Chicken microchromosomes are hypermethylated and can be identified by specific painting probes

Microdissection of single chicken microchromosomes (MICs) followed by degenerate oligonucleotide-primed (DOP) PCR allows the rapid generation of MIC-specific DNA libraries. Since some libraries derived from a single (or a few) chromosome(s) label the entire MIC fraction, the majority of chicken MICs share repetitive DNA sequences that are not found on the macrochromosomes. In evolutionarily distant bird species, MICs are invariably hypermethylated. Methylcytosine staining provides additional in situ evidence for the high gene content of MICs and strong compartmentalization of avian genomes.     

Outer membrane proteins can be simply identified using secondary structure element alignment

Background  

Outer membrane proteins (OMPs) are frequently found in the outer membranes of gram-negative bacteria, mitochondria and chloroplasts and have been found to play diverse functional roles. Computational discrimination of OMPs from globular proteins and other types of membrane proteins is helpful to accelerate new genome annotation and drug discovery.     

Latent Marek's disease virus can be activated from its chromosomally integrated state in herpesvirus-transformed lymphoma cells.

Marek's disease virus (MDV), a lymphotropic herpesvirus, induces T-cell lymphomas in chicken, its natural host. The lymphoma cells are latently infected with MDV but the viral contribution to the transformed phenotype is not understood. To investigate the virus-cell interaction, we focused on the status of MDV in the transformed cells. By the use of highly sensitive fluorescent in situ hybridization with metaphase chromosomes, we found (i) MDV DNA to be randomly integrated at multiple sites in the chromosomes of primary lymphoma cells from chicken tissues; (ii) extrachromosomal, circular MDV genomes were absent and linear virion DNA was usually not detectable in the latently infected lymphoma cells; (iii) the pattern of integration sites revealed the clonal origin of the tumour cells; which (iv) was retained in in vitro established cell lines derived from primary lymphomas; (v) activation of the lytic phase of MDV's life cycle occurred in vitro suggesting that MDV can escape from its integrated status by an unknown mechanism.     

Colonic microbiome profiles for improved feed efficiency can be identified despite major effects of farm of origin and contemporary group in pigs

While feed efficiency (FE) is a trait of great economic importance to the pig industry, the influence of the intestinal microbiome in determining FE is not well understood. The objective of this experiment was to determine the relative influence of FE and farm of birth on the pig colonic microbiome. Animals divergent in residual feed intake (RFI) were sourced from two geographically distinct locations (farms A + B) in Ireland. The 8 most efficient (low RFI (LRFI)) and 8 least efficient (high RFI, (HRFI)) pigs from farm A and 12 LRFI and 12 HRFI pigs from farm B were sacrificed. Colonic digesta was collected for microbial analysis using 16S ribosomal RNA gene sequencing and also for volatile fatty acid analysis. The α-diversity differed between the farms in this study, with pigs from farm A having greater diversity based on Shannon and InvSimpson measures compared to pigs from farm B (P < 0.05), with no difference identified in either Chao1 or observed measures of diversity (P > 0.05). In the analysis of β-diversity, pigs clustered based on farm of birth rather than RFI. Variation in the management of piglets, weight of the piglets, season of the year, sanitary status and dam dietary influence could potentially be causative factors in this large variation between farms. However, despite significant variation in the microbial profile between farms, consistent taxonomic differences were identified between RFI groups. Within the phylum Bacteroidetes, the LRFI pigs had increased abundance of BS11 (P < 0.05) and a tendency toward increased Bacteroidaceae (P < 0.10) relative to the HRFI group. At genus level, the LRFI pigs had increased abundance of Colinsella (P < 0.05), a tendency toward increased Bacteroides and CF231 (P < 0.10). At species level, Ruminococcus flavefaciens had increased abundance in the LRFI compared to the HRFI animals. In conclusion, while farm of birth has a substantial influence on microbial diversity in the pig colon, a microbial signature indicative of FE status was apparent.     

Two immunologically distinct types of protofilaments can be identified in Natrialba magadii flagella

A rabbit antiserum to the 15-kDa acetylcholinesterase toxin neutralised the lethal effect of the 15-kDa toxin of Aeromonas hydrophila when injected into trout. However, immunisation of fish with the 15-kDa toxoid failed to induce an antibody response, and a higher molecular mass form of this toxin was purified from the extracellular products with the aim of inducing an immune response in fish. The optimal conditions for production of extracellular products by A. hydrophila strain B32 were studied to increase the concentration of this protoxin. The extracellular products were fractionated by molecular exclusion chromatography to yield a purified protoxin with an estimated molecular mass of 45 kDa by SDS-PAGE and which gave a positive reaction in Western blotting with the rabbit anti-15-kDa toxin serum. Since the 45-kDa protoxin showed lower specific acetylcholinesterase activity than the active 15-kDa toxin, the behaviour of the active site was studied using specific inhibitors. This 45-kDa protoxin was 13.3-fold less toxic than the 15-kDa toxin and induced antibody production in fish.     

