Biochemical Development Research Articles

Exploration of teaching reform of biochemistry for seven-year program clinical medical students

Biochemistry is an important basic medical course, and it is also a difficult course. In order to improve the comprehensive ability of seven-year program clinical medical students in Capital Medical University, teaching reform of Biochemistry was carried out. Teaching content was redesigned to strengthen the learning of basic knowledge of Biochemistry and to increase the depth of teaching content, while expanding the content by introducing new achievements and new technology to keep up with the forefront in the development of Biochemistry. Various methods such as the comparative method, case teaching and so on, were used flexibly in the teaching practice in order to improve teaching effects. The experiments carried out in the course were also redesigned and integrated, some distinctive experiments such as designing experiments, comprehensive experiments and innovative experiments were opened to improve students' hands-on ability and to cultivate students' scientific thinking. Key words: Biochemistry; Teaching reform; Seven-year program clinical medicine specialty

Developmental Changes for the Hemolymph Metabolome of Silkworm (Bombyx mori L.).

Silkworm (Bombyx mori) is a lepidopteran-holometabolic model organism. To understand its developmental biochemistry, we characterized the larval hemolymph metabonome from the third instar to prepupa stage using (1)H NMR spectroscopy whilst hemolymph fatty acid composition using GC-FID/MS. We unambiguously assigned more than 60 metabolites, among which tyrosine-o-β-glucuronide, mesaconate, homocarnosine, and picolinate were reported for the first time from the silkworm hemolymph. Phosphorylcholine was the most abundant metabolite in all developmental stages with exception for the periods before the third and fourth molting. We also found obvious developmental dependence for the hemolymph metabonome involving multiple pathways including protein biosyntheses, glycolysis, TCA cycle, the metabolisms of choline amino acids, fatty acids, purines, and pyrimidines. Most hemolymph amino acids had two elevations during the feeding period of the fourth instar and prepupa stage. Trehalose was the major blood sugar before day 8 of the fifth instar, whereas glucose became the major blood sugar after spinning. C16:0, C18:0 and its unsaturated forms were dominant fatty acids in hemolymph. The developmental changes of hemolymph metabonome were associated with dietary nutrient intakes, biosyntheses of cell membrane, pigments, proteins, and energy metabolism. These findings offered essential biochemistry information in terms of the dynamic metabolic changes during silkworm development.

Past achievements, current status and future perspectives of studies on 3-hydroxy-3-methylglutaryl-CoA synthase (HMGS) in the mevalonate (MVA) pathway

HMGS functions in phytosterol biosynthesis, development and stress responses. F-244 could specifically-inhibit HMGS in tobacco BY-2 cells and Brassica seedlings. An update on HMGS from higher plants is presented. 3-Hydroxy-3-methylglutaryl-coenzyme A synthase (HMGS) is the second enzyme in the mevalonate pathway of isoprenoid biosynthesis and catalyzes the condensation of acetoacetyl-CoA and acetyl-CoA to produce S-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). Besides HMG-CoA reductase (HMGR), HMGS is another key enzyme in the regulation of cholesterol and ketone bodies in mammals. In plants, it plays an important role in phytosterol biosynthesis. Here, we summarize the past investigations on eukaryotic HMGS with particular focus on plant HMGS, its enzymatic properties, gene expression, protein structure, and its current status of research in China. An update of the findings on HMGS from animals (human, rat, avian) to plants (Brassica juncea, Hevea brasiliensis, Arabidopsis thaliana) will be discussed. Current studies on HMGS have been vastly promoted by developments in biochemistry and molecular biology. Nonetheless, several limitations have been encountered, thus some novel advances in HMGS-related research that have recently emerged will be touched on.

Focus Areas for Computer Animation Development in Biochemistry for Ist Year MBBS Students

Background: Understanding complex molecular biochemical processes is crucial to Ist year MBBS students in solving clinical problems. Though animations have been developed to aid understanding of molecular processes, they are not medically relevant. There is a need to develop animations in specific areas that cater to the requirements of MBBS students. There are no studies that have recommended the focus areas for the development of medically relevant animations for biochemical processes for MBBS students. Objectives: In this study our objective was to select the focus areas for animation development in Biochemistry for the students of Ist year MBBS. Methods: The study was conducted in Department of Biochemistry MVJ Medical College & Research Hospital, Hoskote, Bangalore. Eight textbooks of Biochemistry commonly referred by Ist year MBBS students were used to delineate topics and sub topics that could become focus areas for animation development for the Ist year MBBS students. Results: The topics and subtopics that need animations in Biochemistry for Ist year MBBS were shortlisted. These include 18 topics and 52 subtopics. Conclusion: We recommend that medically relevant animations should be developed in specific focus areas of Biochemistry for the Ist year MBBS students to help in better understanding and application of Biochemistry in solving clinical problems.

