Life Science Disciplines Research Articles

Sample Treatment for Tissue Proteomics in Cancer, Toxicology, and Forensics.

Since the birth of proteomics science in the 1990, the number of applications and of sample preparation methods has grown exponentially, making a huge contribution to the knowledge in life science disciplines. Continuous improvements in the sample treatment strategies unlock and reveal the fine details of disease mechanisms, drug potency, and toxicity as well as enable new disciplines to be investigated such as forensic science.This chapter will cover the most recent developments in sample preparation strategies for tissue proteomics in three areas, namely, cancer, toxicology, and forensics, thus also demonstrating breath of application within the domain of health and well-being, pharmaceuticals, and secure societies.In particular, in the area of cancer (human tumor biomarkers), the most efficient and multi-informative proteomic strategies will be covered in relation to the subsequent application of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and liquid extraction surface analysis (LESA), due to their ability to provide molecular localization of tumor biomarkers albeit with different spatial resolution.With respect to toxicology, methodologies applied in toxicoproteomics will be illustrated with examples from its use in two important areas: the study of drug-induced liver injury (DILI) and studies of effects of chemical and environmental insults on skin, i.e., the effects of irritants, sensitizers, and ionizing radiation. Within this chapter, mainly tissue proteomics sample preparation methods for LC-MS/MS analysis will be discussed as (i) the use of LC-MS/MS is majorly represented in the research efforts of the bioanalytical community in this area and (ii) LC-MS/MS still is the gold standard for quantification studies.Finally, the use of proteomics will also be discussed in forensic science with respect to the information that can be recovered from blood and fingerprint evidence which are commonly encountered at the scene of the crime. The application of proteomic strategies for the analysis of blood and fingerprints is novel and proteomic preparation methods will be reported in relation to the subsequent use of mass spectrometry without any hyphenation. While generally yielding more information, hyphenated methods are often more laborious and time-consuming; since forensic investigations need quick turnaround, without compromising validity of the information, the prospect to develop methods for the application of quick forensic mass spectrometry techniques such as MALDI-MS (in imaging or profiling mode) is of great interest.

The Chemistry Connections Challenge: Encouraging Students To Connect Course Concepts with Real-World Applications

A thought-provoking activity called the “Chemistry Connections Challenge” (CCC) has been introduced to an introductory organic chemistry course as a method of highlighting the real-world applications of course content. Identifying how course material can be utilized in the world around them may be difficult for students in introductory organic chemistry courses, particularly those geared toward life science disciplines. This activity was created as a means to improve student attitudes toward organic chemistry by encouraging them to explore how course content is applied to nature, research, and everyday life. In preparation for the activity, students are exposed to several instructor-generated “Chemistry Connections” slides shown in class during the first 4 weeks of the semester. Then, students are invited to create their own slide as part of the “Chemistry Connections Challenge” activity. As students complete the activity they engage with the course material in a meaningful way which can stimulate new way...

Usefulness of Ejournals Consortium in Pakistan: Academic Staff’s Perceptions and Expectations

This study aimed to investigate academic staff’s perceived usefulness and expectations regarding accessibility of the Higher Education Commission (HEC) consortium of ejournals at the University of the Punjab. The oldest and largest university in Pakistan, the University of the Punjab was selected as a sample for a self-administered questionnaire-based survey. The results of the study indicated that the majority of the academic staff found HEC ejournals useful for their research tasks; these resources also improved their teaching experience. Academic staff (47%) also found core ejournals relevant to their subject through the consortium. Academic staff, mostly from the disciplines of life sciences, sciences, and engineering and technology, expressed their wish to expand subscription to even more ejournals specific to their discipline.

Selective Enrichment of Phosphopeptides and Phospholipids from Biological Matrixes on TiO2 Nanowire Arrays for Direct Molecular Characterization by Internal Extractive Electrospray Ionization Mass Spectrometry.

