A new marker based on the avian spindlin gene that is able to sex most birds,including species problematic to sex with CHD markers

We have developed a new marker (Z43B) that can be successfully used to identify the sex of most birds (69%), including species difficult or impossible to sex with other markers. We utilized the zebra finch Taeniopygia guttata EST microsatellite sequence (CK309496) which displays sequence homology to the 5′ untranslated region (UTR) of the avian spindlin gene. This gene is known to be present on the Z and W chromosomes. To maximize cross‐species utility, the primer set was designed from a consensus sequence created from homologs of CK309496 that were isolated from multiple distantly related species. Both the forward and reverse primer sequences were 100% identical to 14 avian species, including the Z chromosome of eight species and the chicken Gallus gallus W chromosome, as well as the saltwater crocodile Crocodylus porosus. The Z43B primer set was assessed by genotyping individuals of known sex belonging to 61 non‐ratite species and a single ratite. The Z and W amplicons differed in size making it possible to distinguish between males (ZZ) and females (ZW) for the majority (69%) of non‐ratite species tested, comprising 10 orders of birds. We predict that this marker will be useful for obtaining sex‐typing data for ca 6,869 species of birds (69% of non‐ratites but not galliforms). A wide range of species could be sex‐typed including passerines, shorebirds, eagles, falcons, bee‐eaters, cranes, shags, parrots, penguins, ducks, and a ratite species, the brown kiwi, Apteryx australis. Those species sexed include species impossible or problematic to sex‐type with other markers (magpie, albatross, petrel, eagle, falcon, crane, and penguin species). Zoo Biol. 35:533–545, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.     

Labour's ‘strange blindness’ and the end of Jubilee

ABSTRACT

This essay responds to David Roediger's Seizing Freedom: Slave Emancipation and Liberty for All. After a brief examination of the central themes of the book, I turn to the author's emphasis upon political agency. I argue that this emphasis is necessary, given the political and scholarly aims of the book. At the same time, I suggest that the agency depicted in Seizing Freedom was simultaneously constrained by the cultural, political, and social forces discussed in Roediger's earlier companion volume, The Wages of Whiteness. I end the essay with a short discussion of the labour leader William Sylvis that attempts to synthesize insights from Seizing Freedom and The Wages of Whiteness in order to explain the ‘strange blindness’ that led white labour to systematically ignore and repress the activity of black workers.     

Can you hear me now? Range‐testing a submerged passive acoustic receiver array in a Caribbean coral reef habitat

Submerged passive acoustic technology allows researchers to investigate spatial and temporal movement patterns of many marine and freshwater species. The technology uses receivers to detect and record acoustic transmissions emitted from tags attached to an individual. Acoustic signal strength naturally attenuates over distance, but numerous environmental variables also affect the probability a tag is detected. Knowledge of receiver range is crucial for designing acoustic arrays and analyzing telemetry data. Here, we present a method for testing a relatively large‐scale receiver array in a dynamic Caribbean coastal environment intended for long‐term monitoring of multiple species. The U.S. Geological Survey and several academic institutions in collaboration with resource management at Buck Island Reef National Monument (BIRNM), off the coast of St. Croix, recently deployed a 52 passive acoustic receiver array. We targeted 19 array‐representative receivers for range‐testing by submersing fixed delay interval range‐testing tags at various distance intervals in each cardinal direction from a receiver for a minimum of an hour. Using a generalized linear mixed model (GLMM), we estimated the probability of detection across the array and assessed the effect of water depth, habitat, wind, temperature, and time of day on the probability of detection. The predicted probability of detection across the entire array at 100 m distance from a receiver was 58.2% (95% CI: 44.0–73.0%) and dropped to 26.0% (95% CI: 11.4–39.3%) 200 m from a receiver indicating a somewhat constrained effective detection range. Detection probability varied across habitat classes with the greatest effective detection range occurring in homogenous sand substrate and the smallest in high rugosity reef. Predicted probability of detection across BIRNM highlights potential gaps in coverage using the current array as well as limitations of passive acoustic technology within a complex coral reef environment.     

Identification of protein W,the elusive sixth subunit of the Rhodopseudomonas palustris reaction center-light harvesting 1 core complex

The X-ray crystal structure of the Rhodopseudomonas (Rps.) palustris reaction center-light harvesting 1 (RC-LH1) core complex revealed the presence of a sixth protein component, variably referred to in the literature as helix W, subunit W or protein W. The position of this protein prevents closure of the LH1 ring, possibly to allow diffusion of ubiquinone/ubiquinol between the RC and the cytochrome bc₁ complex in analogous fashion to the well-studied PufX protein from Rhodobacter sphaeroides. The identity and function of helix W have remained unknown for over 13 years; here we use a combination of biochemistry, mass spectrometry, molecular genetics and electron microscopy to identify this protein as RPA4402 in Rps. palustris CGA009. Protein W shares key conserved sequence features with PufX homologs, and although a deletion mutant was able to grow under photosynthetic conditions with no discernible phenotype, we show that a tagged version of protein W pulls down the RC-LH1 complex. Protein W is not encoded in the photosynthesis gene cluster and our data indicate that only approximately 10% of wild-type Rps. palustris core complexes contain this non-essential subunit; functional and evolutionary consequences of this observation are discussed. The ability to purify uniform RC-LH1 and RC-LH1-protein W preparations will also be beneficial for future structural studies of these bacterial core complexes.     

