Investigating pre‐analytical requirements for serum and plasma based infrared spectro‐diagnostic

Infrared spectroscopy is a rapid, easy‐to‐operate, label‐free and therefore cost‐effective technique. Many studies performed on biofluids (eg, serum, plasma, urine, sputum, bile and cerebrospinal fluid) have demonstrated its promising application as a clinical diagnostic tool. Given all these characteristics, infrared spectroscopy appears to be an ideal candidate to be implemented into the clinics. However, before considering its translation, a clear effort is needed to standardise protocols for biofluid spectroscopic analysis. To reach this goal, careful investigations to identify and track errors that can occur during the pre‐analytical phase is a crucial step. Here, we report for the first time, results of investigations into pre‐analytical factors that can affect the quality of the spectral data acquired on serum and plasma, such as the impact of long‐term freezing time storage of samples as well as the month‐to‐month reproducibility of the spectroscopic analysis. The spectral data discrimination has revealed to be majorly impacted by a residual water content variation in serum and plasma dried samples.      

Method development in high-performance liquid chromatography for high-throughput profiling and metabonomic studies of biofluid samples

"Metabonomics" has in the past decade demonstrated enormous potential in furthering the understanding of, for example, disease processes, toxicological mechanisms, and biomarker discovery. The same principles can also provide a systematic and comprehensive approach to the study of food ingredient impact on consumer health. However, "metabonomic" methodology requires the development of rapid, advanced analytical tools to comprehensively profile biofluid metabolites within consumers. Until now, NMR spectroscopy has been used for this purpose almost exclusively. Chromatographic techniques and in particular HPLC, have not been exploited accordingly. The main drawbacks of chromatography are the long analysis time, instabilities in the sample fingerprint and the rigorous sample preparation required. This contribution addresses these problems in the quest to develop generic methods for high-throughput profiling using HPLC. After a careful optimization process, stable fingerprints of biofluid samples can be obtained using standard HPLC equipment. A method using a short monolithic column and a rapid gradient with a high flow-rate has been developed that allowed rapid and detailed profiling of larger numbers of urine samples. The method can be easily translated into a slow, shallow-gradient high-resolution method for identification of interesting peaks by LC-MS/NMR. A similar approach has been applied for cell culture media samples. Due to the much higher protein content of such samples non-porous polymer-based small particle columns yielded the best results. The study clearly shows that HPLC can be used in metabonomic fingerprinting studies.     

A fluorescence-based high-throughput assay for the discovery of exchange protein directly activated by cyclic AMP (EPAC) antagonists

Background

The discovery, more than ten years ago, of exchange proteins directly activated by cAMP (EPAC) as a new family of intracellular cAMP receptors revolutionized the cAMP signaling research field. Extensive studies have revealed that the cAMP signaling network is much more complex and dynamic as many cAMP-related cellular processes, previously thought to be controlled by protein kinase A, are found to be also mediated by EPAC proteins. Although there have been many important discoveries in the roles of EPACs greater understanding of their physiological function in cAMP-mediated signaling is impeded by the absence of EPAC-specific antagonist.

Methodology/Principal Findings

To overcome this deficit, we have developed a fluorescence-based high throughput assay for screening EPAC specific antagonists. Our assay is highly reproducible and simple to perform using the “mix and measure” format. A pilot screening using the NCI-DTP diversity set library led to the identification of small chemical compounds capable of specifically inhibiting cAMP-induced EPAC activation while not affecting PKA activity.

Conclusions/Significance

Our study establishes a robust high throughput screening assay that can be effectively applied for the discovery of EPAC-specific antagonists, which may provide valuable pharmacological tools for elucidating the biological functions of EPAC and for promoting an understanding of disease mechanisms related to EPAC/cAMP signaling.     

Protein functional features are reflected in the patterns of mRNA translation speed

Background

The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These “synonymous mRNAs” may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of “silent” single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins.

Results

We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein’s important structural and functional features.

Conclusions

This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein’s functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1734-7) contains supplementary material, which is available to authorized users.     

