Growth rate, size, and sex ratio of last-laid, last-hatched offspring in the tree swallow Tachycineta bicolor

In tree swallows Tachycineta bicolor, last‐laid eggs typically hatch one to two days after the other eggs in the clutch hatch, putting last‐hatched offspring at a disadvantage when competing for food delivered by parents. We studied the biology of last‐laid, last‐hatched tree swallow offspring over two years in a Wyoming, USA, population. Our first objective was to compare the growth of last‐hatched offspring to that of their earlier‐hatched nestmates. One previous study had suggested that last‐hatched, competitively disadvantaged offspring grow feathers faster than senior nestmates, even at the expense of other aspects of growth. This may allow last‐hatched offspring to fledge with senior nestmates and avoid abandonment by parents. A second objective was to determine the sex of nestlings from last‐laid eggs. If last‐laid eggs typically produce undersized, weak adults that are poor competitors for resources, and if the fitness costs of being undersized/weak are more severe for males than for females, then selection may favour having offspring from last‐laid eggs to be female. In this study, last‐laid eggs hatched in 63 of 66 (94%) nests and hatched last in 93% of cases. At hatching, offspring from last‐laid eggs weighed, on average, 63% as much as their three heaviest nestmates (range: 26–107%). Offspring from last‐laid eggs fledged from 71% of the nests that produced at least one fledgling and apparently starved to death in remaining nests. Last‐hatched offspring who were presumably at a substantial competitive disadvantage (those whose mass at hatching was no more than about 75% of the mean mass of their three heaviest nestmates), gained mass more slowly than their senior nestmates but they eventually attained the same peak mass before fledging. Last‐hatched offspring grew primary feathers more slowly than their senior nestmates although the difference in growth rate was slight (0.2 mm/d) and only marginally significant. As a group, offspring from last‐laid eggs did not differ from offspring from all other eggs in either maximum mass attained before fledging or tarsus length at fledging. This is atypical for species with asynchronous hatching and is possibly the result of another unusual trait: the tendency of parent tree swallows to distribute food equally among young within broods. The sex ratio of offspring from last‐laid eggs did not deviate from 1:1 (22 males, 21 females). Given that last‐hatched eggs do not routinely produce undersized/weak individuals in our study population, there should be little selection on parent females to bias the sex ratio of last‐laid offspring towards females.     

Modelling the niche for a marine vertebrate: a case study incorporating behavioural plasticity,proximate threats and climate change

The integration of satellite telemetry, remotely sensed environmental data, and habitat/environmental modelling has provided for a growing understanding of spatial and temporal ecology of species of conservation concern. The Republic of Cape Verde comprises the only substantial rookery for the loggerhead turtle Caretta caretta in the eastern Atlantic. A size related dichotomy in adult foraging patterns has previously been revealed for adult sea turtles from this population with a proportion of adults foraging neritically, whilst the majority forage oceanically. Here we describe observed habitat use and employ ecological niche modelling to identify suitable foraging habitats for animals utilising these two distinct behavioural strategies. We also investigate how these predicted habitat niches may alter under the influence of climate change induced oceanic temperature rises. We further contextualise our niche models with fisheries catch data and knowledge of fisheries ‘hotspots’ to infer threat from fisheries interaction to this population, for animals employing both strategies. Our analysis revealed repeated use of coincident oceanic habitat, over multiple seasons, by all smaller loggerhead turtles, whilst larger neritic foraging turtles occupied continental shelf waters. Modelled habitat niches were spatially distinct, and under the influence of predicted sea surface temperature rises, there was further spatial divergence of suitable habitats. Analysis of fisheries catch data highlighted that the observed and modelled habitats for oceanic and neritic loggerhead turtles could extensively interact with intensive fisheries activity within oceanic and continental shelf waters of northwest Africa. We suggest that the development and enforcement of sustainable management strategies, specifically multi‐national fisheries policy, may begin to address some of these issues; however, these must be flexible and adaptive to accommodate potential range shift for this species.     

POLYMORPHISM IN THE DESMID XANTHIDIUM REGULARE AND ITS TAXONOMIC IMPLICATIONS

This paper refers to a case of polymorphism in the desmid genus Xanthidium Ehr. It is based on material from Lake Dais Irmaios, the main body of water in the Zoological and Botanical Garden in Recife, Pernambuco, northeastern Brazil, collected at 4 different times of the year during 1967 and 1968. A detailed examination of almost 1300 specimens showed an enormous variety in form of Xanthidium regulare Nordst., X. fragile Borge, and X. pseudoregulare Borge, thus allowing the authors to draw the following conclusions: (1) the name X. regulare Nordst. should be retained until further and more detailed studies on form variation within the species are available; (2) the names X. regulare Nordst. var. asteptum Nordst. in Borge, X. regulare Nordst. var. sexangulare Grönbl., X. regulare Nordst. var. sexangulare Grönbl. f. robustior Grönbl., X. fragile Borge, X. fragile Borge forma, and X. fragile Borge var. depauperatum Borge should be considered synonymous, all referring to a single variety of X. regulare Nordst., var. asteptum Nordst. in Borge emend. C. Bic. & L. M. Carv.; (3) X. pseudoregulare Borge must be treated as a variety of X. regulare Nordst. and must be called X. regulare Nordst. var. pseudoregulare (Barge) C. Bic. & L. M. Carv. Finally, a key is given to the 3 varieties of X. regulare Nordst. proposed in the present paper.     

