Illuminating the complexity of GPCR pathway selectivity – advances in biosensor development

It should come as no surprise that G protein-coupled receptors (GPCRs) continue to occupy the focus of drug discovery efforts. Their widespread expression and broad role in signal transduction underline their importance in human physiology. Despite more than 800 GPCRs sharing a common architecture, unique differences govern ligand specificity and pathway selectivity. From the relatively simplified view offered by classical radioligand binding assays and contractility responses in organ baths, the road from ligand binding to biological action has become more and more complex as we learn about the molecular mediators that underly GPCR activation and translate it to physiological outcomes. In particular, the development of biosensors has evolved over the years to dissect the capacity of a given receptor to activate individual pathways. Here, we discuss how recent biosensor development has reinforced the idea that biased signaling may become mainstream in drug discovery programs.     

A critical review of the ‘neugliederung’ concept in relation to the development of the vertebral column

Summary The literature on the early embryonic development of the vertebral column in various animal species was analyzed to evaluate so many unrelated or contradictory observations. The recurring problems are described. One of the first was the lack of correspondence between the metameric boundaries of the primitive vertebral bodies arising from the somites and those of the adult vertebral bodies, as presumably shown by their relationship to the vertebral processes and spinal nerves. A century ago, Remak introduced the concept of Neugliederung, according to which the ultimate vertebral body boundaries are determined by a shift of a half segment in comparison with the earlier segment boundaries.     

Genetics,development and composition of the insect head – A beetle’s view

Many questions regarding evolution and ontogeny of the insect head remain open. Likewise, the genetic basis of insect head development is poorly understood. Recently, the investigation of gene expression data and the analysis of patterning gene function have revived interest in insect head development. Here, we argue that the red flour beetle Tribolium castaneum is a well suited model organism to spearhead research with respect to the genetic control of insect head development. We review recent molecular data and discuss its bearing on early development and morphogenesis of the head. We present a novel hypothesis on the ontogenetic origin of insect head sutures and review recent insights into the question on the origin of the labrum. Further, we argue that the study of developmental genes may identify the elusive anterior non-segmental region and present some evidence in favor of its existence. With respect to the question of evolution of patterning we show that the head Anlagen of the fruit fly Drosophila melanogaster and Tribolium differ considerably and we review profound differences of their genetic regulation. Finally, we discuss which insect model species might help us to answer the open questions concerning the genetic regulation of head development and its evolution.     

The development of policy approaches for reducing nitro-gen pollution to coastal waters of the USA

Two-thirds of the coastal rivers and bays in the United States are degraded from nutrient pollution, and nitrogen inputs these waters continue to increase. The nitrogen comes from a variety of sources, including runoff from agricultural fields, concentrated animal feeding operations, atmospheric deposition from fossil fuel combustion, and sewage and septic wastes. Technical solutions for nitrogen pollution exist at reasonable cost. That most of these solutions have not yet been implemented to any significant extent across the United States suggests that new policy approaches are necessary. The best solution may involve a combination of voluntary and mandatory approaches, applying different approaches to different sources of nitrogen pollution. A watershed-based approach that relies heavily on voluntary mechanisms (such as crop-yield insurance to reduce over-fertilization) is likely to be the most effective for some sources of nitrogen (such as runoff from agricultural fields), while a uniform national regulatory approach may be better for others (such as NOx emissions from fossil fuel combustion). Implementation of management strategies should be carefully coupled to monitoring programs to assess the effectiveness of these strategies. While both nitrogen and phosphorus are important to control, the focus should be on nitrogen management, in part because nitrogen is more generally the causal agent of coastal eutrophication. Also, while nitrogen-control practices tend to also reduce phosphorus pollution, phosphorus-control practices often have little effect on nitrogen. Although current scientific and technical knowledge is sufficient to begin to make substantial progress toward solving coastal nitrogen pollution, progress will be made more quickly and more cost effectively with increased investment in appropriate scientific research.     

