Positional Homology in Bacterial Genomes

In comparative genomic studies, syntenic groups of homologous sequence in the same order have been used as supplementary information that can be used in helping to determine the orthology of the compared sequences. The assumption is that ortholo-gous gene copies are more likely to share the same genome positions and share the same gene neighbors. In this study we have defined positional homologs as those that also have homologous neighboring genes and we investigated the usefulness of this distinction for bacterial comparative genomics. We considered the identification of positionaly homologous gene pairs in bacterial genomes using protein and DNA sequence level alignments and found that the positional homologs had on average relatively lower rates of substitution at the DNA level (synonymous substitutions) than duplicate homologs in different genomic locations, regardless of the level of protein sequence divergence (measured with non-synonymous substitution rate). Since gene order conservation can indicate accuracy of orthology assignments, we also considered the effect of imposing certain alignment quality requirements on the sensitivity and specificity of identification of protein pairs by BLAST and FASTA when neighboring information is not available and in comparisons where gene order is not conserved. We found that the addition of a stringency filter based on the second best hits was an efficient way to remove dubious ortholog identifications in BLAST and FASTA analyses. Gene order conservation and DNA sequence homology are useful to consider in comparative genomic studies as they may indicate different orthology assignments than protein sequence homology alone

Identité biologique des artisans moustériens de Kebara (Mont Carmel, Israël) Réflexions sur le concept de néanderthalien au Levant méditerranéen

Dès les premières découvertes de fossiles humains provenant du Bassin Méditerranéen oriental et datés du Pléistocène supérieur, il est apparu évident que la documentation anthropologique illustrait une hétérogénéité biologique, suscitant des interprétations différentes. Par la suite, l’enrichissement de la documentation avec de nouvelles fouilles est venu alimenter, au sein de la communauté scientifique, les discussions portant aussi bien sur les affinités phylogénétiques des fossiles que sur leur position chronologique. La prise en compte, sur ces fossiles proche-orientaux, de l’originalité de l’assemblage de caractères anatomiques présents ne doit pas être sous-estimée pour une meilleure évaluation des composantes régionales. C’est ce qui est proposé à propos de Kebara, l’objectif étant de favoriser une approche cohérente de la diversité biologique des hommes du Paléolithique moyen dans la région, qui n’exclut pas les influences extra-européennes.The southern Mediterranean Levant has attracted the attention of the scientific community since the early excavations conducted at the beginning of the 20th century on several sites, which provided a significant sample of Upper Pleistocene hominids. Additional skeletal material, circumscribed geographically and chronologically, raises several questions concerning the biological differences and similarities between the hominid samples represented, and their geographical position at the crossroads of Africa and Eurasia. The excellent state of preservation of the hominid remains enables a new insight into the anatomy of Levantine Middle Palaeolithic populations and provides important data for reconstructing the pattern of human evolution in the Near East. With this in view, re-examination of some skeletal remains recovered at Kebara Cave suggests. that biological differences and similarities may have existed between Neanderthals and Levantine Middle Palaeolithic hominids, strengthening the existence of regional variation

Perikymata number and spacing on early modern human teeth: evidence from Qafzeh cave, Israel

The microscopic anatomy of dental enamel has been employed in numerous studies of fossil hominin teeth. This research has focused on the use of microstructure, primarily perikymata and, when available, their internal manifestations, in the construction of phylogenetic relationships as well as in the reconstruction of hominin patterns of growth and development. The literature on perikymata numbers and packing as reported over the last 20 years, shows a huge range of variation within modern humans. The variation is so large in fact that virtually every fossil hominin species can be encompassed within the range except for some but not most of the robust australopithecines. The sample of Mousterian level hominins from the site of Qafzeh, in northern Israel represents some of the earliest recognized members of Homo sapiens sapiens. Included in this sample are a number of immature individuals (N = 5) whose permanent incisor crowns have observable perikymata. The number of perikymata on complete and unworn teeth is within the range of variation of other hominins and does not provide specific evidence for attributing these specimens to one hominin taxon or another. Similarly, the pattern of perikymata compaction toward the cemento-enamel junction of the Qafzeh specimens is compared to published sources.La structure microscopique de l’émail dentaire est employée dans de nombreuses études des dents des Homininés fossiles. Cette recherche se concentre sur l’emploi de la microstructure et, en premier, celui des périkymaties et de leur disposition interne quand cela est possible, pour traiter des relations phylogénétiques et reconstruire des processus de croissance et de développement au sein du groupe. Depuis une vingtaine d’années, les travaux publiés sur le nombre et la distribution des périkymaties permettent de dégager une variation importante dans les populations actuelles, qui intègre pratiquement toutes les espèces d’Homininés fossiles, à l’exception peut-être de quelques-uns des Australopithèques robustes. Les niveaux moustériens du site de Qafzeh au Nord d’Israël ont livré un large échantillon des plus anciens représentants des Homo sapiens sapiens, dont un grand nombre de sujets non adultes. Parmi ces derniers, se trouvent des individus (N = 5) dont les germes d’incisives permanentes portent des périkymaties observables. Le nombre de périkymaties sur les couronnes complètes et non usées s’intègre dans la variation connue des Homininés. La distribution, sur ces quelques dents, des périkymaties le long de la couronne jusqu’à la jonction cémento-énamélaire, est comparée aux données publiées

