Comparison of the A–Cc curve fitting methods in determining maximum ribulose 1·5-bisphosphate carboxylase/oxygenase carboxylation rate, potential light saturated electron transport rate and leaf dark respiration

A review of the literature revealed that a variety of methods are currently used for fitting net assimilation of CO₂–chloroplastic CO₂ concentration (A–C_c) curves, resulting in considerable differences in estimating the A–C_c parameters [including maximum ribulose 1·5‐bisphosphate carboxylase/oxygenase (Rubisco) carboxylation rate (V_cmax), potential light saturated electron transport rate (J_max), leaf dark respiration in the light (R_d), mesophyll conductance (g_m) and triose‐phosphate utilization (TPU)]. In this paper, we examined the impacts of fitting methods on the estimations of V_cmax, J_max, TPU, R_d and g_m using grid search and non‐linear fitting techniques. Our results suggested that the fitting methods significantly affected the predictions of Rubisco‐limited (A_c), ribulose 1,5‐bisphosphate‐limited (A_j) and TPU‐limited (A_p) curves and leaf photosynthesis velocities because of the inconsistent estimate of V_cmax, J_max, TPU, R_d and g_m, but they barely influenced the J_max : V_cmax, V_cmax : R_d and J_max : TPU ratio. In terms of fitting accuracy, simplicity of fitting procedures and sample size requirement, we recommend to combine grid search and non‐linear techniques to directly and simultaneously fit V_cmax, J_max, TPU, R_d and g_m with the whole A–C_c curve in contrast to the conventional method, which fits V_cmax, R_d or g_m first and then solves for V_cmax, J_max and/or TPU with V_cmax, R_d and/or g_m held as constants.     

Wheat stripe rust resistance genes <Emphasis Type="Italic">Yr5</Emphasis> and <Emphasis Type="Italic">Yr7</Emphasis> are allelic

Stripe rust is one of the most destructive diseases of wheat. Breeding for resistance is the most economical and environmentally acceptable means to control stripe rust. Genetic studies on resistance sources are very important. Previous inheritance studies on Triticum aestivum subsp. spelta cv. album and wheat cultivar Lee showed that each possessed a single dominant gene for stripe rust resistance, i.e., Yr5 and Yr7, respectively. Both were located on the long arm of chromosome 2B, but due to the complexities caused by genetic background effects there was no clear evidence on the allelism or linkage status of these genes. Our study, involving an intercross of Avocet S near-isogenic lines possessing the genes, provided clear evidence for allelism or extremely close linkage of Yr5 and Yr7 based on phenotypic and molecular studies.     

A re-investigation of saliva collection procedures that highlights the risk of potential positive interference in cortisol immunoassay

Background

The use of saliva for measurement of cortisol permits non-invasive study of adrenal function, but collection can be technically difficult, particularly in small infants. Saliva collection can be assisted by citric acid to increase saliva flow, or by the use of cotton or polyester swabs in the mouth.

Aim

To determine whether different methods of saliva collection affect cortisol radioimmunoassay (RIA) performance.

Experimental

Cortisol was measured in saliva collected from 16 adults using intra-oral cotton swabs or polyester swabs, compared with saliva dribbled directly into a pot either alone (plain saliva) or after citric acid had been placed on the tongue. An in-house RIA, without prior extraction, was used to measure cortisol with an encapsulated sheep antibody.

Results

Mean (median) salivary cortisol was 10.9 (10.5) nmol L⁻¹ in plain saliva, 10.4 (8.4) nmol L⁻¹ in citric acid stimulated saliva; 25.3 (25.1) nmol L⁻¹ in saliva collected on cotton swabs, and 27.9 (27.3) nmol L⁻¹ collected on polyester swabs. Cortisol in saliva collected using citric acid was not significantly different from plain saliva (p = 0.997), but cortisol in saliva collected using cotton and polyester swabs was significantly higher than that of plain saliva (p < 0.01).

Conclusion

The use of cotton or polyester swabs for collection of saliva can result in spuriously high levels of cortisol when measured by RIA.     

Temporal Patterns of Apparent Leg Band Retention in North American Geese

ABSTRACT An important assumption of mark—recapture studies is that individuals retain their marks, which has not been assessed for goose reward bands. We estimated aluminum leg band retention probabilities and modeled how band retention varied with band type (standard vs. reward band), band age (1–40 months), and goose characteristics (species and size class) for Canada (Branta canadensis), cackling (Branta hutchinsii), snow (Chen caerulescens), and Ross's (Chen rossii) geese that field coordinators double-leg banded during a North American goose reward band study (N = 40,999 individuals from 15 populations). We conditioned all models in this analysis on geese that were encountered with ≥1 leg band still attached (n = 5,747 dead recoveries and live recaptures). Retention probabilities for standard aluminum leg bands were high ( = 0.9995, SE < 0.001) and constant over 1–40 months. In contrast, apparent retention probabilities for reward bands demonstrated an interactive relationship between 5 size and species classes (small cackling, medium Canada, large Canada, snow, and Ross's geese). In addition, apparent retention probabilities for each of the 5 classes varied quadratically with time, being lower immediately after banding and at older age classes. The differential retention probabilities among band type (reward vs. standard) that we observed suggests that 1) models estimating reporting probability should incorporate differential band loss if it is nontrivial, 2) goose managers should consider the costs and benefits of double-banding geese on an operational basis, and 3) the United States Geological Survey Bird Banding Lab should modify protocols for receiving recovery data.     