Aquaporins in development – a review

Water homeostasis during fetal development is of crucial physiologic importance. It depends upon maternal fetal fluid exchange at the placenta and fetal membranes, and some exchange between fetus and amniotic fluid can occur across the skin before full keratinization. Lungs only grow and develop normally with fluid secretion, and there is evidence that cerebral spinal fluid formation is important in normal brain development. The aquaporins are a growing family of molecular water channels, the ontogeny of which is starting to be explored. One question that is of particular importance is how well does the rodent (mouse, rat) fetus serve as a model for long-gestation mammals such as sheep and human? This is particularly important for organs such as the lung and the kidney, whose development before birth is very much less in rodents than in the long-gestation species.     

Arrested development and the great escape – The role of cellular senescence in pancreatic cancer

The outcomes of pancreatic cancer remain dismal due to late clinical presentation and the aggressive nature of the disease. A heterogeneous combination of genetic mutations, including KRAS, INK4a/CDKN2A and p53, underpin the propensity of pancreatic cancer to rapidly invade and disseminate. These oncogenes and tumour suppressors are strongly associated with cellular senescence, therefore suggesting this process as having a key role in malignant transformation. In the context of cancer, oncogenic stimuli trigger the senescent phenotype resulting in cell cycle growth arrest and prevention of progression of premalignant lesions such as PanINs. However mutations of the aforementioned oncogenes or tumour suppressors result in cells escaping senescence and thus allowing tumours to progress. This review presents current evidence regarding both senescence induction and escape with respect to pancreatic cancer, highlighting the key roles of p19ARF, p53, Rb and P16INK4a. The epigenetic regulatory component is also discussed, with relevance to DNA methylation and HDACs. Lastly the role of the tumour microenvironment, and in particular pancreatic stellate cells, is discussed with regards to the induction of a senescence associated secretory phenotype (SASP), with SASP-associated secretory factors contributing to the pro-tumorigenic effects of the surrounding activated stroma. Further work is required in this field to elucidate the most important pathways relating to cellular senescence that contribute to the belligerent nature of this disease, with the aim of discovering therapeutic targets to improve patient outcomes.     

Characterizing the role of the dark kinome in neurodegenerative disease – A mini review

BackgroundDrugs that modulate previously unexplored targets could potentially slow or halt the progression of neurodegenerative diseases. Several candidate proteins lie within the dark kinome, those human kinases that have not been well characterized. Much of the kinome (~80%) remains poorly studied, and these targets likely harbor untapped biological potential.Scope of reviewThis review highlights the significance of kinases as mediators of aberrant pathways in neurodegeneration and provides examples of published high-quality small molecules that modulate some of these kinases.Major conclusionsThere is a need for continued efforts to develop high-quality chemical tools to illuminate the function of understudied kinases in the brain. Potent and selective small molecules enable accurate pairing of an observed phenotype with a protein target.General significanceThe examples discussed herein support the premise that validation of therapeutic hypotheses surrounding kinase targets can be accomplished via small molecules and they can serve as the basis for disease-focused drug development campaigns.     

Hydrophilicity Matching – A Potential Prerequisite for the Formation of Protein-Protein Complexes in the Cell

A binding event between two proteins typically consists of a diffusional search of binding partners for one another, followed by a specific recognition of the compatible binding sites resulting in the formation of the complex. However, it is unclear how binding partners find each other in the context of the crowded, constantly fluctuating, and interaction-rich cellular environment. Here we examine the non-specific component of protein-protein interactions, which refers to those physicochemical properties of the binding partners that are independent of the exact details of their binding sites, but which can affect their localization or diffusional search for one another. We show that, for a large set of high-resolution experimental 3D structures of binary, transient protein complexes taken from the DOCKGROUND database, the binding partners display a surprising, statistically significant similarity in terms of their total hydration free energies normalized by a size-dependent variable. We hypothesize that colocalization of binding partners, even within individual cellular compartments such as the cytoplasm, may be influenced by their relative hydrophilicity, potentially in response to local hydrophilic gradients.     

