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Current Opinion in Structural Biology Jun 2024Specimen preparation is a critical but challenging step in high-resolution cryogenic electron microscopy (cryo-EM) structural analysis of macromolecules. In the past... (Review)
Review
Specimen preparation is a critical but challenging step in high-resolution cryogenic electron microscopy (cryo-EM) structural analysis of macromolecules. In the past decade, graphene has gained much recognition as the supporting substrate to optimize cryo-EM specimen preparation. It improves macromolecule embedding in ice, reduces beam-induced motion, while imposing negligible background noise. Various types of graphene-coated cryo-EM grids were implemented to improve the robustness and efficiency of specimen preparation. Graphene functionalization by different means has been proved specifically useful in addressing challenges related to the air-water interface (AWI), such as preferential orientation and sample denaturation. Graphene sandwich specimen preparation sets a new direction to explore in cryo-EM analysis of biological specimens. In this review, we discuss the current challenges and future prospects of graphene application in cryo-EM analysis of macromolecules.
Topics: Cryoelectron Microscopy; Graphite; Macromolecular Substances; Specimen Handling
PubMed: 38688075
DOI: 10.1016/j.sbi.2024.102823 -
Frontiers in Chemistry 2023Toxicology testing is performed in clinical settings, forensic settings, and for controlling doping. Drug screening is a toxicology test to determine if drugs are... (Review)
Review
Toxicology testing is performed in clinical settings, forensic settings, and for controlling doping. Drug screening is a toxicology test to determine if drugs are present in biological samples. The most common specimen type for drug testing is urine, as drugs and/or their metabolites are often more concentrated in the urine, extending the detection window of drugs. The dilute-and-shoot method is a simple procedure used in toxicology testing, where a sample is diluted before being directly injected into the liquid chromatography-mass spectrometry (LC-MS) system. This method is easy, quick, and cost-saving, and can be used for protein-poor liquid specimens such as urine. Thus, it is reasonable and attractive for busy toxicology laboratories to combine the dilute-and-shoot method with high-resolution hyphenated-MS for urine drug screening. This method has several disadvantages, including a suboptimal detection capability for certain analytes, as well as interference from co-eluting matrix components called matrix effects, in which co-eluting matrix molecules alter the ionization efficiency of the analyte molecules at the ionization source in LC-MS, altering (mostly reducing) the analyte detection capability. The matrix effect testing is essential for the validation of LC-MS-based assays. A reasonable approach to addressing these undesirable effects would be to minimize these components. The most straightforward approach is to reduce the amounts of matrix components by using a higher dilution of the specimen and a lower volume for specimen injection. Optimization of the chromatographic separation is another reasonable approach for reducing co-eluting matrix components with the analyte.
PubMed: 38146427
DOI: 10.3389/fchem.2023.1278313 -
Frontiers in Public Health 2023Metagenomic next-generation sequencing (mNGS) has been gradually applied to the diagnosis of tuberculosis (TB) due to its rapid and highly sensitive characteristics.... (Meta-Analysis)
Meta-Analysis Review
OBJECTIVE
Metagenomic next-generation sequencing (mNGS) has been gradually applied to the diagnosis of tuberculosis (TB) due to its rapid and highly sensitive characteristics. Despite numerous studies on this subject, their results vary significantly. Thus, the current meta-analysis was performed to assess the performance of the mNGS on tuberculosis.
METHODS
PubMed, Embase, Web of Science, and The Cochrane Library were searched up to June 21, 2023. Studies utilizing the mNGS for tuberculosis detection were included. The risk of bias was assessed by QUADAS-2, and a meta-analysis was performed with STATA14.0 software.
RESULTS
Seventeen studies comprising 3,205 specimens were included. The combined sensitivity and specificity of mNGS for clinical specimens were 0.69[0.58-0.79] and 1.00[0.99-1.00], respectively. Subgroup analysis identified sequencing platform, diagnostic criteria, study type, sample size, and sample types as potential sources of heterogeneity. Cerebrospinal Fluid (CSF) has a lower sensitivity of 0.58 (0.39-0.75). In a population with a 10% prevalence rate, the accuracy of sensitivity reached 94%.
