Modern Biomedical Research Research Articles

Parabolic maneuvers of the Swiss Air Force fighter jet F-5E as a research platform for cell culture experiments in microgravity

Long-term sensitivity of human cells to reduced gravity has been supposed since the first Apollo missions and was demonstrated during several space missions in the past. However, little information is available on primary and rapid gravi-responsive elements in mammalian cells. In search of rapid-responsive molecular alterations in mammalian cells, short-term microgravity provided by parabolic flight maneuvers is an ideal way to elucidate such initial and primary effects. Modern biomedical research at the cellular and molecular level requires frequent repetition of experiments that are usually performed in sequences of experiments and analyses. Therefore, a research platform on Earth providing frequent, easy and repeated access to real microgravity for cell culture experiments is strongly desired. For this reason, we developed a research platform onboard the military fighter jet aircraft Northrop F-5E “Tiger II”. The experimental system consists of a programmable and automatically operated system composed of six individual experiment modules, placed in the front compartment, which work completely independent of the aircraft systems. Signal transduction pathways in cultured human cells can be investigated after the addition of an activator solution at the onset of microgravity and a fixative or lysis buffer after termination of microgravity. Before the beginning of a regular military training flight, a parabolic maneuver was executed. After a 1 g control phase, the parabolic maneuver starts at 13,000 ft and at Mach 0.99 airspeed, where a 22 s climb with an acceleration of 2.5 g is initiated, following a free-fall ballistic Keplerian trajectory lasting 45 s with an apogee of 27,000 ft at Mach 0.4 airspeed. Temperature, pressure and acceleration are monitored constantly during the entire flight. Cells and activator solutions are kept at 37 °C during the entire experiment until the fixative has been added. The parabolic flight profile provides up to 45 s of microgravity at a quality of 0.05 g in all axes. Access time is 30 min before take-off; retrieval time is 30 min after landing. We conclude that using military fighter jets for microgravity research is a valuable tool for frequent and repeated cell culture experiments and therefore for state-of-the art method of biomedical research.

Exploring In Vitro/In Vivo Correlation: Lessons Learned from Analyzing Phase I Results of the US EPA's ToxCast Project

The research on alternative toxicological methods provides, among other things, a privileged viewpoint on one of the central issues of modern biomedical research—the relationship between (a) biological phenomena observed at the level of tissues and organisms and (b) their cellular and molecular bases as studied in isolated systems in vitro. The newly released ToxCast Phase 1 results, subject to initial analysis, converge with evidence from other fields (e.g., research on drug design with intensive use of omics technologies, traditional research on alternative tests) in indicating a low degree of the in vitro/in vivo correlation overall. In addition, this and other approaches point to the need for combining biological and chemical information in exploring the in vitro to in vivo connection.

Epigenetic modulation of host: new insights into immune evasion by viruses

Viruses have evolved with their hosts, which include all living species. This has been partly responsible for the development of highly advanced immune systems in the hosts. However, viruses too have evolved ways to regulate and evade the host's immune defence. In addition to mutational mechanisms that viruses employ to mimic the host genome and undergo latency to evade the host's recognition of the pathogen, they have also developed epigenetic mechanisms by which they can render the host's immune responses inactive to their antigens. The epigenetic regulation of gene expression is intrinsically active inside the host and is involved in regulating gene expression and cellular differentiation. Viral immune evasion strategies are an area of major concern in modern biomedical research. Immune evasion strategies may involve interference with the host antigen presentation machinery or host immune gene expression capabilities, and viruses, in these manners, introduce and propagate infection. The aim of this review is to elucidate the various epigenetic changes that viruses are capable of bringing about in their host in order to enhance their own survivability and pathogenesis.

Salinosporamide natural products: Potent 20 S proteasome inhibitors as promising cancer chemotherapeutics.

