Assessing factors associated with changes in the numbers of birds visiting gardens in winter: Are predators partly to blame?

The factors governing the recent declines observed in many songbirds have received much research interest, in particular whether increases of avian predators have had a negative effect on any of their prey species. In addition, further discussion has centered on whether or not the choice of model formulation has an effect on model inference. The study goal was to evaluate changes in the number of 10 songbird species in relation to a suite of environmental covariates, testing for any evidence in support of a predator effect using multiple model formulations to check for consistency in the results. We compare two different approaches to the analysis of long‐term garden bird monitoring data. The first approach models change in the prey species between 1970 and 2005 as a function of environmental covariates, including the abundance of an avian predator, while the second uses a change–change approach. Significant negative relationships were found between Eurasian Sparrowhawk Accipiter nisus and three of the 10 species analyzed, namely house Sparrow Passer domesticus, starling Sturnus vulgaris, and blue tit Cyanistes caeruleus. The results were consistent under both modeling approaches. It is not clear if this is a direct negative impact on the overall populations of these species or a behavioral response of the prey species to avoid feeding stations frequented by Sparrowhawks (which may in turn have population consequences, by reducing available resources). The species showing evidence of negative effects of Sparrowhawks were three of the four species most at risk to Sparrowhawk predation according to their prevalence in the predator's diet. The associations could be causal in nature, although in practical terms the reduction in the rate of change in numbers visiting gardens accredited to Sparrowhawks is relatively small, and so unlikely to be the main driver of observed population declines.     

Notch receptor expression in human brain arteriovenous malformations

The roles of the Notch pathway proteins in normal adult vascular physiology and the pathogenesis of brain arteriovenous malformations are not well‐understood. Notch 1 and 4 have been detected in human and mutant mice vascular malformations respectively. Although mutations in the human Notch 3 gene caused a genetic form of vascular stroke and dementia, its role in arteriovenous malformations development has been unknown. In this study, we performed immunohistochemistry screening on tissue microarrays containing eight surgically resected human brain arteriovenous malformations and 10 control surgical epilepsy samples. The tissue microarrays were evaluated for Notch 1–4 expression. We have found that compared to normal brain vascular tissue Notch‐3 was dramatically increased in brain arteriovenous malformations. Similarly, Notch 4 labelling was also increased in vascular malformations and was confirmed by western blot analysis. Notch 2 was not detectable in any of the human vessels analysed. Using both immunohistochemistry on microarrays and western blot analysis, we have found that Notch‐1 expression was detectable in control vessels, and discovered a significant decrease of Notch 1 expression in vascular malformations. We have demonstrated that Notch 3 and 4, and not Notch 1, were highly increased in human arteriovenous malformations. Our findings suggested that Notch 4, and more importantly, Notch 3, may play a role in the development and pathobiology of human arteriovenous malformations.     

Eye size and the time of arrival of birds at garden feeding stations in winter

A nationwide volunteer survey was conducted to investigate the time at which common species of birds arrived at garden feeders in the morning during winter, and over 5,800 participants submitted observations. We examined the relationship between species’ eye size and their time of arrival at feeders, in order to investigate whether the time at which foraging was initiated was constrained by visual capability. There was a negative correlation between eye size and time of arrival at garden feeders across species, and this relationship remained significant when body mass was taken into account. This suggests that the time at which garden birds begin to forage on winter mornings may be limited by their visual capability at low light intensities.     

Isolation and characterization of a new non-toxic two-chain ribosome-inactivating protein from fruits of elder (Sambucus nigra L.)

