Research Laboratory Research Articles

Laboratory success 101: how to excel in your first lab project

The majority of biochemistry research is based on wet laboratory experiments, yet undergraduate degrees strongly focus on the theoretical aspects of this discipline. The first lab project can be a significant learning curve for students, involving challenges in laboratory techniques, research reproducibility, consistency, resilience, and practical skills. Drawing from my experience in two research internships, a master’s project, and completing three rotations in a PhD program, I have outlined here valuable tips and advice to help undergraduates navigate this transition smoothly, enabling them to excel in their first lab project.

Predicting blood–brain barrier permeability of molecules with a large language model and machine learning

Predicting the blood–brain barrier (BBB) permeability of small-molecule compounds using a novel artificial intelligence platform is necessary for drug discovery. Machine learning and a large language model on artificial intelligence (AI) tools improve the accuracy and shorten the time for new drug development. The primary goal of this research is to develop artificial intelligence (AI) computing models and novel deep learning architectures capable of predicting whether molecules can permeate the human blood–brain barrier (BBB). The in silico (computational) and in vitro (experimental) results were validated by the Natural Products Research Laboratories (NPRL) at China Medical University Hospital (CMUH). The transformer-based MegaMolBART was used as the simplified molecular input line entry system (SMILES) encoder with an XGBoost classifier as an in silico method to check if a molecule could cross through the BBB. We used Morgan or Circular fingerprints to apply the Morgan algorithm to a set of atomic invariants as a baseline encoder also with an XGBoost classifier to compare the results. BBB permeability was assessed in vitro using three-dimensional (3D) human BBB spheroids (human brain microvascular endothelial cells, brain vascular pericytes, and astrocytes). Using multiple BBB databases, the results of the final in silico transformer and XGBoost model achieved an area under the receiver operating characteristic curve of 0.88 on the held-out test dataset. Temozolomide (TMZ) and 21 randomly selected BBB permeable compounds (Pred scores = 1, indicating BBB-permeable) from the NPRL penetrated human BBB spheroid cells. No evidence suggests that ferulic acid or five BBB-impermeable compounds (Pred scores < 1.29423E−05, which designate compounds that pass through the human BBB) can pass through the spheroid cells of the BBB. Our validation of in vitro experiments indicated that the in silico prediction of small-molecule permeation in the BBB model is accurate. Transformer-based models like MegaMolBART, leveraging the SMILES representations of molecules, show great promise for applications in new drug discovery. These models have the potential to accelerate the development of novel targeted treatments for disorders of the central nervous system.

An Integrated DAIDS Laboratory Oversight Framework: Application of the DAIDS GCLP Guidelines.

The Division of AIDS (DAIDS) Good Clinical Laboratory Practice (GCLP) Guidelines establish a framework to guide the oversight of laboratories supporting DAIDS-sponsored clinical research or trials. Compliance with these guidelines promotes data reliability, consistency, validity, and the safety of the clinical research or trial participants and laboratory staff, as well as ensures adherence to regulatory requirements. This article describes the application of the DAIDS GCLP Guidelines, the DAIDS Integrated Laboratory Oversight Framework, and the coordinated efforts of the collaborative oversight team of laboratory experts to support and monitor the performance of over 175 participating laboratories worldwide. Data from two self-administered online surveys conducted in 2017 and 2023 assessed the laboratory staff's experience implementing the GCLP Guidelines. The results of the 2017 survey were instrumental in informing changes to GCLP audit activities and promoting harmonization in the approach to laboratory oversight. A key finding from the 2023 survey results is the preference for hybrid GCLP training encompassing face-to-face and online modules. Overall, both surveys acknowledged satisfaction with applying and implementing GCLP Guidelines. The need to effectively disseminate information about DAIDS laboratory oversight requirements to support the improved implementation of GCLP Guidelines was notable from both survey results. The collaborative team of laboratory experts and the integrated oversight approach promote knowledge-sharing and accountability to support the application of the GCLP Guidelines and compliance monitoring. The systematic implementation of the integrated laboratory oversight activities helped identify valuable lessons for improving laboratory performance and opportunities to strengthen quality oversight for laboratories participating in clinical research or trials. .

