Diet of a rare herbivore based on DNA metabarcoding of feces: Selection,seasonality, and survival

In herbivores, survival and reproduction are influenced by quality and quantity of forage, and hence, diet and foraging behavior are the foundation of an herbivore's life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: (a) They are difficult to observe, (b) collecting stomach contents requires sacrificing animals, and (c) microhistology requires accurately identifying taxa from partially digested plant fragments and likely overemphasizes less‐digestible taxa. The northern Idaho ground squirrel (Urocitellus brunneus) is federally threatened in the United States under the Endangered Species Act. We used DNA metabarcoding techniques to identify the diet of 188 squirrels at 11 study sites from fecal samples. We identified 42 families, 126 genera, and 120 species of plants in the squirrel's diet. Our use of three gene regions was beneficial because reliance on only one gene region (e.g., only trnL) would have caused us to miss >30% of the taxa in their diet. Northern Idaho ground squirrel diet differed between spring and summer, frequency of many plants in the diet differed from their frequency within their foraging areas (evidence of selective foraging), and several plant genera in their diet were associated with survival. Our results suggest that while these squirrels are generalists (they consume a wide variety of plant species), they are also selective and do not eat plants relative to availability. Consumption of particular genera such as Perideridia may be associated with higher overwinter survival.     

Unusual nonmarine burrows from the Middle Jurassic of Scotland

The Kilmaluag Formation of the Great Estuarine Group (Middle Jurassic) of Scotland represents deposition of mixed carbonate and clastic sediments in a low‐salinity coastal lagoon to floodplain lake setting. Large, unusual trace fossils occur at two horizons within the formation. One type consists of platelike structures about 50 cm in diameter, which are found on wave‐rippled sandstone. These structures, strikingly similar to burrows produced by modern mudskippers, are assigned to fish that shallowly burrowed into the lagoon‐shore sediment.

The second type of burrows, found in brecciated, dolomitic limestones, are pipelike, about 4 to 7 cm in diameter and as much as 50 cm deep. One example has a chamber at the base of the pipe. Although most features of these structures appear similar to modern lungfish burrows, the chamber is most similar to structures produced by modern crayfish. The animal probably burrowed into the moist, mudflat sediment to escape desiccation during seasonal aridity.     

Aromatic interactions with naphthylalanine in a β‐hairpin peptide

Stable peptides have been explored as epitope mimics for protein–protein and protein–nucleic acid interactions; however, presentation of a regular structure is critical. Aromatic interactions are ubiquitous and are competent at stabilizing a β‐hairpin fold. The greatest stabilization has been reported from pairs of tryptophan side chains. Naphthylalanine residues are often used as tryptophan replacements, but it is not clear if 1‐naphthylalanine or 2‐naphthylalanine is adequate at replicating the geometry and stability observed with tryptophan aromatic interactions. Herein, a 12‐residue peptide has been constructed with laterally disposed aromatic amino acids. A direct comparison is made between tryptophan and other bicyclic, unnatural amino acids. Significant stabilization is gained from all bicyclic amino acids; however, geometric analysis shows that only 1‐naphthylalanine adopts a similar edge to face geometry as tryptophan, whereas the 2‐naphthylalanine appears most similar to a substituted phenylalanine. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Evaluating atmospheric CO2 inversions at multiple scales over a highly inventoried agricultural landscape

