Novel Distances for Dollo Data

We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. We introduce a novel distance, the Additive Dollo Distance (ADD), which is consistent for data generated under a Dollo model, and show that it has some useful theoretical properties including an intriguing link to the LogDet distance. Simulations of Dollo data are used to compare a number of binary distances including ADD, LogDet, Nei Li and some simple, but to our knowledge previously unstudied, variations on common binary distances. The simulations suggest that ADD outperforms other distances on Dollo data. Interestingly, we found that the LogDet distance performs poorly in the context of a Dollo process, which may have implications for its use in connection with conditioned genome reconstruction. We apply the ADD to two Diversity Arrays Technology (DArT) datasets, one that broadly covers Eucalyptus species and one that focuses on the Eucalyptus series Adnataria. We also reanalyse gene family presence/absence data on bacteria from the COG database and compare the results to previous phylogenies estimated using the conditioned genome reconstruction approach

Intestinal activation of Notch signaling induces rapid onset hepatic steatosis and insulin resistance.

Here we investigate the effects of expressing an activated mutant of Notch (ICD-E) in an inducible transgenic mouse model. Hepatic expression of ICD-E in adult animals has no detectable phenotype, but simultaneous induction of ICD-E in both the liver and small intestine results in hepatic steatosis, lipogranuloma formation and mild insulin resistance within 96 hours. This supports work that suggests that fatty liver disease may result from disruption of the gut-liver axis. In the intestine, ICD-E expression is known to produce a transient change in the proportion of goblet cells followed by shedding of the recombinant epithelium. We report additional intestinal transcriptional changes following ICD-E expression, finding significant transcriptional down-regulation of rpL29 (ribosomal protein L29), which is implicated in the regulation of intestinal flora. These results provide further evidence of a gut-liver axis in the development of fatty liver disease and insulin resistance and validate a new model for future studies of hepatic steatosis

Polychromatic solar energy conversion in pigment-protein chimeras that unite the two kingdoms of (bacterio)chlorophyll-based photosynthesis

Natural photosynthesis can be divided between the chlorophyll-containing plants, algae and cyanobacteria that make up the oxygenic phototrophs and a diversity of bacteriochlorophyll-containing bacteria that make up the anoxygenic phototrophs. Photosynthetic light harvesting and reaction centre proteins from both kingdoms have been exploited for solar energy conversion, solar fuel synthesis and sensing technologies, but the energy harvesting abilities of these devices are limited by each protein’s individual palette of pigments. In this work we demonstrate a range of genetically-encoded, self-assembling photosystems in which recombinant plant light harvesting complexes are covalently locked with reaction centres from a purple photosynthetic bacterium, producing macromolecular chimeras that display mechanisms of polychromatic solar energy harvesting and conversion. Our findings illustrate the power of a synthetic biology approach in which bottom-up construction of photosystems using naturally diverse but mechanistically complementary components can be achieved in a predictable fashion through the encoding of adaptable, plug-and-play covalent interfaces

Sustaining Electron Transfer Pathways Extends Biohybrid Photoelectrode Stability to Years

The exploitation of natural photosynthetic enzymes in semi-artificial devices constitutes an attractive and potentially sustainable route for the conversion of solar energy into electricity and solar fuels. However, the stability of photosynthetic proteins after incorporation in a biohybrid architecture typically limits the operational lifetime of biophotoelectrodes to a few hours. Here, we demonstrate ways to greatly enhance the stability of a mesoporous electrode coated with the RC-LH1 photoprotein from Rhodobacter sphaeroides. By preserving electron transfer pathways, we extended operation under continuous high-light to 33 days, and operation after storage to over two years. Coupled with large photocurrents that reached peak values of 4.6 mA cm−2, the optimized biophotoelectrode produced a cumulative output of 86 C cm−2, the largest reported performance to date. Our results demonstrate that the factor limiting stability is the architecture surrounding the photoprotein, and that biohybrid sensors and photovoltaic devices with operational lifetimes of years are feasible

Failure of microvenous valves in small superficial veins is a key to the skin changes of venous insufficiency

