The Glasgow Metabolism Suite: undergraduate software for intermediary metabolism

The Glasgow Metabolism Suite is a “standalone” Macintosh software application developed for use in conjunction with the teaching of intermediary metabolism to undergraduate students. It is not a vehicle for delivery of primary information, but provides an interactive environment in which students can review their knowledge of a range of metabolic pathways and the integration of mammalian metabolism in exercise and in the fed and fasted state.     

A Biochemistry of Human Disease course for undergraduate and graduate students

This paper describes the experience of members of a medical school faculty who have been offering for more than 10 years a two-course series in the biochemistry of human disease to undergraduate students majoring in biochemistry, biology, or chemistry. Each of the two 3-credit courses meets twice a week for 90 min per session. The courses are divided into five three-week blocs (total number of sessions per bloc, six), each of which is taught by a different instructor. The sixth and last class in each of the blocs is devoted to an exam; there is no cumulative final exam. The topics that are covered include the following: diabetes mellitus, alcoholism, Alzheimer's disease, trophoblastic diseases of pregnancy, molecular and cellular mechanisms of cancer (including chemical carcinogenesis), disorders of calcium metabolism, biochemical and nutritional causes of anemia, collagen diseases, and gene replacement therapy. The various teaching formats and kinds of reading assignments that are used are discussed, as are the reactions of selected faculty who have participated in these courses. The positive experience we have had with a bloc approach to topics-based, multi-instructor courses in human disease should encourage basic science faculty at other medical schools in the US and elsewhere to become involved in teaching specialized, advanced courses to undergraduate, pre-professional students.     

Imaging Cellular Inorganic Phosphate in Caenorhabditis elegans Using a Genetically Encoded FRET-Based Biosensor

Inorganic phosphate (Pi) has central roles in metabolism, cell signaling and energy conversion. The distribution of Pi to each cell and cellular compartment of an animal must be tightly coordinated with its dietary supply and with the varied metabolic demands of individual cells. An analytical method for monitoring Pi dynamics with spatial and temporal resolution is therefore needed to gain a comprehensive understanding of mechanisms governing the transport and recycling of this essential nutrient. Here we demonstrate the utility of a genetically encoded FRET-based Pi sensor to assess cellular Pi levels in the nematode Caenorhabditis elegans. The sensor was expressed in different cells and tissues of the animal, including head neurons, tail neurons, pharyngeal muscle, and the intestine. Cytosolic Pi concentrations were monitored using ratiometric imaging. Injection of phosphate buffer into intestinal cells confirmed that the sensor was responsive to changes in Pi concentration in vivo. Live Pi imaging revealed cell-specific and developmental stage-specific differences in cytosolic Pi concentrations. In addition, cellular Pi levels were perturbed by food deprivation and by exposure to the respiratory inhibitor cyanide. These results suggest that Pi concentration is a sensitive indicator of metabolic status. Moreover, we propose that live Pi imaging in C. elegans is a powerful approach to discern mechanisms that govern Pi distribution in individual cells and throughout an animal.     

Heard it through the grapevine: Proteomic perspective on grape and wine

Grapevine (Vitis ssp.) is currently considered as the most important fruit plant throughout the world, both due to its economic importance and to its role as a non climacteric model species. The relevance of the studies devoted to the dissection of grapevine biology and biochemistry underlines the great amount of attention that this plant has attracted over the last decade. The milestones among these studies are represented by the accomplishment of the genome sequencing programmes in 2007 [1], [2]. Since then, the investigation of grape OMICS has been implemented, and the number of reports published on grape and wine protein investigations using proteomic techniques have significantly improved knowledge in the field.     

Rapid Identification and Enumeration of Saccharomyces cerevisiae Cells in Wine by Real-Time PCR

Despite the beneficial role of Saccharomyces cerevisiae in the food industry for food and beverage production, it is able to cause spoilage in wines. We have developed a real-time PCR method to directly detect and quantify this yeast species in wine samples to provide winemakers with a rapid and sensitive method to detect and prevent wine spoilage. Specific primers were designed for S. cerevisiae using the sequence information obtained from a cloned random amplified polymorphic DNA band that differentiated S. cerevisiae from its sibling species Saccharomyces bayanus, Saccharomyces pastorianus, and Saccharomyces paradoxus. The specificity of the primers was demonstrated for typical wine spoilage yeast species. The method was useful for estimating the level of S.cerevisiae directly in sweet wines and red wines without preenrichment when yeast is present in concentrations as low as 3.8 and 5 CFU per ml. This detection limit is in the same order as that obtained from glucose-peptone-yeast growth medium (GPY). Moreover, it was possible to quantify S. cerevisiae in artificially contaminated samples accurately. Limits for accurate quantification in wine were established, from 3.8 × 10⁵ to 3.8 CFU/ml in sweet wine and from 5 × 10⁶ to 50CFU/ml in red wine.     

