Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21

Human chromosome 21 is the only chromosome in human genome that exhibits oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near the right telomere). We aim at establishing the existence of similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and a putative tendency for nucleosome formation.Comment: submitted to Physical Review

Effective Field Theory of Triangular-Lattice Three-Spin Interaction Model

We discuss an effective field theory of a triangular-lattice three-spin interaction model defined by the ${\mathbb Z}_p$ variables. Based on the symmetry properties and the ideal-state graph concept, we show that the vector dual sine-Gordon model describes the long-distance properties for $p\ge5$; we then compare its predictions with the previous argument. To provide the evidences, we numerically analyze the eigenvalue structure of the transfer matrix for $p=6$, and we check the criticality with the central charge $c=2$ of the intermediate phase and the quantization condition of the vector charges.Comment: 4 pages, 3 figure

Support for UNRWA's survival

The United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA) provides life-saving humanitarian aid for 5·4 million Palestine refugees now entering their eighth decade of statelessness and conflict. About a third of Palestine refugees still live in 58 recognised camps. UNRWA operates 702 schools and 144 health centres, some of which are affected by the ongoing humanitarian disasters in Syria and the Gaza Strip. It has dramatically reduced the prevalence of infectious diseases, mortality, and illiteracy. Its social services include rebuilding infrastructure and homes that have been destroyed by conflict and providing cash assistance and micro-finance loans for Palestinians whose rights are curtailed and who are denied the right of return to their homeland

Increased T-cell immunity against aquaporin-4 and proteolipid protein in neuromyelitis optica.

In neuromyelitis optica (NMO), B-cell autoimmunity to aquaporin-4 (AQP4) has been shown to be essential. However, the role of T cells remains ambiguous. Here, we first showed an increase in CD69+ activated T cells in PBMCs during NMO relapses. Next, T-cell responses to AQP4 and myelin peptides were studied in 12 NM0 patients, 10 multiple sclerosis (MS) patients and 10 healthy subjects (HS). Four hours after adding 1 of 28 overlapping AQP4 peptides, a mixture of AQP4 peptides (AQP4-M) or one of six distinct myelin peptides to 2-day cultured PBMC, CD69 expression on CD4+ T cells was examined. Data were analyzed by paired t-test, frequency of samples with 3-fold increase of CD69 on CD4+ cells (fSI3) and mean stimulation index (mSI). The T-cell response to AQP4-M was significantly increased in NMO (fSI3 = 10/12, mSI = 5.50), with AQP4 (11-30) and AQP4 (91-110) representing the two major epitopes (AQP4 (11-30), fSI3 = 11/12, mSI = 16.0 and AQP4 (91-110), fSI3 = 11/12, mSI = 13.0). Significant but less extensive responses to these two epitopes were also observed in MS and HS. Significant reactivities against AQP4 (21-40), AQP4 (61-80), AQP4 (101-120), AQP4 (171-190) and AQP4 (211-230) were exclusively found in NMO. In addition, responses to AQP4 (81-100) were higher and more frequently detected in NMO, without reaching statistical significance. Interestingly, among the six myelin peptides studied, proteolipid protein (95-116) induced a significant T-cell response in NMO (fSI3 = 7/12, mSI = 4.60). Our study suggests that cellular as well as humoral responses to AQP4 are necessary for NMO development and that the immune response to myelin protein may contribute to disease pathogenesis

Frequency of Chlamydia trachomatis in Ureaplasma-positive healthy women attending their first prenatal visit in a community hospital in Sapporo, Japan

<p>Abstract</p> <p>Background</p> <p>Although <it>Chlamydia trachomatis </it>is the most commonly reported pathogen that causes urogenital infection such as urethritis or cervicitis, <it>Ureaplasma parvum </it>and <it>Ureaplasma urealyticum</it>, which are commensals in the genital tract, have also now been recognized as contributors to urogenital infection. However, whether the presence of either <it>U. parvum </it>or <it>U. urealyticum </it>is related to that of <it>C. trachomatis </it>in the urogenital tract remains unknown. We therefore attempted to estimate by PCR the prevalence of <it>C. trachomatis, U. parvum </it>and <it>U. urealyticum </it>in endocervical samples obtained from healthy women attending their first prenatal visit in Sapporo, Japan.</p> <p>Methods</p> <p>The samples were taken from 303 apparently healthy women, and the extracted DNAs (<it>n </it>= 280) were used for PCR detection targeting <it>C. trachomatis, U. parvum </it>and <it>U. urealyticum</it>. Statistical analysis of the data was performed by Fisher's exact test.</p> <p>Results</p> <p>PCR detection revealed that the prevalence of <it>C. trachomatis, U. parvum </it>and <it>U. urealyticum </it>was 14.3% (40/280), 41.7% (117/280) and 8.9% (25/280), respectively. <it>C. trachomatis ompA </it>genotype D was most frequently identified. Surprisingly, either <it>C. trachomatis </it>or <it>Ureaplasma </it>spp. was detected in almost half of the healthy women. Mixed infection of <it>C. trachomatis </it>with either <it>U. parvum </it>or <it>U. urealyticum </it>was also observed in 9.2% (26/280) of the women. There was a significant association between <it>C. trachomatis </it>and either <it>U. parvum </it>(<it>p </it>= 0.023) or <it>Ureaplasma </it>total (<it>p </it>= 0.013), but not <it>U. urealyticum </it>(<it>p </it>= 0.275).</p> <p>Conclusion</p> <p>This study demonstrated that the presence of <it>Ureaplasma </it>had a significant effect on the presence of <it>C. trachomatis </it>in the genital tract of healthy women, suggesting that mixed infection is an important factor in bacterial pathogenesis in the genital tract.</p

