

2021 ◽  
Vol 66 (1) ◽  
pp. 22-30
Author(s):  
E. A. Nikolaeva ◽  
A. N. Semyachkina
Keyword(s):  
Connective Tissue ◽  
Clinical Symptoms ◽  
Molecular Genetic ◽  
Symptomatic Treatment ◽  
Pathological Process ◽  
Social Adaptation ◽  
Molecular Defect ◽  
Ehlers Danlos Syndrome ◽  
Pathogenetic Therapy ◽  
Danlos Syndrome

Veltischev Researchand Clinical Institutefor Pediatricsofthe Pirogov Russian National Research Medical University, Moscow, Russia The article presents modern data on the most common monogenic connective tissue disease – Ehlers–Danlos syndrome. The authors describe two previous classifications of the syndrome: Berlin (1988) classification, which distinguishes 11 types of the disease, and Beyton (1998) classification, which includes 6 types of the syndrome and takes into account the results of molecular genetic studies. Particular attention is paid to a new classification, proposed by the International Consortium in 2017. This classification is based on the clinical and molecular genetic data and unites 13 types of Ehlers–Danlos syndrome, divided in 7 groups (A–G), depending on the main molecular defect. This defect determines the violation of various collagen structures (primary, spatial, cross-linking) and others constituents of the connective tissue (myomatrix, glycosaminoglycans, complement component, etc.). The classification provides general clinical symptoms for all types of the disease and comprehensive information on the specific signs of each of the 13 types of the syndrome.The authors discuss approaches to the pathogenetic therapy of the syndrome, the possibilities of symptomatic treatment, including both medications of different spectrum of action, and physiotherapeutic measures, exercise therapy. The complex of the listed therapeutic measures is aimed at stabilizing the main pathological process, preventing complications, improving the patient’s quality of life and social adaptation. The authors emphasize that correct patient management, targeted medical supervision and medical genetic counseling requires molecular genetic verification of the diagnosis.

scholarly journals An Integrated Framework for Genome Analysis Reveals Numerous Previously Unrecognizable Structural Variants in Leukemia Patients’ Samples

2019 ◽  
Author(s):  
Jie Xu ◽  
Fan Song ◽  
Emily Schleicher ◽  
Christopher Pool ◽  
Darrin Bann ◽  
...  
Keyword(s):  
Genome Mapping ◽  
Large Fraction ◽  
Genomic Analysis ◽  
Structural Variants ◽  
Driver Genes ◽  
Pediatric Leukemia ◽  
Cis Acting ◽  
Cancer Driver ◽  
The Status ◽  
Intergenic Regions

AbstractWhile genomic analysis of tumors has stimulated major advances in cancer diagnosis, prognosis and treatment, current methods fail to identify a large fraction of somatic structural variants in tumors. We have applied a combination of whole genome sequencing and optical genome mapping to a number of adult and pediatric leukemia samples, which revealed in each of these samples a large number of structural variants not recognizable by current tools of genomic analyses. We developed computational methods to determine which of those variants likely arose as somatic mutations. The method identified 97% of the structural variants previously reported by karyotype analysis of these samples and revealed an additional fivefold more such somatic rearrangements. The method identified on average tens of previously unrecognizable inversions and duplications and hundreds of previously unrecognizable insertions and deletions. These structural variants recurrently affected a number of leukemia associated genes as well as cancer driver genes not previously associated with leukemia and genes not previously associated with cancer. A number of variants only affected intergenic regions but caused cis-acting alterations in expression of neighboring genes. Analysis of TCGA data indicates that the status of several of the recurrently mutated genes identified in this study significantly affect survival of AML patients. Our results suggest that current genomic analysis methods fail to identify a majority of structural variants in leukemia samples and this lacunae may hamper diagnostic and prognostic efforts.

scholarly journals Can 2-Aticyto Complex be an Effective Agent for Recovery of The Symptoms and Enhancing Laboratory Parameters in COVID-19 Patients?

