Transgenic biofortification of the starchy staple cassava (Manihot esculenta) generates a novel sink for protein

Although calorie dense, the starchy, tuberous roots of cassava provide the lowest sources of dietary protein within the major staple food crops (Manihot esculenta Crantz). (Montagnac JA, Davis CR, Tanumihardjo SA. (2009) Compr Rev Food Sci Food Saf 8:181-194). Cassava was genetically modified to express zeolin, a nutritionally balanced storage protein under control of the patatin promoter. Transgenic plants accumulated zeolin within de novo protein bodies localized within the root storage tissues, resulting in total protein levels of 12.5% dry weight within this tissue, a fourfold increase compared to non-transgenic controls. No significant differences were seen for morphological or agronomic characteristics of transgenic and wild type plants in the greenhouse and field trials, but relative to controls, levels of cyanogenic compounds were reduced by up to 55% in both leaf and root tissues of transgenic plants. Data described here represent a proof of concept towards the potential transformation of cassava from a starchy staple, devoid of storage protein, to one capable of supplying inexpensive, plant-based proteins for food, feed and industrial applications.     

Analytical lessons learned from selected therapeutic protein drug comparability studies

The successful implementation of process and product changes for a therapeutic protein drug, both during clinical development and after commercialization, requires a detailed evaluation of their impact on the protein's structure and biological functionality. This analysis is called a comparability exercise and includes a data driven assessment of biochemical equivalence and biological characterization using a cadre of analytical methodologies. This review focuses on describing analytical results and lessons learned from selected published therapeutic protein comparability case studies both for bulk drug substance and final drug product. An overview of the currently available analytical methodologies typically used is presented as well as a discussion of new emerging analytical techniques. The potential utility of several novel analytical approaches to comparability studies is discussed including distribution and stability of protein drugs in vivo, and enhanced evaluation of higher-order protein structure in actual formulations using hydrogen/deuterium exchange mass spectrometry, two-dimensional nuclear magnetic resonance fingerprinting or empirical phase diagrams. In addition, new methods for detecting and characterizing protein aggregates and particles are presented as these degradants are of current industry-wide concern. The critical role that analytical methodologies play in elucidating the structure–function relationships for therapeutic protein products during the overall assessment of comparability is discussed.     

Eight lucky lessons learned

Since my father, Ray Wu, would have been 80 years old this past August, the eighth month of 2008, and since 8 is a lucky number in China-associated with good luck and good fortune (as seen so dramatically in the Beijing Olympics)-I thought I would write about 8 important things that I was lucky to have the chance to learn from my father.     

Protein name tagging guidelines: lessons learned

Interest in information extraction from the biomedical literature is motivated by the need to speed up the creation of structured databases representing the latest scientific knowledge about specific objects, such as proteins and genes. This paper addresses the issue of a lack of standard definition of the problem of protein name tagging. We describe the lessons learned in developing a set of guidelines and present the first set of inter-coder results, viewed as an upper bound on system performance. Problems coders face include: (a) the ambiguity of names that can refer to either genes or proteins; (b) the difficulty of getting the exact extents of long protein names; and (c) the complexity of the guidelines. These problems have been addressed in two ways: (a) defining the tagging targets as protein named entities used in the literature to describe proteins or protein-associated or -related objects, such as domains, pathways, expression or genes, and (b) using two types of tags, protein tags and long-form tags, with the latter being used to optionally extend the boundaries of the protein tag when the name boundary is difficult to determine. Inter-coder consistency across three annotators on protein tags on 300 MEDLINE abstracts is 0.868 F-measure. The guidelines and annotated datasets, along with automatic tools, are available for research use.     

VTEC: lessons learned from British outbreaks

Important Escherichia coli O157 outbreaks in England and Scotland since 1982-83 are reviewed. The scientific lessons learned from them are described and their legal consequences outlined. The light shed by them on relationships between law and science is discussed, and questions of blame are analysed in the context of Reason's 'resident pathogen' metaphor and Vaughan's study of the 1986 Challenger Space Shuttle disaster.     

