Journal of biological methods最新文献

{"title":"Side effects of prostate cancer therapies and potential management.","authors":"Jinfeng Xiao, Meihui Zhang, Donghai Wu","doi":"10.14440/jbm.2024.0019","DOIUrl":"10.14440/jbm.2024.0019","url":null,"abstract":"<p><p>Prostate cancer (PCa) remains a significant health challenge, necessitating diverse therapeutic interventions to manage the disease effectively. While these treatments offer promising outcomes, they are often accompanied by a range of side effects that can impact patient quality of life and treatment compliance. This review provides an overview of the common side effects associated with various PCa therapies, including prostatectomy, radiation therapy, thermal therapy, hormone therapy, chemotherapy, and targeted drug therapy, among others. We summarized and discussed the reported side effects encompassing ureteral problems, sexual issues, gastrointestinal symptoms, fatigue, anemia, thrombocytopenia, hematologic abnormalities, nausea, vomiting, and liver enzyme elevation. Specific managements, such as personalized treatment plans, proactive symptom monitoring, supportive care interventions, and hematological assessments, are crucial in mitigating these side effects and optimizing treatment outcomes. By prioritizing patient-centered care and tailored interventions, health-care providers can enhance treatment efficacy and improve the overall well-being of individuals undergoing PCa therapies.</p>","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":"11 3","pages":"e99010018"},"PeriodicalIF":0.0,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11557297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142634034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cancer genetics and deep learning applications for diagnosis, prognosis, and categorization","authors":"M. Sokouti, B. Sokouti","doi":"10.14440/jbm.2024.0016","DOIUrl":"https://doi.org/10.14440/jbm.2024.0016","url":null,"abstract":"Gene expression data are used to discover meaningful hidden information in gene datasets. Cancer and other disorders may be diagnosed based on differences in gene expression profiles, and this information can be gleaned by gene sequencing. Thanks to the tremendous power of artificial intelligence (AI), healthcare has become a significant user of deep learning (DL) for predicting cancer diseases and categorizing gene expression. Gene expression Microarrays have been proved effective in predicting cancer diseases and categorizing gene expression. Gene expression datasets contain only limited samples, but the features of cancer are diverse and complex. To overcome their dimensionality, gene expression datasets must be enhanced. By learning and analyzing features of input data, it is possible to extract features, as multidimensional arrays, from the data. Synthetic samples are needed to strengthen the range of information. DL strategies may be used when gene expression data are used to diagnose and classify cancer diseases.","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":"49 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141922973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring molecular targets in cancer: Unveiling the anticancer potential of Paeoniflorin through a comprehensive analysis of diverse signaling pathways and recent advances","authors":"Kounser Jan, Neelofar Hassan, Antonisamy James, Ishraq Hussain, S. Rashid","doi":"10.14440/jbm.2024.0003","DOIUrl":"https://doi.org/10.14440/jbm.2024.0003","url":null,"abstract":"Tumors have posed significant threats to human health for over 250 years, emerging as the foremost cause of death. While chemotherapeutic drugs are effective in treating tumors, their side effects can sometimes be challenging to manage during therapy. Nonetheless, there is growing interest in exploring natural compounds as alternatives, which potentially achieve therapeutic outcomes comparable to conventional chemotherapeutics with fewer adverse effects. Paeoniflorin (PF), a monoterpene glycoside derived from the root of Paeonia lactiflora, has garnered significant attention lately due to its promising anti-cancer properties. This review offers an updated outline of the molecular mechanisms underlying PF’s anti-tumor function, with a focus on its modulation of various signaling pathways. PF exerts its anti-tumor activity by regulating crucial cellular processes including apoptosis, angiogenesis, proliferation, and metastasis. We explored the multifaceted impact of PF while modulating through signaling pathways, encompassing nuclear factor kappa B, NOTCH, caspase cascade, transforming growth factor-β, NEDD4, P53/14-3-3, STAT 3, MAPK, MMP-9, and SKP2 signaling pathways, highlighting its versatility in targeting diverse malignancies. Furthermore, we discuss future research directions aimed at exploring innovative and targeted cancer therapies facilitated by PF.\u0000","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":"127 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141835042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Calcium chloride and arginine show diametrically opposite effects on antibody elution in Protein A and Protein L chromatography","authors":"Ju Qu, Yan Wan, Yifeng Li","doi":"10.14440/jbm.2024.0006","DOIUrl":"https://doi.org/10.14440/jbm.2024.0006","url":null,"abstract":"Protein A and Protein L affinity chromatographies are extensively used in mAb and bispecific antibody (bsAb) purification. In addition to product capture, they are both capable of separating certain product-related by-products and aggregates under appropriate conditions. For both types of chromatography, previous studies suggested that adding a salt additive to the mobile phase can significantly improve the resolution between product and by-products/aggregates. Nevertheless, the effects of different salt additives on antibody elution in Protein A and Protein L chromatography have not been compared. In the current study, we compared the effects of three salt additives, sodium chloride (NaCl), calcium chloride (CaCl2), and arginine hydrochloride (Arg·HCl), on antibody elution in Protein A and Protein L chromatography. Interestingly, while NaCl suppressed antibody elution in both types of chromatography, CaCl2, and Arg·HCl promoted antibody elution in Protein A chromatography but suppressed antibody elution in Protein L chromatography. In addition, we evaluated the effect of each salt gradient on aggregate removal by Protein L chromatography. The information provided by the current study should be useful to the selection of conditions/additives for improving by-product removal by Protein A and Protein L chromatography.