2021 ◽  
Vol 3 (2) ◽  
pp. 35-39
Author(s):  
Ferhan Kerget ◽  
Buğra Kerget ◽  
Alperen Aksakal ◽  
Abdullah Osman Koçak
Keyword(s):  
Clinical Symptoms ◽  
Clinical Course ◽  
Symptomatic Treatment ◽  
Clinical Situation ◽  
National Guideline ◽  
Control Group ◽  
Effective Agent ◽  
Laboratory Parameters ◽  
Taste And Smell ◽  
D Dimer

Background: SARS-CoV-2 (Covid-19) pandemic which was firstly identified in Wuhan/China in December 2019.There still exists no precise treatment for this pandemic yet despite many agents are tried in prophylaxis and treatment for Covid-19. In this study, we aimed to investigate the efficacy of 2-aticyto complex in clinical course in these patients. Materials and Methods: 150 patients who applied to the Infection Diseases Polyclinics between dates September 2020-November 2020 having diagnosed with Covid-19 were included in our study. The patients were randomized into 2 groups (75 in each group) of which the first group only had the treatment of National Guideline and the second group had Viruthol® including 2-aticyto complex (at the dose of 27000 mcg/day) in addition to the treatment of the National Guideline. The laboratory parameters, clinical outcomes and the first day on which PCR result turned into negative of the patients were compared. Results: In Viruthol® group, LDH, CRP, D-Dimer and ferritin levels were significantly decreased compared to the control group, while lymphocyte levels were higher. (p=0.02, p=0.001, p=0.01, p=0.02, p=0,001 respectively).  In addition to that, clinical symptoms such as fever, headache, weakness, loss of taste and smell and muscle-joint pain recovered more rapidly in contrast with the control group (p=0.001, p=0.05, p=0.001, p=0.001, p=0.001, respectively). PCR results of the Viruthol® group turned negative in a statistically significant shorter period of time with respect to the control group (p=0.001). Conclusion: Viruthol® containing 2-aticyto complex may be an agent that can be used both symptomatic treatment and improving the clinical situation and recovery of the patients followed up for Covid-19.

scholarly journals Community-based study to demonstrate the presence and local perspectives of the Critically Endangered Chinese Pangolin Manis pentadactyla in Zhejiang Wuyanling, China

2020 ◽  
Vol 12 (5) ◽  
pp. 15547-15556
Author(s):  
Hongying Li ◽  
Shusheng Zhang ◽  
Ji Zhang ◽  
Zupei Lei ◽  
Fangdong Zheng ◽  
...  
Keyword(s):  
Mainland China ◽  
Infrared Camera ◽  
Critically Endangered ◽  
Community Based ◽  
Illegal Hunting ◽  
Critically Endangered Species ◽  
The Status ◽  
In The Wild ◽  
Manis Pentadactyla ◽  
Camera Surveillance

Illegal hunting and trading of the Chinese Pangolin Manis pentadactyla has pushed this Critically Endangered species close to extinction.  While local reports have suggested its continued presence in mainland China, this has not been confirmed by a research group except for a survey of presumed pangolin burrows in 2004.  We conducted a six-month field study using infrared camera surveillance and community questionnaire survey in Zhejiang Wuyanling National Nature Reserve in China, to determine the status of Chinese Pangolins and understand local attitudes towards the conservation of this species.  Our study details the first verifiable documentation of two visual records of a Chinese Pangolin in the wild, demonstrating the suitability of pangolin habitat in Wuyanling region, and suggests an increasing awareness and strong willingness in local communities to conserve the Chinese Pangolin.  

scholarly journals Current concepts in the treatment of hereditary ataxias

2016 ◽  
Vol 74 (3) ◽  
pp. 244-252 ◽  
Author(s):  
Pedro Braga Neto ◽  
José Luiz Pedroso ◽  
Sheng-Han Kuo ◽  
C. França Marcondes Junior ◽  
Hélio Afonso Ghizoni Teive ◽  
...  
Keyword(s):  
Autosomal Recessive ◽  
Autosomal Dominant ◽  
Clinical Symptoms ◽  
Genetic Diagnosis ◽  
Symptomatic Treatment ◽  
Hereditary Ataxias ◽  
Disease Modifying Therapy ◽  
Progressive Ataxia ◽  
Cerebellar Ataxias ◽  
Disease Modifying

ABSTRACT Hereditary ataxias (HA) represents an extensive group of clinically and genetically heterogeneous neurodegenerative diseases, characterized by progressive ataxia combined with extra-cerebellar and multi-systemic involvements, including peripheral neuropathy, pyramidal signs, movement disorders, seizures, and cognitive dysfunction. There is no effective treatment for HA, and management remains supportive and symptomatic. In this review, we will focus on the symptomatic treatment of the main autosomal recessive ataxias, autosomal dominant ataxias, X-linked cerebellar ataxias and mitochondrial ataxias. We describe management for different clinical symptoms, mechanism-based approaches, rehabilitation therapy, disease modifying therapy, future clinical trials and perspectives, genetic counseling and preimplantation genetic diagnosis.

