Materials science: Carbon sheet solutions

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62936/1/442254a.pd

RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes

<p>Abstract</p> <p>Background -</p> <p>The availability of multiple whole genome sequences has facilitated <it>in silico </it>identification of fixed and polymorphic transposable elements (TE). Whereas polymorphic loci serve as makers for phylogenetic and forensic analysis, fixed species-specific transposon insertions, when compared to orthologous loci in other closely related species, may give insights into their evolutionary significance. Besides, TE insertions are not isolated events and are frequently associated with subtle sequence changes concurrent with insertion or post insertion. These include duplication of target site, 3' and 5' flank transduction, deletion of the target locus, 5' truncation or partial deletion and inversion of the transposon, and post insertion changes like inter or intra element recombination, disruption etc. Although such changes have been studied independently, no automated platform to identify differential transposon insertions and the associated array of sequence changes in genomes of the same or closely related species is available till date. To this end, we have designed RISCI - 'Repeat Induced Sequence Changes Identifier' - a comprehensive, comparative genomics-based, <it>in silico </it>subtractive hybridization pipeline to identify differential transposon insertions and associated sequence changes using specific alignment signatures, which may then be examined for their downstream effects.</p> <p>Results -</p> <p>We showcase the utility of RISCI by comparing full length and truncated L1HS and AluYa5 retrotransposons in the reference human genome with the chimpanzee genome and the alternate human assemblies (Celera and HuRef). Comparison of the reference human genome with alternate human assemblies using RISCI predicts 14 novel polymorphisms in full length L1HS, 24 in truncated L1HS and 140 novel polymorphisms in AluYa5 insertions, besides several insertion and post insertion changes. We present comparison with two previous studies to show that RISCI predictions are broadly in agreement with earlier reports. We also demonstrate its versatility by comparing various strains of <it>Mycobacterium tuberculosis </it>for IS 6100 insertion polymorphism.</p> <p>Conclusions -</p> <p>RISCI combines comparative genomics with subtractive hybridization, inferring changes only when exclusive to one of the two genomes being compared. The pipeline is generic and may be applied to most transposons and to any two or more genomes sharing high sequence similarity. Such comparisons, when performed on a larger scale, may pull out a few critical events, which may have seeded the divergence between the two species under comparison.</p

The formation of human populations in South and Central Asia

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages

Knowledge transmission patterns at the border: ethnobotany of Hutsuls living in the Carpathian Mountains of Bukovina (SW Ukraine and NE Romania)

Background Cross-border research is a novel and important tool for detecting variability of ecological knowledge. This is especially evident in regions recently divided and annexed to different political regimes. Therefore, we conducted a study among Hutsuls, a cultural and linguistic minority group living in Northern and Southern Bukovina (Ukraine and Romania, respectively). Indeed, in the 1940s, a border was created: Northern Bukovina was annexed by the USSR while Southern Bukovina remained part of the Kingdom of Romania. In this research, we aim to document uses of plants for food and medicinal preparations, discussing the different dynamics of Local Ecological Knowledge (LEK) transmission among Hutsuls living in Ukraine and Romania. Methods Field research was conducted using convenience and snowball sampling techniques to recruit 31 Hutsuls in Ukraine and 30 in Romania for participation in semi-structured interviews regarding the use of plants for medicinal and food preparation purposes and the sources of such knowledge. Results The interviews revealed that, despite a common cultural and linguistic background, ethnobotanical knowledge transmission occurs in different ways on each side of the border. Family is a primary source of ethnobotanical knowledge transmission on both sides of the border; however, in Romania, knowledge from other sources is very limited, whereas in Ukraine interviewees reported several other sources including books, magazines, newspapers, the Internet and television. This is especially evident when analysing the wild plants used for medicinal purposes as we found 53 taxa that were common to both, 47 used only in Ukraine and 11 used only in Romania. While Romanian Hutsuls used almost exclusively locally available plants, Ukrainian Hutsuls often reported novel plants such as Aloe vera, Aronia melanocarpa and Elaeagnus rhamnoides. Knowledge related to these plants was transferred by sources of knowledge other than oral transmission among members of the same family. Therefore, this may imply hybridization of the local body of knowledge with foreign elements originating in the Soviet context which has enriched the corpus of ethnobotanical knowledge held by Ukrainian Hutsuls. Conclusions While ethnobotanical knowledge among Romanian Hutsuls is mainly traditional and vertically transmitted, among Ukrainian Hutsuls there is a considerable proportion of LEK that is transmitted from other (written and visual) sources of knowledge. This cross-border research reveals that despite a common cultural background, socio-political scenarios have impacted Hutsul ethnobotanical knowledge and its transmission patterns

T cell fate and clonality inference from single-cell transcriptomes.

We developed TraCeR, a computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. We found that T cell clonotypes in a mouse Salmonella infection model span early activated CD4(+) T cells as well as mature effector and memory cells

Crystal structure and Hirshfeld surface analysis of 5, 7-diphenyl-1, 2, 3, 5, 6, 7-hexahydroimidazo [1, 2-a] pyridine-6, 6, 8-tricarbonitrile methanol monosolvate

TARAMAWOSWOS:000661118800004TARAMAPUBMEDTARAMASCOPUSIn the title compound, C22H17N5·CH4O, the imidazolidine ring of the 1,2,3,5,6,7-hexahydroimidazo[1,2-a]pyridine ring system is a twisted envelope, while the 1,2,3,4-tetrahydropyridine ring adopts a twisted boat conformation. In the crystal, pairs of molecules are linked by O—H⋯N and N—H⋯O hydrogen bonds via two methanol molecules, forming a centrosymmetric R44(16) ring motif. These motifs are connected to each other by C—H⋯N hydrogen bonds and form columns along the a axis. The columns form a stable molecular packing, being connected to each other by van der Waals interactions. A Hirshfeld surface analysis indicates that the most significant contributions to the crystal packing are from H⋯H (43.8%), N⋯H/H⋯N (31.7%) and C⋯H/H⋯C (18.4%) contacts