Termination of protein synthesis in mammalian mitochondria

All mechanisms of protein synthesis can be considered in four stages: initiation, elongation, termination, and ribosome recycling. Remarkable progress has been made in understanding how these processes are mediated in the cytosol of many species; however, details of organellar protein synthesis remain sketchy. This is an important omission, as defects in human mitochondrial translation are known to cause disease and may contribute to the aging process itself. In this minireview, we focus on the recent advances that have been made in understanding how one of these processes, translation termination, occurs in the human mitochondrion.     

What biogeography is: a place for process

The search for understanding of the past and present processes that have and/or continue to generate observed biotic distribution patterns substantially involves historical reconstruction based on present patterns (both phylogenetic and geographical). How this should be undertaken has been a cause for major debate over many decades. Residual patterns do not always provide explicit pointers to the causal processes, and in addition to applying our understanding of earth history, we need also to carefully explore the implications of contemporary processes as a means for unravelling pattern. Some biogeographers assert that earth and life evolve together, but knowledge of distributions and ecologies indicate that this is sometimes true and sometimes false. Just as general patterns may sometimes indicate a commonality of the means that generated the patterns so, too, do observable processes sometimes indicate commonalities. Vicariance and dispersal are fundamental attributes of biotic distributions. Phylogeography has the potential to assist us in determining which of these mechanisms has generated observable patterns.     

Identification of new cell size control genes in <Emphasis Type="Italic">S. cerevisiae</Emphasis>

Cell size homeostasis is a conserved attribute in many eukaryotic species involving a tight regulation between the processes of growth and proliferation. In budding yeast S. cerevisiae, growth to a “critical cell size” must be achieved before a cell can progress past START and commit to cell division. Numerous studies have shown that progression past START is actively regulated by cell size control genes, many of which have implications in cell cycle control and cancer. Two initial screens identified genes that strongly modulate cell size in yeast. Since a second generation yeast gene knockout collection has been generated, we screened an additional 779 yeast knockouts containing 435 new ORFs (~7% of the yeast genome) to supplement previous cell size screens. Upon completion, 10 new strong size mutants were identified: nine in log-phase cells and one in saturation-phase cells, and 97% of the yeast genome has now been screened for cell size mutations. The majority of the logarithmic phase size mutants have functions associated with translation further implicating the central role of growth control in the cell division process. Genetic analyses suggest ECM9 is directly associated with the START transition. Further, the small (whi) mutants mrpl49Δ and cbs1Δ are dependent on CLN3 for cell size effects. In depth analyses of new size mutants may facilitate a better understanding of the processes that govern cell size homeostasis.     

The impact of AUG start codon context on maize gene expression in vivo

Summary In mammals, the sequence context surrounding an AUG start codon can alter the efficiency at which translation is initiated. Less is known about the AUG context requirements for translation initiation in plants. Using a maize transient assay, we present evidence that the naturally occurring AUG start codon of the Alcohol dehydrogenase-1 is efficiently used in vivo. We have also tested the effects of upstream, out-of-frame AUGs on the translation of firefly luciferase reporter gene mRNAs. The presence of an upstream out-of-frame AUG, even when surrounded by a poor context, eliminated most luciferase expression, suggesting efficient translation initiation at the upstream AUG. The relaxed requirements for AUG context in maize suggest that plants and mammals may differ in their requirements for efficient translation initiation.     

