Peptide redesign for inhibition of the complement system: Targeting age-related macular degeneration.

PurposeTo redesign a complement-inhibiting peptide with the potential to become a therapeutic for dry and wet age-related macular degeneration (AMD).MethodsWe present a new potent peptide (Peptide 2) of the compstatin family. The peptide is developed by rational design, based on a mechanistic binding hypothesis, and structural and physicochemical properties derived from molecular dynamics (MD) simulation. The inhibitory activity, efficacy, and solubility of Peptide 2 are evaluated using a hemolytic assay, a human RPE cell-based assay, and ultraviolet (UV) absorption properties, respectively, and compared to the respective properties of its parent peptide (Peptide 1).ResultsThe sequence of Peptide 2 contains an arginine-serine N-terminal extension (a characteristic of parent Peptide 1) and a novel 8-polyethylene glycol (PEG) block C-terminal extension. Peptide 2 has significantly improved aqueous solubility compared to Peptide 1 and comparable complement inhibitory activity. In addition, Peptide 2 is more efficacious in inhibiting complement activation in a cell-based model that mimics the pathobiology of dry AMD.ConclusionsWe have designed a new peptide analog of compstatin that combines N-terminal polar amino acid extensions and C-terminal PEGylation extensions. This peptide demonstrates significantly improved aqueous solubility and complement inhibitory efficacy, compared to the parent peptide. The new peptide overcomes the aggregation limitation for clinical translation of previous compstatin analogs and is a candidate to become a therapeutic for the treatment of AMD

Multi-valued, singular stochastic evolution inclusions

We provide an abstract variational existence and uniqueness result for multi-valued, monotone, non-coercive stochastic evolution inclusions in Hilbert spaces with general additive and Wiener multiplicative noise. As examples we discuss certain singular diffusion equations such as the stochastic 1-Laplacian evolution (total variation flow) in all space dimensions and the stochastic singular fast diffusion equation. In case of additive Wiener noise we prove the existence of a unique weak-* mean ergodic invariant measure.Comment: 39 pages, in press: J. Math. Pures Appl. (2013

Parameterized vertex deletion problems for hereditary graph classes with a block property

For a class of graphs P, the Bounded P-Block Vertex Deletion problem asks, given a graph G on n vertices and positive integers k and d, whether there is a set S of at most k vertices such that each block of G − S has at most d vertices and is in P. We show that when P satisfies a natural hereditary property and is recognizable in polynomial time, Bounded P-Block Vertex Deletion can be solved in time 2O(k log d)nO(1), and this running time cannot be improved to 2o(k log d)nO(1), in general, unless the Exponential Time Hypothesis fails. On the other hand, if P consists of only complete graphs, or only K1,K2, and cycle graphs, then Bounded P-Block Vertex Deletion admits a cknO(1)-time algorithm for some constant c independent of d. We also show that Bounded P-Block Vertex Deletion admits a kernel with O(k2d7) vertices. © Springer-Verlag GmbH Germany 2016

Impacts of organic and conventional crop management on diversity and activity of free-living nitrogen fixing bacteria and total bacteria are subsidiary to temporal effects

A three year field study (2007-2009) of the diversity and numbers of the total and metabolically active free-living diazotophic bacteria and total bacterial communities in organic and conventionally managed agricultural soil was conducted at the Nafferton Factorial Systems Comparison (NFSC) study, in northeast England. The result demonstrated that there was no consistent effect of either organic or conventional soil management across the three years on the diversity or quantity of either diazotrophic or total bacterial communities. However, ordination analyses carried out on data from each individual year showed that factors associated with the different fertility management measures including availability of nitrogen species, organic carbon and pH, did exert significant effects on the structure of both diazotrophic and total bacterial communities. It appeared that the dominant drivers of qualitative and quantitative changes in both communities were annual and seasonal effects. Moreover, regression analyses showed activity of both communities was significantly affected by soil temperature and climatic conditions. The diazotrophic community showed no significant change in diversity across the three years, however, the total bacterial community significantly increased in diversity year on year. Diversity was always greatest during March for both diazotrophic and total bacterial communities. Quantitative analyses using qPCR of each community indicated that metabolically active diazotrophs were highest in year 1 but the population significantly declined in year 2 before recovering somewhat in the final year. The total bacterial population in contrast increased significantly each year. Seasonal effects were less consistent in this quantitative study

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

Genes in durophage intersection set at 15 dpf. This is a comma separated table of the genes in the 15 dpf durophage intersection set. Given are edgeR results for each pairwise comparison. Columns indicating whether a gene is included in the intersection set at a threshold of 1.5 or 2 fold are provided. (CSV 13 kb