Rapid analysis of phosphopeptides and phospholipids in biological matrixes is of significant interest in multiple disciplines of life sciences. Herein, trace phospholipids in human plasma, whole blood, and undiluted human urine as well as phosphopeptides in protein digest were selectively captured on a homemade array of TiO2 nanowires for sensitive characterization by internal extractive electrospray ionization mass spectrometry (TiO2-iEESI-MS). Sequential release of captured chemicals from TiO2 array was achieved by tuning pH of the extraction solvent. A single sample analysis, including sample loading, chemical extraction and MS detection, was accomplished within 3 min. As far as the quantification of phospholipids, acceptable linearity ( R2 ≥ 0.9985) and relative standard deviations (RSDs ≤ 8.9%) were obtained within the range of 0.1-500 μg L-1 for LysoPC(14:0) and LysoPC(16:0) in raw urine samples. Limit of detection (LOD) ≤ 0.025 μg L-1 and recovery rates of 94.8-101.6% were obtained for these phospholipids. As far as the quantification of phosphopeptides, R2 ≥ 0.9994 and RSDs ≤ 9.2% within the range of 0.3-200 μg L-1 were obtained for two phosphopeptides in nonphosphopeptides mixtures. LODs ≤ 0.09 μg L-1 and recovery rates of 83.4-107.0% were obtained for these phosphopeptides. On the basis of the orthogonal partial least-squares discriminant analysis, TiO2-iEESI-MS patterns from the blood of 46 patients with ovarian cancer were confidently discriminated from the MS patterns of 46 healthy volunteers. Our results indicate the strong potential of TiO2-iEESI-MS approach for the selective detection of trace phosphopeptides and phospholipids in various biological matrixes with high sensitivity, high specificity, low sample consumption, and high throughput.

Health policies, a transdisciplinary field of study

Nowadays, proposing policies or recommendations regarding intervention requires recognizing that our health policies aim to resolve health conditions caused by extreme poverty and inequity in different styles and living conditions. It is necessary to unveil the interests of actors closer to efficiency than to health equity, in scenarios of inequality that are made evident through gradients in health among disadvantaged populations of our country. Health policy analyzes require integrating measurement, description and political participation with recognition policies in a health context, generating awareness of fundamental human rights and capabilities. The contributions of knowledge from different disciplines of life sciences or other sciences may show transdisciplinary fields of knowledge generation, training and applied research that seek to distance themselves from rational analysis. This is fundamental to emphasize cognitive, rhetorical and narrative factors that portray the dominant ideologies that make up a public health policy at different decision times. The construction of a transdisciplinary field of study in health policies would link critical approaches to understanding social justice based on emerging theories on recognition and skills in different spheres of social life. This could also be useful to investigate how health systems and social practices in health are constituted, as well as to understand study categories that express health inequities and allow for a methodological theoretical approach to emerging individual and collective health expressions such as chronic illness, violence, physical abuse, and social exclusion.

Obituary: Prof Johannes Joseph van Rood (1926‐2017)

Obituary: Prof Johannes Joseph van Rood (1926‐2017)

“ Metabolic Ride” - One Concept Evaluation Tool For Metabolic Biochemistry Teaching For Graduate Students In Biological Sciences And Related Areas.

Biochemistry subject in general has a high degree of difficulty and complexity. Therefore, application of playful and creative games as teaching methodology has spread in various disciplines of life sciences. "METABOLIC RIDE" board game is a conceptual and perceptual evaluation tool for metabolic biochemistry teaching, aiming to review concepts transmitted in classroom, promoting a competitive challenge to students without denying tools that are at their disposal, stimulating their skills. OBJECTIVES. Correlate metabolic routes importance and their interconnections to establish that metabolic pathways are interconnected, such as a railway map. MATERIAL AND METHODS. This game was developed based on a board game Ticket to Ride. Players purchase enzyme cards, which must be used to claim metabolic routes. The goal is to complete the route previously drawn to earn points and the player who builds the longest continuous route will also earn bonus points. In each turn, players can: buy more card, claim a route or pick up additional destination tickets. The game should be played in groups of 5 to 6 students in 6 to 8 groups. Previously there will be theoretical classes. The activity was designed to last 4 hours. Use of didatic books and internet by players are encouraged. RESULTS. This game proved to be an excellent tool for student’s complementary evaluation, which stimulated teamwork and competitiveness within classroom, which allowed to analyze student’s perception regarding metabolic subjects. On the other hand, for teacher and students participating in compulsory traineeship program this game demonstrated to students new ways to approach complex subjects in biochemistry using creativity. CONCLUSION: Overall, students had a good impression of “Metabolic Ride” game since it helped to secure and administer metabolism subject in a competitive and team work way.