Health Perceptions,Self and Body Image,Physical Activity and Nutrition among Undergraduate Students in Israel

Purpose

This study examines health perceptions, self and body image, physical exercise and nutrition among undergraduate students.

Methods

A structured, self-reported questionnaire was administered to more than 1500 students at a large academic institute in Israel. The study population was heterogenic in both gender and fields of academic study.

Results

High correlations between health perceptions, appropriate nutrition, and positive self and body image were found. The relationships between these variables differed between the subpopulation in the sample and the different genders. Engagement in physical exercise contributed to positive body image and positive health perceptions more than engagement in healthy nutrition. Nutrition students reported higher frequencies of positive health perceptions, positive self and body image and higher engagement in physical exercise in comparison to all other students in the sample.

Conclusions

This study suggests, as have many before, that successful health promotion policy should reflect a collectivist rather than an individualist ethos by providing health prerequisites through a public policy of health-promotion, where the academic settings support a healthy lifestyle policy, by increasing availability of a healthy, nutritious and varied menu in the cafeterias, and offering students various activities that enhance healthy eating and exercise.

Implications and contribution

This study examined health perceptions, self-image, physical exercise and nutrition among undergraduate students and found high correlations between these topics. Nutrition students reported higher frequencies of positive health perceptions, and positive self and body image and engaged more in physical exercise when compared with all other students in the sample.     

Evolution of Acetic Acid Bacteria During Fermentation and Storage of Wine

Acetic acid bacteria were present at all stages of wine making, from the mature grape through vinification to conservation. A succession of Gluconobacter oxydans, Acetobacter pasteurianus, and Acetobacter aceti during the course of these stages was noted. Low levels of A. aceti remained in the wine; they exhibited rapid proliferation on short exposure of the wine to air and caused significant increases in the concentration of acetic acid. Higher temperature of wine storage and higher wine pH favored the development and metabolism of these species.     

Learning biochemistry through manga — helping students learn and remember,and making lectures more exciting

Panels taken from manga, Japanese comics and cartoons, were used to supplement explanations of biochemical terms and topics in biochemistry classes. The results showed that the use of manga helped students remember what they had learned. Manga also had the effect of making biochemistry classes less serious and increased the number of students interested in biochemistry.     

Effects of harvest dates on microbial communities of ice grape skins from Xinjiang of China

Ice wine is a sweet dessert wine made from pressing grapes naturally frozen on the vines. The structure and metabolic characteristics of native microbial community dominated by organics and nutrients transformation in fermenting process of ice wine on the grape skin are likely to change due to climate events. Our objective was to evaluate the influence of harvest time on structure and metabolic characteristics of bacterial and fungal communities on Vidal ice grape surface. Vidal grape samples were picked between October and December in 2018; Harvest 1 (VG1): 14 October; Harvest 2 (VG2): 16 November; Harvest 3 (VG3): 18 December. Vishniacozyma, Alternaria, Cladosporium, Stenotrophomonas, unidentified_Cyanobacteria and Sphingomonas existed in all harvest dates and were the main genera widespread in most grape samples from the three harvest periods. Saprotrophic fungi and bacteria involved in metabolism were also dominant. For fungi, wood saprotrophs and unidentified saprotrophs were detected comprising Phoma, Didymella, Filobasidium and Clavaria. Delayed harvest of ice grapes has a distinct advantage for pathogen reduction compared with that of normally harvested grapes. Among bacteria, the most frequently occurring types in the metabolism category were energy metabolism, carbohydrate metabolism and lipid metabolism. In short, the harvest period can positively regulate the function of Vidal ice grape epidermal microorganisms.     