New Data on the Origin of Modern Man in the Levant

Anthropolog

Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

Copyright: © 2015 Solà et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

Оцінка якості життя у вікових першовагітних та вагітних з великим інтергенетичним інтервалом

Проведено изучение показателей качества жизни у 120 возрастных первобеременных и 240 беременных с большим интергенетическим интервалом с использованием опросника SF-36 Health Status Survey, разработанного The Health Institute, New England Medical Center, Boston, USA. Исследование показало, что пациентки обеих групп имеют низкие показатели качества жизни. При сравнении большинство изучаемых параметров оценки качества жизни в обследованных группах не отличались, однако у пациенток с большим интергенетическим интервалом – достоверно выше оценка социальной роли и энергетичности. Оценка качества жизни у возрастных первобеременных и беременных с большим интергенетическим интервалом является важным сегментом наблюдения во время беременности, который оценивает перспективы развития беременности в психологическом, физическом и социальном аспектах.A study of the life quality of 120 over-age primigravidas and of 240 women with a large intergenetic interval has been carried out using the questionnaire SF-36 Health Status Survey developed by The Health Institute, New England Medical Center, Boston, USA. This research has shown that the patients in the both groups have a low quality of life. The major part of the life quality parameters were the same in the both groups, however, in patients with a large interval between births the values of the social role and the energy level were significantly higher. The life quality of over-age primigravidas and pregnant women with a large interval between successive births is an important sector of observation during pregnancy, which allows assessing the prospects of pregnancy in the psychological, physical, and social aspects

Charge and current-sensitive preamplifiers for pulse shape discrimination techniques with silicon detectors

New charge and current-sensitive preamplifiers coupled to silicon detectors and devoted to studies in nuclear structure and dynamics have been developed and tested. For the first time shapes of current pulses from light charged particles and carbon ions are presented. Capabilities for pulse shape discrimination techniques are demonstrated.Comment: 14 pages, 12 figures, to be published in Nucl. Inst. Meth.

SEIS: Insight's Seismic Experiment for Internal Structure of Mars.

By the end of 2018, 42 years after the landing of the two Viking seismometers on Mars, InSight will deploy onto Mars' surface the SEIS (Seismic Experiment for Internal Structure) instrument; a six-axes seismometer equipped with both a long-period three-axes Very Broad Band (VBB) instrument and a three-axes short-period (SP) instrument. These six sensors will cover a broad range of the seismic bandwidth, from 0.01 Hz to 50 Hz, with possible extension to longer periods. Data will be transmitted in the form of three continuous VBB components at 2 sample per second (sps), an estimation of the short period energy content from the SP at 1 sps and a continuous compound VBB/SP vertical axis at 10 sps. The continuous streams will be augmented by requested event data with sample rates from 20 to 100 sps. SEIS will improve upon the existing resolution of Viking's Mars seismic monitoring by a factor of ∼ 2500 at 1 Hz and ∼ 200 000 at 0.1 Hz. An additional major improvement is that, contrary to Viking, the seismometers will be deployed via a robotic arm directly onto Mars' surface and will be protected against temperature and wind by highly efficient thermal and wind shielding. Based on existing knowledge of Mars, it is reasonable to infer a moment magnitude detection threshold of M w ∼ 3 at 40 ∘ epicentral distance and a potential to detect several tens of quakes and about five impacts per year. In this paper, we first describe the science goals of the experiment and the rationale used to define its requirements. We then provide a detailed description of the hardware, from the sensors to the deployment system and associated performance, including transfer functions of the seismic sensors and temperature sensors. We conclude by describing the experiment ground segment, including data processing services, outreach and education networks and provide a description of the format to be used for future data distribution.Electronic supplementary materialThe online version of this article (10.1007/s11214-018-0574-6) contains supplementary material, which is available to authorized users

Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea)

Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level