Observations of phase changes in monoolein during high viscous injection.

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.

Control of sheep gastrointestinal nematodes on pasture in the tropical semiarid region of Brazil, using Bioverm® (Duddingtonia flagrans).

We aimed to evaluate a Brazilian commercial formulation of the fungus Duddingtonia flagrans (Bioverm®) for controlling gastrointestinal nematodes in sheep kept on native pasture in the Caatinga biome, in the semiarid region of Brazil. Twenty ewes, aged between 12 and 18 months, were divided into two groups. In the treated group, each animal received 1 g of the Bioverm® product for each 10 kg of live weight, daily, together with commercial feed, for 6 months. In the control group, the animals received feed without Bioverm®. Each group remained throughout the experiment in a 1.2-ha paddock. Monthly counts of eggs per gram (EPG) of feces, fecal cultures, packed cell volume (PCV), weight measurements, and collection of leaf mass from the pasture were performed. There was greater reduction in EPG, greater weight gain, and less infestation by infective larvae in the paddock of the Bioverm® group, compared with the control group (p < 0.05). There was no significant difference (p ≥ 0.05) in the mean PCV percentage between the Bioverm® and control groups. In coprocultures, Haemonchus sp. was the most prevalent helminth. Bioverm® (D. flagrans) was efficient for biological control of sheep gastrointestinal nematodes in the semiarid region of Brazil.

Biodepuration of domestic sewage, textile effluents and acid mine drainage using starch-based xerogel from recycled potato peels.

Water is a finite resource. Its safety and cleanliness are highly important to meet current and future human needs. Compared to other resources, water represents a main factor to achieve development in several areas and leads to economic progress of a nation. However, in recent years, the excessive demographic and industrial growth has exacerbated water contamination. In this study, the biodepuration process of domestic sewage (DS), textile effluents (TE) and acid mine drainage (AMD) is conducted using starch-based xerogel from potato (Solanum tuberosum) peels. Results showed that the treatment is effective to achieve the reduction of 5-day biochemical oxygen demand. The most important result was the achievement of heavy metals removal for the three components. Firstly, there was a reduction of barium, zinc, and cadmium (91, 60 and 46%, respectively) for raw AMD. Secondly, there was a reduction in the levels of zinc, aluminum, and barium (89, 86 and 64%, respectively) for TE biodepuration. Finally, results showed a reduction in zinc, iron and cadmium levels (81, 78 and 57%, respectively) for DS biodepuration.

Disentangling genetic and epigenetic determinants of ultrafast adaptation.

A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical-experimental framework for disclosing the presence of such adaptation-speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation-accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity. Causative mutations were identified by deep sequencing of the arsenic-adapted populations and reconstructed for validation. Mutation effects on growth phenotypes, and the associated mutational target sizes were quantified and embedded in data-driven individual-based evolutionary population models. We found that the experimentally observed homogeneity of adaptation speed and heterogeneity of molecular solutions could only be accounted for if the mutation rate had been near estimates of the basal mutation rate. The ultrafast adaptation could be fully explained by extensive positive pleiotropy such that all beneficial mutations dramatically enhanced multiple fitness components in concert. As our approach can be exploited across a range of model organisms exposed to a variety of environmental challenges, it may be used for determining the importance of epigenetic adaptation-speeding mechanisms in general.

ChemProt: a disease chemical biology database.

Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). We assembled more than 700,000 unique chemicals with biological annotation for 30,578 proteins. We gathered over 2-million chemical-protein interactions, which were integrated in a quality scored human PPI network of 428,429 interactions. The PPI network layer allows for studying disease and tissue specificity through each protein complex. ChemProt can assist in the in silico evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram, an antidepressant, with osteogenesis imperfect and leukemia and bisphenol A, an endocrine disruptor, with certain types of cancer, respectively. The server can be accessed at http://www.cbs.dtu.dk/services/ChemProt/.

Using electronic patient records to discover disease correlations and stratify patient cohorts.

Electronic patient records remain a rather unexplored, but potentially rich data source for discovering correlations between diseases. We describe a general approach for gathering phenotypic descriptions of patients from medical records in a systematic and non-cohort dependent manner. By extracting phenotype information from the free-text in such records we demonstrate that we can extend the information contained in the structured record data, and use it for producing fine-grained patient stratification and disease co-occurrence statistics. The approach uses a dictionary based on the International Classification of Disease ontology and is therefore in principle language independent. As a use case we show how records from a Danish psychiatric hospital lead to the identification of disease correlations, which subsequently can be mapped to systems biology frameworks.

Prevalence and isolation of Toxoplasma gondii in goats slaughtered for human consumption in the semi-arid of northeastern Brazil.

