Disorder‐Induced Open‐Circuit Voltage Losses in Organic Solar Cells During Photoinduced Burn‐In

The photoinduced open‐circuit voltage (V_oc) loss commonly observed in bulk heterojunction organic solar cells made from amorphous polymers is investigated. It is observed that the total charge carrier density and, importantly, the recombination dynamics are unchanged by photoinduced burn‐in. Charge extraction is used to monitor changes in the density of states (DOS) during degradation of the solar cells, and a broadening over time is observed. It is proposed that the V_oc losses observed during burn‐in are caused by a redistribution of charge carriers in a broader DOS. The temperature and light intensity dependence of the V_oc losses can be described with an analytical model that contains the amount of disorder broadening in a Gaussian DOS as the only fit parameter. Finally, the V_oc loss in solar cells made from amorphous and crystalline polymers is compared and an increased stability observed in crystalline polymer solar cells is investigated. It is found that solar cells made from crystalline materials have a considerably higher charge carrier density than those with amorphous materials. The effects of a DOS broadening upon aging are suppressed in solar cells with crystalline materials due to their higher carrier density, making crystalline materials more stable against V_oc losses during burn‐in.     

Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction

Genetic drift of influenza virus genomic sequences occurs through the combined effects of sequence alterations introduced by a low-fidelity polymerase and the varying selective pressures experienced as the virus migrates through different host environments. While traditional phylogenetic analysis is useful in tracking the evolutionary heritage of these viruses, the specific genetic determinants that dictate important phenotypic characteristics are often difficult to discern within the complex genetic background arising through evolution. Here we describe a novel influenza virus sequence feature variant type (Flu-SFVT) approach, made available through the public Influenza Research Database resource (www.fludb.org), in which variant types (VTs) identified in defined influenza virus protein sequence features (SFs) are used for genotype-phenotype association studies. Since SFs have been defined for all influenza virus proteins based on known structural, functional, and immune epitope recognition properties, the Flu-SFVT approach allows the rapid identification of the molecular genetic determinants of important influenza virus characteristics and their connection to underlying biological functions. We demonstrate the use of the SFVT approach to obtain statistical evidence for effects of NS1 protein sequence variations in dictating influenza virus host range restriction.     

Indole RSK inhibitors. Part 2: optimization of cell potency and kinase selectivity

A series of inhibitors for the 90 kDa ribosomal S6 kinase (RSK) based on an 1-oxo-2,3,4,5-tetrahydro-1H-[1,4]diazepino[1,2-a]indole-8-carboxamide scaffold were optimized for cellular potency and kinase selectivity. This led to the identification of compound 24, BIX 02565, an attractive candidate for use in vitro and in vivo to explore the role of RSK as a target for the treatment heart failure.     

Non-proteinogenic amino acids in the pThr-2 position of a pentamer peptide that confer high binding affinity for the polo box domain (PBD) of polo-like kinase 1 (Plk1)

We report herein that incorporating long-chain alkylphenyl-containing non-proteinogenic amino acids in place of His at the pT-2 position of the parent polo-like kinase 1 (Plk1) polo box domain (PBD)-binding pentapeptide, PLHSpT (1a) increases affinity. For certain analogs, approximately two orders-of-magnitude improvement in affinity was observed. Although, none of the new analogs was as potent as our previously described peptide 1b, in which the pT-2 histidine imidazole ring is alkylated at its π nitrogen (N3), our current finding that the isomeric His(N1)-analog (1c) binds with approximately 50-fold less affinity than 1b, indicates the positional importance of attachment to the His imidazole ring. Our demonstration that a range of modified residues at the pT-2 position can enhance binding affinity, should facilitate the development of minimally-sized Plk1 PBD-binding antagonists.     

