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Briefings in Bioinformatics Jan 2022Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, over 100 million people have been infected by COVID-19, millions...
Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, over 100 million people have been infected by COVID-19, millions of whom have died. In the latest year, a large number of omics data have sprung up and helped researchers broadly study the sequence, chemical structure and function of SARS-CoV-2, as well as molecular abnormal mechanisms of COVID-19 patients. Though some successes have been achieved in these areas, it is necessary to analyze and mine omics data for comprehensively understanding SARS-CoV-2 and COVID-19. Hence, we reviewed the current advantages and limitations of the integration of omics data herein. Firstly, we sorted out the sequence resources and database resources of SARS-CoV-2, including protein chemical structure, potential drug information and research literature resources. Next, we collected omics data of the COVID-19 hosts, including genomics, transcriptomics, microbiology and potential drug information data. And subsequently, based on the integration of omics data, we summarized the existing data analysis methods and the related research results of COVID-19 multi-omics data in recent years. Finally, we put forward SARS-CoV-2 (COVID-19) multi-omics data integration research direction and gave a case study to mine deeper for the disease mechanisms of COVID-19.
Topics: Antiviral Agents; COVID-19; Genomics; Humans; SARS-CoV-2; COVID-19 Drug Treatment
PubMed: 34718395
DOI: 10.1093/bib/bbab446 -
Nature Communications Jun 2023Chemical probes have reached a prominent role in biomedical research, but their impact is governed by experimental design. To gain insight into the use of chemical...
Chemical probes have reached a prominent role in biomedical research, but their impact is governed by experimental design. To gain insight into the use of chemical probes, we conducted a systematic review of 662 publications, understood here as primary research articles, employing eight different chemical probes in cell-based research. We summarised (i) concentration(s) at which chemical probes were used in cell-based assays, (ii) inclusion of structurally matched target-inactive control compounds and (iii) orthogonal chemical probes. Here, we show that only 4% of analysed eligible publications used chemical probes within the recommended concentration range and included inactive compounds as well as orthogonal chemical probes. These findings indicate that the best practice with chemical probes is yet to be implemented in biomedical research. To achieve this, we propose 'the rule of two': At least two chemical probes (either orthogonal target-engaging probes, and/or a pair of a chemical probe and matched target-inactive compound) to be employed at recommended concentrations in every study.
Topics: Biomedical Research; Molecular Probes
PubMed: 37270653
DOI: 10.1038/s41467-023-38952-1 -
Frontiers in Psychiatry 2021premutation is defined by 55-200 CGG repeats in the Fragile X Mental Retardation 1 () gene. premutation carriers are at risk of developing a neurodegenerative disease...
premutation is defined by 55-200 CGG repeats in the Fragile X Mental Retardation 1 () gene. premutation carriers are at risk of developing a neurodegenerative disease called fragile X-associated tremor/ataxia syndrome (FXTAS) and Fragile X-associated primary ovarian insufficiency (FXPOI) in adulthood. In the last years an increasingly board spectrum of clinical manifestations including psychiatric disorders have been described as occurring at a greater frequency among premutation carriers. Herein, we reviewed the neuroimaging findings reported in relation with psychiatric symptomatology in adult premutation carriers. A structured electronic literature search was conducted on premutation and neuroimaging yielding a total of 3,229 articles examined. Of these, 7 articles were analyzed and are included in this review. The results showed that the main radiological findings among adult premutation carriers presenting neuropsychiatric disorders were found on the amygdala and hippocampus, being the functional abnormalities more consistent and the volumetric changes more inconsistent among studies. From a molecular perspective, CGG repeat size, mRNA and FMRP levels have been investigated in relation with the neuroimaging findings. Based on the published results, FMRP might play a key role in the pathophysiology of the psychiatric symptoms described among premutation carriers. However, additional studies including further probes of brain function and a broader scope of psychiatric symptom measurement are required in order to obtain a comprehensive landscape of the neuropsychiatric phenotype associated with the premutation.
PubMed: 34721105
DOI: 10.3389/fpsyt.2021.728952 -
Surgical Infections 2018Conventional antibiotic agents are overused, leading to decreased efficacy because of a rising incidence in antimicrobial resistance. Further, conventional antibiotic...
