SARS-CoV-2 virtual biochemistry labs on bioinformatics and drug design

Colleges and universities are learning to provide relevant virtual lab experiences for students due to the COVID-19 pandemic. Even schools attempting in-person instruction often need to utilize virtual experiences for students absent due to quarantine or illness. Much of biochemistry is amenable to molecular visualization and/or computational study; however, many faculty face learning how to utilize new computational and molecular visualization software. We present a set of virtual lab exercises with detailed instructions to engage students in the discovery of novel antiviral compounds against the SARS-CoV-2 main protease.

The transition from objectively structured practical examination (OSPE) to electronic OSPE in the era of COVID-19

The coronavirus (COVID-19) pandemic is forcing the medical educators to innovate and embrace online education and assessment platform. One of the most significant challenges we are facing is the formative assessment of practical skills in the undergraduate medical biochemistry education. We have designed the electronic objectively structured practical examination to facilitate the formative assessment.

Benchtop mass spectrometry in clinical biochemistry

Mass spectrometry has for many years enabled us to rapidly identify and quantify many different compounds in biological samples. The equipment is currently available in specialist centres investigating metabolic disorders and in toxicology laboratories. Improvements in sample introduction and refinements in the mass spectrometry hardware now allow higher sample throughput without extensive sample purification. Many mass spectrometers are compact and operated by computers that also assist data handling.

Mass spectrometry has the potential to change hospital laboratory operations generally. Consideration of the practical and financial aspects of its application may reveal cost-effective means of improving the specificity of analyte assay. Considerable advantages are expected in the analysis of metabolites and drugs and in proteomics.

Nothing to lose: why early career scientists make ideal entrepreneurs

An entrepreneurial movement within science strives to invert the classical trajectory of academic research careers by positioning trainees at the apex of burgeoning industries. Young scientists today have nothing to lose and everything to gain by pursuing this 'third road', and academic institutes and established companies only stand to benefit from supporting this emerging movement of discovery research with economic purpose.

An economical method for production of (2)H, (13)CH3-threonine for solution NMR studies of large protein complexes: application to the 670 kDa proteasome

NMR studies of very high molecular weight protein complexes have been greatly facilitated through the development of labeling strategies whereby ¹³CH₃ methyl groups are introduced into highly deuterated proteins. Robust and cost-effective labeling methods are well established for all methyl containing amino acids with the exception of Thr. Here we describe an inexpensive biosynthetic strategy for the production of L-[α-²H; β−²H;γ-¹³C]-Thr that can then be directly added during protein expression to produce highly deuterated proteins with Thr methyl group probes of structure and dynamics. These reporters are particularly valuable, because unlike other methyl containing amino acids, Thr residues are localized predominantly to the surfaces of proteins, have unique hydrogen bonding capabilities, have a higher propensity to be found at protein nucleic acid interfaces and can play important roles in signaling pathways through phosphorylation. The utility of the labeling methodology is demonstrated with an application to the 670 kDa proteasome core particle, where high quality Thr ¹³C,¹H correlation spectra are obtained that could not be generated from samples prepared with commercially available U-[¹³C,¹H]-Thr.

An economical method for cell-free protein synthesis using glucose and nucleoside monophosphates

Cell-free protein synthesis reactions have not been seriously considered as a viable method for commercial protein production mainly because of high reagent costs and a lack of scalable technologies. Here we address the first issue by presenting a cell-free protein synthesis system with comparable protein yields that removes the most expensive substrates and lowers the cell-free reagent cost by over 75% (excluding extract, polymerase, and plasmid) while maintaining high energy levels. This system uses glucose as the energy source and nucleoside monophosphates (NMPs) in place of nucleoside triphosphates (NTPs) as the nucleotide source. High levels of nucleoside triphosphates are generated from the monophosphates within 20 min, and the subsequent energy charge is similar in reactions beginning with either NTPs or NMPs. Furthermore, significant levels (>0.2 mM) of all NTPs are still available at the end of a 3-h incubation, and the total nucleotide pool is stable throughout the reaction. The glucose/NMP reaction was scaled up to milliliter scale using a thin film approach. Significant yields of active protein were observed for two proteins of vastly different size: chloramphenicol acetyl transferase (CAT, 25 kDa) and beta-galactosidase (472 kDa). The glucose/NMP cell-free reaction system dramatically reduces reagent costs while supplying high protein yields.