An intensive regional research campaign was conducted by the North American Carbon Program (NACP) in 2007 to study the carbon cycle of the highly productive agricultural regions of the Midwestern United States. Forty‐five different associated projects were conducted across five US agencies over the course of nearly a decade involving hundreds of researchers. One of the primary objectives of the intensive campaign was to investigate the ability of atmospheric inversion techniques to use highly calibrated CO₂ mixing ratio data to estimate CO₂ flux over the major croplands of the United States by comparing the results to an inventory of CO₂ fluxes. Statistics from densely monitored crop production, consisting primarily of corn and soybeans, provided the backbone of a well studied bottom‐up inventory flux estimate that was used to evaluate the atmospheric inversion results. Estimates were compared to the inventory from three different inversion systems, representing spatial scales varying from high resolution mesoscale (PSU), to continental (CSU) and global (CarbonTracker), coupled to different transport models and optimization techniques. The inversion‐based mean CO₂‐C sink estimates were generally slightly larger, 8–20% for PSU, 10–20% for CSU, and 21% for CarbonTracker, but statistically indistinguishable, from the inventory estimate of 135 TgC. While the comparisons show that the MCI region‐wide C sink is robust across inversion system and spatial scale, only the continental and mesoscale inversions were able to reproduce the spatial patterns within the region. In general, the results demonstrate that inversions can recover CO₂ fluxes at sub‐regional scales with a relatively high density of CO₂ observations and adequate information on atmospheric transport in the region.     

A Naturalistic Study of the Acceptability and Effectiveness of Internet-Delivered Cognitive Behavioural Therapy for Psychiatric Disorders in Older Australians

Objectives

The current study investigates the acceptability, effectiveness and uptake of internet-delivered cognitive behavioural therapy (iCBT) amongst older individuals (>60 years) seeking psychiatric treatment in general practice.

Methods

The sample consisted of 2413 (mean age 39.5; range 18–83 years) patients prescribed iCBT through This Way Up clinic by their primary care clinician. The intervention consisted of six fully automated, unassisted online lessons specific to four disorders major depression, generalised anxiety disorder, panic disorder or social phobia. Patients were categorised into five age groups (18–29 years, 30–39 years, 40–49 years, 50–59 years, 60 years and above). 225 (9.3%) patients were aged over 60 years. Analyses were conducted across the four disorders to ensure sufficient sample sizes in the 60 years and older age group. Age differences in adherence to the six lesson courses were assessed to demonstrate acceptability. Age-based reductions in psychological distress (Kessler Psychological Distress Scale; K10) and disability (the World Health Organisation Disability Assessment Schedule; WHODAS-II) were compared to demonstrate effectiveness. To evaluate the uptake of iCBT, the age distribution of those commencing iCBT was compared with the prevalence of these disorders in the 2007 Australian National Survey of Mental Health and Well-Being.

Results

Older adults were more likely to complete all six lessons when compared with their younger counterparts. Marginal model analyses indicated that there were significant reductions in the K10 and WHODAS-II from baseline to post-intervention, regardless of age (p<0.001). The measurement occasion by age interactions were not significant, indicating that individuals showed similar reductions in the K10 and WHODAS-II regardless of age. In general, the age distribution of individuals commencing the iCBT courses matched the age distribution of the four diagnoses in the Australian general population, indicating that iCBT successfully captures older individuals who need treatment.

Conclusion

iCBT is effective and acceptable for use in older populations.     

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.     

The Effectiveness of Internet Cognitive Behavioural Therapy (iCBT) for Depression in Primary Care: A Quality Assurance Study

Background

Depression is a common, recurrent, and debilitating problem and Internet delivered cognitive behaviour therapy (iCBT) could offer one solution. There are at least 25 controlled trials that demonstrate the efficacy of iCBT. The aim of the current paper was to evaluate the effectiveness of an iCBT Program in primary care that had been demonstrated to be efficacious in two randomized controlled trials (RCTs).

Method

Quality assurance data from 359 patients prescribed the Sadness Program in Australia from October 2010 to November 2011 were included.

Results

Intent-to-treat marginal model analyses demonstrated significant reductions in depressive symptoms (PHQ9), distress (K10), and impairment (WHODAS-II) with medium-large effect sizes (Cohen''s d = .51–1.13.), even in severe and/or suicidal patients (Cohen''s d = .50–1.49.) Secondary analyses on patients who completed all 6 lessons showed levels of clinically significant change as indexed by established criteria for remission, recovery, and reliable change.