Conventional antibiotic agents are overused, leading to decreased efficacy because of a rising incidence in antimicrobial resistance. Further, conventional antibiotic agents result in widespread effects to human microbiota, which can lead directly to adverse events such as infection. This review provides a narrative summary of anti-sense therapies, an approach to managing bacterial infections by pursuing specific molecular targets that disrupt the flow of information from deoxyribonucleic acid to ribonucleic acid to protein, leading to the loss of bacterial functions. Included in this article is the rationale for this approach, the current data supporting its further investigation, and the challenges and future directions in this area of research. There is a compelling proof-of-concept against both gram-positive and gram-negative organisms to commend the use of modified anti-sense oligonucleotides as antimicrobial therapy. There are data demonstrating that anti-sense therapies are capable of killing bacteria, silencing antimicrobial resistance mechanisms to restore sensitivity to conventional antibiotic agents, and to target virulence pathways such as biofilm production. Further, these drugs have a significantly greater degree of organismal specificity, limiting antibiotic-associated diarrhea and lowering the risk of antibiotic-related infections such as infection. Anti-sense therapies show promise as a new class of antibiotic agents, providing molecular precision that leads to specific targeting of bacterial species and bacterial functions, including virulence mechanisms beyond the reach of current antibiotic agents. Further, changing the sequence of an anti-sense oligonucleotide provides a method of dealing with antimicrobial resistance that is more time- and cost-flexible than the available options with current conventional antibiotic agents.
Topics: Anti-Bacterial Agents; Bacterial Infections; Biomedical Research; Humans; Molecular Targeted Therapy; Oligonucleotides, Antisense
PubMed: 30256744
DOI: 10.1089/sur.2018.200 -
Orphanet Journal of Rare Diseases Dec 2018Cystic fibrosis (CF) is a rare disease most commonly seen in Caucasians. Only a few Chinese CF patients have been described in literature, taking into account the large...
Cystic fibrosis (CF) is a rare disease most commonly seen in Caucasians. Only a few Chinese CF patients have been described in literature, taking into account the large population of China. In this systematic review, we collected the clinical and genetic information of 71 Chinese CF patients based on all available data. Compared with Caucasians, Chinese CF patients often present atypical symptoms, mainly displaying symptoms of pulmonary infection with fewer digestive symptoms. An ethnicity-specific CFTR variant spectrum was also observed in CF patients of Chinese origin, with p.Gly970Asp as the most common mutation while p.Phe508del, the most common pathogenic mutation in CF patients of Caucasian origin, is rare, suggesting the necessity of a Chinese-specific CFTR variant screening panel. Besides, multiplex ligation-dependent probe amplification analysis should be routinely considered, especially for those with unidentified mutations. Potential under-diagnosis of CF in Chinese patients might be caused by a combination of atypical clinical features and genetic heterogeneity in Chinese CF patients, the inaccessibility of sweat and genetic testing facilities, and the one-child policy in China. With the approval of promising small molecule correctors and potentiators, molecular characterization of Chinese-specific CFTR mutations will help to realize more precise treatment for Chinese CF patients.
Topics: Asian People; Cystic Fibrosis; Cystic Fibrosis Transmembrane Conductance Regulator; Humans; Phenotype
PubMed: 30558651
DOI: 10.1186/s13023-018-0968-2 -
International Journal of Molecular... Sep 2020Intrinsic resistance to ionizing radiation is the major impediment in the treatment and clinical management of esophageal squamous cell carcinoma (ESCC), leading to... (Meta-Analysis)
Meta-Analysis
Intrinsic resistance to ionizing radiation is the major impediment in the treatment and clinical management of esophageal squamous cell carcinoma (ESCC), leading to tumor relapse and poor prognosis. Although several biological and molecular mechanisms are responsible for resistance to radiotherapy in ESCC, the molecule(s) involved in predicting radiotherapy response and prognosis are still lacking, thus requiring a detailed understanding. Recent studies have demonstrated an imperative correlation amongst several long non-coding RNAs and their involvement in complex cellular networks like DNA damage and repair, cell cycle, apoptosis, proliferation, and epithelial-mesenchymal transition. Additionally, accumulating evidence has suggested abnormal expression of lncRNAs in malignant tumor cells before and after radiotherapy effects in tumor cells' sensitivity. Thus, lncRNAs indeed represent unique molecules that can influence tumor cell susceptibility for various clinical interventions. On this note, herein, we have summarized the current status of lncRNAs in augmenting resistance/sensitivity in ESCC against radiotherapy. In addition, we have also discussed various strategies to increase the radiosensitivity in ESCC cells under clinical settings.
