High levels of Paleolithic Y-chromosome lineages characterize Serbia

Whether present-day European genetic variation and its distribution patterns can be attributed primarily to the initial peopling of Europe by anatomically modern humans during the Paleolithic, or to latter Near Eastern Neolithic input is still the subject of debate. Southeastern Europe has been a crossroads for several cultures since Paleolithic times and the Balkans, specifically, would have been part of the route used by Neolithic farmers to enter Europe. Given its geographic location in the heart of the Balkan Peninsula at the intersection of Central and Southeastern Europe, Serbia represents a key geographical location that may provide insight to elucidate the interactions between indigenous Paleolithic people and agricultural colonists from the Fertile Crescent. In this study, we examine, for the first time, the Y-chromosome constitution of the general Serbian population. A total of 103 individuals were sampled and their DNA analyzed for 104 Y-chromosome bi-allelic markers and 17 associated STR loci. Our results indicate that approximately 58% of Serbian Y-chromosomes (I1-M253, I2a-P37.2 and R1a1a-M198) belong to lineages believed to be pre-Neolithic. On the other hand, the signature of putative Near Eastern Neolithic lineages, including E1b1b1a1-M78, G2a-P15, J1-M267, J2-M172 and R1b1a2-M269 accounts for 39% of the Y-chromosome. Haplogroup frequency distributions in Western and Eastern Europe reveal a spotted landscape of paleolithic Y chromosomes, undermining continental-wide generalizations. Furthermore, an examination of the distribution of Y-chromosome filiations in Europe indicates extreme levels of Paleolithic lineages in a region encompassing Serbia, Bosnia-Herzegovina and Croatia, possibly the result of Neolithic migrations encroaching on Paleolithic populations against the Adriatic Sea.     

Concepts on charge transfer through naturally vibrating DNA molecule

Delocalization of charges thorough DNA occurs due to the natural and continuous movements of molecule which stimulates the charge transfer through the molecule. A model is presented showing that the mechanism of electrical conduction occurs mainly by thermally-activated drift motion of holes under control of the localized carriers; where electrons are localized in the conduction band. These localized (stationary-trapped) electrons control the movements of the positive charges and do not play an effective role in the electrical conduction itself. It is found that the localized charge-carriers in the bands have characteristic relaxation times at 5×10(^-2)s, 1.94×10(^-4)s, 5×10(^-7)s, and 2×10(^-11)s respectively which are corresponding to four intrinsic thermal activation energies 0.56eV, 0.33eV, 0.24eV, and 0.05eV respectively. The ac-conductivity of some published data are well fitted with the presented model and the total charge density in DNA molecule is calculated to be n=1.88×10(^19)cm(^-3) at 300K which is corresponding to a linear electron density n=8.66×10(^3)cm(^-1) at 300K. The model shed light on the role of transfer and/or localization of charges through DNA which has multiple applications in medical, nano-technical, bio-sensing and different domains. So, repair DNA by adjusting the charge transport through the molecule is future challenges to new medical applications.     

Functional Glycomic Analysis of Human Milk Glycans Reveals the Presence of Virus Receptors and Embryonic Stem Cell Biomarkers

Human milk contains a large diversity of free glycans beyond lactose, but their functions are not well understood. To explore their functional recognition, here we describe a shotgun glycan microarray prepared from isolated human milk glycans (HMGs), and our studies on their recognition by viruses, antibodies, and glycan-binding proteins (GBPs), including lectins. The total neutral and sialylated HMGs were derivatized with a bifunctional fluorescent tag, separated by multidimensional HPLC, and archived in a tagged glycan library, which was then used to print a shotgun glycan microarray (SGM). This SGM was first interrogated with well defined GBPs and antibodies. These data demonstrated both the utility of the array and provided preliminary structural information (metadata) about this complex glycome. Anti-TRA-1 antibodies that recognize human pluripotent stem cells specifically recognized several HMGs that were then further structurally defined as novel epitopes for these antibodies. Human influenza viruses and Parvovirus Minute Viruses of Mice also specifically recognized several HMGs. For glycan sequencing, we used a novel approach termed metadata-assisted glycan sequencing (MAGS), in which we combine information from analyses of glycans by mass spectrometry with glycan interactions with defined GBPs and antibodies before and after exoglycosidase treatments on the microarray. Together, these results provide novel insights into diverse recognition functions of HMGs and show the utility of the SGM approach and MAGS as resources for defining novel glycan recognition by GBPs, antibodies, and pathogens.     