The Eukaryotic Ribosome: Current Status and Challenges

Despite having been identified first, their greater degree of complexity has resulted in our understanding of eukaryotic ribosomes lagging behind that of their bacterial and archaeal counterparts. A much more complicated biogenesis program results in ribosomes that are structurally, biochemically, and functionally more complex. However, recent advances in molecular genetics and structural biology are helping to reveal the intricacies of the eukaryotic ribosome and to address many longstanding questions regarding its many roles in the regulation of gene expression.Since its initial discovery using differential ultracentrifugation of rat liver homogenates (reviewed in Ref. 1), the ribosome has remained a foundational platform upon which our understanding of the relationship between structure and function at the molecular level has been built. There is a rich history of biochemistry and genetics of eukaryotic ribosomes, including the discovery in the 1950s that they 32 are the site of protein synthesis, the elucidation of the function of the nucleolus, and even the discovery of the first eukaryotic RNA polymerase (reviewed in Ref. 2). Whereas early studies using mammalian ribosomes defined the “integral requirements” for protein synthesis, a switch to bacterial ribosomes in the 1960s facilitated the identification of the “minimal requirements” for the translational machinery, giving rise to a “golden age” of translation. In particular, the greater degree of structural and functional complexity makes eukaryotic ribosomes more challenging to work with than their bacterial and archaeal counterparts. For example, whereas bacterial translation initiation requires only a small set of trans-acting factors and is facilitated by the Shine-Dalgarno sequence, this process in eukaryotes requires a multifactorial complex of trans-acting factors that is almost as massive as the ribosome itself (reviewed in Ref. 3). Here, some of the current topics and challenges in the study of the eukaryotic ribosome are reviewed.     

Genetics of parkin-linked disease

Research into Parkinsons disease (PD), once considered the archetypical non-genetic neurodegenerative disorder, has been revolutionized by the identification of a number of genes, mutations of which underlie various familial forms of the disease. Whereas such mutations appear to exist in a relatively small number of individuals from a few families, the study of the function of these genes promises to reveal the fundamental disease pathogenesis, not only of familial forms of the disease, but also of the much more common sporadic PD. The observation that mutations in the second identified PD locus (parkin) are common in juvenile- and early-onset PD and increasing evidence supporting a direct role for parkin in late-onset disease make this gene a particularly compelling candidate for intensified investigation. The determination of the frequency and effect of parkin mutations in various subsets of PD will be crucial for understanding the way in which parkin is related to neurodegenerative mechanisms, and whether these subsets might be effectively identified and treated. In addition, many aspects of parkin-linked disease, originally thought to be well defined, have now been obscured both by genetic studies that preclude a simple model of disease transmission and by clinical and pathological studies that demonstrate broad variability in cases with parkin mutations. Future studies that address the issues in question should have a far-reaching impact in downstream biochemical studies and our understanding of parkins role in PD.     

Immuno‐ and Correlative Light Microscopy‐Electron Tomography Methods for 3D Protein Localization in Yeast

Compartmentalization of eukaryotic cells is created and maintained through membrane rearrangements that include membrane transport and organelle biogenesis. Three‐dimensional reconstructions with nanoscale resolution in combination with protein localization are essential for an accurate molecular dissection of these processes. The yeast Saccharomyces cerevisiae is a key model system for identifying genes and characterizing pathways essential for the organization of cellular ultrastructures. Electron microscopy studies of yeast, however, have been hampered by the presence of a cell wall that obstructs penetration of resins and cryoprotectants, and by the protein dense cytoplasm, which obscures the membrane details. Here we present an immuno‐electron tomography (IET) method, which allows the determination of protein distribution patterns on reconstructed organelles from yeast. In addition, we extend this IET approach into a correlative light microscopy‐electron tomography procedure where structures positive for a specific protein localized through a fluorescent signal are resolved in 3D. These new investigative tools for yeast will help to advance our understanding of the endomembrane system organization in eukaryotic cells.      

Cascading Walks Model for Human Mobility Patterns

Background

Uncovering the mechanism behind the scaling laws and series of anomalies in human trajectories is of fundamental significance in understanding many spatio-temporal phenomena. Recently, several models, e.g. the explorations-returns model (Song et al., 2010) and the radiation model for intercity travels (Simini et al., 2012), have been proposed to study the origin of these anomalies and the prediction of human movements. However, an agent-based model that could reproduce most of empirical observations without priori is still lacking.

Methodology/Principal Findings

In this paper, considering the empirical findings on the correlations of move-lengths and staying time in human trips, we propose a simple model which is mainly based on the cascading processes to capture the human mobility patterns. In this model, each long-range movement activates series of shorter movements that are organized by the law of localized explorations and preferential returns in prescribed region.

