Recent developments in ligands and chemical probes targeting solute carrier transporters

Solute carrier (SLC) membrane transporters remain a largely unexploited target class, despite their central roles in cell identity and metabolism. This gap is reflected in the lack of high-quality chemical ligands or probes and in the small number of compounds that have progressed toward clinical development. In this review, we discuss recent advancements in SLC ligand discovery as well as new candidates that have been added to the investigational toolkit, with a particular focus on first-in-class ligands and the cognate discovery strategies. The availability of new probes expands the opportunity to elucidate the functions of SLCs and their relevance in physiology and explores any future potential of SLC druggability.     

Flanking Regions Determine the Structure of the Poly-Glutamine in Huntingtin through Mechanisms Common among Glutamine-Rich Human Proteins

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Expanding the concepts and tools of metabolic engineering to elucidate cancer metabolism

The metabolic engineer's toolbox, comprising stable isotope tracers, flux estimation and analysis, pathway identification, and pathway kinetics and regulation, among other techniques, has long been used to elucidate and quantify pathways primarily in the context of engineering microbes for producing small molecules of interest. Recently, these tools are increasingly finding use in cancer biology due to their unparalleled capacity for quantifying intracellular metabolism of mammalian cells. Here, we review basic concepts that are used to derive useful insights about the metabolism of tumor cells, along with a number of illustrative examples highlighting the fundamental contributions of these methods to elucidating cancer cell metabolism. This area presents unique opportunities for metabolic engineering to expand its portfolio of applications into the realm of cancer biology and help develop new cancer therapies based on a new class of metabolically derived targets. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Role of stable isotopes in life--testing isotopic resonance hypothesis

Stable isotopes of most important biological elements, such as C, H, N and O, affect living organisms. In rapidly growing species, deuterium and to a lesser extent other heavy isotopes reduce the growth rate. At least for deuterium it is known that its depletion also negatively impacts the speed of biological processes. As a rule, living organisms "resist" changes in their isotopic environment, preferring natural isotopic abundances. This preference could be due to evolutionary optimization; an additional effect could be due to the presence of the "isotopic resonance". The isotopic resonance phenomenon has been linked to the choice of earliest amino acids, and thus affected the evolution of genetic code. To test the isotopic resonance hypothesis, literature data were analyzed against quantitative and qualitative predictions of the hypothesis. Four studies provided five independent datasets, each in very good quantitative agreement with the predictions. Thus, the isotopic resonance hypothesis is no longer simply plausible; it can now be deemed likely. Additional testing is needed, however, before full acceptance of this hypothesis.     

Carbon and nitrogen partitioning during the post‐anthesis period is conditioned by N fertilisation and sink strength in three cereals

Further knowledge of the processes conditioning nitrogen use efficiency (NUE) is of great relevance to crop productivity. The aim of this paper was characterise C and N partitioning during grain filling and their implications for NUE. Cereals such as bread wheat (Triticum aestivum L. cv Califa sur), triticale (× Triticosecale Wittmack cv. Imperioso) and tritordeum (× Tritordeum Asch. & Graebn line HT 621) were grown under low (LN, 5 mm NH₄NO₃) and high (HN, 15 mm NH₄NO₃) N conditions. We conducted simultaneous double labelling (¹²CO₂ and ¹⁵NH₄¹⁵NO₃) in order to characterise C and N partitioning during grain filling. Although triticale plants showed the largest total and ear dry matter values in HN conditions, the large investment in shoot and root biomass negatively affected ear NUE. Tritordeum was the only genotype that increased NUE in both N treatments (NUE_total), whereas in wheat, no significant effect was detected. N labelling revealed that N fertilisation during post‐anthesis was more relevant for wheat and tritordeum grain filling than for triticale. The study also revealed that the investments of C and N in flag leaves and shoots, together with the ‘waste’ of photoassimilates in respiration, conditioned the NUE of plants, and especially under LN. These results suggest that C and N use by these plants needs to be improved in order to increase ear C and N sinks, especially under LN. It is also remarkable that even though tritordeum shows the largest increase in NUE, the low yield of this cereal limits its agronomic value.     

Characterization and quantitation of membrane proteomes using multidimensional MS-based proteomic technologies

A major goal of proteomics is to develop methods that enable the systematic characterization of every protein within the cell or particular subcellular proteome using a single analytical platform. Although the equivalent has already been achieved in genomics, reaching this goal in proteomics represents a much greater challenge due to the wide dynamic range of protein expression, numerous post-translational modifications and remarkable physicochemical heterogeneity of proteins. A major analytical challenge has involved developing more effective means for proteome-scale investigations of membrane proteins, whose solubility differs drastically from that of cytoplasmic proteins. Fortunately, rapid progress has increased the ability to characterize this critically important class of proteins on a scale analogous to that of aqueous soluble proteins.     