Proteasome inhibitors are rapidly evolving as potent treatment options in cancer therapy. One of the most promising drug candidates of this type is salinosporamide A from the bacterium Salinispora tropica. This marine natural product possesses a complex, densely functionalized γ-lactam-β-lactone pharmacophore, which is responsible for its irreversible binding to its target, the β subunit of the 20S proteasome. Salinosporamide A entered phase I clinical trials for the treatment of multiple myeloma only three years after its discovery. The strong biological activity and the challenging structure of this compound have fueled intense academic and industrial research in recent years, which has led to the development of more than ten syntheses, the elucidation of its biosynthetic pathway, and the generation of promising structure-activity relationships and oncological data. Salinosporamide A thus serves as an intriguing example of the successful interplay of modern drug discovery and biomedical research, medicinal chemistry and pharmacology, natural product synthesis and analysis, as well as biosynthesis and bioengineering.

A proteogenomic update to Yersinia: enhancing genome annotation

BackgroundModern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the time and effort that can be invested in genome annotation. The resulting gene set contains numerous errors in even the most basic form of annotation: the primary structure of the proteins.ResultsThe application of experimental proteomics data to genome annotation, called proteogenomics, can quickly and efficiently discover misannotations, yielding a more accurate and complete genome annotation. We present a comprehensive proteogenomic analysis of the plague bacterium, Yersinia pestis KIM. We discover non-annotated genes, correct protein boundaries, remove spuriously annotated ORFs, and make major advances towards accurate identification of signal peptides. Finally, we apply our data to 21 other Yersinia genomes, correcting and enhancing their annotations.ConclusionsIn total, 141 gene models were altered and have been updated in RefSeq and Genbank, which can be accessed seamlessly through any NCBI tool (e.g. blast) or downloaded directly. Along with the improved gene models we discover new, more accurate means of identifying signal peptides in proteomics data.

Male Mice Not Alone in Research

![Figure][1] CREDIT: COURTESY OF MIN LIU/UNIVERSITY OF CINCINNATI ACADEMIC HEALTH CENTER The NewsFocus story by C. Wald and C. Wu, “Of Mice and Women: The Bias in Animal models” (26 March, p. [1571][2]), is one-sided. We agree that the choice of animal model requires care and that extrapolating data from one sex to the other can be misleading. However, we disagree with their statement that researchers use predominantly male mice because they are “cheaper and easier to work with.” First, many factors influence the choice of research subject. The most obvious are inherent differences in behavior (males fight) and physiology (female hormonal fluctuations); cost (more animals cost more money); and the incidence of strain-specific disorders (such as cancer and epilepsy). Our collective experience is that many researchers select less aggressive females because they can be group-housed to save money. This female bias will persist indefinitely given financial constraints on basic biomedical research, especially in academic laboratories. Second, “best practice” by U.S. federal regulatory agencies and research institutes as well as industry already requires that animal data used to predict human responses be obtained from both sexes. Examples include analysis of genetically engineered animals for translational medicine ([ 1 ][3]) and preclinical studies to investigate chemical carcinogenicity ([ 2 ][4]) or to develop new drugs ([ 3 ][5]) and pesticides ([ 4 ][6]). Definitive information on the role of gender in human disease must be obtained in humans because of intrinsic interspecies physiological differences, but animal studies remain the essential foundation for designing rational human clinical trials. Contributing to the issue of identifying whether there is a male or female bias in modern biomedical research is the consistent failure of researchers to report the critical experimental details—age, sex, strain or stock (with correct nomenclature), animal source, husbandry conditions, and health status—that are necessary to interpret studies. Including experienced comparative pathologists as co-investigators or journal reviewers [such as those recruited through the Center for Genomic Pathology ( )] would substantially enhance study designs and the credibility of data acquisition, analysis, interpretation, and reporting. 1. [↵][7] 1. C. Brayton, 2. M. Justice, 3. C. A. Montgomery , Vet. Pathol. 38, 1 (2001). [OpenUrl][8][Abstract/FREE Full Text][9] 2. [↵][10] U.S. Department of Health and Human Services, National Toxicology Program, “Studies in genetically modified models” ( ). 3. [↵][11] U.S. Department of Health and Human Services, Food and Drug Administration (FDA), “Guidance for industry: S6 preclinical safety evaluation of biotechnology-derived pharmaceuticals” ([www.fda.gov/downloads/RegulatoryInformation/Guidances/UCM129171.pdf][12]). 4. [↵][13] U.S. Environmental Protection Agency (EPA), Chemical Safety and Pollution Prevention, OCSPP Harmonized Test Guidelines ( ). [1]: pending:yes [2]: /lookup/doi/10.1126/science.327.5973.1571 [3]: #ref-1 [4]: #ref-2 [5]: #ref-3 [6]: #ref-4 [7]: #xref-ref-1-1 View reference 1 in text [8]: {openurl}?query=rft.jtitle%253DVeterinary%2BPathology%26rft.stitle%253DVeterinary%2BPathology%26rft.issn%253D0300-9858%26rft.aulast%253DBrayton%26rft.auinit1%253DC.%26rft.volume%253D38%26rft.issue%253D1%26rft.spage%253D1%26rft.epage%253D19%26rft.atitle%253DEvaluating%2BMutant%2BMice%253A%2BAnatomic%2BPathology%26rft_id%253Dinfo%253Adoi%252F10.1354%252Fvp.38-1-1%26rft_id%253Dinfo%253Apmid%252F11199155%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [9]: /lookup/ijlink/YTozOntzOjQ6InBhdGgiO3M6MTQ6Ii9sb29rdXAvaWpsaW5rIjtzOjU6InF1ZXJ5IjthOjQ6e3M6ODoibGlua1R5cGUiO3M6NDoiQUJTVCI7czoxMToiam91cm5hbENvZGUiO3M6NToic3B2ZXQiO3M6NToicmVzaWQiO3M6NjoiMzgvMS8xIjtzOjQ6ImF0b20iO3M6MjU6Ii9zY2kvMzI4LzU5ODIvMTEwMy4xLmF0b20iO31zOjg6ImZyYWdtZW50IjtzOjA6IiI7fQ== [10]: #xref-ref-2-1 View reference 2 in text [11]: #xref-ref-3-1 View reference 3 in text [12]: http://www.fda.gov/downloads/RegulatoryInformation/Guidances/UCM129171.pdf [13]: #xref-ref-4-1 View reference 4 in text