Interactions of the Human LIP5 Regulatory Protein with Endosomal Sorting Complexes Required for Transport

The endosomal sorting complex required for transport (ESCRT) pathway remodels membranes during multivesicular body biogenesis, the abscission stage of cytokinesis, and enveloped virus budding. The ESCRT-III and VPS4 ATPase complexes catalyze the membrane fission events associated with these processes, and the LIP5 protein helps regulate their interactions by binding directly to a subset of ESCRT-III proteins and to VPS4. We have investigated the biochemical and structural basis for different LIP5-ligand interactions and show that the first microtubule-interacting and trafficking (MIT) module of the tandem LIP5 MIT domain binds CHMP1B (and other ESCRT-III proteins) through canonical type 1 MIT-interacting motif (MIM1) interactions. In contrast, the second LIP5 MIT module binds with unusually high affinity to a novel MIM element within the ESCRT-III protein CHMP5. A solution structure of the relevant LIP5-CHMP5 complex reveals that CHMP5 helices 5 and 6 and adjacent linkers form an amphipathic “leucine collar” that wraps almost completely around the second LIP5 MIT module but makes only limited contacts with the first MIT module. LIP5 binds MIM1-containing ESCRT-III proteins and CHMP5 and VPS4 ligands independently in vitro, but these interactions are coupled within cells because formation of stable VPS4 complexes with both LIP5 and CHMP5 requires LIP5 to bind both a MIM1-containing ESCRT-III protein and CHMP5. Our studies thus reveal how the tandem MIT domain of LIP5 binds different types of ESCRT-III proteins, promoting assembly of active VPS4 enzymes on the polymeric ESCRT-III substrate.     

Signal transduction in receptor for advanced glycation end products (RAGE): solution structure of C-terminal rage (ctRAGE) and its binding to mDia1

The receptor for advanced glycation end products (RAGE) is a multiligand cell surface macromolecule that plays a central role in the etiology of diabetes complications, inflammation, and neurodegeneration. The cytoplasmic domain of RAGE (C-terminal RAGE; ctRAGE) is critical for RAGE-dependent signal transduction. As the most membrane-proximal event, mDia1 binds to ctRAGE, and it is essential for RAGE ligand-stimulated phosphorylation of AKT and cell proliferation/migration. We show that ctRAGE contains an unusual α-turn that mediates the mDia1-ctRAGE interaction and is required for RAGE-dependent signaling. The results establish a novel mechanism through which an extracellular signal initiated by RAGE ligands regulates RAGE signaling in a manner requiring mDia1.     

An experimental study of the multiple effects of brown trout Salmo trutta on the bioenergetics of two Arctic charr Salvelinus alpinus morphs

This study investigated the importance of competition with brown trout Salmo trutta as a driver of the morphological and behavioural divergence of two morphs of Arctic charr Salvelinus alpinus. The morphs originated from two lakes differing in absence or presence of the competitor. The bioenergetics and behaviour of S. alpinus were quantified in replicate experimental enclosures (mean volume: 150 m(3) ) stocked with 15 S. alpinus of one morph or the other and in the absence or presence of nine S. trutta. The presence of S. trutta decreased growth rate, affected food consumption and increased activity costs in S. alpinus, but provided little support for the hypothesis that competition with S. trutta is a major driver of the divergence of the two S. alpinus morphs. Both morphs responded similarly in terms of mean growth and consumption rates per enclosure, but the association between individual morphology and growth rate reversed between allopatric and sympatric enclosures. While the activity patterns of the two morphs were unaffected by the presence of S. trutta, their swimming speed and activity rate differed. Since the profound differences in the structure of the physical habitat of the source lakes provided a more likely explanation for the difference observed among these two morphs than interspecific competition, it is hypothesized that physical habitat may sometimes be a significant driving force of the phenotypic divergence.     