Advances in Proteomics in Cancer Research

Proteases are a family of proteolytically active enzymes whose dysfunction is implicated in a wide variety of human diseases. Although an estimated 2% of the human genome encodes for proteases, only a small fraction of these enzymes have well-characterized functions. Identification of the specificity and natural substrates of proteases in complex biological samples is challenging, but proteomic screens for proteases are currently experiencing impressive progress. Such proteomic screens include peptide-based libraries, fluorescent 2D difference gel electrophoresis with mass spectrometry, differential isotope labeling in combination with mass spectrometry, quantitative degradomics analysis of proteolytically generated neo-N-termini, and activity-based protein profiling. In the present article, we summarize and discuss the current status of proteomic techniques to identify protease specificity, cleavage sites and natural substrates with a particular focus on the cytotoxic lymphocyte granule serine proteases granzymes.     

Niche overlap and diet composition of three sympatric coastal dolphin species in the southwest Atlantic Ocean

Sympatric species are expected to differ in ecological requirements to minimize niche overlap and avoid competition. Here we assess the trophic interactions among three coexisting dolphin species from southern Brazil: the franciscana dolphin (Pontoporia blainvillei), the Guiana dolphin (Sotalia guianensis), and the Lahille's bottlenose dolphin (Tursiops truncatus gephyreus). We evaluated temporal variation in carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope values of bone collagen to examine potential dietary shifts resulting from increased fishing activity over the past three decades. We estimated the degree of niche overlap among these species and the contribution of potential prey sources to their diet. δ¹⁵N values were consistent among species and across years, while δ¹³C values increased for Guiana dolphins and decreased for bottlenose dolphins, suggesting changes in diet and/or foraging habitats through time. The similar δ¹³C and δ¹⁵N values and the high niche overlap between Guiana and bottlenose dolphins indicate that these species are primarily feeding on demersal prey. The franciscana diet is primarily composed of pelagic prey, resulting in a lower niche overlap in comparison with the other dolphin species. Our study provides further information about the foraging ecology of this unique dolphin community in southern Brazil with implications for its management and conservation.     

Tracing site‐specific isotopic signatures along a Blue Tit Cyanistes caeruleus food chain

Food chains culminating with temperate insectivorous passerines are well described, yet whether trophic webs can be site‐specific remains a largely unexplored question. In the case of site‐ or habitat‐specificity of food webs, stable isotope signatures of bird feathers may enable assignment of unmarked individuals to a site or a habitat of origin. We address this question in landscapes that include contrasting forest habitat patches with either deciduous Downy Oak Quercus humilis or evergreen Holm Oak Quercus ilex as dominant tree species. First, we examine the spatial variation across habitats and sites in the stable isotope ratios of carbon (δ¹³C) and nitrogen (δ¹⁵N) along the oak leaf–Tortrix moth Tortrix viridana caterpillar–Blue Tit Cyanistes caeruleus food chain. Secondly, we assess whether the isotopic signatures allow for correct assignment of individual birds to their site or habitat of origin. At the scale of the landscape, stable isotope values enabled identification of the different components of the Blue Tit food chain: from oak leaves to Blue Tit nestlings and yearling birds. However, isotopic signatures were site‐specific (i.e. geographical) more than habitat‐specific (i.e. deciduous vs. evergreen oaks). Discriminant analyses correctly assigned 85% of nestlings and 83% of resident yearling birds, indicating a pronounced effect of site on Blue Tit feather isotopic signatures. We thereby demonstrate that isotopes reflect a stronger association of locally born birds to the local features of their habitat than that of un‐ringed yearling birds, whose plumage may have grown while in a wider geographical area. This study provides evidence of site‐specific isotopic signatures from oak leaves to Blue Tit feathers at a fine spatial scale.     

Comparing pellet and stable isotope analyses of nestling Bonelli's Eagle Aquila fasciata diet

Diet analyses are central to the study of avian trophic ecology, and stable isotope analyses have made an increasing contribution in the last two decades. Few isotopic studies have assessed the diet of raptor species, which are more frequently analysed by conventional diet methods such as pellet analysis. In this study, we compare prey consumption estimates of nestling Bonelli's Eagles Aquila fasciata from conventional pellet analysis (in terms of items and biomass) and stable isotopic mixing models (SIAR) using δ¹³C, δ¹⁵N and δ³⁴S of feathers. The pellet analysis showed that European Rabbits Oryctolagus cuniculus, pigeons (mainly Common Wood Pigeons Columba palumbus and Domestic Pigeons Columba livia dom.), Red‐legged Partridges Alectoris rufa, passerines, Yellow‐legged Gulls Larus michahellis and Eurasian Red Squirrels Sciurus vulgaris were the main prey, so they were selected for diet reconstructions in SIAR. At the population level, mean prey consumption estimates were similar for pellets (both items and biomass) and SIAR. At the territory level, the weighted kappa statistic showed good ordinal scale agreement in main prey consumption between items or biomass and SIAR. Although the intraclass correlation coefficient showed poor method agreement when considering all prey in the same analysis, the intraclass correlation coefficients for each prey category showed significant agreement between pellets and SIAR when estimating the consumption of Rabbits, pigeons and Gulls, with lower agreement for passerines and Squirrels. Lastly, there was poor method agreement for estimates of Partridges. Our results suggest an overall agreement between the pellet analysis and SIAR when estimating nestling Bonelli's Eagle diet at both the population and, to a lesser extent, the territory level, supporting the usefulness of isotopic mixing models when identifying the terrestrial and marine components of raptor diets.