Severe obstetric brachial plexus palsies can be identified at one month of age

Objective

To establish whether severe obstetric brachial plexus palsy (OBPP) can be identified reliably at or before three months of age.

Methods

Severe OBPP was defined as neurotmesis or avulsion of spinal nerves C5 and C6 irrespective of additional C7-T1 lesions, assessed during surgery and confirmed by histopathological examination. We first prospectively studied a derivation group of 48 infants with OBPP with a minimal follow-up of two years. Ten dichotomous items concerning active clinical joint movement and needle electromyography of the deltoid, biceps and triceps muscles were gathered at one week, one month and three months of age. Predictors for a severe lesion were identified using a two-step forward logistic regression analysis. The results were validated in two independent cohorts of OBPP infants of 60 and 13 infants.

Results

Prediction of severe OBPP at one month of age was better than at one week and at three months. The presence of elbow extension, elbow flexion and of motor unit potentials in the biceps muscle correctly predicted whether lesions were mild or severe in 93.6% of infants in the derivation group (sensitivity 1.0, specificity 0.88), in 88.3% in the first validation group (sensitivity 0.97, specificity 0.76) and in 84.6% in the second group (sensitivity of 1.0, specificity 0.66).

Interpretation

Infants with OBPP with severe lesions can be identified at one month of age by testing elbow extension, elbow flexion and recording motor unit potentials (MUPs) in the biceps muscle. The decision rule implies that children without active elbow extension at one month should be referred to a specialized center, while children with active elbow extension as well as active flexion should not. When there is active elbow extension, but no active elbow flexion an EMG is needed; absence of MUPs in the biceps muscle is an indication for referral.     

Analysis of CD38 and ZAP70 mRNA expression among cytogenetic subgroups of Iranian chronic-lymphocytic-leukemia patients

Chromosomal abnormalities and ZAP70 expression profile are two major independent prognostic markers in B-cell chronic lymphocytic leukemia. We investigated a possible correlation between these two markers. ZAP70 expression using real-time RT-PCR was examined in 20 B-cell chronic lymphocytic leukemia patients with del13q14, 13 patients with del11q22, 15 patients with trisomy 12, and 16 patients with no detected chromosomal abnormalities. Molecular analysis revealed that ZAP70 expression in the del13q subgroup was the same as in the control group, while it increased 2.78-fold in the del11q subgroup and 2.95-fold in the trisomy 12 subgroup, compared to the 15 cases in the control group. Comparison of the mean and standard deviation of the ZAP70 expression profile within the subgroups showed it to be highly variable among the individuals of the del11q and trisomy 12 subgroups, versus tight clustering for the del13q subgroup. Therefore, there is a correlation between del13q aberration, which has good prognosis with normal levels of ZAP70 expression. Due to a high degree of variation, no conformity is seen for del11q and trisomy 12 subgroups, making this grouping poor for prognostic discrimination. As a result, neither of these markers can serve as sole discriminators to determine the course of the disease; the use of both markers improves prognostic assessment.     

Three major somatic embryogenesis related proteins in Cichorium identified as PR proteins

In Cichorium hybrid clone '474' (C. intybus L., var. sativum x C. endivia L., var. latifolia), the direct somatic embryogenesis process in leaf tissues is accompanied by an overall increase in the amount of proteins secreted into the culture medium. Amongst these, three major protein bands of 38 kDa, 32 kDa and 25 kDa were found in the conditioned media. These extracellular protein bands accumulated in the medium of the embryogenic Cichorium hybrid up to 8-fold compared with those in the medium of a nonembryogenic variety. 32 and 25 kDa proteins were purified from the medium and their identities were determined as already described for 38 kDa beta-1,3-glucanases. To investigate their possible function in somatic embryogenesis, peptide sequences, serological relationships or biochemical properties revealed that there were at least two acidic chitinases of 32 kDa and one glycosylated osmotin-like protein of 25 kDa in the embryogenic culture medium. Comparing the amounts of the 38 kDa glucanases, the 32 kDa chitinases, and the 25 kDa osmotin-like protein present in the conditioned media of the embryogenic '474' hybrid and of a non-embryogenic variety, a 2-8-fold higher accumulation of these proteins was observed in the embryogenic hybrid culture medium. This may suggest that part of the accumulation of these three pathogenesis-related (PR) proteins could be correlated with the somatic embryogenesis process. Their possible involvement in this developmental process is discussed.     

