Packing analysis of carbohydrates and polysaccharides. V. Crystal structures of two polymorphs of pachyman triacetate

The crystal structures of two polymorphic forms of pachyman triacetate, the fully acetylated derivative of a naturally occuring β-(1 → 3)-D -glucan, were determined by a combination of stereochemical and x-ray diffraction analysis. The two polymorphs could be obtained depending on the temperature and the degree of stretching of film specimens of the substance: polymorph I resulted from stretching 25–50% at 125°C and polymorph II resulted from further stretching to 300% at 215°C. Both polymorphs had previously been shown to have sixfold helical chain conformations, but of unequal pitch. Subsequent detailed structure refinement performed with bond lengths, bond angles, conformational angles, and helix-packing parameters as refinement variables, and the simultaneous minimization of packing and conformational energy and the crystallographic R-factor as refinement criteria, resulted in a complete determination of the two crystal structures. Pachyman triacetate I was found to be a right-handed helix packing with antiparallel polarity and space group P2₁2₁2₁ symmetry (unit-cell parameters a = 11.0, b = 19.0, c (fiber repeat) = 22.38 Å). The acetate groups were nearly planar and the O(2) and O(4) acetates were oriented in such a fashion that the carbonyl double-bond nearly eclipsed the corresponding C—H bond of the ring. The O(6) was in the tg position and its acetate was oriented in such a fashion that the bond sequence C(6)—O(6)—C(6C)—C(6M) was nearly trans-planar, with the carbonyl double-bond bisecting the tetrahedral angle formed by C(6) and its two hydrogens. The final R = 0.221. Pachyman triacetate II was similarly found to be a right-handed helix, but packing as a 50:50 mixture of parallel and antiparallel polarities (unit-cell parameters a = 11.49, b = 20.13, c (fiber repeat) = 18.6 Å). The acetate positions in pachyman triacetate II were substantially the same as in pachyman triacetate I. The final R for the 50:50 mixture was 0.234. Probable reasons for the change in packing polarities are discussed, as are the difficulties encountered in the structure refinement of acetate derivatives.     

Microbial composition affects the functioning of estuarine sediments

Although microorganisms largely drive many ecosystem processes, the relationship between microbial composition and their functioning remains unclear. To tease apart the effects of composition and the environment directly, microbial composition must be manipulated and maintained, ideally in a natural ecosystem. In this study, we aimed to test whether variability in microbial composition affects functional processes in a field setting, by reciprocally transplanting riverbed sediments between low- and high-salinity locations along the Nonesuch River (Maine, USA). We placed the sediments into microbial ‘cages'' to prevent the migration of microorganisms, while allowing the sediments to experience the abiotic conditions of the surroundings. We performed two experiments, short- (1 week) and long-term (7 weeks) reciprocal transplants, after which we assayed a variety of functional processes in the cages. In both experiments, we examined the composition of bacteria generally (targeting the 16S rDNA gene) and sulfate-reducing bacteria (SRB) specifically (targeting the dsrAB gene) using terminal restriction fragment length polymorphism (T-RFLP). In the short-term experiment, sediment processes (CO₂ production, CH₄ flux, nitrification and enzyme activities) depended on both the sediment''s origin (reflecting differences in microbial composition between salt and freshwater sediments) and the surrounding environment. In the long-term experiment, general bacterial composition (but not SRB composition) shifted in response to their new environment, and this composition was significantly correlated with sediment functioning. Further, sediment origin had a diminished effect, relative to the short-term experiment, on sediment processes. Overall, this study provides direct evidence that microbial composition directly affects functional processes in these sediments.     

Population Structure of Peronospora effusa in the Southwestern United States

Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales.     

The Protein Data Bank: unifying the archive

The Protein Data Bank (PDB; http://www.pdb.org/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the progress that has been made in validating all data in the PDB archive and in releasing a uniform archive for the community. We have now produced a collection of mmCIF data files for the PDB archive (ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software.     

Effect of Sublethal Heat on the Metabolic Activity of Staphylococcus aureus

Cells of Staphylococcus aureus MF-31 which have been heat-injured at 52 C have an altered metabolic activity. Analyses of whole-cell preparations by means of the Thunberg technique and Warburg manometry showed decreased dehydrogenase activity and oxygen uptake on a variety of substrates. In cell-free extracts prepared from injured cells, it was demonstrated that the specific activity of fructose diphosphate aldolase, lactate dehydrogenase, and butanediol dehydrogenase was less than that of extracts prepared from normal unheated cells. Recovery of the heat-injured cells in a suitable medium supported a return of the dehydrogenase activity and oxygen uptake, but the activity of the enzymes in cell-free extracts prepared from such partially recovered cells did not fully return to the level of normal (unheated) preparations. Addition of chloramphenicol or actinomycin D to the recovery medium, singly or in combination, retarded the return of the normal metabolic activity. Radiorespirometric experiments indicated that the percentage participation of the Embden-Meyerhoff Parnas and hexose monophosphate pathways remained the same for normal and heat-injured cells. The sublethal heat treatment decreased the catabolic capabilities of S. aureus and the production of selected end products associated with the metabolism of glucose.     

