BACE-1 inhibitors part 3: identification of hydroxy ethylamines (HEAs) with nanomolar potency in cells

This article is focusing on further optimization of previously described hydroxy ethylamine (HEA) BACE-1 inhibitors obtained from a focused library with the support of X-ray crystallography. Optimization of the non-prime side of our inhibitors and introduction of a 6-membered sultam substituent binding to Asn-294 as well as a fluorine in the C-2 position led to derivatives with nanomolar potency in cell-based assays.     

Digestive enzyme activities and gastrointestinal fermentation in wood-eating catfishes

To determine what capabilities wood-eating and detritivorous catfishes have for the digestion of refractory polysaccharides with the aid of an endosymbiotic microbial community, the pH, redox potentials, concentrations of short-chain fatty acids (SCFAs), and the activity levels of 14 digestive enzymes were measured along the gastrointestinal (GI) tracts of three wood-eating taxa (Panaque cf. nigrolineatus “Marañon”, Panaque nocturnus, and Hypostomus pyrineusi) and one detritivorous species (Pterygoplichthys disjunctivus) from the family Loricariidae. Negative redox potentials (?600 mV) were observed in the intestinal fluids of the fish, suggesting that fermentative digestion was possible. However, SCFA concentrations were low (<3 mM in any intestinal region), indicating that little GI fermentation occurs in the fishes’ GI tracts. Cellulase and xylanase activities were low (<0.03 U g^?1), and generally decreased distally in the intestine, whereas amylolytic and laminarinase activities were five and two orders of magnitude greater, respectively, than cellulase and xylanase activities, suggesting that the fish more readily digest soluble polysaccharides. Furthermore, the Michaelis–Menten constants (K _m) of the fishes’ β-glucosidase and N-acetyl-β-d-glucosaminidase enzymes were significantly lower than the K _m values of microbial enzymes ingested with their food, further suggesting that the fish efficiently digest soluble components of their detrital diet rather than refractory polysaccharides. Coupled with rapid gut transit and poor cellulose digestibility, the wood-eating catfishes appear to be detritivores reliant on endogenous digestive mechanisms, as are other loricariid catfishes. This stands in contrast to truly “xylivorous” taxa (e.g., beavers, termites), which are reliant on an endosymbiotic community of microorganisms to digest refractory polysaccharides.     

Pesticide ecotoxicological effect factors and their uncertainties for freshwater ecosystems

Background, aim, and scope  Characterization factors for ecotoxicity in the Life Cycle Impact Assessment (LCIA) are used to convert emissions into ecotoxicological impacts. Deriving them involves a fate and an effect analysis step. The fate factor quantifies the change in environmental concentration per unit of emission, while the effect factor quantifies the change in impact on the ecosystem per unit of environmental concentration. This paper calculates freshwater ecotoxicological effect factors for 397 pesticides belonging to 11 pesticide-specific toxic modes of action (TMoA), such as acetylcholinesterase inhibition and photosynthesis inhibition. Moreover, uncertainties in the effect factors due to uncertain background concentrations and due to limited toxicity data are quantified. Methods  To calculate median ecotoxicological effect factors (EEFs), toxic pressure assessments were made, based on the species sensitivity distribution—and the multisubstance potentially affected fraction—concept. The EEF quantifies an estimate of the fraction of species that is probably affected due to a marginal change in concentration of a pesticide. EEFs were divided into a TMoA-specific and a chemical-specific part, which were calculated on the basis of physicochemical properties, emissions, and toxicity data. Propagation of parameter uncertainty in the EEFs and the TMoA- and chemical-specific parts was quantified by Monte Carlo simulation and results were reported as 90% confidence intervals. Results  Median EEFs range from 2·10⁻³ to 7·10⁶ l/g. Uncertainty in the TMoA-specific part is dominated by uncertainty in the TMoA-specific spread in species sensitivity and by uncertainty in the effective toxicity of a TMoA. Uncertainty in the chemical-specific part of the EEFs depends on the number of species for which toxicity data are available to calculate average toxicity (n _s) and ranges from a median uncertainty of 2.6 orders of magnitude for n _s = 2 to one order of magnitude for n _s ≥ 4. The TMoA-specific effect factor for systemic fungicides shows the largest uncertainty range. For seven TMoAs, uncertainty ranges of the TMoA-specific effect factor are less than two orders of magnitude. For the other four TMoAs, the EEF uncertainty range is between two and eight orders of magnitude. For the chemical-specific part of the EEFs, we found that variation in uncertainty readily decreases for pesticides for which toxicity data are available for at least three species. Discussion  The same parameters that contributed most to uncertainty were found for pesticides as were found before for high-production-volume chemicals. However, uncertainty in concentrations of pesticides was lower. TMoA-specific factors obtained with the applied nonlinear method differ up to nine orders of magnitude from the factor of 0.5, which is used in the linear method. With the applied method, a distinction in EEFs can be made among different TMoAs. Conclusions   Ecotoxicological effect factors are presented, including overviews of their uncertainty ranges and the main contributors to uncertainty. The applied nonlinear method provides the possibility to quantify parameter uncertainty in the TMoA-specific part of the ecotoxicological effect factor, which is helpful to get more insight in how uncertainty in ecotoxicological characterization factors can be reduced. Recommendations and perspectives  The calculated uncertainty ranges can be included in life cycle assessment (LCA) case studies, which allows for better interpretation of LCA results obtained with the EEFs. To put the uncertainty in effect factors into perspective within LCIA, more information on the uncertainty in fate factors should be derived. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Nucleoid-associated proteins in Crenarchaea