Allosteric sites can be identified based on the residue–residue interaction energy difference

Allosteric drugs act at a distance to regulate protein functions. They have several advantages over conventional orthosteric drugs, including diverse regulation types and fewer side effects. However, the rational design of allosteric ligands remains a challenge, especially when it comes to the identification allosteric binding sites. As the binding of allosteric ligands may induce changes in the pattern of residue–residue interactions, we calculated the residue–residue interaction energies within the allosteric site based on the molecular mechanics generalized Born surface area energy decomposition scheme. Using a dataset of 17 allosteric proteins with structural data for both the apo and the ligand‐bound state available, we used conformational ensembles generated by molecular dynamics simulations to compute the differences in the residue–residue interaction energies in known allosteric sites from both states. For all the known sites, distinct interaction energy differences (>25%) were observed. We then used CAVITY, a binding site detection program to identify novel putative allosteric sites in the same proteins. This yielded a total of 31 “druggable binding sites,” of which 21 exhibited >25% difference in residue interaction energies, and were hence predicted as novel allosteric sites. Three of the predicted allosteric sites were supported by recent experimental studies. All the predicted sites may serve as novel allosteric sites for allosteric ligand design. Our study provides a computational method for identifying novel allosteric sites for allosteric drug design. Proteins 2015; 83:1375–1384. © 2014 Wiley Periodicals, Inc.     

Two progressive substrates of the M-intermediate can be identified in glucose-embedded, wild-type bacteriorhodopsin.

Glucose-embedded bacteriorhodopsin shows M-intermediates with different Amide I infrared bands when samples are illuminated at 240 or 260 K, in contrast with fully hydrated samples where a single M-intermediate is formed at all temperatures. In hydrated, but not in glucose-embedded specimens, the N intermediate is formed together with M at 260 K. Both Fourier transform infrared and electron diffraction data from glucose-embedded bacteriorhodopsin suggest that at 260 K a mixture is formed of the M-state that is trapped at 240 K, and a different M-intermediate (MN) that is also formed by mutant forms of bacteriorhodopsin that lack a carboxyl group at the 96 position, necessary for the M to N transition. The fact that an MN species is trapped in glucose-embedded, wild-type bacteriorhodopsin suggests that the glucose samples lack functionally important water molecules that are needed for the proton transfer aspartate 96 to the Schiff base (and, thus, to form the N-intermediate); thus, aspartate 96 is rendered ineffective as a proton donor.     

The yeast oligosaccharyltransferase complex can be replaced by STT3 from Leishmania major

The key step of protein N-glycosylation is catalyzed by the multimeric oligosaccharyltransferase complex (OST). Biochemical and genetic studies have revealed that OST from Saccharomyces cerevisiae consists of nine subunits: Wbp1, Swp1, Stt3, Ost1, Ost2, Ost3, Ost4, Ost5, and Ost6. With the exception of Stt3, assumed to contain the catalytic site, little is known about the function of other OST subunits. The existence of the OST complex is suggested to allow substrate specificity and efficient transfer, a close interaction with the translocon and the prevention of protein folding to ensure the efficient co-translational modification of proteins. However, in the recently completed genome of the trypanosomatid parasite Leishmania major STT3 (of which four paralogs exist, STT3-1, STT3-2, STT3-3, and STT3-4) is the only OST subunit that can be identified. Here we report that L.m.STT3 proteins, except STT3-3, are able to complement stt3 deficiency in yeast during vegetative growth, but only poorly during sporulation. By blue native electrophoresis we demonstrate that the L.mSTT3 is active mainly as a free, monomeric enzyme. In cell-free assays and also in vivo we find that L.mSTT3, expressed in yeast, has a broad specificity for nonglucosylated lipid-linked mannose-oligosaccharides, typical for several protists. But when incorporated into the OST complex, L.mSTT3 transfers also the common eukaryotic Glc(3)Man(9)GlcNAc(2)-PP-Dol donor. Finally, three L.m.STT3 paralogs were shown to complement not only stt3 but also ost1, ost2, wbp1, or swp1 mutants. Thus, STT3 from Leishmania can substitute for the whole OST complex.     

Selfish punishment: altruism can be maintained by competition among cheaters

Altruistic punishment refers to a class of behaviors that deters cheating at a cost to the punisher, making it a form of second-order altruism. Usually, it is assumed that the punishers are themselves "solid citizens" who refrain from cheating. We show in a simulation model that altruism and punishment paradoxically become negatively correlated, leading to a form of selfish punishment. Examples of selfish punishment can be found in organisms as diverse as wasps, birds, and humans.     