CONCLUSION
Metagenomic next-generation sequencing technology exhibits high sensitivity and speed in diagnosing . Its application in mono and mixed infections peoples shows promise, and mNGS is likely to be increasingly used to address challenges posed by complexes in the future.
Topics: Humans; Mycobacterium tuberculosis; High-Throughput Nucleotide Sequencing; Coinfection; Research Design; Technology
PubMed: 37637815
DOI: 10.3389/fpubh.2023.1224993 -
Journal of Clinical Microbiology Aug 2023Twelve high-risk alpha human papillomavirus (HPV) genotypes cause approximately 690,000 cancer cases annually, with cervical and oropharyngeal cancer being the two most... (Review)
Review
Twelve high-risk alpha human papillomavirus (HPV) genotypes cause approximately 690,000 cancer cases annually, with cervical and oropharyngeal cancer being the two most prominent types. HPV testing is performed in laboratory settings for various applications of a clinical, epidemiological, and research nature using a range of clinical specimens collected by clinicians or by individuals (self-collected specimens). Here, we reflect on the importance and justification of using the right test for the right application and provide practical updates for laboratories either participating in or anticipating involvement in HPV testing in three specimen types, namely, urine, blood, and oral specimens, which are considered "alternative" specimens by many. In addition to clinician-collected cervical samples and self-collected cervicovaginal samples, first-void urine is emerging as a credible specimen for HPV-based cervical cancer screening, triage of HPV screen-positive women, monitoring HPV vaccine impact, and HPV testing in groups for which a less invasive sample is preferred. Detection of cell-free DNA (including HPV DNA) in blood has great promise for the early detection of HPV-attributable oropharyngeal cancer (HPV-AOC) and potentially other HPV-driven cancers and as an adjunct prognostic marker in long-term tumor surveillance, including treatment response. The moderate sensitivity of HPV testing in oral rinses or swabs at HPV-AOC diagnosis prevents its use in HPV-AOC secondary prevention but represents a promising prognostic tool in HPV-AOC tertiary prevention, where the HPV persistence in oral rinses throughout treatment may predict early HPV-AOC recurrences and/or the development of secondary HPV-AOC. The increasing sophistication of specific collection devices designed for alternative samples and the enhanced precision of novel molecular technologies are likely to support the evolution of this field and catalyze potential translation into routine practice.
Topics: Humans; Female; Uterine Cervical Neoplasms; Human Papillomavirus Viruses; Uterine Cervical Dysplasia; Papillomavirus Infections; Early Detection of Cancer; Laboratories; Papillomaviridae; Oropharyngeal Neoplasms; DNA, Viral; Sensitivity and Specificity; Vaginal Smears
PubMed: 37439692
DOI: 10.1128/jcm.01403-22 -
AIDS Research and Therapy Aug 2023The goal of the AIDS and Cancer Specimen Resource (ACSR) is to play a major role in the advancement of HIV/AIDS cancer-related research/treatment by providing richly... (Review)
Review
The goal of the AIDS and Cancer Specimen Resource (ACSR) is to play a major role in the advancement of HIV/AIDS cancer-related research/treatment by providing richly annotated biospecimens and data to researchers at no cost. The ACSR acquires, stores, and equitably distributes these samples and associated clinical data to investigators conducting HIV/AIDS-related research, at no costs. Currently, it is the only biorepository of human biospecimens from people with HIV and cancer available to eligible researchers globally who are studying HIV associated malignancies.This review describes the history and organizational structure of the ACSR, its types of specimens in its inventory, and the process of requesting specimens. In addition, the review provides an overview of research that was performed over the last 5 years with its support and gives a summary of important new findings acquired by this research into the development of cancers in people with HIV, including both Aids-related and non-Aids-related malignancies.
Topics: Humans; HIV Infections; Neoplasms; Acquired Immunodeficiency Syndrome
PubMed: 37641153
DOI: 10.1186/s12981-023-00558-4 -
The Journal of Infectious Diseases Nov 2023Adding additional specimen types (eg, serology or sputum) to nasopharyngeal swab (NPS) reverse transcription polymerase chain reaction (RT-PCR) increases respiratory... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Adding additional specimen types (eg, serology or sputum) to nasopharyngeal swab (NPS) reverse transcription polymerase chain reaction (RT-PCR) increases respiratory syncytial virus (RSV) detection among adults. We assessed if a similar increase occurs in children and quantified underascertainment associated with diagnostic testing.
