Within trophic level shifts in collagen–carbonate stable carbon isotope spacing are propagated by diet and digestive physiology in large mammal herbivores

Stable carbon isotope analyses of vertebrate hard tissues such as bones, teeth, and tusks provide information about animal diets in ecological, archeological, and paleontological contexts. There is debate about how carbon isotope compositions of collagen and apatite carbonate differ in terms of their relationship to diet, and to each other. We evaluated relationships between δ¹³C_collagen and δ¹³C_carbonate among free‐ranging southern African mammals to test predictions about the influences of dietary and physiological differences between species. Whereas the slopes of δ¹³C_collagen–δ¹³C_carbonate relationships among carnivores are ≤1, herbivore δ¹³C_collagen increases with increasing dietary δ¹³C at a slower rate than does δ¹³C_carbonate, resulting in regression slopes >1. This outcome is consistent with predictions that herbivore δ¹³C_collagen is biased against low protein diet components (¹³C‐enriched C₄ grasses in these environments), and δ¹³C_carbonate is ¹³C‐enriched due to release of ¹³C‐depleted methane as a by‐product of microbial fermentation in the digestive tract. As methane emission is constrained by plant secondary metabolites in browse, the latter effect becomes more pronounced with higher levels of C₄ grass in the diet. Increases in δ¹³C_carbonate are also larger in ruminants than nonruminants. Accordingly, we show that Δ¹³C_collagen‐_carbonate spacing is not constant within herbivores, but increases by up to 5 ‰ across species with different diets and physiologies. Such large variation, often assumed to be negligible within trophic levels, clearly cannot be ignored in carbon isotope‐based diet reconstructions.     

Identification,mapping, and marker development of stem rust resistance genes in durum wheat ‘Lebsock’

Wheat production in many wheat-growing regions is vulnerable to stem rust, caused by Puccinia graminis f. sp. tritici (Pgt). Several previous studies showed that most of the durum cultivars adapted to the upper Great Plains in the USA have good resistance to the major Pgt pathotypes, including the Ug99 race group. To identify the stem rust resistance (Sr) genes in the durum cultivar ‘Lebsock’, a tetraploid doubled haploid (DH) population derived from a cross between Lebsock and Triticum turgidum ssp. carthlicum PI 94749 was screened with the Pgt races TTKSK, TRTTF, and TTTTF. The stem rust data and the genotypic data previously developed were used to identify quantitative trait loci (QTL) associated with resistance. We identified one QTL each on chromosome arms 4AL, 6AS, 6AL, and 2BL. Based on marker and race-specification analysis, we postulated that the QTL on 4AL, 6AS, 6AL, and 2BL correspond to Sr7a, Sr8155B1, Sr13, and likely Sr9e, respectively. The results indicated that most of the US durum germplasm adapted to the upper Great Plains likely harbors the four major Sr genes characterized in this study. Among these genes, Sr8155B1 was recently identified and shown to be unique in that it conferred susceptibility to TTKSK but resistance to variant race TTKST. Two, three, and one thermal asymmetric reverse PCR (STARP) markers were developed for Sr7a, Sr8155-B1, and Sr13, respectively. Knowledge of the Sr genes in durum germplasm and the new STARP markers will be useful to pyramid and deploy multiple Sr genes in future durum and wheat cultivars.     

Myosin Heads Are Displaced from Actin Filaments in the In Situ Beating Rat Heart in Early Diabetes

Diabetes is independently associated with a specific cardiomyopathy, characterized by impaired cardiac muscle relaxation and force development. Using synchrotron radiation small-angle x-ray scattering, this study investigated in the in situ heart and in real-time whether changes in cross-bridge disposition and myosin interfilament spacing underlie the early development of diabetic cardiomyopathy. Experiments were conducted using anesthetized Sprague-Dawley rats 3 weeks after treatment with either vehicle (control) or streptozotocin (diabetic). Diffraction patterns were recorded during baseline and dobutamine infusions simultaneous with ventricular pressure-volumetry. From these diffraction patterns myosin mass transfer to actin filaments was assessed as the change in intensity ratio (I_1,0/I_1,1). In diabetic hearts cross-bridge disposition was most notably abnormal in the diastolic phase (p < 0.05) and to a lesser extent the systolic phase (p < 0.05). In diabetic rats only, there was a transmural gradient of contractile depression. Elevated diabetic end-diastolic intensity ratios were correlated with the suppression of diastolic function (p < 0.05). Furthermore, the expected increase in myosin head transfer by dobutamine was significantly blunted in diabetic animals (p < 0.05). Interfilament spacing did not differ between groups. We reveal that impaired cross-bridge disposition and radial transfer may thus underlie the early decline in ventricular function observed in diabetic cardiomyopathy.     

Zooplankton dynamics in response to the transition from drought to flooding in four Murray–Darling Basin rivers affected by differing levels of flow regulation

A review of stratigraphic, radiocarbon, pollen, and aerial photographic data on the Swan Coastal Plain, south-western Australia, allows interpretation of long-term changes in climate and its effects on wetlands during the Holocene, whereas monitoring wetland hydrology and vegetation provides a measure of shorter-term changes. The information provides models for basin wetland response to changing climate. Drying climates shift wetlands to drier conditions, turning lakes into seasonally inundated or waterlogged basins, or resulting in an overall loss of wetlands, and favours more saline conditions, and development of carbonate deposits. Wetter conditions results in more frequent inundation, shifting damplands to sumplands or lakes, and resulting in fresher water conditions, and development of peat and/or organic matter enriched deposits. Examples of wetland basin responses to climate change across the Swan Coastal Plain show differential responses depending on setting, spatial distribution, hydrology, hydrochemistry and geochemistry, different temporal frameworks, and biological resilience.     