Next generation sequencing in functional genomics

Genome-wide sequencing has enabled modern biomedical research to relate more and more events in healthy as well as disease-affected cells and tissues to the genomic sequence. Now next generation sequencing (NGS) extends that reach into multiple almost complete genomes of the same species, revealing more and more details about how individual genomes as well as individual aspects of their regulation differ from each other. The inclusion of NGS-based transcriptome sequencing, chromatin-immunoprecipitation (ChIP) of transcription factor binding and epigenetic analyses (usually based on DNA methylation or histone modification ChIP) completes the picture with unprecedented resolution enabling the detection of even subtle differences such as alternative splicing of individual exons. Functional genomics aims at the elucidation of the molecular basis of biological functions and requires analyses that go far beyond the primary analysis of the reads such as mapping to a genome template sequence. The various and complex interactions between the genome, gene products and metabolites define biological function, which necessitates inclusion of results other than sequence tags in quite elaborative approaches. However, the extra efforts pay off in revealing mechanisms as well as providing the foundation for new strategies in systems biology and personalized medicine. This review emphasizes the particular contribution NGS-based technologies make to functional genomics research with a special focus on gene regulation by transcription factor binding sites.

Cyclopamine and Hedgehog Signaling: Chemistry, Biology, Medical Perspectives

When Odysseus left the devastated city of Troy after ten years of siege he could not foresee the perils he still had to face. The encounter with the cyclops, a giant with only one eye placed in the middle of its forehead, was doubtlessly one of the creepiest and most dangerous of his adventures. In the end, Odysseus could only escape with the help of a sheep. Whether Homers cyclops was inspired by the observation of terribly malformed neonates remains speculative. However, when sheep herders in Idaho in the middle of the 20th century faced an increasing number of cyclops-like sheep in their herds, a unique cascade of chemical, biological, and medicinal discoveries was initiated. This Minireview tells this story and shows its impact on modern biomedical research.