Development and cancer: lessons learned in the pancreas

Cancer progression and organ development are similar phenomena. Both involve rapid bursts of proliferation, angiogenesis, tissue remodeling, and cell migration. Therefore, it is not surprising that both processes utilize similar signaling machinery. In fact, many recent studies have suggested that cancer is a disease triggered by the erroneous re-activation of signaling pathways that are typically downregulated after the completion of embryonic development. This link between embryonic development and cancer is particularly exciting because it suggests that we might be able to exploit the knowledge gained in studies of Developmental Biology to obtain novel insights into tumor biology. Our evolving understanding of pancreatic adenocarcinoma is an excellent example of this relationship between development and cancer. Here we discuss recent studies have indicated important roles for two major developmental signaling pathways in pancreatic cancer: Notch and Hedgehog (Hh).     

Amazonia and the modern carbon cycle: lessons learned

In this paper, we review some critical issues regarding carbon cycling in Amazonia, as revealed by several studies conducted in the Large Scale Biosphere Atmosphere Experiment in Amazonia (LBA). We evaluate both the contribution of this magnificent biome for the global net primary productivity/net ecosystem exchange (NPP/NEE) and the feedbacks of climate change on the dynamics of Amazonia. In order to place Amazonia in a global perspective and make the carbon flux obtained through the LBA project comparable with global carbon budgets, we extrapolated NPP/NEE values found by LBA studies to the entire area of the Brazilian Amazon covered by rainforest. The carbon emissions due to land use changes for the tropical regions of the world produced values from 0.96 to 2.4 Pg C year⁻¹, while atmospheric CO₂ inversion models have recently indicated that tropical lands in the Americas could be exchanging a net 0.62±1.15 Pg C year⁻¹ with the atmosphere. The difference calculated from these two methods would imply a local sink of approximately 1.6–1.7 Pg C year⁻¹, or a source of 0.85 ton C ha⁻¹ year⁻¹. Using our crude extrapolation of LBA values for the Amazon forests (5 million km²) we estimate a range for the C flux in the region of −3.0 to 0.75 Pg C year⁻¹. The exercise here does not account for environmental variability across the region, but it is an important driver for present and future studies linking local process (i.e. nutrient availability, photosynthetic capacity, and so forth) to global and regional dynamic approaches.     

Mitochondrial efficiency: lessons learned from transgenic mice

Metabolic research has, like most areas of research in the life sciences, been affected dramatically by the application of transgenic technologies. Within the specific area of bioenergetics it has been thought that transgenic approaches in mice would provide definitive proof for some longstanding metabolic theories and assumptions. Here we review a number of transgenic approaches that have been used in mice to address theories of mitochondrial efficiency. The focus is largely on genes that affect the coupling of energy substrate oxidation to ATP synthesis, and thus, mice in which the uncoupling protein (Ucp) genes are modified are discussed extensively. Transgenic approaches have indeed provided proof-of-concept in some instances, but in many other instances they have yielded results that are in contrast to initial hypotheses. Many studies have also shown that genetic background can affect phenotypic outcomes, and that the upregulated expression of genes that are related to the modified gene often complicates the interpretation of findings.     

Dissecting phosphorylation networks: lessons learned from yeast

Protein phosphorylation continues to be regarded as one of the most important post-translational modifications found in eukaryotes and has been implicated in key roles in the development of a number of human diseases. In order to elucidate roles for the 518 human kinases, phosphorylation has routinely been studied using the budding yeast Saccharomyces cerevisiae as a model system. In recent years, a number of technologies have emerged to globally map phosphorylation in yeast. In this article, we review these technologies and discuss how these phosphorylation mapping efforts have shed light on our understanding of kinase signaling pathways and eukaryotic proteomic networks in general.     

Clinical trials in systemic sclerosis: lessons learned and outcomes

The pathogenesis of systemic sclerosis (SSc) is complex and largely unclear. The clinical heterogeneity of the disease and its progression over a number of years makes the choice of endpoints in the design of clinical trials difficult. The overwhelming need in this disease is to diagnose it early and identify those patients who will benefit most from early, aggressive treatment that potentially can alter the clinical disease course. To achieve this, innumerable challenges must be overcome. This article reviews data from recent clinical trials and the lessons derived from retrospective observational studies, databases, and patient registries. Taken together, these observations will help to improve our understanding of the diverse clinical course of SSc and permit refinement of existing outcome measures for the design of future clinical trials, in which the likelihood of observing a positive treatment effect with the drugs at our disposal will be maximized.     