Topics: DNA Damage; Esophageal Squamous Cell Carcinoma; Gene Expression Regulation, Neoplastic; Genetic Therapy; Humans; MicroRNAs; Molecular Targeted Therapy; RNA, Antisense; RNA, Long Noncoding; RNA, Neoplasm; Radiation Tolerance
PubMed: 32947897
DOI: 10.3390/ijms21186787 -
Scientific Reports Mar 2018Antisense oligonucleotide (AON)-based therapies hold promise for a range of neurodegenerative and neuromuscular diseases and have shown benefit in animal models and... (Meta-Analysis)
Meta-Analysis
Antisense oligonucleotide (AON)-based therapies hold promise for a range of neurodegenerative and neuromuscular diseases and have shown benefit in animal models and patients. Success in the clinic is nevertheless still limited, due to unfavourable biodistribution and poor cellular uptake of AONs. Extensive research is currently being conducted into the formulation of AONs to improve delivery, but thus far there is no consensus on which of those strategies will be the most effective. This systematic review was designed to answer in an unbiased manner which delivery strategies most strongly enhance the efficacy of AONs in animal models of heritable neurodegenerative and neuromuscular diseases. In total, 95 primary studies met the predefined inclusion criteria. Study characteristics and data on biodistribution and toxicity were extracted and reporting quality and risk of bias were assessed. Twenty studies were eligible for meta-analysis. We found that even though the use of delivery systems provides an advantage over naked AONs, it is not yet possible to select the most promising strategies. Importantly, standardisation of experimental procedures is warranted in order to reach conclusions about the most efficient delivery strategies. Our best practice guidelines for future experiments serve as a step in that direction.
Topics: Animals; Disease Models, Animal; Drug Delivery Systems; Heredodegenerative Disorders, Nervous System; Neuromuscular Diseases; Oligonucleotides, Antisense
PubMed: 29520012
DOI: 10.1038/s41598-018-22316-7 -
Molecular and Cellular Probes Feb 2021The newly emerged coronavirus (SARS-CoV-2) continues to infect humans, and no effective treatment has yet been found. Antibody therapy is one way to control infection...
The newly emerged coronavirus (SARS-CoV-2) continues to infect humans, and no effective treatment has yet been found. Antibody therapy is one way to control infection caused by COVID-19. However, the use of classical antibodies raises complex issues. Heavy chain antibodies (HCAbs) are single-domain antibodies derived from the Camelidae family. The variable part of these antibodies (Nanobodies or VHH) has interesting properties such as small size, cost-effective production, and good tissue permeability, causing VHH to be regarded as an antiviral therapeutics. However, the small size of nanobodies may lead to low antigen binding affinity and rapid renal clearance. In this systematic review, the application of nanobodies in the treatment of COVID-19 infection and other similar infections (MERS and SARS) was reviewed.
Topics: Antibodies, Neutralizing; COVID-19; COVID-19 Testing; Humans; SARS-CoV-2; Single-Domain Antibodies
PubMed: 33358936
DOI: 10.1016/j.mcp.2020.101692 -
BMJ Open Jan 2019We evaluated the performance of nucleic acid amplification tests (NAATs) using vaginal specimens in comparison to specimens from the cervix or urine in their ability to...
Evaluation of the performance of nucleic acid amplification tests (NAATs) in detection of chlamydia and gonorrhoea infection in vaginal specimens relative to patient infection status: a systematic review.