Conclusions/Significance

Based on the numerical simulations and analytical studies, we show more than five statistical characters that are well consistent with the empirical observations, including several types of scaling anomalies and the ultraslow diffusion properties, implying the cascading processes associated with the localized exploration and preferential returns are indeed a key in the understanding of human mobility activities. Moreover, the model shows both of the diverse individual mobility and aggregated scaling displacements, bridging the micro and macro patterns in human mobility. In summary, our model successfully explains most of empirical findings and provides deeper understandings on the emergence of human mobility patterns.     

An expanding role for cell biologists in drug discovery and pharmacology

The profound challenges facing clinicians, who must prescribe drugs in the face of dramatic variability in response, and the pharmaceutical industry, which must develop new drugs despite ever-rising costs, represent opportunities for cell biologists interested in rethinking the conceptual basis of pharmacology and drug discovery. Much better understanding is required of the quantitative behaviors of networks targeted by drugs in cells, tissues, and organisms. Cell biologists interested in these topics should learn more about the basic structure of drug development campaigns and hone their quantitative and programming skills. A world of conceptual challenges and engaging industry–academic collaborations awaits, all with the promise of delivering real benefit to patients and strained healthcare systems.Four decades of molecular and cellular biology has fundamentally improved our understanding of human disease, but this undeniable revolution has had less impact than hoped on human health, particularly in the area of discovery and use of therapeutic drugs. The missing link between basic science and useful therapeutics is the quantitative, multifactorial understanding of networks that operate within and between cells and of the changes that drugs induce in these networks (Berger and Iyengar, 2009 ). Contributing to this understanding of drugs and network dynamics represents a significant opportunity for cell biologists interested in careers in industry and for academic scientists seeking industrial collaborations. Success in such “translational” research is not simply a matter of applying known concepts to practical problems; interesting new ideas and science are required (Loscalzo and Barabasi, 2011 ). Fifty years ago, pharmacology and pathophysiology provided cell biologists with many fundamental research problems, and there is every reason to believe this will also be true in the future.Insufficient understanding of pathological and therapeutic mechanisms at a cellular level has contributed to the growing difficulty of bringing new drugs to market. Even when drugs win approval, it is rare that we can predict which patients will benefit from them. As a result, patients have too few treatment options, many serious illnesses remain difficult to treat, and the cost of new medicines is too high (often at the limit of what healthcare systems can support). High-throughput “-omic” approaches have been hailed as a means to understand disease and develop new drugs, but an outstanding opportunity exists for fundamental contributions from cell biologists. A central feature of cell biology is its emphasis on applying diverse conceptual and analytical approaches to biological processes that are inherently multifactorial. This is in contrast to “-omic” approaches, in which the focus is usually on one type of data collected in volume (gene sequences being one example).The role of cell biology in unraveling disease mechanisms is well established, but the value of cell biology in drug development is less well appreciated. Cell and molecular biologists currently play a role during the earliest preclinical stages of drug development in the identification and evaluation of potential drug targets (Figure 1). However, it is increasingly apparent that existing procedures for qualifying targets are inadequate, and this manifests itself as frequent and expensive late-stage failures of efficacy (typically during phase II and III clinical studies (Paul et al., 2010 ). To overcome this problem, we require a much better understanding of the functions of target proteins within the context of cellular networks in normal and diseased cells, both in culture and in the organism (“network biology”). Opportunities exist for cell biologists to help define optimal therapeutic strategies (e.g., aiding in the choice between using a recombinant antibody or small molecule) and to ascertain exposure/response relationships in tissues. Cell biologists also have an important role to play in understanding acquired resistance. A lack of durable responses is the bane of many recently approved targeted drugs. Finally, in diseases such as cancer, we have many plausible targets (the Akt kinase, for example), but it is not clear how to inhibit the target without causing excessive toxicity. It is also unclear why only a subset of patients responds to even the most potent and selective inhibitors. In our opinion, many drugs fail because cell biology is ignored during the later stages of drug development, when selecting indications and drug combinations and determining dosing schedules are the key tasks.Open in a separate windowFIGURE 1:Traditional and emerging roles for cell biologists in drug development and pharmacology. Traditionally, cell biologists have worked on the earliest phases of drug discovery, during the identification and