Search results for "alignment"
showing 10 items of 627 documents
The genomic history of the Aegean palatial civilizations
2021
Summary The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as e…
Variable-order reference-free variant discovery with the Burrows-Wheeler Transform
2020
Abstract Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precision of previous de Bruijn graphs based tools by overcoming several of their limitations, namely: (i) the need to establish a fixed value, usually small, for the order k, (ii) the loss of important information such as k-mer coverage and adjacency of k-mers within the same read, and (iii) bad performance in repeated regions longer than k bases. The preliminary tool, however, was able to identify only SNPs and it was too slow and memory con…
Molecular Basis for the Interaction of the Hepatitis B Virus Core Antigen with the Surface Immunoglobulin Receptor on Naive B Cells
2001
ABSTRACTThe nucleocapsid of the hepatitis B virus (HBV) is composed of 180 to 240 copies of the HBV core (HBc) protein. HBc antigen (HBcAg) capsids are extremely immunogenic and can activate naive B cells by cross-linking their surface receptors. The molecular basis for the interaction between HBcAg and naive B cells is not known. The functionality of this activation was evidenced in that low concentrations of HBcAg, but not the nonparticulate homologue HBV envelope antigen (HBeAg), could prime naive B cells to produce anti-HBc in vitro with splenocytes from HBcAg- and HBeAg-specific T-cell receptor transgenic mice. The frequency of these HBcAg-binding B cells was estimated by both hybridom…
Alignment of the ATLAS Inner Detector and Single Top Studies
2016
Alineamiento del detector interno de ATLAS y estudios del single top Esta tesis esta compuesta por dos partes bien diferenciadas. La primera trata de los estudios de alineamiento del detector interno del experimento ATLAS en el CERN. La segunda se centra en los estudios sobre el quark top cuando es producido como partícula aislada. ATLAS es uno de los grandes experimentos del LHC (Gran colisionador de hadrones) situado en el CERN. ATLAS es un detector de propósito general. Se diseñó para aprovechar la alta energía disponible en el LHC y observar fenómenos de física a muy altas energías. ATLAS está formado por varios sub-sistemas, como el detector interno de trazas, los calorímetros electrom…
Controlling molecular alignment rephasing through interference of Raman-induced rotational coherence
2000
0021-9606; Quantum control over molecular alignment rephasing is experimentally investigated in gaseous CO2. The control process is achieved by illuminating the medium with a pair of pump-pulses separated in time by approximately an integer value of T0=1/8B(0), where B(0) is the rotational constant. Through a Raman-type process, each pulse alone produces rotational coherence leading to a periodic orientational anisotropy. It is the combination of the two pulses that yields to quantum interference, resulting in a modification of this anisotropy probed by a third delayed pulse. The effect is accurately analyzed for different time delays between the two pulses. A theoretical analysis supplies …
EcFLO, a FLORICAULA-like gene from Eschscholzia californica is expressed during organogenesis at the vegetative shoot apex.
2003
FLORICAULA/ LEAFY-like genes were initially characterized as flower meristem identity genes. In a range of angiosperms, expression occurs also in vegetative shoot apices and developing leaves, and in some species with dissected leaves expression is perpetuated during organogenesis at the leaf marginal blastozone. The evolution of these expression patterns and associated functions is not well understood. We have isolated and characterized a FLORICAULA-like gene from California Poppy, Eschscholzia californica Cham. (Papaveraceae), a species belonging to the basal eudicot clade Ranunculales. EcFLO encodes a putative 416-amino-acid protein with highest similarity to homologous genes from Trocho…
A urochordate putative homolog of human EB1, the protein which binds APC1
1996
Abstract The human EB1 protein has been cloned by virtue of its interaction with the C-terminus of the APC (adenomatous polyposis coli) protein, whose C-terminal truncated forms have been shown to accompany sporadic and familial forms of colorectal cancer. We have cloned a putative EB1 homolog from Botryllus schlosseri (Urochordata, Ascidiacea). The deduced protein is 287 amino acids long, and is identical with 48% of the residues in human EB1 and 24–25% in two yeast hypothetical proteins. We propose that such a high degree of conservation among EB1 homologs is indicative of an essential regulatory mechanism in eukaryotic cells.
Type I keratin cDNAs from the rainbow trout: independent radiation of keratins in fish
2002
Five different type I keratins from a teleost fish, the rainbow trout Oncorhynchus mykiss, have been sequenced by cDNA cloning and identified at the protein level by peptide mass mapping using MALDI-MS. This showed that the entire range of type I keratins detected biochemically in this fish has now been sequenced. Three of the keratins are expressed in the epidermis (subtype Ie), whereas the other two occur in simple epithelia and mesenchymal cells (subtype Is). Among the Is keratins is an ortholog of human K18; the second Is polypeptide is clearly distinct from K18. We raised a new monoclonal antibody (F1F2, subclass IgG1) that specifically recognizes trout Is keratins, with negative react…
cDNA sequences of the authentic keratins 8 and 18 in zebrafish
2003
From the zebrafish Danio rerio, we have cDNA cloned and sequenced a novel type II and a novel type I keratin, termed DreK8 and DreK18, respectively. We identified DreK8/18 as the true orthologs of the human keratin pair K8/18 as follows: (i) MALDI-MS assignment to the biochemically identified K8 and K18 candidates that are co-expressed in simple epithelia and absent in epidermal keratinocytes; (ii) multiple sequence alignments and phylogenetic tree analysis, showing that DreK8, within the phylogenetic tree of type II keratins, forms a highly bootstrap-supported branch together with K8 from goldfish and rainbow trout, whereas DreK18, within the phylogenetic tree of type I keratins, groups wi…
Fetuin-A and Cystatin C Are Endogenous Inhibitors of Human Meprin Metalloproteases
2010
Meprin α and β, zinc metalloproteinases, play significant roles in inflammation, including inflammatory bowel disease (IBD), possibly by activating cytokines, like interleukin 1β, interleukin 18, or tumor growth factor α. Although a number of potential activators for meprins are known, no endogenous inhibitors have been identified. In this work, we analyzed the inhibitory potential of human plasma and identified bovine fetuin-A as an endogenous meprin inhibitor with a K(i) (inhibition constant) of 4.2 × 10(-5) M for meprin α and a K(i) of 1.1 × 10(-6) M meprin β. This correlated with data obtained for a fetuin-A homologue from carp (nephrosin inhibitor) that revealed a potent meprin α and β…