Amazonia trees have limited capacity to acclimate plant hydraulic properties in response to long‐term drought

The fate of tropical forests under future climate change is dependent on the capacity of their trees to adjust to drier conditions. The capacity of trees to withstand drought is likely to be determined by traits associated with their hydraulic systems. However, data on whether tropical trees can adjust hydraulic traits when experiencing drought remain rare. We measured plant hydraulic traits (e.g. hydraulic conductivity and embolism resistance) and plant hydraulic system status (e.g. leaf water potential, native embolism and safety margin) on >150 trees from 12 genera (36 species) and spanning a stem size range from 14 to 68 cm diameter at breast height at the world's only long‐running tropical forest drought experiment. Hydraulic traits showed no adjustment following 15 years of experimentally imposed moisture deficit. This failure to adjust resulted in these drought‐stressed trees experiencing significantly lower leaf water potentials, and higher, but variable, levels of native embolism in the branches. This result suggests that hydraulic damage caused by elevated levels of embolism is likely to be one of the key drivers of drought‐induced mortality following long‐term soil moisture deficit. We demonstrate that some hydraulic traits changed with tree size, however, the direction and magnitude of the change was controlled by taxonomic identity. Our results suggest that Amazonian trees, both small and large, have limited capacity to acclimate their hydraulic systems to future droughts, potentially making them more at risk of drought‐induced mortality.     

Development of a fluorescent monoclonal antibody‐based assay to measure the allosteric effects of synthetic peptides on self‐oligomerization of AGR2 protein

Many regulatory proteins are homo‐oligomeric and designing assays that measure self‐assembly will provide novel approaches to study protein allostery and screen for novel small molecule modulators of protein interactions. We present an assay to begin to define the biochemical determinants that regulate dimerization of the cancer‐associated oncoprotein AGR2. A two site‐sandwich microtiter assay (^2SMTA) was designed using a DyLight800‐labeled monoclonal antibody that binds to an epitope in AGR2 to screen for synthetic self‐peptides that might regulate dimer stability. Peptides derived from the intrinsically disordered N‐terminal region of AGR2 increase in trans oligomer stability as defined using the ^2SMTA assay. A DSS‐crosslinking assay that traps the AGR2 dimer through K95‐K95 adducts confirmed that Δ45‐AGR2 was a more stable dimer using denaturing gel electrophoresis. A titration of wt‐AGR2, Δ45‐AGR2 (more stable dimer), and monomeric AGR2^E60A revealed that Δ45‐AGR2 was more active in binding to Reptin than either wt‐AGR2 or the AGR2^E60A mutant. Our data have defined a functional role for the AGR2 dimer in the binding to its most well characterized interacting protein, Reptin. The ability to regulate AGR2 oligomerization in trans opens the possibility for developing small molecules that regulate its' biochemical activity as potential cancer therapeutics. The data also highlight the utility of this oligomerization assay to screen chemical libraries for ligands that could regulate AGR2 dimer stability and its' oncogenic potential.     

Quality Control Methods in Accelerometer Data Processing: Defining Minimum Wear Time

Background

When using accelerometers to measure physical activity, researchers need to determine whether subjects have worn their device for a sufficient period to be included in analyses. We propose a minimum wear criterion using population-based accelerometer data, and explore the influence of gender and the purposeful inclusion of children with weekend data on reliability.

Methods

Accelerometer data obtained during the age seven sweep of the UK Millennium Cohort Study were analysed. Children were asked to wear an ActiGraph GT1M accelerometer for seven days. Reliability coefficients(r) of mean daily counts/minute were calculated using the Spearman-Brown formula based on the intraclass correlation coefficient. An r of 1.0 indicates that all the variation is between- rather than within-children and that measurement is 100% reliable. An r of 0.8 is often regarded as acceptable reliability. Analyses were repeated on data from children who met different minimum daily wear times (one to 10 hours) and wear days (one to seven days). Analyses were conducted for all children, separately for boys and girls, and separately for children with and without weekend data.

Results

At least one hour of wear time data was obtained from 7,704 singletons. Reliability increased as the minimum number of days and the daily wear time increased. A high reliability (r = 0.86) and sample size (n = 6,528) was achieved when children with ≥ two days lasting ≥10 hours/day were included in analyses. Reliability coefficients were similar for both genders. Purposeful sampling of children with weekend data resulted in comparable reliabilities to those calculated independent of weekend wear.