validation of targets. However, by expanding their horizons and adding new skills, cell biologists can become well-suited to other roles later in development, roles in which the stakes are higher and sophisticated understanding of the underlying biology less common. Some of these fields are traditional (e.g., pharmacokinetics and pharmacodynamics [PK/PD]; black) and others are newly emerging (e.g., systems pharmacology; red).Cell biology also has an important role to play in discerning the precise mechanisms of action of existing drugs; it is a remarkable fact that we understand very few drug responses in mechanistic detail. This is as true of the latest generations of targeted therapeutics (many of which aim for selective inhibition of disease-specific mutants) as for older drugs that constitute the mainstay of standard-of-care therapy. The challenge lies less in the interaction between a drug and its intended target than in the consequences of target inhibition for cellular phenotype. This is particularly true when we consider genetic variation from one patient to the next and from one cell to the next within a single patient (particularly with diseases such as cancer). Cellular responses to the microtubule inhibitor and anticancer drug Taxol are an excellent example. Despite being an “old-fashioned” cytotoxic drug, Taxol and its various derivatives are a mainstay of contemporary cancer care, and more patients have probably benefited from taxanes than from all the targeted anticancer drugs combined (Ni Chonghaile et al., 2011 ). Understanding responses to taxanes at a cellular level has also been central to understanding the biology of the spindle assembly checkpoint and mitosis in general. Over the past two decades, checkpoint pathways have been identified and studied in many organisms, and we now understand in detail how processes such as mitotic catastrophe cause cell death (Mitchison, 2012 ). Remarkably, however, the factors that determine whether a cell lives or dies when exposed to Taxol differ dramatically between cultured cells and xenografted tumors (never mind real human tumors); progress through mitosis is always required in culture, but apparently not in the mouse (Orth et al., 2011 ). Understanding this difference represents a fascinating problem in cell biology likely to reveal how cell-autonomous processes, such as mitosis, interact with factors from the local environment in controlling cell fate. Such understanding could also have a real and immediate impact on cancer care.Over the past decade, the success of classical antimitotic chemotherapeutics, such as Taxol, has given rise to efforts to develop other antimitotic agents. For example, drugs that target spindle motors promised to combine the therapeutic antimitotic effects of Taxol, while minimizing neuropathy (motors such as Eg5 are not expressed in neurons [ Huszar et al., 2009 ]). Despite a massive effort by multiple companies, these drugs have proven disappointing in the clinic, as have many drugs that target mitotic kinases. It is now clear that inhibiting mitosis in cancer cells simply does not have the effects we have assumed for the past 50 years, and those antimitotic drugs that do work must do something fundamentally more. Working this out is likely to advance our understanding of the complexities of cell division in humans and animals. However, given the time pressures in industry, there is little opportunity to pursue “failed” drugs, and academic cell biologists have largely ignored problems such as the mechanisms of cell killing by antimitotic agents in real tumors. We must adopt a more holistic and physiological perspective in which we admit that detailed mechanistic understanding is required not only in model organisms and HeLa cells, but also in myriad normal and diseased tissues that have low mitotic index, unusual forms of endo-replication, and complex interactions with neighboring cells. New programs sponsored by the National Center for Advancing Translational Sciences promise to provide some support for this type of research (Allison, 2012 ).More generally, while we all recognize that the “one gene–one disease” paradigm is insufficient for understanding human disease and for selecting patients who will respond to therapy, an effective alternative remains to be developed. Even when the multiplicity of factors involved in a particular disease can be discerned, this understanding does not necessarily reveal how to develop a treatment or cure. For therapy, we must elucidate not only the nature of the initial insult (e.g., a cancer-causing mutation) but also the operation of biological networks that attempt to compensate for the insult (to reestablish homeostasis) and variation in network properties from one individual to the next. It is also important that we identify and understand factors that determine the concentrations and biodistribution of drugs in patients with diverse genotypes. This, in turn, requires a multiscale, network-based approach involving systemic and quantitative study of biological processes at the cellular, tissue, and organismal levels and of the effects of drugs on these processes—precisely the areas in which cell biology has much to contribute.Despite these opportunities, several factors stand in the way of a greater role for cell biologists in drug discovery and development. The first is an unfamiliar vocabulary. We are repeatedly amazed by postdocs who have decided they want to pursue a career in biotechnology or the pharmaceutical industry but who have not spent the time to learn the basics of the drug discovery process from preclinical development to phased clinical trials. Anyone