Sambucus (Caprifoliaceae) species contain nigrin b and ebulinI, which are two-chain ribosomeinactivating proteins (RIPs)belonging to a new type of RIPS which are non-toxic to miceand cultured human cells. In this work the presence in fruitsof elder (S. nigra L.) of a new non-toxic type 2 RIP (nigrinf) that co-exists with a lectin known as SNA IV is described.Nigrin f strongly inhibited protein synthesis in mammalian,but not in plant, ribosomes, promoting the depurination of sensitiveribosomes and thus allowing the release of the RIP diagnosticRNA fragment. Nigrin f is composed of two dissimilar subunitslinked by disulphide bridges with apparent M_r values of 31 600and 26 300. The N-terminal amino acid sequence revealed closehomology of the catalytic A chain with type 1 RIPs, especiallythose from Cucurbitaceae, and the B chain with several lectinspreviously isolated from Sambucus species. Nigrin f was nottoxic to mice when injected intraperitoneally up to 2 mg kg^–1.In addition, NHC human cells were also insensitive to nigrinf up to 60 µg ml^–1. Anti-nigrin b rabbit polyclonalantibodies reacted with nigrin f, indicating that nigrin b andnigrin f are proteins with similar structures. Key words: Sambucus nigra, elder fruits, nigrin f, ribosomeinactivating protein, characterization     

Characterizing the normal proteome of human ciliary body

Background

The ciliary body is the circumferential muscular tissue located just behind the iris in the anterior chamber of the eye. It plays a pivotal role in the production of aqueous humor, maintenance of the lens zonules and accommodation by changing the shape of the crystalline lens. The ciliary body is the major target of drugs against glaucoma as its inhibition leads to a drop in intraocular pressure. A molecular study of the ciliary body could provide a better understanding about the pathophysiological processes that occur in glaucoma. Thus far, no large-scale proteomic investigation has been reported for the human ciliary body.

Results

In this study, we have carried out an in-depth LC-MS/MS-based proteomic analysis of normal human ciliary body and have identified 2,815 proteins. We identified a number of proteins that were previously not described in the ciliary body including importin 5 (IPO5), atlastin-2 (ATL2), B-cell receptor associated protein 29 (BCAP29), basigin (BSG), calpain-1 (CAPN1), copine 6 (CPNE6), fibulin 1 (FBLN1) and galectin 1 (LGALS1). We compared the plasma proteome with the ciliary body proteome and found that the large majority of proteins in the ciliary body were also detectable in the plasma while 896 proteins were unique to the ciliary body. We also classified proteins using pathway enrichment analysis and found most of proteins associated with ubiquitin pathway, EIF2 signaling, glycolysis and gluconeogenesis.

Conclusions

More than 95% of the identified proteins have not been previously described in the ciliary body proteome. This is the largest catalogue of proteins reported thus far in the ciliary body that should provide new insights into our understanding of the factors involved in maintaining the secretion of aqueous humor. The identification of these proteins will aid in understanding various eye diseases of the anterior segment such as glaucoma and presbyopia.     

Long-term decline of a winter-resident bird community in Puerto Rico

Despite concern expressed two decades ago, there has been little recent discussion about continuing declines of migrant bird populations. Monitoring efforts have been focused almost exclusively on the breeding grounds. We describe the long-term decline of a winter-resident bird population in Guánica Commonwealth Forest, Puerto Rico, one of the last remaining tracts of high-quality tropical dry forests in the Caribbean. The winter bird community has exhibited dramatic declines, with constant-effort mist netting now capturing about one-third as many birds as it did 20 years ago. Population estimates for the three most common species have declined dramatically, even though survival rates have remained constant, and other species are now virtually absent from a site where they once were fairly common. Although explanations for these declines are speculative, particularly because they involve multiple species, we argue that the strength and duration of these declines in well-preserved dry forest within a biosphere reserve should stimulate renewed discussion of migrant population trends and comparison with other recent monitoring activities.     

The dissociation of avidin–biotin complexes by guanidinium chloride

Avidin molecules in which a fraction of the four binding sites were occupied by biotin did not dissociate completely in 6.4m-guanidinium chloride. Only unoccupied subunits dissociated. The remainder recombined to form the tetrameric avidin-biotin complex. The rate at which unoccupied subunits were unfolded and dissociated was only decreased by one-half in species in which three of the four binding sites were occupied by biotin. These results can be explained by assuming that unfolding of unoccupied subunits followed by dissociation from the tetramer is initiated by penetration of guanidinium ions into the binding site and disorganization of this region of the subunit. When a site is occupied by biotin this pathway is blocked and the subunit does not unfold. Each subunit behaves independently and is not markedly stabilized when neighbouring subunits are occupied.     

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas

Background

Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question.

Results

We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events.

Conclusions

Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0432-0) contains supplementary material, which is available to authorized users.