TGFβ signalling in the development of ovarian function

Ovarian development begins back in the embryo with the formation of primordial germ cells and their subsequent migration and colonisation of the genital ridges. Once the ovary has been defined structurally, the primordial germ cells transform into oocytes and become housed in structures called follicles (in this case, primordial follicles), a procedure that, in most mammals, occurs either shortly before or during the first few days after birth. The growth and differentiation of follicles from the primordial population is termed folliculogenesis. Primordial follicles give rise to primary follicles that transform into preantral follicles, then antral follicles (secondary follicles) and, finally (preovulatory) Graafian follicles (tertiary follicles) in a co-ordinated series of transitions regulated by hormones and local intraovarian factors. Members of the transforming growth factor-β (TGFβ) superfamily have been shown to play important roles in this developmental process starting with the specification of primordial germ cells by the bone morphogenetic proteins through to the recruitment of primordial follicles by anti-Mullerian hormone and, potentially, growth and differentiation factor-9 (GDF9) and, finally, their transformation into preantral and antral follicles in response to activin and TGF-β. Developmental and mutant mouse models have been used to show the importance of this family of growth factors in establishing the first wave of folliculogenesis.The author thanks the NHMRC of Australia for funding (Regkey 241000).     

Utilization of Surveillance after Polypectomy in the Medicare Population – A Cohort Study

Background

Surveillance in patients with previous polypectomy was underused in the Medicare population in 1994. This study investigates whether expansion of Medicare reimbursement for colonoscopy screening in high-risk individuals has reduced the inappropriate use of surveillance.

Methods

We used Kaplan-Meier analysis to estimate time to surveillance and polyp recurrence rates for Medicare beneficiaries with a colonoscopy with polypectomy between 1998 and 2003 who were followed through 2008 for receipt of surveillance colonoscopy. Generalized Estimating Equations were used to estimate risk factors for: 1) failing to undergo surveillance and 2) polyp recurrence among these individuals. Analyses were stratified into three 2-year cohorts based on baseline colonoscopy date.

Results

Medicare beneficiaries undergoing a colonoscopy with polypectomy in the 1998–1999 (n = 4,136), 2000–2001 (n = 3,538) and 2002–2003 (n = 4,655) cohorts had respective probabilities of 30%, 26% and 20% (p<0.001) of subsequent surveillance events within 3 years. At the same time, 58%, 52% and 45% (p<0.001) of beneficiaries received a surveillance event within 5 years. Polyp recurrence rates after 5 years were 36%, 30% and 26% (p<0.001) respectively. Older age (≥ 70 years), female gender, later cohort (2000–2001 & 2002–2003), and severe comorbidity were the most important risk factors for failure to undergo a surveillance event. Male gender and early cohort (1998–1999) were the most important risk factors for polyp recurrence.

Conclusions

Expansion of Medicare reimbursement for colonoscopy screening in high-risk individuals has not reduced underutilization of surveillance in the Medicare population. It is important to take action now to improve this situation, because polyp recurrence is substantial in this population.     

Maternal Smoking and the Risk of Cancer in Early Life – A Meta-Analysis

BackgroundIn spite of the well-known harmful effects on the fetus, many women continue smoking during pregnancy. Smoking as an important source of toxic chemicals may contribute to the developmental origin of diseases.ObjectivesThe aim of this work was to pursue the possible association between maternal smoking and cancer in early life. Specifically, we wanted to identify the associated early life cancer types, and to quantify the associations.MethodsIn a systematic literature search 825 articles were identified in PubMed and Web of Science, and 55 more through the reference lists. Of these 62 fulfilled the criteria for inclusion in meta-analyses. Using Mantel-Haenszel or DerSimonian and Laird method, depending on heterogeneity of the studies, pooled estimates and 95% confidence intervals for eight cancer types were calculated.ResultsSmoking during pregnancy was associated with an increased risk for for brain and central nervous system tumors (OR = 1.09; 95% CI = 1.02–1.17). Although the risk for lymphoma was also associated (OR = 1.21; 95% CI = 1.05–1.34), it did not hold up in subgroup analyses. Leukemia was not found to be associated with maternal smoking. Five other cancer types (bone, soft tissue, renal, hepatic, and germ cell cancer) were also examined, but the number of studies was too limited to exclude the possibility of maternal smoking as a risk factor for cancer in offspring.ConclusionsAccording to our meta-analyses, maternal smoking is associated with nervous system cancers, but not with leukemia in early life. Confirming or rejecting associations of maternal smoking with lymphoma and the five other cancer types requires further studies.     