interested in an industrial career should stay abreast of the lively and interesting debates about the best ways to structure and evaluate trials (Kelloff and Sigman, 2012 ). An industrial career usually requires writing more but shorter reports than an academic career, and familiarity with the language of drug discovery makes report writing much easier. A career in industry also benefits from knowledge of the diverse scientific, medical, and business factors that determine success in a drug development campaign. At the same time, it is important to note that some key drug discovery concepts, such as “target identification” or “target qualification,” are widely used but elusive. They imply that the key task is identifying (or cloning) a specific target protein and then screening for agonists and antagonists. As mentioned above, the current challenge increasingly involves understanding targets in the context of biological networks, homeostatic processes, and pathophysiological mechanisms (Wang et al., 2012 ). This implies a more nuanced and holistic approach to understanding the ways the targets and drugs interact (Chene, 2012 ).Many cell biologists in industry find themselves involved in the development or evaluation of assays, particularly for high-throughput screening. Evaluating such screens requires basic understanding of statistics and the trade-offs between false-positive and false-negative results (Atkinson and Lalonde, 2007 ). If high-content screening by imaging is involved, then it is necessary to develop and apply machine vision approaches. Unfortunately, many cell biologists are insufficiently trained in basic statistics, and they have poor programming skills. In our experience, this can be a significant impediment to employment in industry that can be overcome by taking courses in probability and statistics and by gaining practical experience with MatLab or languages such as Python and R. Particularly in biotech, learning the rudiments of intellectual property law can also be a real asset, since it makes it easier to spot patentable inventions.Even the largest drug companies have come to doubt their ability to pursue development projects all the way from target identification to drug approval. It is widely believed that more frequent and effective collaborations between industry and academe are part of the solution (Rubin and Gilliland, 2012 ). This obviously represents a significant opportunity for academic cell biologists. However, the days in which companies were willing to shower academic institutions with generous and unrestricted financial support are long gone. It is now necessary to develop research programs that revolve around concrete goals and deliverables. In our experience, this can be an exciting process for academics accustomed to the conservatism of federal grants, since industry is often willing to pursue ideas that are risky and innovative. Moreover, we have rarely found the perceived difference between applied and basic research to be a significant issue. However, very different expectations over the duration of projects are a major challenge. Industry typically works on 12- to 18-month time lines and academe on a schedule that is at least twice as long. In our experience, even the most effective industry–academic projects tend to underdeliver over the first 18 months, and then only prove their worth in subsequent years. Industry must be more sensitive to the fact that starting a new project in an academic setting means recruiting a new student or postdoc and that there is no way for such an individual to be trained and to succeed with only 18 months of support. However, academics must learn to accommodate the real need for industrial partners to reevaluate projects after approximately 18 months. In our opinion, academics could speed up the initial stages of a project and industry should slow down. We have personally witnessed many industrial projects that were discontinued without reaching a firm conclusion, only to result in an exciting opportunity being missed or to leave open questions that impede progress many years later. A frank discussion of these issues is essential at the outset of any collaborative project.Despite obvious challenges, we envision an expanding role for cell biologists in drug discovery that extends beyond their traditional involvement in early-stage target identification. Significant opportunities exist in better qualifying potential targets and in identifying the role of target proteins in cellular function and pathophysiology. Better understanding of targets in the context of cellular and tissue networks should make it possible to design better therapeutics based on optimizing selectivity, affinity, and type of molecule. Cell biologists can also become more involved in clinical development of new and standard-of-care drugs, particularly with respect to identifying indications, developing diagnostics, and stratifying populations. In this case, learning more about the clinical phases of drug development is valuable. In our personal experience, the most effective approaches are those that involve quantitative analysis and combine experimentation and modeling. This often goes under the name “systems biology” but can easily be viewed as a natural evolution of cell biology in the face of ever-larger data sets and more complex cellular mechanisms. Thus, if we had a single piece of advice for cell biologists interested in pharmacology or drug discovery, it is to acquire or hone skills in statistics, bioinformatics, programming, and applied mathematics in general.Open in a separate windowP. K. SorgerOpen in a separate windowP. K. Sorger     