Engineering a Monomeric Fc Domain Modality by N-Glycosylation for the Half-life Extension of Biotherapeutics

Human IgG is a bivalent molecule that has two identical Fab domains connected by a dimeric Fc domain. For therapeutic purposes, however, the bivalency of IgG and Fc fusion proteins could cause undesired properties. We therefore engineered the conversion of the natural dimeric Fc domain to a highly soluble monomer by introducing two Asn-linked glycans onto the hydrophobic C_H3-C_H3 dimer interface. The monomeric Fc (monoFc) maintained the binding affinity for neonatal Fc receptor (FcRn) in a pH-dependent manner. We solved the crystal structure of monoFc, which explains how the carbohydrates can stabilize the protein surface and provides the rationale for molecular recognition between monoFc and FcRn. The monoFc prolonged the in vivo half-life of an antibody Fab domain, and a tandem repeat of the monoFc further prolonged the half-life. This monoFc modality can be used to improve the pharmacokinetics of monomeric therapeutic proteins with an option to modulate the degree of half-life extension.     

Identification of coronin‐1a as a novel antibody target for clinically isolated syndrome and multiple sclerosis

Recently, we identified the mimotope UH‐CIS6 as a novel candidate antibody target for clinically isolated syndrome (CIS) and relapsing‐remitting (RR) multiple sclerosis (MS). The purpose of this study was to further validate UH‐CIS6 as an antibody target for CIS and MS and to identify the in vivo antibody target of UH‐CIS6. First, a UH‐CIS6 peptide ELISA was optimized. Next, we investigated the antibody response toward UH‐CIS6 in cerebrospinal fluid (CSF) from patients with CIS (n = 20), MS (n = 43) and other neurological diseases (n = 42). Immunoprecipitation of anti‐UH‐CIS6 antibodies on a normal human brain lysate was performed to identify the in vivo antibody target of UH‐CIS6. The cellular expression of an in vivo candidate target was investigated by immunohistochemistry using MS brain tissue sections. Antibody reactivity toward UH‐CIS6 was detected in a significantly increased proportion of CSF samples from CIS and RR‐MS patients as compared with neurological controls (p = 0.046). We identified and confirmed coronin‐1a as the in vivo antibody target for UH‐CIS6. Furthermore, coronin‐1a was expressed by T cells and macrophages in an active MS lesion. Together, these results demonstrate that coronin‐1a is a novel antibody target for CIS and MS.     

Assessing the Jarman–Bell Principle: Scaling of intake,digestibility, retention time and gut fill with body mass in mammalian herbivores

Differences in allometric scaling of physiological characters have the appeal to explain species diversification and niche differentiation along a body mass (BM) gradient — because they lead to different combinations of physiological properties, and thus may facilitate different adaptive strategies. An important argument in physiological ecology is built on the allometries of gut fill (assumed to scale to BM^1.0) and energy requirements/intake (assumed to scale to BM^0.75) in mammalian herbivores. From the difference in exponents, it has been postulated that the mean retention time (MRT) of digesta should scale to BM^1.0–0.75 = BM^0.25. This has been used to argue that larger animals have an advantage in digestive efficiency and hence can tolerate lower-quality diets. However, empirical data does not support the BM^0.25 scaling of MRT, and the deduction of MRT scaling implies, according to physical principles, no scaling of digestibility; basing assumptions on digestive efficiency on the thus-derived MRT scaling amounts to circular reasoning. An alternative explanation considers a higher scaling exponent for food intake than for metabolism, allowing larger animals to eat more of a lower quality food without having to increase digestive efficiency; to date, this concept has only been explored in ruminants. Here, using data for 77 species in which intake, digestibility and MRT were measured (allowing the calculation of the dry matter gut contents (DMC)), we show that the unexpected shallow scaling of MRT is common in herbivores and may result from deviations of other scaling exponents from expectations. Notably, DMC have a lower scaling exponent than 1.0, and the 95% confidence intervals of the scaling exponents for intake and DMC generally overlap. Differences in the scaling of wet gut contents and dry matter gut contents confirm a previous finding that the dry matter concentration of gut contents decreases with body mass, possibly compensating for the less favorable volume–surface ratio in the guts of larger organisms. These findings suggest that traditional explanations for herbivore niche differentiation along a BM gradient should not be based on allometries of digestive physiology. In contrast, they support the recent interpretation that larger species can tolerate lower-quality diets because their intake has a higher allometric scaling than their basal metabolism, allowing them to eat relatively more of a lower quality food without having to increase digestive efficiency.     

Systematic evaluation of medium-throughput mRNA abundance platforms

Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-seq has become an important tool in both basic and biomedical research. However, these platforms remain prone to systematic errors and have challenges in clinical and industrial applications. As a result, it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from a high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample quality (e.g., for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we fill that gap by comparing two key medium-throughput platforms—NanoString''s nCounter Analysis System and ABI''s OpenArray System—to gold-standard quantitative real-time RT-PCR. We quantified 38 genes and positive and negative controls in 165 samples. Signal:noise ratios, correlations, dynamic range, and detection accuracy were compared across platforms. All three measurement technologies showed good concordance, but with divergent price/time/sensitivity trade-offs. This study provides the first detailed comparison of medium-throughput RNA quantification platforms and provides a template and a standard data set for the evaluation of additional technologies.