METHODS
We searched databases for studies involving RSV detection in persons <18 years using ≥2 specimen types or tests. We assessed study quality using a validated checklist. We pooled detection rates by specimen and diagnostic tests and quantified performance.
RESULTS
We included 157 studies. Added testing of additional specimens to NP aspirate (NPA), NPS, and/or nasal swab (NS) RT-PCR resulted in statistically nonsignificant increases in RSV detection. Adding paired serology testing increased RSV detection by 10%, NS by 8%, oropharyngeal swabs by 5%, and NPS by 1%. Compared to RT-PCR, direct fluorescence antibody tests, viral culture, and rapid antigen tests were 87%, 76%, and 74% sensitive, respectively (pooled specificities all ≥98%). Pooled sensitivity of multiplex versus singleplex RT-PCR was 96%.
CONCLUSIONS
RT-PCR was the most sensitive pediatric RSV diagnostic test. Adding multiple specimens did not substantially increase RSV detection, but even small proportional increases could result in meaningful changes in burden estimates. The synergistic effect of adding multiple specimens should be evaluated.
Topics: Adult; Child; Humans; Respiratory Syncytial Virus Infections; Sensitivity and Specificity; Respiratory Syncytial Virus, Human; Viruses; Diagnostic Techniques and Procedures; Nasopharynx; Reverse Transcriptase Polymerase Chain Reaction
PubMed: 37285396
DOI: 10.1093/infdis/jiad185 -
Radiography (London, England : 1995) Oct 2023The porcine model shows structural features comparable to that of humans and are routinely used within research, due to the ethical, legal, and practical use of...
INTRODUCTION
The porcine model shows structural features comparable to that of humans and are routinely used within research, due to the ethical, legal, and practical use of post-mortem human samples. Methods for obtaining high quality and comparable reference data using standardised acquisition protocols are essential.
METHODS
The decapitated heads of three adult white sows were subjected to radiographic imaging before and after cranial trauma (9 mm, Heckler and Koch MP5). Digital radiographs were generated using a Siemens MULTIX TOP system with an Agfa digital detector, with foam blocks and sandbags as ancillary equipment. An iterative approach was adopted by the authors to generate reproducible radiographic views from two perpendicular angles. Specimens were kept at 5 °C and wrapped in polythene bags to reduce the impact of putrefaction.
RESULTS
Standardised head radiography technique was developed for superior-inferior and lateral views demonstrating porcine anatomy. Key parameters included: automatic exposure control for tube current (∼4 mAs), tube voltage of 73 kVp, 100 cm source to image receptor distance, and an anti-scatter grid. Slight variances in specimen morphology, developmental status, and soft tissue changes did not affect imaging outcomes.
CONCLUSION
The technique and positioning proposed in this study allows for the acquisition of high quality and reproducible radiographic images for comparable ballistic research datasets. Specimen positioning and centring of the primary beam may be applied across porcine breeds, although individual radiographic parameters may differ according to equipment specifications and specimen size.
IMPLICATIONS FOR PRACTICE
Development of a reproducible radiographic technique of porcine heads in forensic and veterinary research.
Topics: Adult; Humans; Swine; Animals; Female; Radiographic Image Enhancement; Phantoms, Imaging; Radiography
PubMed: 37595528
DOI: 10.1016/j.radi.2023.08.001 -
Indian Journal of Cancer Oct 2023Histopathological examination of appendectomy specimens may reveal malignancies. Based on these results, either appendectomy is sufficient or sometimes a further...
BACKGROUND
Histopathological examination of appendectomy specimens may reveal malignancies. Based on these results, either appendectomy is sufficient or sometimes a further treatment protocol can be needed. In this study, malignancy-diagnosed cases on appendectomy specimen were examined.