Decarbonizing research laboratories? The tensions associated with the commensurability of carbon and how it opens up the boundaries of responsibility attribution

Decarbonizing research laboratories? The tensions associated with the commensurability of carbon and how it opens up the boundaries of responsibility attribution

Review of Pseudoloma neurophilia (Microsporidia): A common neural parasite of laboratory zebrafish (Danio rerio).

Zebrafish (Danio rerio) is now the second most used animal model in biomedical research. As with other vertebrate models, underlying diseases and infections often impact research. Beyond mortality and morbidity, these conditions can compromise research end points by producing nonprotocol induced variation within experiments. Pseudoloma neurophilia, a microsporidium that targets the central nervous system, is the most frequently diagnosed pathogen in zebrafish facilities. The parasite undergoes direct, horizontal transmission within populations, and is also maternally transmitted with spores in ovarian fluid and occasionally within eggs. This transmission explains the wide distribution among research laboratories as new lines are generally introduced as embryos. The infection is chronic, and fish apparently never recover following the initial infection. However, most fish do not exhibit outward clinical signs. Histologically, the parasite occurs as aggregates of spores throughout the midbrain and spinal cord and extends to nerve roots. It often elicits meninxitis, myositis, and myodegeneration when it infects the muscle. There are currently no described therapies for the parasite, thus the infection is best avoided by screening with PCR-based tests and removal of infected fish from a facility. Examples of research impacts include reduced fecundity, behavioral changes, transcriptome alterations, and autofluorescent lesions.

A project‐based learning mode for science students: Fluorescent protein expression in trypanosomes

AbstractAn effective, practical approach for incorporating molecular biology tools to biology and biochemistry students is described. For 6 weeks, students are exposed to bacterial transformation, plasmid DNA purification and analysis, parasite transfection, ectopic expression of fluorescent proteins, fluorescence microscopy, and flow cytometry analysis. This research‐oriented laboratory course delves into theoretical and practical concepts of basic techniques in molecular biology to emphasize the logical connections between the obtained results and the resolution of problems that arise daily in a research laboratory, training the students in planning, conducting, discussing, and presenting their own experiments and results.

Revolutionary Point-of-Care Wearable Diagnostics for Early Disease Detection and Biomarker Discovery through Intelligent Technologies.

Early-stage disease detection, particularly in Point-Of-Care (POC) wearable formats, assumes pivotal role in advancing healthcare services and precision-medicine. Public benefits of early detection extend beyond cost-effectively promoting healthcare outcomes, to also include reducing the risk of comorbid diseases. Technological advancements enabling POC biomarker recognition empower discovery of new markers for various health conditions. Integration of POC wearables for biomarker detection with intelligent frameworks represents ground-breaking innovations enabling automation of operations, conducting advanced large-scale data analysis, generating predictive models, and facilitating remote and guided clinical decision-making. These advancements substantially alleviate socioeconomic burdens, creating a paradigm shift in diagnostics, and revolutionizing medical assessments and technology development. This review explores critical topics and recent progress in development of 1) POC systems and wearable solutions for early disease detection and physiological monitoring, as well as 2) discussing current trends in adoption of smart technologies within clinical settings and in developing biological assays, and ultimately 3) exploring utilities of POC systems and smart platforms for biomarker discovery. Additionally, the review explores technology translationfrom research labs to broader applications. It also addresses associated risks, biases, and challenges of widespread Artificial Intelligence (AI) integration in diagnostics systems, while systematically outlining potential prospects, current challenges, and opportunities.

Predicting atrial fibrillation in comorbid patients with arterial hypertension and chronic obstructive pulmonary disease using laboratory research methods: a machine learning approach

Predicting atrial fibrillation in comorbid patients with arterial hypertension and chronic obstructive pulmonary disease using laboratory research methods: a machine learning approach

The Diagnostic Utility of Cervical Spine Proprioception for Adolescent Concussion.