Alien invasions in aquatic ecosystems: Toward an understanding of brook trout invasions and potential impacts on inland cutthroat trout in western North America

Experience from case studies of biologicalinvasions in aquatic ecosystems has motivated aset of proposed empirical rules forunderstanding patterns of invasion and impactson native species. Further evidence is neededto better understand these patterns, andperhaps contribute to a useful predictivetheory of invasions. We reviewed the case ofbrook trout (Salvelinus fontinalis)invasions in the western United States andtheir impacts on native cutthroat trout (Oncorhynchus clarki). Unlike many biologicalinvasions, a considerable body of empiricalresearch on brook trout and cutthroat trout isavailable. We reviewed life histories of eachspecies, brook trout invasions, their impactson cutthroat trout, and patterns and causes ofsegregation between brook trout and cutthroattrout. We considered four stages of theinvasion process: transport, establishment,spread, and impacts to native species. Most ofthe research we found focused on impacts. Interspecific interactions, especiallycompetition, were commonly investigated andcited as impacts of brook trout. In many casesit is not clear if brook trout invasions have ameasurable impact. Studies of speciesdistributions in the field and a variety ofexperiments suggest invasion success of brooktrout is associated with environmental factors,including temperature, landscape structure,habitat size, stream flow, and humaninfluences. Research on earlier stages ofbrook trout invasions (transport,establishment, and spread) is relativelylimited, but has provided promising insights. Management alternatives for controllingbrook trout invasions are limited, and actions tocontrol brook trout focus on direct removal,which is variably successful and can haveadverse effects on native species. Themanagement applicability of research has beenconfounded by the complexity of the problem andby a focus on understanding processes atsmaller scales, but not on predicting patternsat larger scales. In the short-term, animproved predictive understanding of brooktrout invasions could prove to be most useful,even if processes are incompletely understood. A stronger connection between research andmanagement is needed to identify more effectivealternatives for controlling brook troutinvasions and for identifying managementpriorities.     

Seasonality in human zoonotic enteric diseases: a systematic review

Background

Although seasonality is a defining characteristic of many infectious diseases, few studies have described and compared seasonal patterns across diseases globally, impeding our understanding of putative mechanisms. Here, we review seasonal patterns across five enteric zoonotic diseases: campylobacteriosis, salmonellosis, vero-cytotoxigenic Escherichia coli (VTEC), cryptosporidiosis and giardiasis in the context of two primary drivers of seasonality: (i) environmental effects on pathogen occurrence and pathogen-host associations and (ii) population characteristics/behaviour.

Methodology/Principal Findings

We systematically reviewed published literature from 1960–2010, resulting in the review of 86 studies across the five diseases. The Gini coefficient compared temporal variations in incidence across diseases and the monthly seasonality index characterised timing of seasonal peaks. Consistent seasonal patterns across transnational boundaries, albeit with regional variations was observed. The bacterial diseases all had a distinct summer peak, with identical Gini values for campylobacteriosis and salmonellosis (0.22) and a higher index for VTEC (Gini = 0.36). Cryptosporidiosis displayed a bi-modal peak with spring and summer highs and the most marked temporal variation (Gini = 0.39). Giardiasis showed a relatively small summer increase and was the least variable (Gini = 0.18).

Conclusions/Significance

Seasonal variation in enteric zoonotic diseases is ubiquitous, with regional variations highlighting complex environment-pathogen-host interactions. Results suggest that proximal environmental influences and host population dynamics, together with distal, longer-term climatic variability could have important direct and indirect consequences for future enteric disease risk. Additional understanding of the concerted influence of these factors on disease patterns may improve assessment and prediction of enteric disease burden in temperate, developed countries.