Comparison of Plasmodium berghei challenge models for the evaluation of pre-erythrocytic malaria vaccines and their effect on perceived vaccine efficacy

<p>Abstract</p> <p>Background</p> <p>The immunological mechanisms responsible for protection against malaria infection vary among <it>Plasmodium </it>species, host species and the developmental stage of parasite, and are poorly understood. A challenge with live parasites is the most relevant approach to testing the efficacy of experimental malaria vaccines. Nevertheless, in the mouse models of <it>Plasmodium berghei </it>and <it>Plasmodium yoelii</it>, parasites are usually delivered by intravenous injection. This route is highly artificial and particularly in the <it>P. berghei </it>model produces inconsistent challenge results. The initial objective of this study was to compare an optimized intravenous (IV) delivery challenge model with an optimized single infectious mosquito bite challenge model. Finding shortcomings of both approaches, an alternative approach was explored, <it>i.e</it>., the subcutaneous challenge.</p> <p>Methods</p> <p>Mice were infected with <it>P. berghei </it>sporozoites by intravenous (tail vein) injection, single mosquito bite, or subcutaneous injection of isolated parasites into the subcutaneous pouch at the base of the hind leg. Infection was determined in blood smears 7 and 14 days later. To determine the usefulness of challenge models for vaccine testing, mice were immunized with circumsporozoite-based DNA vaccines by gene gun.</p> <p>Results</p> <p>Despite modifications that allowed infection with a much smaller than reported number of parasites, the IV challenge remained insufficiently reliable and reproducible. Variations in the virulence of the inoculum, if not properly monitored by the rigorous inclusion of sporozoite titration curves in each experiment, can lead to unacceptable variations in reported vaccine efficacies. In contrast, mice with different genetic backgrounds were consistently infected by a single mosquito bite, without overwhelming vaccine-induced protective immune responses. Because of the logistical challenges associated with the mosquito bite model, the subcutaneous challenge route was optimized. This approach, too, yields reliable challenge results, albeit requiring a relatively large inoculum.</p> <p>Conclusions</p> <p>Although a single bite by <it>P. berghei </it>infected <it>Anopheles </it>mosquitoes was superior to the IV challenge route, it is laborious. However, any conclusive evaluation of a pre-erythrocytic malaria vaccine candidate should require challenge through the natural anatomic target site of the parasite, the skin. The subcutaneous injection of isolated parasites represents an attractive compromise. Similar to the mosquito bite model, it allows vaccine-induced antibodies to exert their effect and is, therefore not as prone to the artifacts of the IV challenge.</p

Contorted and ordinary body postures in the human brain

Social interaction and comprehension of non-verbal behaviour requires a representation of people’s bodies. Research into the neural underpinnings of body representation implicates several brain regions including extrastriate and fusiform body areas (EBA and FBA), superior temporal sulcus (STS), inferior frontal gyrus (IFG) and inferior parietal lobule (IPL). The different roles played by these regions in parsing familiar and unfamiliar body postures remain unclear. We examined the responses of this body observation network to static images of ordinary and contorted postures by using a repetition suppression design in functional neuroimaging. Participants were scanned whilst observing static images of a contortionist or a group of objects in either ordinary or unusual configurations, presented from different viewpoints. Greater activity emerged in EBA and FBA when participants viewed contorted compared to ordinary body postures. Repeated presentation of the same posture from different viewpoints lead to suppressed responses in the fusiform gyrus as well as three regions that are characteristically activated by observing moving bodies, namely STS, IFG and IPL. These four regions did not distinguish the image viewpoint or the plausibility of the posture. Together, these data define a broad cortical network for processing static body postures, including regions classically associated with action observation

TOLKIN – Tree of Life Knowledge and Information Network: Filling a Gap for Collaborative Research in Biological Systematics

The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email

Experts see it all: configural effects in action observation

Biological motion perception is influenced by observers’ familiarity with the observed action. Here we used classical dance as a means to investigate how visual and motor experience modulates perceptual mechanism for configural processing of actions. While some ballet moves are performed by only one gender, male and female dancers train together and acquire visual knowledge of all ballet moves. 24 expert ballet dancers (12 female) and matched non-expert participants viewed pairs of upright and inverted point light female and common dance movements. Visual discrimination between different exemplars of the same movement presented upright was significantly better in experts than controls, while no differences were found when the same stimuli were presented upside down. These results suggest expertise influences configural action processing. Within the expert group, effects were stronger for female participants than for males, while no differences were found between movement types. This observer gender effect could suggest an additional role for motor familiarity in action perception, over and above visual experience. Our results are consistent with a specific motor contribution to configural processing of action