Cervical spine proprioception may be impaired after concussion. Our objective was to determine the diagnostic utility of cervical spine proprioception for adolescent concussion. Cross-sectional. Research laboratory. Adolescents ≤18 days of concussion and uninjured controls. N/A. Head repositioning accuracy (HRA) testing, a measure of cervical spine proprioception. The HRA test involved patients relocating their head back to a neutral starting position with eyes closed after maximal cervical spine flexion, extension, and right and left rotations. The overall HRA error score was the mean error (distance from the starting point to self-reported return to neutral) across 12 trials: 3 trials in each direction. We used t-tests to compare group means and logistic regression (outcome = group, predictor = HRA, covariates) to calculate odds ratios. We used a receiver operator characteristic curve to evaluate area under the curve (AUC) and calculate the optimal HRA cutpoint to distinguish concussion from controls. We enrolled and tested 46 participants with concussion (age = 15.8 ± 1.3 years, 59% female, mean = 11.3 ± 3.3 days postconcussion) and 83 uninjured controls (age = 16.1 ± 1.4 years, 88% female). The concussion group had significantly worse HRA than controls (4.3 ± 1.6 vs 2.9 ± 0.7 degrees, P < 0.001, Cohen d = 1.19). The univariable HRA model AUC was 0.81 (95% CI = 0.73, 0.90). After adjusting for age, sex, and concussion history, the multivariable model AUC improved to 0.85 (95% CI = 0.77, 0.92). The model correctly classified 80% of participants as concussion/control at a 3.5-degree cutpoint. Adolescents with concussion demonstrated worse cervical spine proprioception than uninjured controls. Head repositioning accuracy may offer diagnostic utility for subacute concussion.

The impact of temperature on Ophthalmic Viscoelastic Devices and clinical implications - a pilot study: Temperature effect on Ophthalmic Viscoelastic Devices.

To evaluate how temperature impacts the rheology of common Ophthalmic Viscoelastic Devices (OVDs) and clinical implications. Tennent Institute of Ophthalmology, Glasgow, with Department of Mechanical and Aerospace Engineering, and Advanced Materials Research Laboratory, University of Strathclyde, Glasgow, UK. Laboratory pilot study. The viscous and elastic responses of three OVDs (Eyefill-SC/Eyefill-C/Eyefill-HD; Bausch & Lomb) were measured using rotational and extensional rheometers at clinically relevant temperatures (5°C, 25°C, 37°C). Thermal properties were evaluated using differential scanning calorimetry and laser-flash analysis. The OVDs tested exhibited viscoelastic properties and shear-thinning behaviour. Apparent viscosities and relaxation time were higher at lower temperatures. The Eyefill-C and Eyefill-SC exhibited predominantly viscous character at low frequencies with a transition to predominantly elastic behaviour at high frequencies. An increase in temperature led to a decrease in relaxation time under shear and extension. At low frequencies, Eyefill-C and Eyefill-SC moduli increase with decreasing temperatures. Eyefill-HD at 25°C and 37°C displays two cross-over points, with the storage modulus dominating at low and high frequencies indicating a predominantly elastic behaviour. Thermal property analysis revealed Eyefill-C had the lowest thermal conductivity. This pilot study confirms our clinical experience that OVD properties are affected by low temperatures, with increased viscosities at low shear rates and higher relaxation times.Cold OVD can cause greater resistance to initiation of IOL injection system forces (compared to warmer OVD). Excessively forced injection using cold OVD could contribute to inadvertent cannula detachment if incorrectly assembled, or uncontrolled IOL release leading to avoidable injury.