Tuberculin immunotherapy: its history and lessons to be learned

The use of tuberculin for the therapy of tuberculosis was attempted more than 100 years ago and abandoned because of its adverse reactions. In this historical review we point out that some of the intensive efforts to avoid the reactions were based on the best scientific rationale available at that time. Balancing the dosage and intervals of tuberculin delivery with clinical and laboratory monitoring of patients achieved a limited success, with implications, toward current research in the field. The role of economical and social aspects at that time is also a lesson to be learned toward current approaches to tuberculosis control.     

Introduction: microbiology and immunology: lessons learned from Salmonella.

Salmonella enterica, a Gram-negative bacterium, causes significant morbidity and mortality worldwide, and is an excellent model to study bacterial pathogenesis and cellular immune responses. With the development of powerful new technologies, there has been a fusion of research on immunology, molecular biology and cellular microbiology of S. enterica infections. This multidisciplinary research will enhance our understanding of the basic mechanisms of bacterial infections and immunity; it also provides new approaches towards therapeutic and control measures.     

Protein folding diseases and neurodegeneration: lessons learned from yeast

Budding yeast Saccharomyces cerevisiae has proven to be a valuable model organism for studying fundamental cellular processes across the eukaryotic kingdom including man. In this respect, complementation assays, in which the yeast protein is replaced by a homologous protein from another organism, have been very instructive. A newer trend is to use the yeast cell factory as a toolbox to understand cellular processes controlled by proteins for which the yeast lacks functional counterparts. An increasing number of studies have indicated that S. cerevisiae is a suitable model system to decipher molecular mechanisms involved in a variety of neurodegenerative disorders caused by aberrant protein folding. Here we review the current knowledge gained by the use of so-called humanized yeasts in the field of Huntington's, Parkinson's and Alzheimer's diseases.     

Protozoa and pathogenic bacteria: lessons learned from Legionella pneumophila

Bacterivorous protozoa and bacteria have been in co-existence since the origin of life. This co-existence has led unequivocally to the evolution of many different co-interactions. Most bacteria are ingested and digested, but many escape ingestion for various reasons. Others are ingested but evade digestion, and a few, notoriously Legionella pneumophila , even have the capacity of multiplying within the protozoan host. The aims of this study were to elucidate the interactions of various multi-drug-resistant Staphylococcus aureus (MRSA) strains, Listeria monocytogenes sv4b, and Escherichia coli K12 with the amoeba, Acanthamoeba polyphaga . To evaluate the interactions, we set up co-cultures in Neffs' amoebic saline, at a multiplicity of invasion (MOI) of 1:100 of amoeba to bacteria, and a temperature of 37°C, although the effects of MOI and temperature were also assessed. Survival of bacteria and amoeba was checked at regular intervals, coupled with microscopy. It was discovered under our test conditions, that E. coli was ingested and digested by A. polyphaga , but in contrast, L. monocytogenes , had the capacity to flourish in the presence of A. polyphaga . We also report, for the first time, that all six MRSA isolates tested, survived and replicated in association with A. polyphaga , in comparison to conditions where amoebae were absent. Indeed, we also have evidence suggesting that increases in MRSA, in the presence of A. polyphaga , may be attributable to intracellular survival and replication. These findings have profound implications for the hospital environment, where Acanthamoeba sp., are also commonly isolated. In conclusion, this study illustrates the significance of protozoa as vehicles augmenting the survival of MRSA and L. monocytogenes in the environment.     

Negative-pressure wound therapy in the military: lessons learned

The utilization of negative pressure for medicinal purposes dates back to 600 bc. The U.S. military has been engaged in continuous overseas combat operations since 2001. Negative-pressure wound therapy has been in use in the treatment of casualties from these operations since 2004. It represents a new standard of practice in combat wound care; it promotes granulation tissue formation and creates mechanical forces supporting wound contraction, facilitating definitive wound closure. This article describes (1) the use of negative-pressure wound therapy in combat casualty care, (2) inherent challenges of its use in theater of operations and across the echelons of care, (3) modifications of this wound therapy to meet military-specific needs, and (4) future directions with this novel wound care modality.