Adjustments of Protein Metabolism in Fasting Arctic Charr,Salvelinus alpinus

Protein metabolism, including the interrelated processes of synthesis and degradation, mediates the growth of an animal. In ectothermic animals, protein metabolism is responsive to changes in both biotic and abiotic conditions. This study aimed to characterise responses of protein metabolism to food deprivation that occur in the coldwater salmonid, Arctic charr, Salvelinus alpinus. We compared two groups of Arctic charr: one fed continuously and the other deprived of food for 36 days. We measured the fractional rate of protein synthesis (K_S) in individuals from the fed and fasted groups using a flooding dose technique modified for the use of deuterium-labelled phenylalanine. The enzyme activities of the three major protein degradation pathways (ubiquitin proteasome, lysosomal cathepsins and the calpain systems) were measured in the same fish. This study is the first to measure both K_S and the enzymatic activity of protein degradation in the same fish, allowing us to examine the apparent contribution of different protein degradation pathways to protein turnover in various tissues (red and white muscle, liver, heart and gills). K_S was lower in the white muscle and in liver of the fasted fish compared to the fed fish. There were no observable effects of food deprivation on the protease activities in any of the tissues with the exception of liver, where the ubiquitin proteasome pathway seemed to be activated during fasting conditions. Lysosomal proteolysis appears to be the primary degradation pathway for muscle protein, while the ubiquitin proteasome pathway seems to predominate in the liver. We speculate that Arctic charr regulate protein metabolism during food deprivation to conserve proteins.     

Microbial acetyl-CoA metabolism and metabolic engineering

Recent concerns over the sustainability of petrochemical-based processes for production of desired chemicals have fueled research into alternative modes of production. Metabolic engineering of microbial cell factories such as Saccharomyces cerevisiae and Escherichia coli offers a sustainable and flexible alternative for the production of various molecules. Acetyl-CoA is a key molecule in microbial central carbon metabolism and is involved in a variety of cellular processes. In addition, it functions as a precursor for many molecules of biotechnological relevance. Therefore, much interest exists in engineering the metabolism around the acetyl-CoA pools in cells in order to increase product titers. Here we provide an overview of the acetyl-CoA metabolism in eukaryotic and prokaryotic microbes (with a focus on S. cerevisiae and E. coli), with an emphasis on reactions involved in the production and consumption of acetyl-CoA. In addition, we review various strategies that have been used to increase acetyl-CoA production in these microbes.     

Physical Activity Differentially Affects the Cecal Microbiota of Ovariectomized Female Rats Selectively Bred for High and Low Aerobic Capacity

The gut microbiota is considered a relevant factor in obesity and associated metabolic diseases, for which postmenopausal women are particularly at risk. Increasing physical activity has been recognized as an efficacious approach to prevent or treat obesity, yet the impact of physical activity on the microbiota remains under-investigated. We examined the impacts of voluntary exercise on host metabolism and gut microbiota in ovariectomized (OVX) high capacity (HCR) and low capacity running (LCR) rats. HCR and LCR rats (age = 27wk) were OVX and fed a high-fat diet (45% kcal fat) ad libitum and housed in cages equipped with (exercise, EX) or without (sedentary, SED) running wheels for 11wk (n = 7-8/group). We hypothesized that increased physical activity would hinder weight gain, increase metabolic health and shift the microbiota of LCR rats, resulting in populations more similar to that of HCR rats. Animals were compared for characteristic metabolic parameters including body composition, lipid profile and energy expenditure; whereas cecal digesta were collected for DNA extraction. 16S rRNA gene-based amplicon Illumina MiSeq sequencing was performed, followed by analysis using QIIME 1.8.0 to assess cecal microbiota. Voluntary exercise decreased body and fat mass, and normalized fasting NEFA concentrations of LCR rats, despite only running one-third the distance of HCR rats. Exercise, however, increased food intake, weight gain and fat mass of HCR rats. Exercise clustered the gut microbial community of LCR rats, which separated them from the other groups. Assessments of specific taxa revealed significant (p<0.05) line by exercise interactions including shifts in the abundances of Firmicutes, Proteobacteria, and Cyanobacteria. Relative abundance of Christensenellaceae family was higher (p = 0.026) in HCR than LCR rats, and positively correlated (p<0.05) with food intake, body weight and running distance. These findings demonstrate that exercise differentially impacts host metabolism and gut microbial communities of female HCR and LCR rats without ovarian function.     