Architectural proteins play an important role in compacting and organizing the chromosomal DNA in all three kingdoms of life (Eukarya, Bacteria and Archaea). These proteins are generally not conserved at the amino acid sequence level, but the mechanisms by which they modulate the genome do seem to be functionally conserved across kingdoms. On a generic level, architectural proteins can be classified based on their structural effect as DNA benders, DNA bridgers or DNA wrappers. Although chromatin organization in archaea has not been studied extensively, quite a number of architectural proteins have been identified. In the present paper, we summarize the knowledge currently available on these proteins in Crenarchaea. By the type of architectural proteins available, the crenarchaeal nucleoid shows similarities with that of Bacteria. It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity.     

Expression of retinaldehyde dehydrogenase enzymes in mucosal dendritic cells and gut-draining lymph node stromal cells is controlled by dietary vitamin A

The vitamin A metabolite retinoic acid (RA) plays a crucial role in mucosal immune responses. We demonstrate in this study that RA-producing retinaldehyde dehydrogenase (RALDH) enzymes are postnatally induced in mesenteric lymph node (MLN) dendritic cells (DCs) and MLN stromal cells. RALDH enzyme activity in lamina propria-derived CD103(+) MLN-DCs did not depend on TLR signaling. Remarkably, RA itself could directly induce RALDH2 in both DCs and stromal cells in vitro. Furthermore, upon provision of a vitamin A-deficient diet, it was found that RA-mediated signaling was strongly reduced within the small intestines, while RALDH2 mRNA and RALDH enzyme activity in lamina propria DCs and MLN-DCs, as well as RALDH2 mRNA expression in MLN stromal cells, were strongly diminished. Moreover, supply of vitamin A to vitamin A-deficient mice restored RA-mediated signaling in the intestine and RALDH activity in lamina propria-derived CD103(+) MLN-DCs. Our results show that RA-dependent signaling within the intestine is indispensable for RALDH activity in the draining MLN.     

The Mn4Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser

The structure of photosystem II and the catalytic intermediate states of the Mn₄CaO₅ cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.     

The antibody response against MART‐1 differs in patients with melanoma‐associated leucoderma and vitiligo

Patients with melanoma may develop skin depigmentation spontaneously or following therapy, referred to as melanoma‐associated leucoderma (MAL). As clinical presentation of MAL may precede primary/metastatic melanoma detection, recognition of MAL is important to prevent its misdiagnosis as vitiligo and the subsequent application of immunosuppressive treatment. To reveal the immunity involved in MAL development, we investigated the presence of antibody and T‐cell immune responses directed against the melanocyte‐differentiation‐antigens MART‐1 (Melan‐A), tyrosinase and gp100 in patients with MAL, as compared to patients with vitiligo. Autoantibodies to gp100 and tyrosinase were commonly found in both diseases. Interestingly, MART‐1 antibodies were only present in patients with MAL. Melanocyte antigen‐specific T cells were found in all patients, with relatively more specific T cells in patients with active vitiligo. Although MAL and vitiligo may appear clinically similar, our results indicate that the humoral immune responses against MART‐1 differ between these diseases, which can help to differentiate MAL from vitiligo.     