Naturalistic Experimental Designs as Tools for Understanding the Role of Genes and the Environment in Prevention Research.

Before genetic approaches were applied in experimental studies with human populations, they were used by animal and plant breeders to observe, and experimentally manipulate, the role of genes and environment on specific phenotypic or behavioral outcomes. For obvious ethical reasons, the same level of experimental control is not possible in human populations. Nonetheless, there are natural experimental designs in human populations that can serve as logical extensions of the rigorous quantitative genetic experimental designs used by animal and plant researchers. Applying concepts such as cross-fostering and common garden rearing approaches from the life science discipline, we describe human designs that can serve as naturalistic proxies for the controlled quantitative genetic experiments facilitated in life sciences research. We present the prevention relevance of three such human designs: (1) children adopted at birth by parents to whom they are not genetically related (common garden approach); (2) sibling designs where one sibling is reared from birth with unrelated adoptive parents and the other sibling is reared from birth by the biological mother of the sibling pair (cross-fostering approach); and (3) in vitro fertilization designs, including egg donation, sperm donation, embryo donation, and surrogacy (prenatal cross-fostering approach). Each of these designs allows for differentiation of the effects of the prenatal and/or postnatal rearing environment from effects of genes shared between parent and child in naturalistic ways that can inform prevention efforts. Example findings from each design type are provided and conclusions drawn about the relevance of naturalistic genetic designs to prevention science.

REU Site: Bio-Grid Initiatives for interdisciplinary research and education

Recently more and more universities have been incorporating HPC (High Performance Computing) in their computing curriculum. The Bio-Grid REU (Research Experience for Undergraduates) Site offers undergraduate students interested or experienced in HPC a summer research opportunity to participate in projects that apply HPC in various life-science disciplines. The projects are associated with the Bio-Grid Initiatives conducted at the University of Connecticut. Training seminars are designed to equip students with background knowledge such as basic parallel programming, large-scale data analytics, and middleware support, etc., as well as some ongoing projects using these computing methods. Students participate in several collaborative projects supported by a campus-wide computational and data grid. The REU project introduces such interdisciplinary research work to students in the early stage of their academic career to spark their interest. The project aims at preparing future software engineers to formalize and solve emerging life-science problems, as well as life-science researchers with a strong background in high-performance computing. The Bio-Grid REU Site was supported by the National Science Foundation from 08–10 and 12–14, with a website located at http://biogrid.engr.uconn.edu/REU.

Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils.

The cavitation of gas bubbles in liquids has been applied to different disciplines in life and natural sciences, and in technologies. To obtain an appropriate theoretical description of effects induced by the bubble cavitation, we develop an all-atom nonequilibrium molecular-dynamics simulation method to simulate bubbles undergoing harmonic oscillation in size. This allows us to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects. The method is then employed to simulate an Aβ fibril model in the presence of bubbles, and the results show that the bubble expansion and contraction exert water pressure on the fibril. This yields to the deceleration and acceleration of the fibril kinetic energy, facilitating the conformational transition between local free energy minima, and leading to the dissociation of the fibril. Our work, which is a proof-of-concept, may open a new, efficient way to dissociate amyloid fibrils using the bubble cavitation technique, and new venues to investigate the complex phenomena associated with amyloidogenesis.

Graphics processing units in bioinformatics, computational biology and systems biology.

Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools.

Elementary teachers’ use of content knowledge to evaluate students’ thinking in the life sciences

ABSTRACTScience learning environments should provide opportunities for students to make sense of and enhance their understanding of disciplinary concepts. Teachers can support students’ sense-making by engaging and responding to their ideas through high-leverage instructional practices such as formative assessment (FA). However, past research has shown that teachers may not understand FA, how to implement it, or have sufficient content knowledge to use it effectively. Few studies have investigated how teachers gather information to evaluate students’ ideas or how content knowledge factors into those decisions, particularly within the life science discipline. We designed a study embedded in a multi-year professional development program that supported elementary teachers’ development of disciplinary knowledge and FA practices within science instruction. Study findings illustrate how elementary teachers’ life science content knowledge influences their evaluation of students’ ideas. Teachers with higher levels of life science content knowledge more effectively evaluated students’ ideas than teachers with lower levels of content knowledge. Teachers with higher content exam scores discussed both content and student understanding to a greater extent, and their analyses of students’ ideas were more scientifically accurate compared to teachers with lower scores. These findings contribute to theory and practice around science teacher education, professional development, and curriculum development.

Development of a structured undergraduate research experience: Framework and implications.

Participating in undergraduate research can be a pivotal experience for students in life science disciplines. Development of critical thinking skills, in addition to conveying scientific ideas in oral and written formats, is essential to ensuring that students develop a greater understanding of basic scientific knowledge and the research process. Modernizing the current life sciences research environment to accommodate the growing demand by students for experiential learning is needed. By developing and implementing a structured, theory-based approach to undergraduate research in the life sciences, specifically biochemistry, it has been successfully shown that more students can be provided with a high-quality, high-impact research experience. The structure of this approach allowed students to develop novel, independent projects in a computational molecular modeling lab. Students engaged in an experience in which career goals, problem-solving skills, time management skills, and independence in a research lab were developed. After experiencing this approach to undergraduate research, students reported feeling challenged to think critically and prepared for future career paths. The approach allowed for a progressive learning environment where more undergraduate students could participate in publishable research. Future areas for development include implementation in a bench-top lab and extension to disciplines beyond biochemistry. In this study, it has been shown that utilizing the structured approach to undergraduate research could allow for more students to experience undergraduate research and develop into more confident, independent life scientists well prepared for graduate schools and professional research environments. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(5):463-474, 2016.

Researchers’ Adoption of an Institutional Central Fund for Open-Access Article-Processing Charges

This article analyzes researchers’ adoption of an institutional central fund (or faculty publication fund) for open-access (OA) article-processing charges (APCs) to contribute to a wider understanding of take-up of OA journal publishing (“Gold” OA). Quantitative data, recording central fund usage at the University of Nottingham from 2006 to 2014, are analyzed alongside qualitative data from institutional documentation. The importance of the settings of U.K. national policy developments and international OA adoption trends are considered. Innovation Diffusion Theory (IDT) is used as an explanatory framework. It is shown that use of the central fund grew during the period from covering less than 1% of the University’s outputs to more than 12%. Health and Life Sciences disciplines made greatest use of the fund. Although highly variable, average APC prices rose during the period, with fully OA publishers setting lower average APCs. APCs were paid largely from internal funds, but external funding became increasingly important. Key factors in adoption are identified to be increasing awareness and changing perceptions of OA, communication, disciplinary differences, and adoption mandates. The study provides a detailed longitudinal analysis of one of the earliest central funds to be established globally with a theoretically informed explanatory model to inform future work on managing central funds and developing institutional and national OA policies.

Niche construction game cancer cells play.

Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.