Piwi/piRNAs control food intake by promoting neuropeptide F expression in locusts

Animal feeding, which directly affects growth and metabolism, is an important physiological process. However, the contribution of PIWI proteins and PIWI‐interacting RNAs (piRNAs) to the regulatory mechanism of animal feeding is unknown. Here, we report a novel function of Piwi and piRNAs in regulating food intake in locusts. Our study shows that the locust can serve as a representative species for determining PIWI function in insects. Knockdown of Piwi1 expression suppresses anabolic processes and reduces food consumption and body weight. The reduction in food intake by knockdown of Piwi1 expression results from decreased expression of neuropeptide NPF1 in a piRNA‐dependent manner. Mechanistically, intronic piRNAs might enhance RNA splicing of NPF1 by preventing hairpin formation at the branch point sites. These results suggest a novel nuclear PIWI/piRNA‐mediated mechanism that controls food intake in the locust nervous system.     

Control of Flavor Development in Wine during and after Malolactic Fermentation by Oenococcus oeni

During malolactic fermentation in wine by Oenococcus oeni, the degradation of citric acid was delayed compared to the degradation of malic acid. The maximum concentration of diacetyl, an intermediary compound in the citric acid metabolism with a buttery or nutty flavor, coincided with the exhaustion of malic acid in the wine. The maximum concentration of diacetyl obtained during malolactic fermentation was strongly dependent on the oxygen concentration and the redox potential of the wine and, to a lesser extent, on the initial citric acid concentration. The final diacetyl concentration in the wine was also dependent on the concentration of SO₂. Diacetyl combines rather strongly with SO₂ (K_f = 7.2 × 10³ M⁻¹ in 0.1 M malate buffer [pH 3.5] at 30°C). The reaction is exothermic and reversible. If the concentration of SO₂ decreases during storage of the wine, the diacetyl concentration increases again.     

Defining the limits of diving biochemistry in marine mammals

The field of marine mammal diving biochemistry was essentially untouched when Peter Hochachka turned his attention to it in the mid-1970s. Over the next 30 years, his work followed three main themes in this area: first, most biologists at that time supported the theory that diving mammals utilized enhanced metabolic pathways for hypoxic energy production (glycolysis to lactate) and reduced their metabolic rate while diving. Peter began his work on potential hypoxic adaptations in marine mammals by working out the details of how these pathways would be regulated. By the 1980s, he started to ask how diving mammals balanced the increased demands of exercise with the apparently conflicting demands to reduce aerobic metabolism while exercising underwater. By the 1990s, his work involved complex models of the interplay between the neural, hormonal, behavioral and evolutionary components of diving biochemistry and animal exercise. From a comparative approach, he excelled at bringing themes of hypoxic adaptation from many different types of animals to the field of diving mammal biochemistry. This review traces the history of Peter Hochachka's work on diving biochemistry from the perspective of those of us who spent time with him both inside the laboratory and outside in the field from Antarctica to Iceland.     

Potential role and therapeutic interests of myo-inositol in metabolic diseases

Several inositol isomers and in particular myo-inositol (MI) and D-chiro-inositol (DCI), were shown to possess insulin-mimetic properties and to be efficient in lowering post-prandial blood glucose. In addition, abnormalities in inositol metabolism are associated with insulin resistance and with long term microvascular complications of diabetes, supporting a role of inositol or its derivatives in glucose metabolism. The aim of this review is to focus on the potential benefits of a dietary supplement of myo-inositol, by far the most common inositol isomer in foodstuffs, in human disorders associated with insulin resistance (polycystic ovary syndrome, gestational diabetes mellitus or metabolic syndrome) or in prevention or treatment of some diabetic complications (neuropathy, nephropathy, cataract). The relevance of such a nutritional strategy will be discussed for each context on the basis of the clinical and/or animal studies. The dietary sources of myo-inositol and its metabolism from its dietary uptake to its renal excretion will be also covered in this review. Finally, the actual insights into inositol insulin-sensitizing effects will be addressed and in particular the possible role of inositol glycans as insulin second messengers.     