Marker-Assisted Selection in Crop Plants

Plant kingdom, the base for every ecological pyramid, serves as a key source for food and evolution. Individualisation and analysis of genetic diversity and relatedness between or within different species, genera and population are the central task for many disciplines of biological science. Till recently, only the morphological traits/markers have been extensively used for this purpose. However, these morphological markers are often influenced by environment, which require special experimental designs to distinguish genotypic and phenotypic variation in a population. Later, the developments in biochemistry and molecular biology complemented many markers like protein, isozyme and DNA markers, which enable the breeders to overcome the limitations faced in the use of morphological markers. They show co-dominance (with exception of Random Amplified Polymorphic DNA (RAPD), mostly a dominant marker) so that all the genotypes can be classified, a large number of samples can be analysed, require only a limited quantity of plant tissue for analysing, thus eliminating the need for raising a large population in the field and one need not wait for the maturity of the plant. All living organisms are made up of cells that are programmed by genetic material called DNA. This molecule is made up of a long chain of nitrogen-containing bases (there are four different bases: adenine (A), cytosine (C), guanine (G) and thymine (T). Only a small fraction of the DNA sequence typically makes up genes, i.e., that code for protein, while the remaining and major share of the DNA represents non-coding sequences, the role of which is not yet clearly understood. The genetic material is organised into sets of chromosomes (e.g., five pairs in Arabidopsis thaliana; 30 pairs in Bos taurus (cow), and the entire set is called the genome. In a diploid individual (i.e., where chromosomes are organised in pairs), there are two alleles of every gene, one from each parent. Marker-assisted selection (MAS) is the breeding strategy in which selection for a gene is based on molecular markers closely linked to the gene of interest, rather than gene itself and the markers are used to monitor the incorporation of desirable allele from the donor source. Molecular markers should not be considered as normal genes as they usually do not have any biological effect. Instead, they can be thought of as constant landmarks in the genome. They are identifiable DNA sequences, found at specific locations of the genome and transmitted by the standard laws of inheritance from one generation to the next. They rely on a DNA assay in contrast to morphological markers that are based on visible traits, and biochemical markers that are based on proteins produced by genes. Different kinds of molecular markers exist, such as restriction fragment length polymorphisms, RAPDs markers, amplified fragment length polymorphisms, microsatellites and single-nucleotide polymorphisms (SNPs). Thus, MAS is the breeding strategy in which selection for a gene is based on molecular markers closely linked to the gene of interest, rather than gene itself and the markers are used to monitor the incorporation of desirable allele from the donor source.

Application of Systems Biology and Bioinformatics Methods in Biochemistry and Biomedicine

Application of Systems Biology and Bioinformatics Methods in Biochemistry and Biomedicine

Biophysical Characterization of the Recombinant Importin-α from Neurospora crassa

Neurospora crassa has been widely used as a model organism and contributed to the development of biochemistry and molecular biology by allowing the identification of many metabolic pathways and mechanisms responsible for gene regulation. Nuclear proteins are synthesized in the cytoplasm and need to be translocated to the nucleus to exert their functions which the importin-α receptor has a key role for the classical nuclear import pathway. In an attempt to get structural information of the nuclear transport process in N. crassa, we present herein the cloning, expression, purification and structural studies with N-terminally truncated IMPα from N. crassa (IMPα-Nc). Circular dichroism analysis revealed that the IMPα-Nc obtained is correctly folded and presents a high structural conservation compared to other importins-α. Dynamic light scattering, analytical size-exclusion chromatography experiments and molecular dynamics simulations indicated that the IMPα-Nc unbound to any ligand may present low stability in solution. The IMPα-Nc theoretical model displayed high similarity of its inner concave surface, which binds the cargo proteins containing the nuclear localization sequences, among IMPα from different species. However, the presence of non-conserved amino acids relatively close to the NLS binding region may influence the binding specificity of IMPα-Nc to cargo proteins.