Human biospecimens collection in the era of Personalized Medicine: challenges and perspectives

Why do we need your tissues? Modern biomedical research requires use of clinically characterized, high‐quality human biospecimens yielding high‐integrity analytes for development of novel medicines and companion diagnostic tests, biomarker assay development and, overall, achieving the goals of the personalized medicine. Effects of most important pre‐analytical biospecimen variables, significantly confounding human tissue research will be discussed: tissue collection specifications, processing materials and methods, storage and shipping procedures, molecular analyte preparation techniques, etc. Other issues include: collection of biospecimens using standard protocols versus project‐based collection protocols; using currently available biorepositories for future studies on the indicated subject; relevant regulatory and legal issues, including international disparities in regulations on using human materials for biomedical research.

Polymer-assisted nanoparticulate contrast-enhancing materials

The application of nanotechnology in medicine research has significant potential in modern biomedical research, disease diagnosis and therapy. Organic fluorophore-based detection techniques have been widely used as imaging and signal transduction tools for the detection of trace levels of analytes. The photosensitivity of the fluorophores, however, limits their application in such complex environments as living bio-systems where degradation or photobleaching occurs. Inorganic nanoparticles have unique and stable optical, electrical, magnetic and catalytic properties because of their various shapes, sizes and compositions. The potential of the nanoparticles as novel imaging agents has been studied as a possible solution to this problem. Surface modification of inorganic nanoparticles could enhance their biostability in physiological conditions and ability of targeting bioactive molecules.

Cell Uptake of Nanoparticles

Nanotechnology, the area of study involving nanoparticles, century; medical fields. The nanotechnology is one of the fastest growing sectors of the high-tech economy in the 21st industry, it is currently undergoing unprecedented development in nowadays especially in areas of biological research for clinical, environmental and life science applications. The most frequently used nanoparticles are superparamagnetic iron oxide (SPIO) nanoparticles and semiconductor quantum dots (QDs). SPIO nanoparticles with nanometer sizes and superparamagnetic properties are widely used for labeling and sorting cells or organelles, magnetic resonance imaging, targeted drug delivery, and hyperthermia. QDs combined the unique size-dependent physical properties, excellent chemical and photochemical stability, controlled and increased endocytosis, enhanced cooperative binding activity, and easy introduction of multi-functionality for targeted delivery and imaging, and became the most promising labeling tool for life science studies. Both types of nanomaterials provide special approaches for complex studies and play very important roles in modern biomedical research. However, non-specific uptake of QDs and SPIO nanoparticles is a major concern because it can lead to false positives or false results. Hence, we report cellular uptake studies on SPIO nanoparticles and QDs conducted on breast cancer cell line SK-BR3. The results show that both QDs and SPIO nanoparticles have very strong non-specific cellular uptake. With specially designed blocking buffer (BBB) the non-specific signals were significantly decreased.

Mammalian Target of Rapamycin Signaling and Autophagy: Roles in Lymphangioleiomyomatosis Therapy

The pace of progress in lymphangioleiomyomatosis (LAM) is remarkable. In the year 2000, TSC2 gene mutations were found in LAM cells; in 2001 the tuberous sclerosis complex (TSC) genes were discovered to regulate cell size in Drosophila via the kinase TOR (target of rapamycin); and in 2008 the results were published of a clinical trial of rapamycin, a specific inhibitor of TOR, in patients with TSC and LAM with renal angiomyolipomas. This interval of just 8 years between a genetic discovery for which the relevant signaling pathway was as yet unknown, to the initiation, completion, and publication of a clinical trial, is an almost unparalleled accomplishment in modern biomedical research. This robust foundation of basic, translational, and clinical research in TOR, TSC, and LAM is now poised to optimize and validate effective therapeutic strategies for LAM. An immediate challenge is to deduce the mechanisms underlying the partial response of renal angiomyolipomas to rapamycin, and thereby guide the design of combinatorial approaches. TOR complex 1 (TORC1), which is known to be active in LAM cells, is a key inhibitor of autophagy. One hypothesis, which will be explored here, is that low levels of autophagy in TSC2-null LAM cells limits their survival under conditions of bioenergetic stress. A corollary of this hypothesis is that rapamycin, by inducing autophagy, promotes the survival of LAM cells, while simultaneously arresting their growth. If this hypothesis proves to be correct, then combining TORC1 inhibition with autophagy inhibition may represent an effective clinical strategy for LAM.