A flexible and economical medium-throughput strategy for protein production and crystallization

Large-scale structural genomics centres rely heavily on robotics to ensure that maximum throughput is achieved. However, the size and cost of these approaches is out of the reach of most academic structural biology efforts. A major challenge for such groups is to adapt current high-throughput schemes to a reasonable scale with the resources available. A flexible medium-throughput approach has been developed that is suitable for typical academic research groups. Following nested PCR, targets are routinely cloned into two Gateway expression vectors (pDEST15 for an N-terminal GST tag and pDEST17 for an N-terminal His tag). Expression of soluble recombinant protein in Escherichia coli is rapidly assessed in 96-well format. An eight-probe sonicator is utilized and a six-buffer lysis screen was incorporated to enhance solubility. Robotics is reserved for crystallization, since this is the key bottleneck for crystallography. Screening proteins with a 480-condition protocol using a Cartesian nanolitre-dispensing robot has increased crystallization success markedly, with an overall success rate (structures solved out of proteins screened) of 19%. The methods are robust and economical -- with the exception of the crystallization robot, investment in additional equipment has been minimal at 9000 US dollars. All protocols are designed for individuals so that graduate students and postdoctoral fellows gain expertise in every aspect of the structural pipeline, from cloning to crystallization.

Downstream Process Synthesis for Biochemical Production of Butanol, Ethanol, and Acetone from Grains: Generation of Optimal and Near-Optimal Flowsheets with Conventional Operating Units

Manufacturing butanol, ethanol, and acetone through grain fermentation has been attracting increasing research interest. In the production of these chemicals from fermentation, the cost of product recovery constitutes the major portion of the total production cost. Developing cost-effective flowsheets for the downstream processing is, therefore, crucial to enhancing the economic viability of this manufacturing method. The present work is concerned with the synthesis of such a process that minimizes the cost of the downstream processing. At the outset, a wide variety of processing equipment and unit operations, i.e., operating units, is selected for possible inclusion in the process. Subsequently, the exactly defined superstructure with minimal complexity, termed maximal structure, is constructed from these operating units with the rigorous and highly efficient graph-theoretic method for process synthesis based on process graphs (P-graphs). Finally, the optimal and near-optimal flowsheets in terms of cost are identified.

An economical method for (15)N/(13)C isotopic labeling of proteins expressed in Pichia pastoris

We report a new and cost-effective approach to prepare (15)N/(13)C labeled proteins for NMR using the Pichia pastoris expression system. Four protocols (P1 to P4) were defined and compared using recombinant Ovine interferon-tau (rOvIFN-tau). Our results demonstrate that in order to get full incorporation of (15)N and (13)C, the isotopes are not totally required during the initial growth phase of P. pastoris culture. The addition of small amounts of (15)N and (13)C compounds 6 h prior to the methanol induction phase is sufficient to obtain 99% incorporation of heavy isotopes into the protein. Our optimized protocol P4 is two-thirds less costly than the classical method using (15)N and (13)C isotopes during the entire growth phase.