Enantioseparation of racecadotril using polysaccharide‐type chiral stationary phases in polar organic mode

Enantioseparation of the antidiarrheal drug, racecadotril, was investigated by liquid chromatography using polysaccharide‐type chiral stationary phases in polar organic mode. The enantiodiscrimininating properties of 4 different chiral columns (Chiralpak AD, Chiralcel OD, Chiralpak AS, Chiralcel OJ) with 5 different solvents (methanol, ethanol, 1‐propanol, 2‐propanol, and acetonitrile) at 5 different temperatures (5–40 °C) were investigated. Apart from Chiralpak AS column the other 3 columns showed significant enantioseparation capabilities. Among the tested mobile phases, alcohol type solvents were superior over acetonitrile, and significant differences in enantioselective performance of the selector were observed depending on the type of alcohol employed. Van't Hoff analysis was used for calculation of thermodynamic parameters which revealed that enantioseparation is mainly enthalpy controlled; however, enthropic control was also observed. Enantiopure standard was used to determine the enantiomer elution order, revealing chiral selector—and mobile‐phase dependent reversal of enantiomer elution order. Using the optimized method (Chiralcel OJ stationary phase, thermostated at 10 °C, 100% methanol, flow rate: 0.6 mL/min) baseline separation of racecadotril enantiomers (resolution = 3.00 ± 0.02) was achieved, with the R‐enantiomer eluting first. The method was validated according to the ICH guidelines, and its application was tested on capsule and granules containing the racemic mixture of the drug.     

基于SSR分子标记的延胡索遗传多样性研究

采用SSR分子标记分析延胡索的遗传多样性,筛选出多态性高、稳定性好的12对引物,对19个居群360份延胡索样品进行了群体遗传分析。结果表明:(1)12对SSR引物共扩增出多态性位点227个,检测到4~9个等位基因,平均等位基因数目为5.25个,表现出丰富的多态性;延胡索居群具有较高的遗传多样性(Na=5.25,I=1.192 6,H=0.387 9),物种间遗传分化程度高(Fst=0.388 3),基因流较弱(Nm=0.393 8)。(2)UPGMA聚类分析和贝叶斯距离分析结果表明,19个居群明显聚为4大支;Mantle Test结果(r=0.326,P=0.01)表明,地理位置相近的种群亲缘关系更近。研究认为,延胡索的遗传结构是该物种自交为主的繁育系统、克隆生长、地理隔离以及居群间有限的基因流共同作用的结果,故对该物种的保护应以就地保护为主。     

Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability

We engineered nucleosome core particles (NCPs) with two site-specific cysteine crosslinks that increase the stability of the particle. The first disulfide was introduced between the two copies of H2A via an H2A-N38C point mutation, effectively crosslinking the two H2A/H2B heterodimers together to stabilize the histone octamer against H2A/H2B dimer dissociation. The second crosslink was engineered between an R40C point mutation on the N-terminal tail of H3 and the NCP DNA ends by the introduction of a convertible nucleotide. This crosslink maintains the nucleosome DNA in a fixed translational setting relative to the histone octamer and prevents dilution-driven dissociation. The X-ray crystal structures of NCPs containing the disulfides in isolation and in combination were determined. Both disulfides stabilize the structure of the NCP without disturbing the overall structure. Nucleosomes containing these modifications will be advantageous for biochemical and structural studies as a consequence of their greater resistance to dissociation during high dilution in purification, elevated salt for crystallization and vitrification for cryogenic electron microscopy.     

Fadenwürmer – fade Würmer?

Nematodes – there is more to it … Nematodes play a central role – not only in a negative way as dreaded parasites of humans, animals and plants, where they may be harmful in terms of health and economy. The majority of nematodes turn out to be highly beneficial: Firstly, they are a vital part of the food web and by this indispensably involved in nutrient cycles. On the other hand, we increasingly make use of nematodes in biological control of pest organisms, in the ecotoxicological assessment of soils and sediments and as excellent model organisms in a broad range of different research fields.     

Accounting for apparent deviations between calorimetric and van't Hoff enthalpies

Background

In theory, binding enthalpies directly obtained from calorimetry (such as ITC) and the temperature dependence of the binding free energy (van't Hoff method) should agree. However, previous studies have often found them to be discrepant.