Facilities available for biomedical science research in the public universities in Lagos, Nigeria

Across the world, basic medical scientists and physician scientists work on common platforms in state-of-the-arts laboratories doing translational research that occasionally results in bedside application. Biotechnology industries capitalise on useful findings for colossal profit.1 In Nigeria and the rest of Africa, biomedical science has not thrived and the contribution of publications to global high impact journals is low.2 This work investigated facilities available for modern biomedical research in Lagos public universities to extract culprit factors. The two public universities in Lagos, Nigeria were investigated by a cross sectional questionnaire survey of the technical staff manning biomedical science departments. They were asked about availability of 47 modern biomedical science research laboratory components such as cold room and microscopes and six research administration components such as director of research and grants administration. For convenient basic laboratory components such as autoclaves and balances, 50% responses indicated "well maintained and always functional" whereas for less convenient complex, high maintenance, state-of-the-arts equipment 19% responses indicated "well maintained and always functional." Respondents indicated that components of modern biomedical science research administration were 44% of expectation. The survey reveal a deficit in state-of the-arts research equipment and also a deficit in high maintenance, expensive equipment indicating that biomedical science in the investigated environment lacks the momentum of global trends and also lacks buoyant funding. In addition, administration supporting biomedical science is below expectation and may also account for the low contributions of research articles to global high impact journals.

Noninvasive <em>In Vivo</em> Small Animal MRI and MRS: Basic Experimental Procedures

Small animal Magnetic Resonance (MR) research has emerged as an important element of modern biomedical research due to its non-invasive nature and the richness of biological information it provides. MR does not require any ionizing radiation and can noninvasively provide higher resolution and better signal-to-noise ratio in comparison to other tomographic or spectroscopic modalities. In this protocol, we will focus on small animal MR imaging and MR spectroscopy (MRI/MRS) to noninvasively acquire relaxation weighted 1H images of mouse and to obtain 31P spectra of mouse muscle. This work does not attempt to cover every aspect of small animal MRI/MRS but rather introduces basic procedures of mouse MRI/MRS experiments. The main goal of this work is to inform researchers of the basic procedures for in vivo MR experiments on small animals. The goal is to provide a better understanding of basic experimental procedures to allow researchers new to the MR field to better plan for non-MR components of their studies so that both MR and non-MR procedures are seamlessly integrated.

Noninvasive <em>In Vivo</em> Small Animal MRI and MRS: Basic Experimental Procedures

Small animal Magnetic Resonance (MR) research has emerged as an important element of modern biomedical research due to its non-invasive nature and the richness of biological information it provides. MR does not require any ionizing radiation and can noninvasively provide higher resolution and better signal-to-noise ratio in comparison to other tomographic or spectroscopic modalities. In this protocol, we will focus on small animal MR imaging and MR spectroscopy (MRI/MRS) to noninvasively acquire relaxation weighted (1)H images of mouse and to obtain (31)P spectra of mouse muscle. This work does not attempt to cover every aspect of small animal MRI/MRS but rather introduces basic procedures of mouse MRI/MRS experiments. The main goal of this work is to inform researchers of the basic procedures for in vivo MR experiments on small animals. The goal is to provide a better understanding of basic experimental procedures to allow researchers new to the MR field to better plan for non-MR components of their studies so that both MR and non-MR procedures are seamlessly integrated.