An Introduction to the Smart Urban Mobility Laboratory at University of South Florida [ITS Research Lab

An Introduction to the Smart Urban Mobility Laboratory at University of South Florida [ITS Research Lab

Effect of varying temperature increases on the microbial community of Pleistocene and Holocene permafrost

The total area covered by permafrost has been continually decreasing over the past decades. This study investigates the effect of various temperature increases on the microbiome of permafrost sampled at the Cold Regions Research and Engineering Laboratory (CRREL) Permafrost Tunnel site in Fox, Alaska, USA, corresponding to the Holocene (around 8,000 years before present (ybp)) and Pleistocene (around 36,000 ybp), respectively. The soil was subjected to two thawing time courses, with temperature increasing from -4°C to either +4°C or +25°C, and total nucleic acid was extracted at each time point. Consistent with previous 16S rRNA amplicon sequencing studies on the Permafrost Tunnel, the Pleistocene was dominated by Clostridia, while the Holocene was mainly composed of Clostridia, Bacteroidia and Alphaproteobacteria at -4°C. Thawing at +25°C resulted in divergent microbial profiles for permafrost of both ages, with the Pleistocene becoming more similar to the active layer, while the Holocene was relatively less impacted. Prediction of metabolic function revealed that bacteria from the Holocene permafrost activated degradation pathways upon thawing at +25°C, while bacteria from the Pleistocene were more involved in amino-acid biosynthesis pathways, suggesting different mechanisms of adaptation.

Effect of varying temperature increases on the microbial community of Pleistocene and Holocene permafrost

The total area covered by permafrost has been continually decreasing over the past decades. This study investigates the effect of various temperature increases on the microbiome of permafrost sampled at the Cold Regions Research and Engineering Laboratory (CRREL) Permafrost Tunnel site in Fox, Alaska, USA, corresponding to the Holocene (around 8,000 years before present (ybp)) and Pleistocene (around 36,000 ybp), respectively. The soil was subjected to two thawing time courses, with temperature increasing from -4°C to either +4°C or +25°C, and total nucleic acid was extracted at each time point. Consistent with previous 16S rRNA amplicon sequencing studies on the Permafrost Tunnel, the Pleistocene was dominated by Clostridia, while the Holocene was mainly composed of Clostridia, Bacteroidia and Alphaproteobacteria at -4°C. Thawing at +25°C resulted in divergent microbial profiles for permafrost of both ages, with the Pleistocene becoming more similar to the active layer, while the Holocene was relatively less impacted. Prediction of metabolic function revealed that bacteria from the Holocene permafrost activated degradation pathways upon thawing at +25°C, while bacteria from the Pleistocene were more involved in amino-acid biosynthesis pathways, suggesting different mechanisms of adaptation.

Mobile Media Content Exposure and Toddlers' Responses to Attention Prompts and Behavioral Requests.

With personalized touch-screen tablets, young children can choose content and engage in play-like activities. However, tablets may also reduce shared engagement as the action of viewing or touching the screen is often not visible to nearby adults. This may impact communicative gazing and pointing, which is critical to the formation of shared awareness and in turn supports language development. To assess the association of tablet media content with toddlers' responses to joint attention prompts and behavioral requests. This cohort study took place at a behavioral research laboratory and included toddlers who were aged 18 to 32 months with neurotypical development who were recruited from a volunteer and community sample. Toddlers engaged with a real toy or 3 different types of tablet content (ie, viewing video of toy play, playing with a digital toy, or playing a commercial game) while an experimenter delivered joint attention prompts. Data were acquired from June 2021 November XX 2022, and data analysis occurred from January 2023 to May 2024. Main outcomes included child response to joint attention (number of prompts with joint attention response per number of prompts delivered) and child response to behavioral request (ie, the prompt on which the child responded to the behavioral request). Measures included crossed random effects, Wald tests, and likelihood ratio tests. In this study, 63 toddlers were enrolled, and data from 62 were included (31 female [49%]; mean [SD] age, 26.1 [3.4] months; median [IQR] age, 25.0 [18.6-32.6] months). When toddlers were playing a commercial game on a tablet, they responded to fewer joint attention prompts (crossed random effects model, -0.15; 95% CI, -0.24 to -0.06 prompts) and male toddlers took longer to acknowledge a behavioral request (interaction of content and sex, -0.75; 95% CI, -1.36 to -0.17). The negative impact of the tablet game was larger as child age increased (τ = -2.30; 95% CI, -0.05 to 0; P = .03). Greater media use at home was associated with decreased responding to joint attention prompts during the tablet game (ρ = -0.47; P < .001), while better language skills were associated with more joint attention during play with a real toy (ρ = 0.31; P = .02). In this cohort study, a touch-screen tablet game was associated with decreased joint attention among toddlers and they were less likely to respond to a behavioral request. In a laboratory setting, it was difficult for toddlers to engage in social-communicative interactions with adults when using a tablet media device.