\u0000","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":"33 S123","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141835328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenomic, cistromic, and transcriptomic profiling of primary kidney tubular cells","authors":"Zhiheng Liu, Lirong Zhang, Yupeng Chen","doi":"10.14440/jbm.2024.0009","DOIUrl":"https://doi.org/10.14440/jbm.2024.0009","url":null,"abstract":"Spatiotemporal regulation of gene expression is essential for maintaining cellular homeostasis throughout kidney development and disease progression. Transcription factors (TFs) and epigenetic modifications play pivotal roles in controlling gene expression. Profiling chromatin modifications across the genome, along with the distribution and target regulation by TFs in specific kidney cell types, is crucial for understanding the dynamic changes in gene expression. Here, we presented a comprehensive workflow for epigenomic, cistromic, and transcriptomic analyses of primary kidney tubular cells. Specifically, our methodologies included the isolation of primary kidney tubular epithelial cells, RNA extraction, assay for transposase-accessible chromatin using sequencing, ultra-low-input micrococcal nuclease-based native chromatin immunoprecipitation, cleavage under targets and release using nuclease, and subsequent bioinformatic analysis. This protocol provides a methodological framework for investigating the roles of TFs and epigenetic modifications in kidney development and diseases.\u0000","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":"100 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141835607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conventional PCR-based versus next-generation sequencing-based approach for T-cell receptor γ gene clonality assessment in mature T-cell lymphomas: A phase 3 diagnostic accuracy study","authors":"Riccardo Donelli, A. Gazzola, C. Mannu, Maryam Etebari, M. Navari, P. Piccaluga","doi":"10.14440/jbm.2024.0002","DOIUrl":"https://doi.org/10.14440/jbm.2024.0002","url":null,"abstract":"Background: Clonality assessment is currently the major molecular analysis utilized to support the diagnosis of suspicious lymphoid malignancies. Clonal rearrangements of the V-J segments of T-cell receptor G chain locus (TCRγ or TRG) have been observed in almost all types of T neoplasms, such as T-cell-related non-Hodgkin lymphomas and leukemias. At present, the gold standard for clonality evaluation is multiplex polymerase chain reaction (PCR), plus subsequent capillary electrophoresis/heteroduplex analyses, and/or Sanger sequencing. This approach overcomes the problem with the conventional Southern blot hybridization and is more efficient, simple, fast, and reproducible. In the recent years, the new next-generation sequencing (NGS) technologies provided alternative techniques for the analysis of antigen receptors genes, which presented several advantages, such as increased efficiency, specificity (SP), sensitivity (ST), resolution, and objectivity of the results, leading to a better classification, stratification, and monitoring of lymphoid malignancies. Nonetheless, these technologies are still far from being the new gold standard since further studies are warranted to prove their utility. The present study aimed to assess the diagnostic accuracy of these two methods by comparing a commercial NGS-based assay for the evaluation of TRG locus with the gold standard PCR-based one, to fulfill the requirements of a phase 3 diagnostic accuracy study. Methods: We assessed the TRG gene rearrangements in 72 cases using the conventional and highly-validated PCR-based assay proposed by EuroClonality consortium, an alternative commercial PCR-based assay, namely, IdentiClone® TCR Gamma Gene Rearrangement Assay 2.0, and a commercial NGS-based assay, that is, Invivoscribe LymphoTrack® Dx MiSeq® (both by Invivoscribe Technologies Inc., San Diego, CA, USA), to determine the diagnostic accuracy of the latter, and compare them with reference diagnoses made based on observation of clinical manifestations, cytohistological, and immunohistochemical analyses. Statistical values were calculated using the Oxford CATmaker software package. Results: Using standardized criteria of interpretation, the obtained results showed a diagnostic accuracy of 90.3% (correspondence in 65 out of 72 cases) of the test under investigation, with a ST of 86%, a SP of 95%, a positive predicting value of 94%, and a negative predicting value of 88%, demonstrating that Invivoscribe LymphoTrack® Dx MiSeq® assay had high efficiency and reliability in detecting clonal TRG gene rearrangements in T-cell non-Hodgkin lymphomas. Conclusions: This diagnostic accuracy study yielded comparable results using a validated PCR-based approach and a new NGS-based one. Subsequent studies and cost-effectiveness evaluation are needed to put the NGS-based clonality assessment into routine diagnostic practice.