Long-term development of the crustacean plankton in the Saidenbach Reservoir (Germany) – changes,causes, consequences

The rates of development and food intake of the copepod Temora longicornis (Müller) were studied using artificial blooms of Phaeocystis globosa Scherffel under different conditions of nutrient limitation. Mesocosms with 800 l of natural seawater were manipulated by inoculation with cultured P. globosa and by addition of nitrogen and/or phosphorus, to obtain N- or P-limited blooms of P. globosa. During development and ageing of these blooms, water from the mesocosms was used as medium for incubation of nauplii of T. longicornis. Only moderate rates of naupliar development as well as high rates of mortality were observed, irrespective of major differences of nutrient conditions and density of P. globosa. Grazing by the nauplii on P. globosa seemed to be low, suggesting a low food quality of this alga at all physiological conditions studied. The results of this study indicate a low capability of T. longicornis nauplii for control of nuisance algal blooms caused by P. globosa.     

Production of the antibiotic gallidermin by Staphylococcus gallinarum – development of a scale-up procedure

A scale-up strategy into 200 l pilot-scale for the production of the antibiotic gallidermin by Staphylococcus gallinarum Tü 3928 was developed. Large-scale fermentations were simulated by consecutive liquid cultures of smaller scale. Afterwards, optimised cultivation conditions were transferred to pilot-scale. Best results were achieved by addition of Maltose during the late production phase leading to a final concentration of 330 mg gallidermin per litre. Compared to the concentrations found in a non-pulsed pilot-scale fermentations this is an increase of 20–30%.     

Advances in the human genome project – A review

While celebrating its fifth official birthday last year it seems that the Human Genome Project (HGP) has and will continue to yield important biochemical information to mankind. It is exhilarating to think about the transition from studying genome structure to understanding genome function. The collective actions of information dessimination, technology development for efficient and faster sequencing, high-volume sequencing and developing model organisms has led to its success sofar. Various genome-wide STS-based human maps were completed in 1995, including a genetic map, a YAC map, a RH map with, and an integrated YAC-RH genetic map. These maps provide comprehensive frameworks for positioning additional loci, with the current genetic and RH maps spanning essentially 100% of the human genome and the YAC maps covering 95%. Few genes, however, have yet been localized on these framework maps. To date the Human Genome Project has experienced gratifying success. The technology and data produced by the genome project will provide a strong stimulus to broad areas of biological research and biotechnology. However, enormous challenges remain.     

SOD1 in amyotrophic lateral sclerosis development – in silico analysis and molecular dynamics of A4F and A4V variants

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that is characterized by the selective loss of motor neurons. Approximately 5% to 10% of patients with ALS have a family history of the disease, and approximately 20% of familial amyotrophic lateral sclerosis (fALS) cases are associated with mutations in Cu/Zn superoxide dismutase (SOD1). In this study, we evaluated the structural and functional effects of human A4F and A4V SOD1 protein mutations. We performed an in silico analysis using prediction algorithms of nonsynonymous single-nucleotide polymorphisms (nsSNPs) associated with the fALS development. Our structural conservation results show that the mutations analyzed (A4V and A4F) were in a highly conserved region. Molecular dynamics simulations using the Linux GROMACS package revealed how these mutations affect protein structure, protein stability, and aggregation. These results suggest that there might be an effect on the SOD1 function. Understanding the molecular basis of disease provides new insights useful for rational drug design and advancing our understanding of the ALS development.