A Bead-Based Nonradioactive Immunoassay for Autoantibody Testing in a Mouse Model of Myasthenia Gravis

Serological testing for anti-acetylcholine receptor (AChR) autoantibodies is not only crucial for the diagnosing, disease monitoring, and treatment management of patients with myasthenia gravis (MG) but also for preclinical studies utilizing MG disease models. However, there are no specific guidelines on which methods to use in clinical diagnostic or research laboratories to detect or quantify any MG-specific autoantibodies. Conventional autoantibody assays, particularly those for anti-AChR antibodies, are varied and mostly laboratory-specific. Here, we report our new nonradioactive immunoprecipitation–immunoblotting method for assessing autoantibodies (anti-AChR antibodies) in a mouse model of MG. This simple, efficient, reproducible, and cost-effective assay appears superior to the enzyme-linked immunosorbent assay but comparable to the radioimmunoprecipitation or cell-based assay in specificity and sensitivity. Thus, the newly developed assay can serve as a valuable alternative to classical assays and is suitable for routine testing of AChR-specific autoantibodies in preclinical studies. The further optimization of our assay may facilitate its application in the diagnosis and therapeutic management of patients with MG.

The Bead Maze Hand Function Test for Children.

There is a need for a pediatric hand function test that can be used to objectively assess movement quality. We have developed a toy-based test, the Bead Maze Hand Function (BMHF) test, to quantify how well a child performs an activity. This is achieved by assessing the control of forces applied while drawing a bead over wires of different complexity. To study the psychometric properties of the BMHF test and understand the influence of age and task complexity on test measures. A cross-sectional, observational study performed in a single visit. Clinical research laboratory. Twenty-three participants (ages 4-15 yr) were recruited locally. They were typically developing children with no illness or conditions that affected their movement. Interventions/Assessments: Participants performed the BMHF test and the Box and Block test with both hands. Total force and completion time were examined according to age and task complexity using a linear mixed-effects model. We calculated intraclass correlation coefficients to measure interrater reliability of the method and estimated concurrent validity using the Box and Block test. Total force and completion time decreased with age and depended on task complexity. The total force was more sensitive to task complexity. The Box and Block score was associated with BMHF completion time but not with total force. We found excellent interrater reliability. A familiar toy equipped with hidden sensors provides a sensitive tool to assess a child's typical hand function. Plain-Language Summary: We developed the Bead Maze Hand Function (BMHF) test to determine how well a child performs an activity with their hands. The BMHF test is a toy equipped with hidden sensors. Twenty-three typically developing children with no illnesses or conditions that affected their hand movement participated in the study. We asked the children to perform the BMHF test with both hands. Our study found that occupational therapists can reliably use the BMHF test to assess a child's hand function.

In vitro evaluation of the mechanical and optical properties of 3D printed vs CAD/CAM milled denture teeth materials

This laboratory research aimed to assess the Flexural strength, fracture toughness, Volumetric wear and optical properties of various recent 3D-printed denture tooth materials and compare them to CAD/CAM milled materials. Four 3D-printed denture tooth materials (Lucitone Tooth, OnX, Flexcera Ultra +, and VarseoSmile Crown Plus) and one CAD/CAM milled denture teeth material (Ivotion Dent) were used to fabricate fifteen specimens for each material (with total no. of 300 specimens). Tests were conducted according to ISO standards to assess flexural strength, fracture toughness, color staining, and volumetric wear. All materials were printed, washed, cured, or milled following the manufacturer’s instructions. Flexural strength and fracture toughness values were obtained by a universal testing machine. Volumetric wear was evaluated using a non-contact optical profilometer. Color stability outcomes were obtained via a spectrophotometer for determining L*a*b* values, with color change (ΔE2000) based on the CIEDE2000 formula. Data were analyzed using one-way ANOVA and Tukey post-hoc analysis (α = 0.05). All 3D-printed materials exhibited higher flexural strength values than the milled material (p < 0.05). For fracture toughness, two of the 3D-printed materials showed higher values than the milled material, while the other two had lower values. Insignificant variances in volumetric wear were detected between the materials (p > 0.05). Color staining results varied, with milled materials generally demonstrating better-staining resistance compared to the 3D-printed materials. 3D-printed denture tooth materials exhibit good mechanical and optical properties, presenting a cost-effective and efficient alternative to CAD/CAM milled materials for denture tooth fabrication.