scholarly journals An Overview of Chinese Pangolin (Manis pentadactyla): Its General Biology, Status, Distribution and Conservation Threats in Nepal

2014 ◽  
Vol 5 ◽  
pp. 164-170 ◽  
Author(s):  
Prakash Thapa
Keyword(s):  
Protected Areas ◽  
Habitat Destruction ◽  
Illegal Trade ◽  
General Biology ◽  
The Status ◽  
Manis Pentadactyla ◽  
Conservation Threats ◽  
Scientific Attention

Chinese Pangolin is nocturnal, shy, non-aggressive, solitary, strange and burrowing mammal which has received low scientific attention. Little information is known about its biology, distribution and status. In Nepal it is distributed in many districts and protected areas. The status of this mammal is decreasing in the country but there is no any research regarding its biology, status and distribution. Although, this mammal is protected nationally and internationally, it is facing too much problems due to habitat destruction and illegal trade. This article mainly focuses on the biology, status, distribution and conservation threats of this ecologically beneficial handsome creature. DOI: http://dx.doi.org/10.3126/init.v5i0.10267   The Initiation 2013 Vol.5; 164-170

scholarly journals Therapeutic effects of combined meloxicam and glucosamine sulfate treatment on patients with osteoarthritis, and its effect on serum CTX-Ⅰ, CTX-Ⅱ, COMP and MMP-3

2021 ◽  
Vol 18 (7) ◽  
pp. 1553-1557
Author(s):  
Lu Zhijun ◽  
Chen Rongchun ◽  
Lin Feixiang ◽  
Wu Yaohong ◽  
Liu Ning ◽  
...  
Keyword(s):  
Treatment Group ◽  
Matrix Protein ◽  
Type I Collagen ◽  
Clinical Symptoms ◽  
Type Ii Collagen ◽  
Symptomatic Treatment ◽  
Glucosamine Sulfate ◽  
Control Group ◽  
Therapeutic Effects ◽  
Type I

Purpose: To study the therapeutic influence of meloxicam-glucosamine sulfate combination in patients with osteoarthritis and their effect on serum CTX-I, CTX-II, COMP and MMP-3. Methods: A total of 88 patients with osteoarthritis were assigned to control (n = 44) and treatment groups (n = 44), using the random number table method. Control group was given 7.5 mg of meloxicam, while treatment group received 0.5 g of glucosamine sulfate capsule in addition to meloxicam. Both groups were treated continuously for 8 weeks. Serum levels of C-terminal telopeptide of type I collagen (CTX-I), C-terminal telopeptide of type II collagen (CTX-II), cartilage oligomeric matrix protein (COMP) and matrix metalloproteinase-3 (MMP-3) were compared for the two groups after treatment. Results: Lysholm score significantly increased in the two groups after treatment. Serum CTX-I, CTX-II, COMP and MMP-3 in the two groups were significantly lower than before treatment, but the reductions were more pronounced in the treatment group (p < 0.05). During treatment, mild vomiting and pruritus of the skin appeared in both groups, but these were relieved after symptomatic treatment without any serious adverse reactions. Conclusion: Treatment with a combination of meloxicam and glucosamine sulfate produces significant beneficial effects in patients with osteoarthritis by reduction of clinical symptoms, pain relief and reduction of serum CTX-I, CTX-II, MMP-3 and COMP.

scholarly journals Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3391 ◽  
Author(s):  
Dariya K. Sydykova ◽  
Claus O. Wilke
Keyword(s):  
Amino Acid ◽  
Conservation Score ◽  
Amino Acid Level ◽  
Sequence Divergence ◽  
Similar Rate ◽  
Amino Acid Sequences ◽  
Evolutionary Rates ◽  
Site Specific ◽  
Relative Conservation ◽  
The Relationship

Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN∕dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it assigns a relative conservation score to each site in an alignment. How site-wise dN∕dS values relate to Rate4Site scores is not known. Here we elucidate the relationship between these two rate measurements. We simulate sequences with known dN∕dS, using either dN∕dS models or mutation–selection models for simulation. We then infer Rate4Site scores on the simulated alignments, and we compare those scores to either true or inferred dN∕dS values on the same alignments. We find that Rate4Site scores generally correlate well with true dN∕dS, and the correlation strengths increase in alignments with greater sequence divergence and more taxa. Moreover, Rate4Site scores correlate very well with inferred (as opposed to true) dN∕dS values, even for small alignments with little divergence. Finally, we verify this relationship between Rate4Site and dN∕dS in a variety of empirical datasets. We conclude that codon-level and amino-acid-level analysis frameworks are directly comparable and yield very similar inferences.

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