A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular mechanism of their choice. Data were collected from interviews, artifacts, and drawings, and then subjected to thematic analysis. We found that biologists explained the specific activities and organization of entities of the mechanism. In addition, they contextualized explanations according to their biological and social significance; integrated explanations with methods, instruments, and measurements; and used analogies and narrated stories. The derived methods, analogies, context, and how themes informed the development of our final MACH model of mechanistic explanations. Future research will test the potential of the MACH model as a guiding framework for instruction to enhance the quality of student explanations.     

Evaluation of Oxidative Stress and hsCRP in Polycystic Ovarian Syndrome in a Tertiary Care Hospital

PCOS is a heterogeneous endocrine disorder with diverse clinical presentation. Oxidative stress plays a key role in the pathophysiology of this disease. Serumhigh sensitive C-reactive protein (hsCRP), a marker of chronic low grade inflammation, is indicative of future development of cardiovascular disease. Our aim is to evaluate the oxidant status and hsCRP levels in PCOS. The study involved 61 cases and 61 controls in the age group of 18–40 years diagnosed with PCOS. Erythrocyte malondialdehyde (MDA), superoxide dismutase (SOD), serum hsCRP, gonadotrophins, thyroid stimulating hormone, prolactin, glycemic status and lipid profile were estimated. Erythrocyte MDA (p < 0.001), SOD (p = 0.007) and serum hsCRP (p < 0.001) were significantly elevated in PCOS patients than controls. Oxidative stress is present in women with PCOS along with elevated hsCRP.     

Association of Aberrations in One Carbon Metabolism with Intimal Medial Thickening in Patients with Type 2 Diabetes Mellitus

The present work was aimed to study the association of one carbon genetic variants, hyperhomocysteinemia and oxidative stress markers, i.e., serum nitrite, plasma malondialdehyde (MDA) and glutathione (GSH) on intimal medial thickening (IMT) in patients with type 2 diabetes mellitus (T2D). A total number of 76 subjects from ACS Medical College and Hospital, Chennai, India were included in the study, i.e., Group I (n = 42) of T2D and Group II (n = 34) of age- and sex matched healthy controls. The glycated haemoglobin was measured by ion-exchange resin method; plasma homocysteine by Enzyme Linked Immunosorbant Assay method; serum nitrite (nitric oxide, NO), plasma MDA and GSH by spectrophotometric methods; the IMT by high frequency ultrasound. The polymorphisms of one carbon genetic variants were genotyped using polymerase chain reaction-restriction fragment length polymorphism and amplified fragment length polymorphism methods. Results indicate that methyltetrahydrofolate homocysteine methyl transferase (MTR) A2756G allele was found to be protective in T2D and the other variants were not significantly associated with T2D. Glutamate carboxypeptidase II (GCP II) C1561T (r = 0.34; p = 0.05) and methylene tetrahydrofolate reductase (MTHFR) C677T (r = 0.35; 0.04) showed positive correlation with plasma homocysteine in T2D cases. In this study, MTR A2756G allele was found to be protective in T2D; GCP II C1561T and MTHFR C677T showed positive association with plasma homocysteine in T2D cases. Among all the genetic variants, MTR A2756G was found influence IMT. RFC 1 G80A and TYMS 5′-UTR 2R3R showed synergistically interact with MTR A2756G in influencing increase in IMT.     

Advances in urinary protein biomarkers for urogenital and non-urogenital pathologies

The discovery of protein biomarkers that reflect the biological state of the body is of vital importance to disease management. Urine is an ideal source of biomarkers that provides a non-invasive approach to diagnosis, prognosis and prediction of diseases. Consequently, the study of the human urinary proteome has increased dramatically over the last 10 years, with many studies being published. This review focuses on urinary protein biomarkers that have shown potential, in initial studies, for diseases affecting the urogenital tract, specifically chronic kidney disease and prostate cancer, as well as other non-urogenital pathologies such as breast cancer, diabetes, atherosclerosis and osteoarthritis. PubMed was searched for peer-reviewed literature on the subject, published in the last 10 years. The keywords used were “urine, biomarker, protein, and/or prostate cancer/breast cancer/chronic kidney disease/diabetes/atherosclerosis/osteoarthritis”. Original studies on the subject, as well as a small number of reviews, were analysed including the strengths and weaknesses, and we summarized the performance of biomarkers that demonstrated potential. One of the biggest challenges found is that biomarkers are often shared by several pathologies so are not specific to one disease. Therefore, the trend is shifting towards implementing a panel of biomarkers, which may increase specificity. Although there have been many advances in urinary proteomics, these have not resulted in similar advancements in clinical practice due to high costs and the lack of large data sets. In order to translate these potential biomarkers to clinical practice, vigorous validation is needed, with input from industry or large collaborative studies.Key words: urine, protein, biomarker     