Deconstructing the ONIOM Hessian: Investigating Method Combinations for Transition Structures.

Developments in biochemistry and materials sciences have led to increasing interest in the reactivity of large chemical systems, presenting theoretical and computational challenges that can be addressed with hybrid methods such as ONIOM. Here, we show that the diagonalized ONIOM Hessian can be partitioned/deconstructed into contributions from the individual subcalculations-indicating the curvature of their potential energy surfaces (PESs)-without increasing the computational cost. The resulting pseudofrequencies have particular application in the study of transition structures and higher-order saddle points with ONIOM, where we find that an imaginary frequency may result from combining subcalculations for which the corresponding vibrational frequencies are all real. Two cycloaddition reactions, including functionalization of a 150 atom (5,5) single-walled carbon nanotube, demonstrate how this analysis of pseudofrequencies allows identification of critical points where further exploratory work should be carried out to ensure that the ONIOM PES correctly approximates the target.

The reaction mechanism of hydroxyethylphosphonate dioxygenase: a QM/MM study

By employing ab initio quantum mechanical/molecular mechanical (QM/MM) and molecular dynamics (MD) simulations, we have provided further evidence against the previously proposed hydroperoxylation or hydroxylation mechanism of hydroxyethylphosphonate dioxygenase (HEPD). HEPD employs an interesting catalytic cycle based on concatenated bifurcations. The first bifurcation is based on the abstraction of hydrogen atoms from the substrate, which leads to a distal or proximal hydroperoxo species (Fe-OOH or Fe-(OH)O). The second and the third bifurcations refer to the carbon-carbon bond cleavage reaction. And this is achieved through a tridentate intermediate, or employing a proton-shuttle assisted mechanism, in which the residue Glu(176) or the Fe(IV)=O group serves as a general base. The reaction directions seem to be tunable and show significant environment dependence. This mechanism can provide a comprehensive interpretation for the seemingly contradicting experimental evidences and provide insight into the development of biochemistry and material sciences.

Re-engineering pharmacology teaching and research: Can we adopt translational approach?

Re-engineering pharmacology teaching and research: Can we adopt translational approach?

History of Biochemistry at the University of Geneva From the Boulevard des Philosophes to Quai Ernest-Ansermet.

A brief account of the developments in biochemistry at the Faculty of Science of the University of Geneva is given from its emergence from organic chemistry at the Ancienne Ecole de chimie to today's Department of Biochemistry at the Section de chimie et biochimie.

The development of biochemistry and molecular biology in China

The development of biochemistry and molecular biology in China

Coupling the development of biochemistry concept inventory questions to the assessment of students' conceptual knowledge in basic chemistry and biology

Like other science disciplines, biochemistry's foundation is built on basic concepts from other disciplines, particularly chemistry and biology. However, biochemistry students often have heterogeneous background training in these disciplines and sometimes lack sufficient mastery of important ancillary concepts (DW Sears et al BAMBEd 35:105‐118, 2007). To be successful then, concept inventory (CI) development in biochemistry may depend in part on the co‐evaluation of students' basic conceptual knowledge in these other areas. Inspired by CI questions that K Garvin‐Doxas and MW Klymkowsky (Life Sci. Ed. 7:227, 2008) developed to probe biology students' conceptual understanding of molecular diffusion and random movement in solution, assessment questions where devised to probe biochemistry students' conceptual understanding of the pH‐dependent migratory behavior of ionizable molecules in an aqueous solution in the presence of an electric field. Preliminary results of the assessment data presented here suggest that many students have difficulty coupling several basic chemical concepts related to random and electrophoretic movement of molecules that also undergo reversible ionization.

Early development of biochemistry and molecular biology in Israel

Early development of biochemistry and molecular biology in Israel

The Spanish Society of Biochemistry and Molecular Biology, the development of biochemistry in Spain, and IUBMB

FOREWORD An account such as this includes lots of important actors. To avoid forgetting anybody, I have preferred to forget all: I give only the names for the older ones, although I also mention a few returned or half-returned distinguished expatriates who are leading now a new (for Spain) brand of Spanish research institutes. This text is purely a personal perspective based on my experience as a SEBMB member since 1973 (although I am a full member from 1980 only). For information before that time, I have resorted to the book ‘‘Cuarenta anos de la Sociedad Espanola de Bioquimica y Biologia Molecular 1963–2003,’’ edited by Emilio Munoz et al. (see ref. 9), as well as other written records (see reference list). I have resorted also to oral stories, such as the recollections of the Madrid FEBS meeting by Julio Rodriguez Villanueva and Carlos Gancedo, both ex-Chairmen of FEBS, and both privileged participants in that event. I have had first-hand accounts of other aspects of Spanish biochemical history from Santiago Grisolia and from Severo Ochoa, Alberto Sols and Francisco Grande Covian, the last three regrettably deceased. Since I did not take written notes, I may have misinterpreted or misremembered something of what they told me. Therefore, any errors that might be found are my entire responsibility.