Eudicot primary cell wall glucomannan is related in synthesis,structure, and function to xyloglucan

Hemicellulose polysaccharides influence assembly and properties of the plant primary cell wall (PCW), perhaps by interacting with cellulose to affect the deposition and bundling of cellulose fibrils. However, the functional differences between plant cell wall hemicelluloses such as glucomannan, xylan, and xyloglucan (XyG) remain unclear. As the most abundant hemicellulose, XyG is considered important in eudicot PCWs, but plants devoid of XyG show relatively mild phenotypes. We report here that a patterned β-galactoglucomannan (β-GGM) is widespread in eudicot PCWs and shows remarkable similarities to XyG. The sugar linkages forming the backbone and side chains of β-GGM are analogous to those that make up XyG, and moreover, these linkages are formed by glycosyltransferases from the same CAZy families. Solid-state nuclear magnetic resonance indicated that β-GGM shows low mobility in the cell wall, consistent with interaction with cellulose. Although Arabidopsis β-GGM synthesis mutants show no obvious growth defects, genetic crosses between β-GGM and XyG mutants produce exacerbated phenotypes compared with XyG mutants. These findings demonstrate a related role of these two similar but distinct classes of hemicelluloses in PCWs. This work opens avenues to study the roles of β-GGM and XyG in PCWs.

Patterned β-GGM resembles xyloglucan in structure, biosynthesis, and function.

In a Nutshell Background: Plant primary cell walls (PCWs) need to be rigid enough to define the plant shape and yet allow cell expansion at the same time. Plants achieve this by forming a complex network that is composed of cellulose and various non-cellulosic polysaccharides, such as hemicelluloses. Cell walls differ in the abundance of the various hemicelluloses, and their roles are poorly understood. In contrast to xyloglucan (XyG), which has been the most extensively studied hemicellulose in the PCWs, neither the structure nor functions of glucomannan has been resolved. Question: Are the functions of the glucomannan in PCWs distinct from the roles of the most abundant hemicellulose, XyG? Findings: We discovered a type of glucomannan in eudicot PCWs, which we named β-galactoglucomannan (β-GGM) because of its distinctive structures: disaccharide side chains of β-Gal-α-Gal and alternating repeats of Glc-Man in the backbone. Similarity to XyG in structure and biosynthesis led us to identify a β-galactosyltransferase for the β-GGM biosynthesis. We found that β-GGM contributed to normal cell expansion, in a way that was masked by the presence of XyG. These results suggest related functions of β-GGM to XyG, highlighting the necessity to consider the contribution of multiple hemicelluloses in the functional study of plant cell walls. Next steps: We would like to know how β-GGM binds to cellulose, and how this differs to cellulose binding of XyG. Investigation of the precise arrangements and interactions of cellulose and hemicelluloses including β-GGM and XyG will help further understanding of the enigmatic functions of hemicelluloses.     

Response to a Respiratory Survey

Respondents to a respiratory survey of Berlin, New Hampshire, residents in 1961 have been studied to assess the relationship between co-operation and respiratory disease prevalence. Two hundred and forty-three unco-operative subjects, interviewed at home, had significantly more morning phlegm and a lower vital capacity than carefully matched subjects who attended the central clinic. Fifty-one volunteers had the same prevalence of respiratory disease symptoms and physiological abnormalities as carefully matched subjects drawn from a probability sample of the city.It is concluded that respiratory disease prevalence will be underestimated if calculated from studies of co-operative subjects who attend a clinic. Case-finding by respiratory disease screening clinics will also miss many persons who suffer from chronic bronchitis.