METHODS
Patients who underwent appendectomy between January 2013 and December 2018 with a pre-diagnosis of acute appendicitis were evaluated retrospectively and those cases with malignancy were included in the study. Patients' age, sex, tumor type, tumor diameter, tumor grade, tumor localization, surgical margin, Ki-67 index, state of lymphovascular invasion, state of peri-neural invasion, and follow-up period duration were recorded.
RESULTS
On examination of 2336 appendectomy specimens, 16 patients (0.7%) were found to have neuroendocrine tumors (NET), 11 patients (0.5%) were found to have low-grade mucinous neoplasm (LAMN), and five patients (0.2%) were found to have primary appendix carcinomas. Appendix tumors usually present with acute appendicitis symptoms. Despite re-operation with right hemicolectomy (RHC) being required in the treatment of adenocarcinoma cases, appendectomy provides adequate treatment in most cases with NET and LAMN. With these tumors, which usually have a benign prognosis, it is important to perform the necessary screening in the postoperative period and not to interrupt follow-up.
Topics: Humans; Appendiceal Neoplasms; Appendicitis; Retrospective Studies; Appendectomy; Neuroendocrine Tumors
PubMed: 38159212
DOI: 10.4103/ijc.IJC_450_20 -
Emerging Infectious Diseases Jul 2023In 2008, bacilli from 2 Hansen disease (leprosy) cases were identified as a new species, Mycobacterium lepromatosis. We conducted a systematic review of studies...
In 2008, bacilli from 2 Hansen disease (leprosy) cases were identified as a new species, Mycobacterium lepromatosis. We conducted a systematic review of studies investigating M. lepromatosis as a cause of HD. Twenty-one case reports described 27 patients with PCR-confirmed M. lepromatosis infection (6 dual M. leprae/M. lepromatosis): 10 case-patients in the United States (7 originally from Mexico), 6 in Mexico, 3 in the Dominican Republic, 2 each in Singapore and Myanmar, and 1 each in Indonesia, Paraguay, Cuba, and Canada. Twelve specimen surveys reported 1,098 PCR-positive findings from 1,428 specimens, including M. lepromatosis in 44.9% (133/296) from Mexico, 3.8% (5/133) in Colombia, 12.5% (10/80) in Brazil, and 0.9% (2/224) from the Asia-Pacific region. Biases toward investigating M. lepromatosis as an agent in cases of diffuse lepromatous leprosy or from Mesoamerica precluded conclusions about clinicopathologic manifestations and geographic distribution. Current multidrug treatments seem effective for this infection.
Topics: Humans; Mycobacterium; Leprosy; Leprosy, Lepromatous; Mycobacterium leprae
PubMed: 37347507
DOI: 10.3201/eid2907.230024 -
Journal of Microbiology & Biology... Aug 2023Active learning tools, such as gamification, have facilitated teamwork and improved decision-making skills in Anatomy and Physiology classes. However, most Anatomy and...
Active learning tools, such as gamification, have facilitated teamwork and improved decision-making skills in Anatomy and Physiology classes. However, most Anatomy and Physiology labs currently contain dissection activities where students are not likely to engage in inquiry, critical thinking, or problem-solving. Usually, the instructor gives a brief lecture on the topic, and students are left to dissect without understanding how the lecture relates to what is in front of them, which is frustrating. Coupled with the frustration, some students have adverse opinions on dissecting specimens, including hesitation to dissect the specimen and religious or ethical concerns with dissection. Utilizing similar game mechanics to Taboo (Hasbro) and Milton Bradley's Operation, Incision Precision is a card game that was made to engage students in the dissection lab by allowing them to connect lecture-based information to a physical structure within an organ system. Each card contains an anatomical or physiological description of the organs commonly dissected in the undergraduate Anatomy and Physiology laboratory. For effective gameplay and full participation, the class should be divided into groups containing 3 to 4 students. The group will draw two cards where members can either correctly name the organ or identify the named organ on the dissected specimen. Playing Incision Precision resulted in participation from all group members during the dissection activity, including those with negative feelings about touching the dissected specimen. Due to positive student feedback, Incision Precision has been adapted and played with system-specific organ dissections.
PubMed: 37614876
DOI: 10.1128/jmbe.00193-22