Development of biochemistry and molecular biology in Malta

Development of biochemistry and molecular biology in Malta

Molecular markers to assess genetic diversity

Molecular markers play an essential role today in all aspects of plant breeding, ranging from the identification of genes responsible for desired traits to the management of backcrossing programs. The emergence of marker systems has, for the last 30 years, closely tracked developments in biochemistry and molecular biology. Following the demonstration that retrotransposons are ubiquitous, active, and abundant in plant genomes, markers were developed that are based on the insertional polymorphism they create upon replication. They virtually all exploit the joint that is formed, during retrotransposon integration, between genomic DNA and the long terminal repeats at either end of retrotransposon. The various retrotransposon marker systems differ in the nature of the second primer used in the amplification reactions. All except one of these marker methods is dominant (RBIP is co-dominant). Hence, the availability of effective means to generate doubled haploid populations through gametophytic embryogenesis is valuable for the efficient use of these markers. Over the last eight years, retrotransposon-based markers have been developed for crop species and trees across the plant kingdom, as well as for fungi and insects. Many retrotransposons features make them appealing as the basis of molecular marker systems. They are usually dispersed throughout the genome and produce large genetic changes at the point of insertion that can be detected with family-specific amplification primers. The ancestral state of a retrotransposon insertion is known, and subsequent changes at the locus are not subject to homoplasy. Retrotransposon markers are useful in accelerating backcrossing programs, tagging genes of interest, tracking germplasm, verifying and producing pedigrees, and examining crop evolution.

The Development of Biochemistry in China

The Development of Biochemistry in China

Thoughts on the teaching of metabolism

Systems biology, metabolomics, metabolic engineering, and other recent developments in biochemistry suggest that future biochemists will require a detailed familiarity with the compounds and pathways of intermediary metabolism and their biochemical control. The challenge to the biochemistry instructor is the presentation of metabolic pathways in a manner that allows student creativity in learning the pathways and their components. One approach that does permit the use of problem solving for the study of metabolic pathways involves following the fate of (13) C, (14) C, or (15) N labels, presented originally in the structure of an important metabolic starting compound, through relevant metabolic pathways. This method allows the presentation and study of problems in which such an isotopic label can be traced through two or more metabolic pathways, thus illustrating how these pathways are interconnected. The understanding that all the pathways of intermediary metabolism are interconnected provides opportunities to discuss their metabolic control by such mechanisms as signaling, feedback inhibition, location in organelles, coenzyme levels, and coenzyme recycling rates. The method is illustrated by following the fate of (14) C labels through anaerobic glycolysis, gluconeogenesis, and fatty acid transport, β-oxidation, and ketone body formation. Cholesterol biosynthesis and heme formation are used to show that presentations of long and complex pathways can demonstrate important biochemical concepts by following the fate of an isotopic label using only the most important intermediates. Problems based on tracing radioactive labels through one or more metabolic pathways allow the use of cooperative learning techniques.

From components to regulatory motifs in signalling networks

The developments in biochemistry and molecular biology over the past 30 years have produced an impressive parts list of cellular components. It has become increasingly clear that we need to understand how components come together to form systems. One area where this approach has been growing is cell signalling research. Here, instead of focusing on individual or small groups of signalling proteins, researchers are now using a more holistic perspective. This approach attempts to view how many components are working together in concert to process information and to orchestrate cellular phenotypic changes. Additionally, the advancements in experimental techniques to measure and visualize many cellular components at once gradually grow in diversity and accuracy. The multivariate data, produced by experiments, introduce new and exciting challenges for computational biologists, who develop models of cellular systems made up of interacting cellular components. The integration of high-throughput experimental results and information from legacy literature is expected to produce computational models that would rapidly enhance our understanding of the detail workings of mammalian cells.