The development of a noisy brain

Early in life, brain development carries with it a large number of structural changes that impact the functional interactions of distributed neuronal networks. Such changes enhance information processing capacity, moving the brain from a deterministic system to one that is more stochastic. The evidence from empirical studies with EEG and functional MRI suggests that this stochastic property is a result of an increased number of possible functional network configurations for a given situation. This is captured in the variability of endogenous and evoked responses or "brain noise ". In empirical data from infants and children, brain noise increases with maturation and correlates positively with stable behavior and accuracy. The noise increase is best explained through increased noise from network level interactions with a concomitant decrease of local noise. In old adults, brain noise continues to change, although the pattern of changes is not as global as in early development. The relation between high brain noise and stable behavior is maintained, but the relationships differ by region, suggesting changes in local dynamics that then impact potential network configurations. These data, when considered in concert with our extant modeling work, suggest that maturational changes in brain noise represent the enhancement offunctional network potential--the brain's dynamic repertoire.     

Detection of salmonid alphavirus RNA in wild marine fish: implications for the origins of salmon pancreas disease in aquaculture

Salmonid alphaviruses (SAVs), which include the aetiological agents of salmon pancreas disease (SPD) in farmed Atlantic salmon Salmo salar L. and sleeping disease (SD) in rainbow trout Oncorhynchus mykiss (Walbaum), are significant viral pathogens of European salmonid aquaculture. SAV is horizontally transmitted and the virus can survive for extended periods in seawater. A lack of convincing evidence for vertical transmission coupled to the fact that the SPD virus (SPDV) occurs in historically infected sites irrespective of fallow period duration suggests that a substantial reservoir of infection exists in the marine environment. We used a highly sensitive real-time PCR (qPCR) assay targeting a region of the SAV nsP1 gene to screen wild marine fish species for the presence of SAV in an attempt to identify such a potential reservoir. Screened fish species were caught in the vicinity of aquaculture activity in an area with a previous history of SAV infection (Shetland Isles, Scotland). SAV RNA was detected in internal organs (kidney and heart) from the flatfish species common dab Limanda limanda, long rough dab Hippoglossoides platessoides, and plaice Pleuronectes platessa. Based on these findings, sampling was extended to an area remote from aquaculture activity (Stonehaven Bay, NE coast of Scotland) from where heart tissues obtained from common dab also tested positive. While no virus could be cultivated from these samples, qPCR detections were shown to be SAV-specific by sequencing of an alternative gene region (E2) to that targeted by the qPCR assay. Analysis of these nucleotide sequences revealed minor differences to those previously obtained from farmed salmon, and subsequent phylogenetic analysis of an E2 dataset demonstrated a subtype V-like sequence.     

Alpha-conotoxin OmIA is a potent ligand for the acetylcholine-binding protein as well as alpha3beta2 and alpha7 nicotinic acetylcholine receptors

The molluskan acetylcholine-binding protein (AChBP) is a homolog of the extracellular binding domain of the pentameric ligand-gated ion channel family. AChBP most closely resembles the alpha-subunit of nicotinic acetylcholine receptors and in particular the homomeric alpha7 nicotinic receptor. We report the isolation and characterization of an alpha-conotoxin that has the highest known affinity for the Lymnaea AChBP and also potently blocks the alpha7 nAChR subtype when expressed in Xenopus oocytes. Remarkably, the peptide also has high affinity for the alpha3beta2 nAChR indicating that alpha-conotoxin OmIA in combination with the AChBP may serve as a model system for understanding the binding determinants of alpha3beta2 nAChRs. alpha-Conotoxin OmIA was purified from the venom of Conus omaria. It is a 17-amino-acid, two-disulfide bridge peptide. The ligand is the first alpha-conotoxin with higher affinity for the closely related receptor subtypes, alpha3beta2 versus alpha6beta2, and selectively blocks these two subtypes when compared with alpha2beta2, alpha4beta2, and alpha1beta1deltaepsilon nAChRs.     

Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features

Background  

Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and utilizes ideas from statistical information retrieval to discover and characterize properties shared by subsets of the list. The practical utility of this method is demonstrated by employing it in a retrospective study of two non-overlapping sets of genes defined by a published investigation as markers for normal human breast luminal epithelial cells and myoepithelial cells.