The aim of this study was to determine the seroprevalence of anti-Toxoplasma gondii antibodies and factors associated with infection in goats, and to isolate protozoan strains in tissue samples from seropositive goats that were destined for human consumption in the state of Paraíba, northeastern Brazil. Serum samples from 229 slaughtered goats were tested using the indirect fluorescence antibody test (IFAT), with a cutoff point of 1:64. Epidemiological questionnaires were applied to the producers, to acquire information about the sanitary management used in their herds. Tissue samples from the animals were collected during slaughter, in order to perform bioassays in mice. The seroprevalence found was 21.39% (49/229), with antibody titers ranging from 1:64 to 1:32,768. The municipalities of origin, Patos (OR: 3.047; CI: 1.384-6.706) and Sousa (OR: 3.355; CI: 1.536-7.327), were considered to be factors associated with infection by T. gondii. Thirty-eight bioassays were performed in mice, using tissues from seropositive goats, with an isolation rate of 50% (19/38). There was no correlation between isolation rate and antibody titers. Only one mouse died, at 30 days post-infection, which demonstrated that the strains isolated had low virulence towards mice. It was concluded that there is high seroprevalence in goats in northeastern Brazil, as well as a high percentage of viable tissue cysts in slaughtered animals destined for human consumption. These results demonstrate that there is an imminent one health problem relating to toxoplasmosis, especially in the most populous municipalities in the study (Patos and Sousa), which were identified as factors associated with T. gondii infection in goats.

Preferred orientation and its effects on intensity-correlation measurements.

Intensity-correlation measurements allow access to nanostructural information on a range of ordered and disordered materials beyond traditional pair-correlation methods. In real space, this information can be expressed in terms of a pair-angle distribution function (PADF) which encodes three- and four-body distances and angles. To date, correlation-based techniques have not been applied to the analysis of microstructural effects, such as preferred orientation, which are typically investigated by texture analysis. Preferred orientation is regarded as a potential source of error in intensity-correlation experiments and complicates interpretation of the results. Here, the theory of preferred orientation in intensity-correlation techniques is developed, connecting it to the established theory of texture analysis. The preferred-orientation effect is found to scale with the number of crystalline domains in the beam, surpassing the nanostructural signal when the number of domains becomes large. Experimental demonstrations are presented of the orientation-dominant and nanostructure-dominant cases using PADF analysis. The results show that even minor deviations from uniform orientation produce the strongest angular correlation signals when the number of crystalline domains in the beam is large.

Stability, flow alignment and a phase transition of the lipidic cubic phase during continuous flow injection.

Continuous flow injection is a key technology for serial crystallography measurements of protein crystals suspended in the lipidic cubic phase (LCP). To date, there has been little discussion in the literature regarding the impact of the injection process itself on the structure of the lipidic phase. This is despite the fact that the phase of the injection matrix is critical for the flow properties of the stream and potentially for sample stability. Here we report small-angle X-ray scattering measurements of a monoolein:water mixture during continuous delivery using a high viscosity injector. We observe both an alignment and modification of the LCP as a direct result of the injection process. The orientation of the cubic lattice with respect to the beam was estimated based on the anisotropy of the diffraction pattern and does not correspond to a single low order zone axis. The solvent fraction was also observed to impact the stability of the cubic phase during injection. In addition, depending on the distance traveled by the lipid after exiting the needle, the phase is observed to transition from a pure diamond phase (Pn3m) to a mixture containing both gyriod (Ia3d) and lamellar (Lα) phases. Finite element modelling of the observed phase behaviour during injection indicates that the pressure exerted on the lipid stream during extrusion accounts for the variations in the phase composition of the monoolein:water mixture.

Dissecting spatio-temporal protein networks driving human heart development and related disorders.

Aberrant organ development is associated with a wide spectrum of disorders, from schizophrenia to congenital heart disease, but systems-level insight into the underlying processes is very limited. Using heart morphogenesis as general model for dissecting the functional architecture of organ development, we combined detailed phenotype information from deleterious mutations in 255 genes with high-confidence experimental interactome data, and coupled the results to thorough experimental validation. Hereby, we made the first systematic analysis of spatio-temporal protein networks driving many stages of a developing organ identifying several novel signaling modules. Our results show that organ development relies on surprisingly few, extensively recycled, protein modules that integrate into complex higher-order networks. This design allows the formation of a complicated organ using simple building blocks, and suggests how mutations in the same genes can lead to diverse phenotypes. We observe a striking temporal correlation between organ complexity and the number of discrete functional modules coordinating morphogenesis. Our analysis elucidates the organization and composition of spatio-temporal protein networks that drive the formation of organs, which in the future may lay the foundation of novel approaches in treatments, diagnostics, and regenerative medicine.