\u0000","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":"54 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141835717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of relative humidity on SARS-CoV-2 RNA extraction using Nextractor automated extraction system","authors":"R. K. Jain, Archa Sharma, J. Lalwani, D. Chaurasia, Nagaraj Perumal","doi":"10.14440/jbm.2024.0001","DOIUrl":"https://doi.org/10.14440/jbm.2024.0001","url":null,"abstract":"This study investigated the influence of relative humidity (RH) on the efficiency of SARS-CoV-2 RNA extraction using the Nextractor automated system. Experiments employing clinical samples demonstrated satisfactory sensitivity and reproducibility for RNA extraction at low humidity (below 50% RH). Conversely, extractions at high humidity (above 70% RH) resulted in complete failure of reverse transcription-polymerase chain reaction assays, with neither SARS-CoV-2 RNA nor the human RNase P gene (internal control) detected. Analysis suggested that residual ethanol, incompletely evaporating due to high humidity, acted as a potent polymerase chain reaction inhibitor in these samples. These findings highlighted the importance of maintaining optimal laboratory humidity (<50% RH) for reliable SARS-CoV-2 RNA extraction using the Nextractor system. Furthermore, laboratories should implement strategies such as regular humidity monitoring, staff training on humidity’s impact, and system validation under specific humidity conditions to ensure accurate molecular diagnostic workflows for COVID-19 testing.\u0000","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":"65 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141837751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnosis of Alzheimer's disease: Towards accuracy and accessibility","authors":"Yan Mu, Ke-Xin Chang, Yu-Feng Chen, Ke Yan, Chun-Xiang Wang, Qian Hua","doi":"10.14440/jbm.2024.412","DOIUrl":"https://doi.org/10.14440/jbm.2024.412","url":null,"abstract":"Alzheimer’s disease (AD) is a serious dementia afflicting aging population and is characterized by cognitive decline, amyloid-β plaques, and neurofibrillary tangles. AD substantially impairs the life quality of the victims and poses a heavy burden on the society at large. The number of people with dementia due to AD, prodromal AD, and preclinical AD is estimated to stand at roughly 3.2, 69, and 315 million worldwide, respectively. Current clinical diagnosis is based on clinical symptoms, and clinical research demonstrated that positron emission tomography (PET) and cerebrospinal fluid (CSF) biomarkers had excellent diagnostic performance. However, the application of CSF biomarker tests and PET are restricted by the invasiveness and high cost. The presence of clinical symptoms means that AD pathology has been progressing for many years, and only a few drugs have been approved for the traetemnt of AD. Therefore, early diagnosis is extremely important for controlling the outcomes caused by AD. In this review, we provided an overview of developing clinical diagnostic criteria, diagnostic strategies under clinical research, developing blood based-biomarker assays, and promising nanotechnologically-based assays.","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":" 18","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140390585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of an In Situ Hybridization Method for Detection of Akabane Virus","authors":"Nihat Toplu, T. Ç. Oğuzoğlu, A. Akkoç","doi":"10.14440/jbm.2024.413","DOIUrl":"https://doi.org/10.14440/jbm.2024.413","url":null,"abstract":"Akabane virus (AKAV) is an arbovirus belonging to the family Bunyaviridae, genus Orthobunyavirus. AKAV consists of three-segment (L, M, and S RNA segments), negative single-stranded RNA. The aim of this study was to investigate an in situ hybridization method (ISH) in a Vero E6 cell line infected with Akabane virus. The 320 base pair amplicon was obtained by RT-PCR with a primer pair and labeled with digoxigenin. Akabane virus RNAs were seen as a granular pattern in the cytoplasm of infected cells. As a result, the expression of the particular Akabane virus gene area was successfully disclosed in the current investigation using the ISH method with a digoxigenin-labeled probe.","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":"17 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140437393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of 12 Rapid Antigen Tests for the Detection of SARS-CoV-2","authors":"Minghang Yu, Yang Xiong, Pu Liang, Danying Chen, Yuting Zhang, Huan Liu, Yuanyuan Zhang, Xuesen Zhao, Ronghua Jin, Xi Wang","doi":"10.14440/jbm.2024.409","DOIUrl":"https://doi.org/10.14440/jbm.2024.409","url":null,"abstract":"The rapid identification SARS-CoV-2 virus has become the basis for the control of the COVID-19 outbreak. The rapid antigen tests for SARS-CoV-2 are quick, widely available, and inexpensive. Rapid antigen tests have gradually replaced the time-consuming and costly RT-PCR. Currently, although several RAT kits have been extensively used for the diagnosis of COVID-19, validity data are limited due to the inconsistent sensitivity and poor reproducibility. Meanwhile, WHO does not recommend specific commercial RAT kits. Therefore, it is crucial to establish a method to evaluate the effectiveness of different rapid antigen tests kits. This study aimed to develop an evaluation system for rapid antigen tests to provide an efficient and accurate technique for screening SARS-CoV-2 antigen detection kits. Given large number of rapid antigen tests kits available, this study only focused on those that are representative and commonely used in China. By minimzing biases through randomization, concealment, and blinding, we eventually found that the Test 1 had the lowest sensitivity and the Test VI had the highest sensitivity. This study provided an evaluation platform that can potentially serve as a reference for COVID-19 diagnostic strategies.","PeriodicalId":73618,"journal":{"name":"Journal of biological methods","volume":"12 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139532789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}