The hypnotic effect of propofol in the medial preoptic area of the rat

Recent introduction of the intravenous anesthetic propofol as an ICU sedative has allowed a deeply sedated state to be maintained for extended periods in the ICU without delays in emergence. Although such sedation has been advocated to promote physiologic sleep, little evidence exists to support such a strategy. To explore propofol's effect on sleep regulation, we administered propofol directly into the medial preoptic area (MPA) of the rat, an anatomic site where administration of other sedatives (triazolam and phenobarbital) also induce sleep. We performed three two-hour sleep studies in the daytime with the lights on following the administration of propofol (8 ng or 40 ng) or vehicle (intralipid). The higher dose of propofol significantly reduced sleep latency and increased nonREM and total sleep times when compared to vehicle. REM sleep times, intermittent waking times and number of transitions were not altered. Mean nonREM sleep bout length was increased significantly at the higher dose. These findings suggest that propofol may enhance sleep by acting at a hypothalamic site.     

Factors affecting reproductive performance in captive Mallard ducks

Propagation of wild-strain Mallards (Anas platyrhynchos) in captivity is hindered by low egg fertility. Therefore, we studied the effects of captivity, age, mate choice and isolation on reproductive parameters of Mallards. Captive drakes had smaller immature testes than free-flying Mallard drakes. Captive yearling ducks weighed less than adult ducks at the beginning of the breeding season, but no differences were found between their initial clutch size, egg volume or number of clutches laid. Yearling pairs had lower egg fertility (7%) than adult pairs (80%). Egg fertility was higher (51 vs 21%) in self-chosen pairs than in randomly assigned pairs. Isolation of ducks, however did not influence egg production.     

Distribution, standing stock, growth, mortality and production of Strongylocentrotus pallidus (Echinodermata: Echinoidea) in the northern Barents Sea

The regular sea urchin, Strongylocentrotus pallidus (G.O. Sars, 1871), is a widespread epibenthic species in high-Arctic waters. However, little is known about its distribution, standing stock, population dynamics and production. In the northern Barents Sea, S. pallidus was recorded on seabed still photographs at 10 out of 11 stations in water depths of 80–360?m. Mean abundances along photographic transects of 150–300 m length ranged between <0.1 and 14.7?ind. m^?2 yielding a grand average of 3.6?ind.?m^?2. The small-scale distribution along the transects was patchy, with densities varying from nil to an overall maximum of 25.5 ind. m^?2, and exhibited a significant relation to the number of stones present. Sea urchin test diameters, measured on scaled photographs, extended from 7 to 90?mm. Median values at single stations varied from 14 to 46?mm, showing a significant inverse relationship to water depth. Biomass, estimated by combining photographic abundances, size frequencies and a size-mass function established with trawled specimens, ranged between <0.1 and 3.0?g ash-free dry mass m^?2, averaging about 1.0?g ash free dry mass m^?2. An analysis of skeletal growth bands in genital plates was carried out with 143 trawled individuals ranging in test diameter (D) from 4 to 48?mm. Assuming these bands to represent annual growth marks, the ages of the specimens analysed ranged between 3 and 42 years. A von Bertalanffy function was fitted to size-at-age data to model individual growth pattern (D_∞?=?102.3?mm, k?=?0.011 year^?1, t₀?=?0.633?year). The annual mortality rate Z of the population in the northern Barents Sea was estimated from a size-converted catch curve to be 0.08 year^?1. Applying the weight-specific growth rate method, the average P/B ratio and the mean annual production of this population were estimated as 0.07 year^?1 and 0.076?g AFDM m^?2 year^?1, respectively. In conclusion, S. pallidus is characterized by slow growth, low mortality, high longevity and low productivity. Because of its relatively high biomass, it is considered to contribute significantly to total benthic standing stock and carbon flux in the study area.     

Effects of outplanting time on growth,shedding and quality of Saccharina latissima (Phaeophyceae) in its northern distribution range

Journal of Applied Phycology - To reach the goal of large-scale seaweed cultivation in Norway and the rest of Europe, new knowledge about the commercially important kelp species Saccharina...     

SorCS1 variants and amyloid precursor protein (APP) are co‐transported in neurons but only SorCS1c modulates anterograde APP transport

Processing of amyloid precursor protein (APP) into amyloid‐β peptide (Aβ) is crucial for the development of Alzheimer's disease (AD). Because this processing is highly dependent on its intracellular itinerary, altered subcellular targeting of APP is thought to directly affect the degree to which Aβ is generated. The sorting receptor SorCS1 has been genetically linked to AD, but the underlying molecular mechanisms are poorly understood. We analyze two SorCS1 variants; one, SorCS1c, conveys internalization of surface‐bound ligands whereas the other, SorCS1b, does not. In agreement with previous studies, we demonstrate co‐immunoprecipitation and co‐localization of both SorCS1 variants with APP. Our results suggest that SorCS1c and APP are internalized independently, although they mostly share a common post‐endocytic pathway. We introduce functional Venus‐tagged constructs to study SorCS1b and SorCS1c in living cells. Both variants are transported by fast anterograde axonal transport machinery and about 30% of anterograde APP‐positive transport vesicles contain SorCS1. Co‐expression of SorCS1b caused no change of APP transport kinetics, but SorCS1c reduced the anterograde transport rate of APP and increased the number of APP‐positive stationary vesicles. These data suggest that SorCS1 and APP share trafficking pathways and that SorCS1c can retain APP from insertion into anterograde transport vesicles.