Evaluation of the Fertility Status of Rice Fields in Giri Jaya Village, Nagrak District, Sukabumi Regency

The research comprises three stages, which include: Field research, Laboratory research, encompassing the analysis of soil chemical properties. Data analysis, conducted both descriptively and quantitatively. Composite soil samples from rice fields were collected at three different elevations (top, middle, and bottom) at a depth of 1-20 cm in the surface layer of the rice field soil. Analysis of paddy soil samples involved measuring pH H2O using the electrometric method, total N, and cation exchange capacity (CEC) using the titrimetric method, potential K2O using the flame photometric method, potential P2O5 and organic C using the spectrophotometric method, K exchangeability and Na exchangeability using the flame photometric method, and Ca exchangeability and Mg exchangeability using the AAS method. Data obtained from soil analysis at different elevations were compared based on soil type for each observed parameter. The research results indicate that the evaluation of nutrient status is influenced by altitude. Land situated at lower elevations exhibits better soil fertility status, followed by land at the upper and middle elevations.

Генотипни различия в растежната активност на семената от сортове зимен ечемик

At the Institute of Agriculture - Karnobat, Bulgaria, laboratory research was conducted on 5 varieties of two-row and 5 varieties of multi-row winter barley. The aim of the research is to determine the genotypic differences in the initial growth of winter barley varieties. The varieties were studied in a laboratory experiment using the roll method. Number of indicators number of roots (number), length of roots (cm), length of the first leaf (cm) were recorded. 20 seeds of each variety were placed on filter paper in 3 replicates. The rolls are immersed in water and after 10 days the length of the first leaf, the number of roots and their length are counted. The results of the analysis show that Zahir and Alexan varieties form the largest number of roots. The Lardeya and Bozhin varieties form the smallest number of roots. The Kuber and Siela varieties have the longest root length and the first leaf. The varieties Zahir and Achinora have the smallest root length, and Lardea and Zemela have the smallest length of the first leaf. To improve the length of the first leaf, good combinations are expected when crossing the varieties Daria, Bozhin with Alexan, Achinora. Siela, Zemela, Alexan and Achinora varieties are genetically the most distant from Lardea, Kuber and Zahir in terms of length and number of roots. It is recommended to use them for crosses in order to create a better root system.

Identifying ice wedges in ground-penetrating radar data from the Cold Regions Research and Engineering Laboratory permafrost tunnel, Fox, Alaska

The warming of Alaska’s permafrost has been leading to thawing within its discontinuous permafrost. This can cause ice wedges to melt, resulting in thermokarst formations such as sinkholes and landslides, which are causing damage to Alaskan infrastructure. To avoid developing further infrastructure in areas containing ice wedges, it is necessary to improve methods of detecting subsurface ground ice. Ground-penetrating radar (GPR) is a nonintrusive remote sensing method of locating and characterizing permafrost and other subsurface features that are not evident on a cut face or surface. When applied to the detection of ice wedges at the Cold Regions Research and Engineering Laboratory permafrost tunnel in Fox, Alaska, a few identifying features have been observed which corresponded with prior research. We first use GPR reflections of areas along the tunnel walls holding known ice wedges to verify the identifying features of an ice wedge within GPR data. We use these reflections as test data to identify possible ice wedges in locations where they were not observed on the tunnel walls.