Modelling biochemical features of mitochondrial neuropathology

Background

The neuropathology of mitochondrial disease is well characterised. However, pathophysiological mechanisms at the level of biochemistry and cell biology are less clear. Progress in this area has been hampered by the limited accessibility of neurologically relevant material for analysis.

Scope of review

Here we discuss the recent development of a variety of model systems that have greatly extended our capacity to understand the biochemical features associated with mitochondrial neuropathology. These include animal and cell based models, with mutations in both nuclear and mitochondrial DNA encoded genes, which aim to recapitulate the neuropathology and cellular biochemistry of mitochondrial diseases.

Major conclusions

Analysis of neurological tissue and cells from these models suggests that although there is no unifying mode of pathogenesis, dysfunction of the oxidative phosphorylation (OXPHOS) system is often central. This can be associated with altered reactive oxygen species (ROS) generation, disruption of the mitochondrial membrane potential (ΔΨ_m) and inadequate ATP synthesis. Thus, other cellular processes such as calcium (Ca^2 +) homeostasis, cellular signaling and mitochondrial morphology could be altered, ultimately compromising viability of neuronal cells.

General significance

Mechanisms of neuronal dysfunction in mitochondrial disease are only just beginning to be characterised, are system dependent and complex, and not merely driven by energy deficiency. The diversity of pathogenic mechanisms emphasises the need for characterisation in a wide range of models, as different therapeutic strategies are likely to be needed for different diseases.This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.     

The confounding effects of sub-thermoneutral housing temperatures on aerobic exercise-induced adaptations in mouse subcutaneous white adipose tissue

Mice are the most commonly used model organism for human biology, and failure to acknowledge fundamental differences in thermal biology between these species has confounded the study of adipose tissue metabolism in mice and its translational relevance to humans. Here, using exercise biochemistry as an example, we highlight the subtle yet detrimental effects sub-thermoneutral housing temperatures can have on the study of adipose tissue metabolism in mice. We encourage academics and publishers to consider ambient housing temperature as a key determinant in the methodological conception and reporting of all research on rodent white adipose tissue metabolism.     

Genetic Basis of Variations in Nitrogen Source Utilization in Four Wine Commercial Yeast Strains

The capacity of wine yeast to utilize the nitrogen available in grape must directly correlates with the fermentation and growth rates of all wine yeast fermentation stages and is, thus, of critical importance for wine production. Here we precisely quantified the ability of low complexity nitrogen compounds to support fast, efficient and rapidly initiated growth of four commercially important wine strains. Nitrogen substrate abundance in grape must failed to correlate with the rate or the efficiency of nitrogen source utilization, but well predicted lag phase length. Thus, human domestication of yeast for grape must growth has had, at the most, a marginal impact on wine yeast growth rates and efficiencies, but may have left a surprising imprint on the time required to adjust metabolism from non growth to growth. Wine yeast nitrogen source utilization deviated from that of the lab strain experimentation, but also varied between wine strains. Each wine yeast lineage harbored nitrogen source utilization defects that were private to that strain. By a massive hemizygote analysis, we traced the genetic basis of the most glaring of these defects, near inability of the PDM wine strain to utilize methionine, as consequence of mutations in its ARO8, ADE5,7 and VBA3 alleles. We also identified candidate causative mutations in these genes. The methionine defect of PDM is potentially very interesting as the strain can, in some circumstances, overproduce foul tasting H₂S, a trait which likely stems from insufficient methionine catabolization. The poor adaptation of wine yeast to the grape must nitrogen environment, and the presence of defects in each lineage, open up wine strain optimization through biotechnological endeavors.     

A single protein research integrated advanced biochemistry laboratory course: design and general outline

An advanced biochemistry laboratory has been designed to focus on a detoxifying enzyme, glutathione-S-transferase, which is involved in the metabolism of polycyclic aromatic hydrocarbons (PAHs), pesticides, herbicides, and other electrophilic xenobiotic compounds. The enzyme is known to catalyze conjugation of glutathione to xenobiotics, which makes them water-soluble so that they can be easily discarded through further metabolism and excretion. About two-thirds of the laboratory course incorporates nine advanced biochemical techniques, all focused to analyze various chemical characteristics of the glutathione-S-transferase. The remaining third of the semester time students work on a project that involves application of all the newly acquired techniques to solve a biochemical problem that encompasses the same detoxifying enzyme.