Patterns of loggerhead turtle ontogenetic shifts revealed through isotopic analysis of annual skeletal growth increments

Ontogenetic changes in resource use often delimit transitions between life stages. Ecological and individual factors can cause variation in the timing and consistency of these transitions, ultimately affecting community and population dynamics through changes in growth and survival. Therefore, it is important to document and understand behavioral and life history polymorphisms, and the processes that drive intraspecific variation in them. To evaluate juvenile loggerhead sea turtle (Caretta caretta) life history variation and to detect shifts in habitat and diet that occur during an oceanic-to-neritic ontogenetic shift, we sequentially analyzed the stable isotope composition of humerus bone growth increments from turtles that stranded dead on Southeastern U.S. beaches between 1997 and 2013 (n = 84). In one-half of the sampled turtles, growth increment-specific nitrogen stable isotope (δ¹⁵N) data showed significant increases in δ¹⁵N values over each turtle's life. These data were used to provide a new line of evidence that juvenile Northwest Atlantic loggerheads exhibit two major ontogenetic shift patterns: discrete shifts (n = 24), which were completed within one year, and facultative shifts (n = 14), which were completed over multiple years (up to five). The mean difference in pre- and post-ontogenetic shift δ¹⁵N values was 4.3‰. Differences in isotopic baselines between neritic and oceanic habitats of the Northwest Atlantic Ocean make it likely these patterns are driven by a coupled change in both habitat and diet, and that facultative shifters utilize both neritic and oceanic resources within transitional growth years. Mean size and age at transition between habitats (54.2 cm straightline carapace length, SCL; 11.98 yr) was within the range of previous estimates and did not differ between discrete and facultative shifters. Our results further expand our understanding of loggerhead sea turtle life history polymorphisms and demonstrate the value of bone tissue analysis to the study of this variation. Sequential analysis of annual skeletal growth increments provides a valuable method for reconstructing long-term ontogenetic changes in foraging ecology and habitat use in long-lived, cryptic marine species

Neuroendocrine factors regulate retinoic acid receptors in normal and hypoplastic lung development

Congenital diaphragmatic hernia (CDH) is characterised by a spectrum of lung hypoplasia and consequent pulmonary hypertension, leading to high morbidity and mortality rates. Moreover, CDH has been associated with an increase in the levels of pulmonary neuroendocrine factors, such as bombesin and ghrelin, and a decrease in the action of retinoic acid (RA). The present study aimed to elucidate the interaction between neuroendocrine factors and RA. In vitro analyses were performed on Sprague-Dawley rat embryos. Normal lung explants were treated with bombesin, ghrelin, a bombesin antagonist, a ghrelin antagonist, dimethylsulfoxide (DMSO), RA dissolved in DMSO, bombesin plus RA and ghrelin plus RA. Hypoplastic lung explants (nitrofen model) were cultured with bombesin, ghrelin, bombesin antagonist or ghrelin antagonist. The lung explants were analysed morphometrically, and retinoic acid receptor (RAR) α, β and γ expression levels were assessed via Western blotting. Immunohistochemistry analysis of RAR was performed in normal and hypoplastic lungs 17.5 days post-conception (dpc). Compared with the controls, hypoplastic lungs exhibited significantly higher RARα/γ expression levels. Furthermore considering hypoplastic lungs, bombesin and ghrelin antagonists decreased RARα/γ expression. Normal lung explants (13.5 dpc) treated with RA, bombesin plus RA, ghrelin plus RA, bombesin or ghrelin exhibited increased lung growth. Moreover, bombesin and ghrelin increased RARα/γ expression levels, whereas the bombesin and ghrelin antagonists decreased RARα/γ expression. This study demonstrates for the first time that neuroendocrine factors function as lung growth regulators, sensitising the lung to the action of RA through up-regulation of RARα and RARγ.P.P.-T. was supported by the Fundação para a Ciência e a Tecnologia (ref. SFRH/BD/73660/2010). R.S.M. was supported by the ON.2 SR&TD Integrated Program (N-01-01-01-24-01-07) (ref. UMINHO/BPD/31/2013). The funding bodies had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Computing H/D-Exchange rates of single residues from data of proteolytic fragments

<p>Abstract</p> <p>Background</p> <p>Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex. In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides generated from the protease digest of the protein is related to the solvent accessibility of amide protons within the original protein construct.</p> <p>Results</p> <p>In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue resolution.</p> <p>Conclusions</p> <p>With our new method it is possible to automatically determine deuterium exchange with higher spatial resolution than the level of digested fragments.</p

A Functional Proteomic Method for Biomarker Discovery

The sequencing of the human genome holds out the hope for personalized medicine, but it is clear that analysis of DNA or RNA content alone is not sufficient to understand most disease processes. Proteomic strategies that allow unbiased identification of proteins and their post-transcriptional and -translation modifications are an essential complement to genomic strategies. However, the enormity of the proteome and limitations in proteomic methods make it difficult to determine the targets that are particularly relevant to human disease. Methods are therefore needed that allow rational identification of targets based on function and relevance to disease. Screening methodologies such as phage display, SELEX, and small-molecule combinatorial chemistry have been widely used to discover specific ligands for cells or tissues of interest, such as tumors. Those ligands can be used in turn as affinity probes to identify their cognate molecular targets when they are not known in advance. Here we report an easy, robust and generally applicable approach in which phage particles bearing cell- or tissue-specific peptides serve directly as the affinity probes for their molecular targets. For proof of principle, the method successfully identified molecular binding partners, three of them novel, for 15 peptides specific for pancreatic cancer

Challenging the Logics of Reformism and Humanism in Juvenile Justice Rhetoric

This article draws on contemporary policy discourse in order to advance claims about the intractable figure of the “bad” child in contemporary juvenile justice reforms in the United States (US). The article focuses in particular on the discourses of trauma and “brain science” to point to a form of neo-positivism that has arguably emerged and which challenges efforts to engage in systematic decarceration. The article also focuses on the idea of the “bad child” that persists in the commitment of some reformers to the necessity of confinement for some children. The article questions the extent to which new forms of positivism challenge our ability to leverage structural claims