The effects of pH change and NO(-) (3) pulse on microbial community structure and function: a vernal pool microcosm study

Forest vernal pools experience strong environmental fluctuations, such as changes in water chemistry, which are often correlated with changes in microbial community structure. However, very little is known about the extent to which these community changes influence ecosystem processes in vernal pools. This study utilized experimental vernal pool microcosms to simulate persistent pH alteration and a pulse input of nitrate (NO3 -), which are common perturbations to temperate vernal pool ecosystems. pH was manipulated at the onset and microbial respiration was monitored throughout the study (122?days). On day 29, NO3 - was added and denitrification rate was measured and bacterial, fungal, and denitrifier communities were profiled on day 30 and day 31. Microbial respiration and both bacterial and fungal community structure were altered by the pH treatment, demonstrating both structural and functional microbial responses. The NO3 - pulse increased denitrification rate without associated changes in community structure, suggesting that microbial communities responded functionally without structural shifts. The functioning of natural vernal pools, which experience both persistent and short-term environmental change, may thus depend on the type and duration of the change or disturbance.     

High throughput sequencing approaches to mutation discovery in the mouse

Phenotype-driven approaches in mice are powerful strategies for the discovery of genes and gene functions and for unravelling complex biological mechanisms. Traditional methods for mutation discovery are reliable and robust, but they can also be laborious and time consuming. Recently, high-throughput sequencing (HTS) technologies have revolutionised the process of forward genetics in mice by paving the way to rapid mutation discovery. However, successful application of HTS for mutation discovery relies heavily on the sequencing approach employed and strategies for data analysis. Here we review current HTS applications and resources for mutation discovery and provide an overview of the practical considerations for HTS implementation and data analysis.     

The ability of serum from alpha 1-antitrypsin-deficient patients to inhibit PRT-201, a recombinant human type I pancreatic elastase

PRT-201 is a recombinant human pancreatic elastase under development as a treatment for blood vessels to promote hemodialysis access patency. Proteases such as elastase are normally inactivated by antiproteases such as alpha 1-antitrypsin. It is unknown if serum from patients with alpha 1-antitrypsin deficiency will inhibit PRT-201 elastase activity. An assay for PRT-201 elastase activity in the presence of serum was developed and validated. PRT-201 elastase activity inhibition curves were developed using serum and also using purified alpha 1-antitrypsin and alpha 2-macroglobulin. Serum from 15 patients with documented alpha 1-antitrypsin deficiency, some of whom were receiving alpha 1-antitrypsin augmentation therapy, and four normal volunteers was analyzed. Serum from normal volunteers and patients with alpha 1-antitrypsin deficiency completely inactivated PRT-201 elastase activity in vitro. In the alpha 1-antitrypsin-deficient patients, the volume of serum necessary to inhibit elastase activity was related to the serum concentration of alpha 1-antitrypsin and augmentation therapy. Purified alpha 1-antitrypsin and alpha 2-macroglobulin were each alone capable of completely inhibiting PRT-201 elastase activity. It is unlikely that the use of PRT-201 will be associated with negative outcomes in patients with alpha 1-antitrypsin deficiency.     

Super folds,networks, and barriers

Exhaustive enumeration of sequences and folds is conducted for a simple lattice model of conformations, sequences, and energies. Examination of all foldable sequences and their nearest connected neighbors (sequences that differ by no more than a point mutation) illustrates the following: (i) There exist unusually large number of sequences that fold into a few structures (super‐folds). The same observation was made experimentally and computationally using stochastic sampling and exhaustive enumeration of related models. (ii) There exist only a few large networks of connected sequences that are not restricted to one fold. These networks cover a significant fraction of fold spaces (super‐networks). (iii) There exist barriers in sequence space that prevent foldable sequences of the same structure to “connect” through a series of single point mutations (super‐barrier), even in the presence of the sequence connection between folds. While there is ample experimental evidence for the existence of super‐folds, evidence for a super‐network is just starting to emerge. The prediction of a sequence barrier is an intriguing characteristic of sequence space, suggesting that the overall sequence space may be disconnected. The implications and limitations of these observations for evolution of protein structures are discussed. Proteins 2012. © 2011 Wiley Periodicals, Inc.