Conclusion

Quality control procedures should be undertaken before analysing accelerometer data in large-scale studies. Using data from children with ≥ two days lasting ≥10 hours/day should provide reliable estimates of physical activity. It’s unnecessary to include only children with accelerometer data collected during weekends in analyses.     

Methodological Deficits in Diagnostic Research Using ‘-Omics’ Technologies: Evaluation of the QUADOMICS Tool and Quality of Recently Published Studies

Background

QUADOMICS is an adaptation of QUADAS (a quality assessment tool for use in systematic reviews of diagnostic accuracy studies), which takes into account the particular challenges presented by ‘-omics’ based technologies. Our primary objective was to evaluate the applicability and consistency of QUADOMICS. Subsequently we evaluated and describe the methodological quality of a sample of recently published studies using the tool.

Methodology/Principal Findings

45‘-omics’- based diagnostic studies were identified by systematic search of Pubmed using suitable MeSH terms (“Genomics”, “Sensitivity and specificity”, “Diagnosis”). Three investigators independently assessed the quality of the articles using QUADOMICS and met to compare observations and generate a consensus. Consistency and applicability was assessed by comparing each reviewer''s original rating with the consensus. Methodological quality was described using the consensus rating. Agreement was above 80% for all three reviewers. Four items presented difficulties with application, mostly due to the lack of a clearly defined gold standard. Methodological quality of our sample was poor; studies met roughly half of the applied criteria (mean ± sd, 54.7±18.4%). Few studies were carried out in a population that mirrored the clinical situation in which the test would be used in practice, (6, 13.3%); none described patient recruitment sufficiently; and less than half described clinical and physiological factors that might influence the biomarker profile (20, 44.4%).

Conclusions

The QUADOMICS tool can consistently be applied to diagnostic ‘-omics’ studies presently published in biomedical journals. A substantial proportion of reports in this research field fail to address design issues that are fundamental to make inferences relevant for patient care.     

Increased levels of galactose-deficient anti-Gal immunoglobulin G in the sera of hepatitis C virus-infected individuals with fibrosis and cirrhosis

Hepatitis B and C viruses are major causative agents of liver fibrosis, cirrhosis, and liver cancer. Using comparative glycoproteomics, we identified a glycoprotein that is altered both in amount and in glycosylation as a function of liver fibrosis and cirrhosis. Specifically, this altered glycoprotein is an immunoglobulin G (IgG) molecule reactive to the heterophilic alpha-Gal epitope [Galα-1-3Galβ1-(3)4GlcNAc-R]. While similar changes in glycosylation have been observed in several autoimmune diseases, the specific immunoglobulins and their antigen recognition profiles were not determined. Thus, we provide the first report identifying the specific antigenic recognition profile of an immunoglobulin molecule containing altered glycosylation as a function of liver disease. This change in glycosylation allowed increased reactivity with several fucose binding lectins and permitted the development of a plate-based assay to measure this change. Increased lectin reactivity was observed in 100% of the more than 200 individuals with stage III or greater fibrosis and appeared to be correlated with the degree of fibrosis. The reason for the alteration in the glycosylation of anti-Gal IgG is currently unclear but may be related to the natural history of the disease and may be useful in the noninvasive detection of fibrosis and cirrhosis.     

Use of Tetrahymena thermophila To Study the Role of Protozoa in Inactivation of Viruses in Water

The ability of a ciliate to inactivate bacteriophage was studied because these viruses are known to influence the size and diversity of bacterial populations, which affect nutrient cycling in natural waters and effluent quality in sewage treatment, and because ciliates are ubiquitous in aquatic environments, including sewage treatment plants. Tetrahymena thermophila was used as a representative ciliate; T4 was used as a model bacteriophage. The T4 titer was monitored on Escherichia coli B in a double-agar overlay assay. T4 and the ciliate were incubated together under different conditions and for various times, after which the mixture was centrifuged through a step gradient, producing a top layer free of ciliates. The T4 titer in this layer decreased as coincubation time increased, but no decrease was seen if phage were incubated with formalin-fixed Tetrahymena. The T4 titer associated with the pellet of living ciliates was very low, suggesting that removal of the phage by Tetrahymena inactivated T4. When Tetrahymena cells were incubated with SYBR gold-labeled phage, fluorescence was localized in structures that had the shape and position of food vacuoles. Incubation of the phage and ciliate with cytochalasin B or at 4°C impaired T4 inactivation. These results suggest the active removal of T4 bacteriophage from fluid by macropinocytosis, followed by digestion in food vacuoles. Such ciliate virophagy may be a mechanism occurring in natural waters and sewage treatment, and the methods described here could be used to study the factors influencing inactivation and possibly water quality.