Does spatial variation in egg thiamine and fatty‐acid concentration of Lake Michigan lake trout Salvelinus namaycush lead to differential early mortality syndrome and yolk oedema mortality in offspring?

Individual variation in fatty-acid and thiamine concentrations were determined in lake trout Salvelinus namaycush eggs collected at two spawning grounds in Lake Michigan. A suite of predictor variables, including spawning location, egg fatty-acid and thiamine concentrations, were used to attempt to explain cause-and-effect in early life stage mortality among S. namaycush families. Lipid and fatty-acid composition of S. namaycush eggs differed between spawning locations. Salvelinus namaycush offspring from south-western Lake Michigan were affected by a high occurrence of yolk oedema, whereas a higher frequency of early mortality syndrome (EMS) was observed among offspring from the north-western part of the lake. Random-forest regressions revealed location as the most influential predictor of yolk oedema mortality, whereas thiamine level in eggs was the strongest predictor of EMS-related mortality. Several polyunsaturated fatty acids were also found to be predictors of both mortalities. There is evidence of spatial variability in egg fatty-acid concentration among S. namaycush in Lake Michigan that, together with diminished thiamine concentration, contribute to low survival of S. namaycush progeny.     

Detection of feeding behaviour in common carp Cyprinus carpio by using an acceleration data logger to identify mandibular movement

Miniaturized acceleration data loggers were attached to the lower mandible of common carp Cyprinus carpio to remotely identify feeding behaviour. Whether the acceleration signal could distinguish the quantity and quality of food was also investigated. The frequency and amplitude of the lower mandible stroke, calculated from surging acceleration determined by continuous wavelet transformation, significantly increased during the feeding period compared to that during the non-feeding period. These characteristic movement patterns were maintained for mean ±s.e. 187·3 ± 38·2 s when the fish were fed a single item of food and for mean ±s.e. 419·3 ± 28·6 s when they consumed multiple items. The dominant cycle and amplitude calculated according to feeding event duration, however, did not differ significantly between the two types of diets the fish consumed. Surging acceleration could detect mean ±s.e. 89·8 ± 13·5% of feeding events, although the false detection rate was mean ±s.e. 25·9 ± 10·9%. The results indicate that the mandible acceleration measurement method could be utilized to detect and record the feeding events in fishes that use a suction feeding mode similar to C. carpio.     

Small‐plot studies comparing pheromone and juice baits for mass‐trapping invasive Synanthedon myopaeformis in Canada

Recent introduction of Synanthedon myopaeformis (Borkhausen) (Lepidoptera: Sesiidae) into organic apple‐growing areas of Canada has stimulated research on semiochemical‐based management of this European pest. Replicated, small‐plot (0.16 ha) experiments were conducted to compare sex pheromone, 3Z,13Z‐octadecadienyl acetate (10 mg), Concord grape juice (300 ml), or their combination, as mass‐trapping lures at trap densities equivalent to 12.5, 25, 50, and 100 traps ha^?1. Total numbers of male and female moths removed from test plots increased significantly with trap density in all juice‐based mass‐trapping experiments. In pheromone mass‐trapping experiments, however, total catches of males did not increase significantly as trap densities were increased and catches appeared to plateau with 25–50 traps ha^?1. With pheromone‐based mass‐trapping, significantly fewer males were caught in pheromone‐baited assessment traps at the centre of each mass‐trapping plot than in identical traps in untreated plots. This reduction is indicative of significant trap interference or trap ‘shut‐down’. Increasing the density of juice‐based mass‐trapping had no effect on catches of male or female moths in juice‐baited assessment traps, indicating a short range of attraction and lack of interference between juice traps. Pheromone‐ and juice‐based mass trapping removed similar numbers of males at each trap density tested, respectively, but summed catches of males and females were greatest with juice baits. Combining pheromone and juice into a single mass‐trapping treatment (50 traps ha^?1) did not significantly increase catches of males or females relative to either treatment alone. If a practical bisexual mass‐trapping system is going to be developed for S. myopaeformis, then identification of volatile kairomones in Concord grape juice may be useful.