A Novel Dual-Core Architecture for the Analysis of DNA Microarray Images

A deoxyribonucleic acid (DNA) microarray is a collection of microscopic DNA spots attached to a solid surface, such as a glass, plastic, or silicon chip forming an array. DNA microarray technologies are an essential part of modern biomedical research. DNA microarray allows compressing hundreds of thousands of different DNA nucleotide sequences in a little microscope glass and permits having all this information on a single image. The analysis of DNA microarray images allows the identification of gene expressions to draw biological conclusions for applications ranging from genetic profiling to diagnosis of cancer. Unfortunately, DNA microarray technology has a high variation of data quality. Therefore, to obtain reliable results, complex and extensive image analysis algorithms should be applied before the actual DNA microarray information can be used for biomedical purposes. In this paper, we present a novel hardware architecture that is specifically designed to analyze DNA microarray images. The architecture is based on a dual-core system that implements several units working in a single-instruction/multiple-data fashion. A field-programmable-gate-array (FPGA)-based prototypal implementation of the proposed architecture is presented. The effectiveness of the novel dual-core architecture is demonstrated by several analyses performed on original DNA microarray images, showing that the capability of detecting DNA spots increases by more than the 30% with respect to that of previously developed software techniques.

Lineage-specific biology revealed by a finished genome assembly of the mouse.

Author SummaryThe availability of an accurate genome sequence provides the bedrock upon which modern biomedical research is based. Here we describe a high-quality assembly, Build 36, of the mouse genome. This assembly was put together by aligning overlapping individual clones representing parts of the genome, and it provides a more complete picture than previous assemblies, because it adds much rodent-specific sequence that was previously unavailable. The addition of these sequences provides insight into both the genomic architecture and the gene complement of the mouse. In particular, it highlights recent gene duplications and the expansion of certain gene families during rodent evolution. An improved understanding of the mouse genome and thus mouse biology will enhance the utility of the mouse as a model for human disease.

The MurC Ligase Essential for Peptidoglycan Biosynthesis Is Regulated by the Serine/Threonine Protein Kinase PknA in Corynebacterium glutamicum

The Mur ligases play an essential role in the biosynthesis of bacterial cell-wall peptidoglycan and thus represent attractive targets for the design of novel antibacterials. These enzymes catalyze the stepwise formation of the peptide moiety of the peptidoglycan disaccharide peptide monomer unit. MurC is responsible of the addition of the first residue (L-alanine) onto the nucleotide precursor UDP-MurNAc. Phosphorylation of proteins by Ser/Thr protein kinases has recently emerged as a major physiological mechanism of regulation in prokaryotes. Herein, the hypothesis of a phosphorylation-dependent mechanism of regulation of the MurC activity was investigated in Corynebacterium glutamicum. We showed that MurC was phosphorylated in vitro by the PknA protein kinase. An analysis of the phosphoamino acid content indicated that phosphorylation exclusively occurred on threonine residues. Six phosphoacceptor residues were identified by mass spectrometry analysis, and we confirmed that mutagenesis to alanine residues totally abolished PknA-dependent phosphorylation of MurC. In vitro and in vivo ligase activity assays showed that the catalytic activity of MurC was impaired following mutation of these threonine residues. Further in vitro assays revealed that the activity of the MurC-phosphorylated isoform was severely decreased compared with the non-phosphorylated protein. To our knowledge, this is the first demonstration of a MurC ligase phosphorylation in vitro. The finding that phosphorylation is correlated with a decrease in MurC enzymatic activity could have significant consequences in the regulation of peptidoglycan biosynthesis.

A transgenic mouse model for “lipid hang-up”, or why pathologists need to be involved in genetically engineered mouse modelling

Current technology can be used to knock out specific genes in the offspring of mice, to knock in genes with specific mutations, to selectively silence or express gene products in...

The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and Their Assemblies Using Mass Spectrometry-Based Approaches

Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research laboratory or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a Web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of this is to not only provide a common data sharing and archiving system, but also to assist in the building of new collaborations and to spur the development of new tools and technologies.