The Traditional Training of PhDs Threatens the Technology Transfer and Entrepreneurship Pipeline While Innovative Programs Provide Unique Recovery Opportunities

The flaws in the training of PhDs in life science disciplines are impacting the state of academic biomedical science in the United States (U.S.) as well as the fate of PhD students and postdoctoral fellows. In the absence of sweeping changes to the U.S. graduate training model, these circumstances will degrade the pipeline of highly educated scientific innovators and entrepreneurs. To counter this, a wide range of unique programs are emerging with the objective of providing opportunities for PhDs to more easily transition into the job market, where they will be able to sustain and build innovation within the marketplace. In this article, we describe the current challenges faced by emerging PhDs in the life sciences, address the negative implications of the existing training paradigm, and introduce some of the unique programs that will help PhD trainees be better prepared for the non-academic career paths that they are likely to follow. PhDs from all disciplines are key contributors to the innovations that drive technology transfer and entrepreneurship. As such, graduate programs should serve as the common training grounds for these individuals to gain the subject matter expertise, research experience, and vision needed to develop scientific advancements for the benefit of society. Keywords: Careers, entrepreneurship, Innovative training programs, Jobs, PhD training, Research funding, Science PhD, Skill development.

Biologische Anwendungen aus dem Baukasten

Synthetic Biology is concerned with the deliberate design and construction of organisms with new, naturally not occurring functions. To this end, the young discipline combines the classical disciplines of theoretical and experimental life sciences with engineering approaches “to help make biology easy to engineer” [1]. Potential applications of new biological systems and products lie in the areas of industrial biotechnology and medicine.

The F1000Research Antibody Validation Article Collection

Well validated antibodies are crucial to progress in a wide range of life science disciplines, but validating an antibody is a complex and ongoing process. Antibody validation is often carried out as preliminary work to a larger study so the validation data may go unpublished and needless duplication of efforts can occur. This collection of articles in F1000Research provides a home for papers describing antibody validation studies. Our goal is to encourage publishing of all studies, both positive and negative, which increase understanding of how antibodies perform. These could range from large studies with thousands of antibodies to small single figure studies which validate an individual antibody for a specific purpose. Opinion or Correspondence articles considering any aspect of antibody validation are also welcome. Here, we provide an introduction to the collection which we hope will grow and become a valuable resource for the many thousands of researchers who use antibodies.

The F1000Research Antibody Validation Article Collection.

Well validated antibodies are crucial to progress in a wide range of life science disciplines, but validating an antibody is a complex and ongoing process. Antibody validation is often carried out as preliminary work to a larger study so the validation data may go unpublished and needless duplication of efforts can occur. This collection of articles in F1000Research provides a home for papers describing antibody validation studies. Our goal is to encourage publishing of all independent studies, both positive and negative, which increase understanding of how antibodies perform. These could range from large studies with thousands of antibodies to small single figure studies which validate an individual antibody for a specific purpose. Opinion or Correspondence articles considering any aspect of antibody validation are also welcome. Here, we provide an introduction to the collection which we hope will grow and become a valuable resource for the many thousands of researchers who use antibodies.

Immunological tools: engaging students in the use and analysis of flow cytometry and enzyme-linked immunosorbent assay (ELISA).

Flow cytometry and enzyme-linked immunosorbent assay (ELISA) are commonly used techniques associated with clinical and research applications within the immunology and medical fields. The use of these techniques is becoming increasingly valuable in many life science and engineering disciplines as well. Herein, we report the development and evaluation of a novel half-semester course that focused on introducing undergraduate and graduate students to advance conceptual and technical skills associated with flow cytometry and ELISA, with emphasis on applications, experimental design, and data analysis. This course was offered in the North Carolina State University Biotechnology Program over three semesters and consisted of weekly lectures and laboratories. Students performed and/or analyzed flow cytometry and ELISA in three separate laboratory exercises: (1) identification of transgenic zebrafish hematopoietic cells, (2) analysis of transfection efficiency, and (3) analysis of cytokine production upon lipopolysaccharide stimulation. Student learning outcomes were achieved as demonstrated by multiple means of assessment, including three laboratory reports, a data analysis laboratory practicum, and a cumulative final exam. Further, anonymous student self-assessment revealed increased student confidence in the knowledge and skill sets defined in the learning outcomes.