Peer review: still king in the digital age

The article presents one of the main findings of an international study of 4,000 academic researchers that examined how trustworthiness is determined in the digital environment when it comes to scholarly reading, citing, and publishing. The study shows that peer review is still the most trustworthy characteristic of all. There is, though, a common perception that open access journals are not peer reviewed or do not have proper peer‐review systems. Researchers appear to have moved inexorably from a print‐based system to a digital system, but it has not significantly changed the way they decide what to trust. They do not trust social media. Only a minority – although significantly mostly young and early career researchers – thought that social media are anything other than more appropriate to personal interactions and peripheral to their professional/academic lives. There are other significant differences, according to the age of the researcher. Thus, in regard to choosing an outlet for publication of their work, young researchers are much less concerned with the fact that it is peer reviewed.     

Planning for the Budget-ocalypse: The Evolution of a Serials/ER Cancellation Methodology

The University of North Texas (UNT) Libraries are funded almost entirely by undergraduate student use fees. As the undergraduate enrollment has plateaued in recent years, the libraries have not been able to keep up with rising costs, resulting in a series of cuts to the materials budget totaling around $3.25 million. While some of these cuts took the form of reductions in firm orders and dissolution of approval plans, for the past three years the bulk has come from cancellations of serials and electronic resources. With each year’s cuts, the UNT Collection Development department has been forced to modify and refine their deselection process. This article will show the development of UNT’s strategy for determining cancellations using a variety of methods (overlap analysis, usage statistics, faculty input) and tools (EBSCO Usage Consolidation, Serials Solutions 360).     

Thermally multiplexed polymerase chain reaction

Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously—each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel.     

Enhanced single-cell printing by acoustophoretic cell focusing

Recent years have witnessed a strong trend towards analysis of single-cells. To access and handle single-cells, many new tools are needed and have partly been developed. Here, we present an improved version of a single-cell printer which is able to deliver individual single cells and beads encapsulated in free-flying picoliter droplets at a single-bead efficiency of 96% and with a throughput of more than 10 beads per minute. By integration of acoustophoretic focusing, the cells could be focused in x and y direction. This way, the cells were lined-up in front of a 40 μm nozzle, where they were analyzed individually by an optical system prior to printing. In agreement with acoustic simulations, the focusing of 10 μm beads and Raji cells has been achieved with an efficiency of 99% (beads) and 86% (Raji cells) to a 40 μm wide center region in the 1 mm wide microfluidic channel. This enabled improved optical analysis and reduced bead losses. The loss of beads that ended up in the waste (because printing them as single beads arrangements could not be ensured) was reduced from 52% ± 6% to 28% ± 1%. The piezoelectric transducer employed for cell focusing could be positioned on an outer part of the device, which proves the acoustophoretic focusing to be versatile and adaptable.     

Introducing novel approaches for examining the variability of individuals’ physical activity

Tudor-Locke and colleagues previously assessed steps/day for 1 year. The aim of this study was to use this data set to introduce a novel approach for the investigation of whether individual’s physical activity exhibits periodicity fluctuating round a mean and, if so, the degree of fluctuation and whether the mean changes over time. Twenty-three participants wore a pedometer for 365 days, recorded steps/day and whether the day was a workday. Fourier transform of each participant’s daily steps data showed the physical activity had a periodicity of 7 days in half of the participants, matching the periodicity of the workday pattern. Activity level remained stable in half of the participants, decreased in ten participants and increased in two. In conclusion, the 7-day periodicity of activity in half of the participants and correspondence with the workday pattern suggest a social or environmental influence. The novel analytical approach introduced herein allows the determination of the periodicity of activity, the degree of variability in activity that is tolerated during day-to-day life and whether the activity level is stable. Results from the use of these methodologies in larger data sets may enable a more focused approach to the design of interventions that aim to increase activity.