OBJECTIVE
We evaluated the performance of nucleic acid amplification tests (NAATs) using vaginal specimens in comparison to specimens from the cervix or urine in their ability to detect chlamydia and gonorrhoea infection in women based on patient infection status (PIS).
DESIGN
Systematic review.
DATA SOURCES
EMBASE and Ovid MEDLINE databases were searched through 3 October 2017.
ELIGIBILITY CRITERIA FOR SELECTING STUDIES
We included studies that tested samples from the vagina and ≥1 other site (cervix and/or urine) with ≥2 NAATs for chlamydia and ≥2 NAATs or 1 NAAT and culture for gonorrhoea for each site.
DATA EXTRACTION AND SYNTHESIS
Performance is defined as the sensitivity of a NAAT using a specimen site and PIS of the patient. We assessed risk of bias using modified QUADAS-2.
RESULTS
Nine publications met the inclusion criteria (eight for chlamydia; six for gonorrhoea) and were narratively reviewed. Pooled summary estimates were not calculated due to the variable methodology and PIS definitions. Tests performed on vaginal specimens accomplished similar performance to cervical and urine specimens for chlamydia (range of performance estimates: vaginal 65%-100%, cervical 59%-97%, urine 57%-100%) and gonorrhoea (vaginal 64%-100%, cervical 85%-100%, urine 67%-94%). Vaginal specimens were estimated to have a performance >80% for chlamydia and gonorrhoea infections in all but one study.
CONCLUSIONS
Performance of the NAATs for chlamydia and gonorrhoea detection using vaginal specimens was similar to that of cervical and urine specimens relative to PIS. As vaginal samples have a higher acceptability and lower cost, the study can support clinical testing guidelines by providing evidence that vaginal samples are a suitable alternative to traditionally used specimens.
Topics: Chlamydia Infections; Chlamydia trachomatis; Cost-Benefit Analysis; Female; Gonorrhea; Humans; Neisseria gonorrhoeae; Nucleic Acid Amplification Techniques; Sensitivity and Specificity; Vagina
PubMed: 30659036
DOI: 10.1136/bmjopen-2018-022510 -
Scientific Reports Mar 2019This systematic review assesses the accuracy of molecular diagnostic methods for the detection of pulmonary tuberculosis in studies performed in China, published in...
This systematic review assesses the accuracy of molecular diagnostic methods for the detection of pulmonary tuberculosis in studies performed in China, published in Chinese and English. We searched for studies that assessed the accuracy of molecular diagnostics for pulmonary TB in China in the China National Knowledge Infrastructure, the Wanfang Database, SinoMed, VIP Information, Pubmed, Embase, and the Cochrane Library. For each index test, a summary estimation for sensitivity and specificity was calculated using the bivariate random-effects model. A total of 59 studies were included in our analysis. Loop-mediated isothermal amplifcation (LAMP) assay (six studies; pooled sensitivity 90%, 95% CI 78-95%; specificity 93%, 85-97%), line probe assay (LPA) (one study; 87%, 84-90%; 94%, 92-95%) and polymerase chain reaction (PCR) (FQ-PCR and RT-PCR) (four studies; 90%, 55-99%; 93%, 71-99%) showed good diagnostic performance in the meta-analysis. The highest pooled sensitivity was from Xpert MTB/RIF (20 studies; pooled sensitivity 91%, 95% CI 87-94%). The highest pooled specificity was from cross-priming amplification (CPA) (six studies; pooled specificity 97%, 95-99%). The lowest pooled sensitivity and specificity were from simultaneous amplification and testing (SAT)-TB (three studies; 79%, 66-88%; 72%, 48-88%). In subgroup analysis, molecular diagnostics demonstrated higher sensitivity for pulmonary TB detection in smear-positive specimens. Xpert MTB/RIF, LAMP, LPA, CPA and PCR demonstrated high accuracy overall for pulmonary tuberculosis detection, while SAT-TB had poor performance.
Topics: China; Humans; Molecular Diagnostic Techniques; Mycobacterium tuberculosis; Pathology, Molecular; Predictive Value of Tests; Tuberculosis, Pulmonary
PubMed: 30872692
DOI: 10.1038/s41598-019-41074-8