Reduced plant competition among kin can be explained by Jensen's inequality

Plants often compete with closely related individuals due to limited dispersal, leading to two commonly invoked predictions on competitive outcomes. Kin selection, from evolutionary theory, predicts that competition between relatives will likely be weaker. The niche partitioning hypothesis, from ecological theory, predicts that competition between close relatives will likely be stronger. We tested for evidence consistent with either of these predictions by growing an annual legume in kin and nonkin groups in the greenhouse. We grew plant groups in treatments of symbiotic nitrogen fixing bacteria differing in strain identity and composition to determine if differences in the microbial environment can facilitate or obscure plant competition patterns consistent with kin selection or niche partitioning. Nonkin groups had lower fitness than expected, based on fitness estimates of the same genotypes grown among kin. Higher fitness among kin groups was observed in mixtures of N‐fixing bacteria strains compared to single inoculations of bacteria strains present in the soil, which increased fitness differences between kin and nonkin groups. Lower fitness in nonkin groups was likely caused by increased competitive asymmetry in nonkin groups due to genetic differences in plant size combined with saturating relationships with plant size and fitness‐ i.e. Jensen's inequality. Our study suggests that microbial soil symbionts alter competitive dynamics among kin and nonkin. Our study also suggests that kin groups can have higher fitness, as predicted by kin selection theory, through a commonly heritable trait (plant size), without requiring kin recognition mechanisms.     

Sinorhizobium fredii isolates can be specifically identified by a 260 bp fragment from the nolXWBTUV locus

A pair of primers homologous to the nolXWBTUV locus generated a 260 bp fragment by PCR only in the presence of Sinorhizobium fredii template DNA of different quality. This resulted in a fast and accurate method for the identification of S. fredii either from pure DNA, whole bacterial cells or nodule extracts. By means of two PCR fragments, one specific for S. fredii (260-bp) and the other specific for Bradyrhizobium japonicum (RSalpha), we found that S. fredii strain SMH12 and B. japonicum E109 were equally efficient at developing nodules on soybean plants grown under controlled environmental conditions.     

How small can the difference among competitors be for coexistence to occur

Closely related competitors comprising ofEscherichia coli strains having the same metabolic system and differing only with a few bases on the glutamine synthetase gene in the plasmid pKGN were previously shown to coexist in a chemostat. The differences among these closely related competitors can be considered large enough to allow coexistence as the level of enzyme activity is different. To bring the difference among competitors to the slightest possible, the mutation was introduced on the noncoding region of the plasmid pKGN harbored in the wild-type strain (strain W). The new strain, strain W’, carries the plasmid pKGN’ with a 4-base insertion at theHind III site in the polycloning site of pKGN. As the noncoding region is a nucleotide segment that is not translated into amino acids, the relatedness between strains W and W’ is the closest possible from the genetic point of view. Interestingly, though both strains are almost identical, they can coexist stably in a chemostat irrespective of the initial population size. These experimental results suggest that in the natural ecosystem, no matter how akin competitors are, coexistence is not impossible.     

A third sublineage of avian T cells can be identified with a T cell receptor-3-specific antibody

Avian homologues of mammalian gamma delta and alpha beta TCR, termed TCR1 and TCR2, have been identified in the chicken with specific mAb. A third TCR, dubbed TCR3, has been identified on a subpopulation of T cells that lack the TCR1 or TCR2 epitopes. We have now produced a mAb that identifies this TCR3 molecule. The anti-TCR3 antibody immunoprecipitates a CD3-associated heterodimer with a relative Mr of 88,000, composed of 48,000 and 40,000 disulfide-linked chains. The Mr 40,000 chains of TCR3 and TCR2 exhibited the same isoelectric points of 5.6 to 6.5 and had core proteins of 34,000. Although the Mr 48,000 chain of TCR3 and the Mr 50,000 chain of TCR2 had the same basic isoelectric point of 6.2 to 7.6, their core proteins were different in size, 31,000 vs 29,000. Immunofluorescence analysis reveals that the TCR3 was present on all of the CD3+ T cells not identified by antibodies specific for TCR1 or TCR2. Thymocytes that expressed the surface CD3/TCR3 complex at relatively low levels were predominantly CD4+ and CD8+, whereas those with higher levels of surface CD3/TCR3 were predominantly CD4+ and CD8+ singles. Mature TCR3+ cells in the periphery were also either CD4+ (80%) or CD8+ (20%). The TCR1+, TCR2+, and TCR3+ subsets of T cells were generated sequentially in the thymus and seeded to the periphery in the same order. Intrathymic development of the TCR3+ cells was selectively inhibited by embryonic treatment with the anti-TCR3 mAb. The pattern of histologic localization of TCR3+ cells in the periphery was similar to the TCR2 subset of cells except that the TCR3+ cells were rarely seen in the intestine. Cross-reactivity patterns of the anti-chicken TCR antibodies suggested that other gallinaceous species share the three types of TCR. We conclude that TCR2 and TCR3 in gallinaceous birds may represent alpha beta subfamilies of TCR that are sequentially expressed on developmentally discrete sublines of T cells.