ObjectiveTo determine the role of microvenous valves in the superficial venous system in the prevention of reflux and skin changes in the progression of venous insufficency.MethodsThe venous anatomy of 15 amputated lower limbs, eight free from clinical venous disease and seven with varicose veins and ulcers, was examined using retrograde venography corrosion casting. Prior to amputation, all limbs were scanned by duplex ultrasound to confirm the presence or absence of reflux in the great (GSV) and small saphenous veins or their tributaries. The resulting resin casts were photographed and mapped to show the position, orientation, and competency of valves in the superficial venous network. Casts were also examined by scanning electron microscopy.ResultsRetrograde venous filling was demonstrated in the “normal” limbs despite a competent GSV. Microvalves were identified down to the sixth generation of tributaries from the GSV. Only in regions where incompetence existed in microvalves out to the third (ie, the “boundary”) generation was the resin able to penetrate deeper into microvenous networks of the dermis. This was despite the presence of subsequent competent valves, which were able to be bypassed in the network. In limbs with varicose veins and venous ulcers, reflux into the small venous networks and capillary loops was more extensive with more dense networks and greater tortuousity.ConclusionsThis study demonstrates that valvular incompetence can occur independently in small superficial veins in the absence of reflux within the GSV and the major tributaries. We have shown that once there is incompetence of the third generation “boundary” microvalves, reflux can extend into the microvenous networks in the skin. These effects are markedly worse in the presence of GSV incompetence. We propose that degenerative changes with valve incompetence are required in both the larger proximal vessels and the small superficial veins, in particular at the “boundary” valve level, for the severe skin changes in venous insufficiency to occur.Clinical RelevanceThis study describes the presence of microvalves in the very small veins in the skin, which may be critical to whether skin changes occur in venous insufficiency. The concept may explain why some people with longstanding varicose veins do not develop venous ulcers. In addition, this article describes degenerative changes in the network of very small veins in the skin of the leg which may relate to appearances of reticular veins, corona phlebectatica, and venous flares. These degenerative changes occur without varicose veins but are much worse when they occur together

Just Bone Tired: Equine Bone Stress

The field of biophotoelectrochemistry and its application in biophotovoltaics and biosensors has gained more and more attention in recent years. Knowledge of the redox potentials of the catalytically active protein cofactors in biophotovoltaic devices is crucial for accurate modelling and in discerning the mechanisms of their operation. Here, for the first time, we used spectroelectrochemical methods to investigate thermodynamic parameters of a biophotoelectrode in situ. We determined redox potentials of two elements of the system: the primary electron donor in photosynthetic reaction centers (RCs) of the bacterium Rhodobacter sphaeroides and osmium-complex based redox mediators that are bound to a hydrogel matrix. We observe that the midpoint potential of the primary donor is shifted towards more positive potentials in comparison to literature data for RCs solubilized in buffered water solution, likely due to interaction with the polymer matrix. We also demonstrate that the osmium-complex modified redox polymer efficiently wires the RCs to the electrode, maintaining a high Internal Quantum Efficiency with approximately one electron per two photons generated (IQE=50±12%). Overall, this biophotoelectrode may be attractive for controlling the redox state of the protein when performing other types of experiments, e.g. time resolved absorption or fluorescence measurements, in order to gain insights into kinetic limitations and thereby help in the rational design of bioelectronic devices

Survey of the Illinois Endangered Kankakee Mallow, Iliamna remota, in Kankakee County

Iliamna remota Greene (Malvaceae), endemic only to Langham Island in the Kankakee River, Kankakee County, Illinois, is a state endangered species. During the present study, the size of the population was determined, the habitat structure in and around the individual colonies analyzed, and management recommendation made to potentially increase the size of the population. During the summer of 2005, the I remota population consisted of 1,074 stems in 12 colonies, located along the northwest side of the island. In late June, flowering appeared to be prolific, where means and standard deviations of floral buds and open flowers were 1.6 :t 1.2 and 2.1 :t 1.7 per stem, respectively. By late July, however, flowering was sporadic, but many flowering stems had set seed with the mean number of fruits being 1.2 :t 0.9 per stem. Forty percent of sampled seeds germinated after being treated in hot water (80°C) for 10 seconds. Common species associated with I remota colonies were the cool-season Eurasian grass, Poa pratensis, and the East Asian shrub Lonicera maackii, along with 22 native species and a few other exotics. Previous management included cutting and burning of the shrubby vegetation in and around the l remota colonies. A return to these management practices is suggested