The Diversity of Planetary Systems Architectures: Contrasting Theory with Observations

We develop a semi-analytical model for computing planetary system formation with the aim of explaining the observed diversity of planetary systems architectures and relate this primordial diversity with the initial properties of the disc where they were born. We adopt different initial conditions based on recent results in protoplanetary discs observations, to generate a variety of planetary systems and analyze them statistically. We explore the relevance of the mass and size of the disc, its metallicity, the mass of the central star and the time-scale of gaseous disc dissipation, in defining the architecture of the planetary system. We also test different values of some key parameters of our model, to find out which factors best reproduce the diverse sample of observed planetary systems. According to this, we predict which systems are the most common in the solar neighbourhood. Our results show that planetary systems with only terrestrial planets are the most common, being the only planetary systems formed when considering low metallicity discs and which also represent the best environment for the developing of rocky, potentially habitable planets. We also found that planetary systems like our own are not rare in the solar neighbourhood, being its formation favoured in massive discs where there is not a large accumulation of solids in the inner region of the disc. Regarding the planetary systems that harbor hot and warm Jupiter planets, we found that this systems are born in very massive, metal-rich discs. Also a fast migration rate is required in order to form these systems. According to our results, most of the hot and warm Jupiter systems are composed by only one giant planet, which is also a tendency of the current observational data.Comment: MNRAS in pres

X-ray Crystallographic Structure of an Artificial β-Sheet Dimer

This paper describes the X-ray crystallographic structure of a designed cyclic beta-sheet peptide that forms a well-defined hydrogen-bonded dimer that mimics beta-sheet dimers formed by proteins. The 54-membered ring macrocyclic peptide (1a) contains molecular template and turn units that induce beta-sheet structure in a heptapeptide strand that forms the dimerization interface. The X-ray crystallographic structure reveals the structures of the two "Hao" amino acids that help template the beta-sheet structure and the two delta-linked ornithine turn units that link the Hao-containing template to the heptapeptide beta-strand. The Hao amino acids adopt a conformation that resembles a tripeptide in a beta-strand conformation, with one edge of the Hao unit presenting an alternating array of hydrogen-bond donor and acceptor groups in the same pattern as that of a tripeptide beta-strand. The delta-linked ornithines adopt a conformation that resembles a hydrogen-bonded beta-turn, in which the ornithine takes the place of the i+1 and i+2 residues. The dimers formed by macrocyclic beta-sheet 1a resemble the dimers of many proteins, such as defensin HNP-3, the lambda-Cro repressor, interleukin 8, and the ribonuclease H domain of HIV-1 reverse transcriptase. The dimers of 1a self-assemble in the solid state into a barrel-shaped trimer of dimers in which the three dimers are arranged in a triangular fashion. Molecular modeling in which one of the three dimers is removed and the remaining two dimers are aligned face-to-face provides a model of the dimers of dimers of closely related macrocyclic beta-sheet peptides that were observed in solution

Lentiviral Vectors and Protocols for Creation of Stable hESC Lines for Fluorescent Tracking and Drug Resistance Selection of Cardiomyocytes

Developmental, physiological and tissue engineering studies critical to the development of successful myocardial regeneration therapies require new ways to effectively visualize and isolate large numbers of fluorescently labeled, functional cardiomyocytes.Here we describe methods for the clonal expansion of engineered hESCs and make available a suite of lentiviral vectors for that combine Blasticidin, Neomycin and Puromycin resistance based drug selection of pure populations of stem cells and cardiomyocytes with ubiquitous or lineage-specific promoters that direct expression of fluorescent proteins to visualize and track cardiomyocytes and their progenitors. The phospho-glycerate kinase (PGK) promoter was used to ubiquitously direct expression of histone-2B fused eGFP and mCherry proteins to the nucleus to monitor DNA content and enable tracking of cell migration and lineage. Vectors with T/Brachyury and alpha-myosin heavy chain (alphaMHC) promoters targeted fluorescent or drug-resistance proteins to early mesoderm and cardiomyocytes. The drug selection protocol yielded 96% pure cardiomyocytes that could be cultured for over 4 months. Puromycin-selected cardiomyocytes exhibited a gene expression profile similar to that of adult human cardiomyocytes and generated force and action potentials consistent with normal fetal cardiomyocytes, documenting these parameters in hESC-derived cardiomyocytes and validating that the selected cells retained normal differentiation and function.The protocols, vectors and gene expression data comprise tools to enhance cardiomyocyte production for large-scale applications