Stereoselective synthesis of (S)-(+)-Naproxen catalyzed by carboxyl esterase in a multicompartment electrolyzer

The stereoselective hydrolysis of racemic 2-substituted propionates, catalyzed by carboxyl esterase, provides a cost-competitive route to produce the optically pure, anti-inflammatory drug Naproxen. In the present work, we describe the application of the multicompartment electrolyzer reactor (ME) for the stereoselective hydrolysis of a racemic Naproxen ester, (R,S)-ethoxyethyl-[2-(6-methoxy-2-naphtyl)]propionate, catalyzed by a carboxyl esterase. The enzyme was trapped in a reactor chamber, delimited by two isoelectric membranes encompassing the pI value of the enzyme, together with the neutral substrate. After 90 min, a conversion of 45% was obtained with an enantiomeric excess of 84%. The reaction product, (S)-(+)-Naproxen, was electrophoretically removed in continuous from the reaction chamber and collected in a contiguous, more acidic chamber, separated from the enzyme and from the unreacted substrate. Moreover, at the end of the reaction, it was possible to recover the enzyme from the reactor and use it again.

Who solved the protein folding problem?

For the third time, techniques for the prediction of three-dimensional structures of proteins were critically assessed in a worldwide blind test. Steady progress is undeniable. How did this happen and what are the implications?

Highly sensitive and stable phosphatidylserine liposome aggregation assay for annexins

Annexins are a gene family of Ca(2+)-dependent membrane binding proteins which interact specifically with acidic phospholipids. We describe here details of highly sensitive and precise assays for annexins I and V, utilizing turbidometric analysis of phosphatidylserine liposome aggregation. In the case of annexin I, the new assay is 7-fold more sensitive than the conventional chromaffin granule aggregation assay in terms of threshold for detection and the rate of increase of initial absorbance is 15-fold greater. Annexin V, which binds but does not aggregate liposomes, can be assayed on the basis of inhibition of Ca(2+)-dependent liposome aggregation. Further comparative advantages of the assay include lower expense and increased shelf life of the liposome reagent.

[Mathematical model of technical equipment of a clinical-diagnostic laboratory]

The paper is concerned with the problems of technical equipment of standard clinico-diagnostic laboratories (CDL) in this country. The authors suggest a mathematic model that may minimize expenditures for laboratory studies. The model enables the following problems to be solved: to issue scientifically-based recommendations for technical equipment of CDL; to validate the medico-technical requirements for newly devised items; to select the optimum types of uniform items; to define optimal technical decisions at the stage of the design; to determine the lab assistant's labour productivity and the cost of some investigations; to compute the medical laboratory engineering requirement for treatment and prophylactic institutions of this country.

Future funding policies from non-government sources: the Wellcome Trust

As we enter the 1990s, the Trust is taking on a new and unsought role as a mainstay of University biomedical research. It is to be hoped that recent statements from Government, which appear to recognize the harm being wreaked on the Universities, will prove to be more than pious platitudes.

Costing clinical biochemistry services as part of an operational management budgeting system

The process of costing clinical biochemistry tests as a component of the commissioning of a unit management budgeting system based on an International Computers Limited (ICL) minicomputer system was examined. Methods of apportioning consumable and labour costs under direct and indirect cost headings and as test and request charges were investigated, and in this currently operational system it was found that 38% of consumable costs and 57% of labour costs were not a direct component of the routine analysis function. Means of assigning test costs to a given request source and the incorporation of such charges into clinical budget statements were looked at. A reduction in laboratory workload did not produce a comparable reduction in laboratory costs. For a theoretical reduction in workload of 20% only a 3.8% laboratory saving in recoverable costs could be expected.

Effectiveness of out-of-hours biochemistry investigations

A survey was carried out of doctors who used their out-of-hours biochemistry service to find out why requests for investigations were made, how often the results altered patient management, and whether they could define areas where investigations were unproductive. Of 107 questionnaires distributed, 147 (88%) were completed. In 86% the requests were for diagnosis or immediate patient management and in 35% the results actually altered management. Senior clinical staff were more efficient than their juniors in instigating biochemical investigations that proved to be effective. In no instance where the clinical staff predicted that it was unlikely that the results would alter management was management altered. It is suggested that joint reviews of case notes by junior and senior clinical staff would prove to be the most appropriate way to increase the effectiveness and efficiency of clinical investigation.