Conclusions

The Sadness Program is effective when prescribed by primary care practitioners and is consistent with a cost-effective stepped-care framework.     

A Glycolipid Adjuvant, 7DW8-5, Enhances CD8+ T Cell Responses Induced by an Adenovirus-Vectored Malaria Vaccine in Non-Human Primates

A key strategy to a successful vaccine against malaria is to identify and develop new adjuvants that can enhance T-cell responses and improve protective immunity. Upon co-administration with a rodent malaria vaccine in mice, 7DW8-5, a recently identified novel analog of α-galactosylceramide (α-GalCer), enhances the level of malaria-specific protective immune responses more strongly than the parent compound. In this study, we sought to determine whether 7DW8-5 could provide a similar potent adjuvant effect on a candidate human malaria vaccine in the more relevant non-human primate (NHP) model, prior to committing to clinical development. The candidate human malaria vaccine, AdPfCA (NMRC-M3V-Ad-PfCA), consists of two non-replicating recombinant adenoviral (Ad) vectors, one expressing the circumsporozoite protein (CSP) and another expressing the apical membrane antigen-1 (AMA1) of Plasmodium falciparum. In several phase 1 clinical trials, AdPfCA was well tolerated and demonstrated immunogenicity for both humoral and cell-mediated responses. In the study described herein, 25 rhesus macaques received prime and boost intramuscular (IM) immunizations of AdPfCA alone or with an ascending dose of 7DW8-5. Our results indicate that 7DW8-5 is safe and well-tolerated and provides a significant enhancement (up to 9-fold) in malaria-specific CD8+ T-cell responses after both priming and boosting phases, supporting further clinical development.     

In silico investigation of novel biological pathways: The role of CD200 in regulation of T cell priming in experimental autoimmune encephalomyelitis

The use of simulation to investigate biological domains will inevitably lead to the need to extend existing simulations as new areas of these domains become more fully understood. Such simulation extensions can entail the incorporation of additional cell types, molecules or molecular pathways, all of which can exert a profound influence on the simulation behaviour. Where the biological domain is not well characterised, a structured development methodology must be employed to ensure that the extended simulation is well aligned with its predecessor. We develop and discuss such a methodology, relying on iterative simulation development and sensitivity analysis. The utility of this methodology is demonstrated using a case study simulation of experimental autoimmune encephalomyelitis (EAE), a murine T cell-mediated autoimmune disease model of multiple sclerosis, where it is used to investigate the activity of an additional regulatory pathway. We discuss how application of this methodology guards against creating inappropriate simulation representations of the biology when investigating poorly characterised biological mechanisms.     

Insights into the Mechanism of Ribosomal Incorporation of Mammalian L13a Protein during Ribosome Biogenesis

In contrast to prokaryotes, the precise mechanism of incorporation of ribosomal proteins into ribosomes in eukaryotes is not well understood. For the majority of eukaryotic ribosomal proteins, residues critical for rRNA binding, a key step in the hierarchical assembly of ribosomes, have not been well defined. In this study, we used the mammalian ribosomal protein L13a as a model to investigate the mechanism(s) underlying eukaryotic ribosomal protein incorporation into ribosomes. This work identified the arginine residue at position 68 of L13a as being essential for L13a binding to rRNA and incorporation into ribosomes. We also demonstrated that incorporation of L13a takes place during maturation of the 90S preribosome in the nucleolus, but that translocation of L13a into the nucleolus is not sufficient for its incorporation into ribosomes. Incorporation of L13a into the 90S preribosome was required for rRNA methylation within the 90S complex. However, mutations abolishing ribosomal incorporation of L13a did not affect its ability to be phosphorylated or its extraribosomal function in GAIT element-mediated translational silencing. These results provide new insights into the mechanism of ribosomal incorporation of L13a and will be useful in guiding future studies aimed at fully deciphering mammalian ribosome biogenesis.