Secondary structure in the core of amyloid fibrils formed from human βm and its truncated variant Δn6

Amyloid fibrils formed from initially soluble proteins with diverse sequences are associated with an array of human diseases. In the human disorder, dialysis-related amyloidosis (DRA), fibrils contain two major constituents, full-length human β-microglobulin (hβm) and a truncation variant, ΔN6 which lacks the N-terminal six amino acids. These fibrils are assembled from initially natively folded proteins with an all antiparallel β-stranded structure. Here, backbone conformations of wild-type hβm and ΔN6 in their amyloid forms have been determined using a combination of dilute isotopic labeling strategies and multidimensional magic angle spinning (MAS) NMR techniques at high magnetic fields, providing valuable structural information at the atomic-level about the fibril architecture. The secondary structures of both fibril types, determined by the assignment of ∼80% of the backbone resonances of these 100- and 94-residue proteins, respectively, reveal substantial backbone rearrangement compared with the location of β-strands in their native immunoglobulin folds. The identification of seven β-strands in hβm fibrils indicates that approximately 70 residues are in a β-strand conformation in the fibril core. By contrast, nine β-strands comprise the fibrils formed from ΔN6, indicating a more extensive core. The precise location and length of β-strands in the two fibril forms also differ. The results indicate fibrils of ΔN6 and hβm have an extensive core architecture involving the majority of residues in the polypeptide sequence. The common elements of the backbone structure of the two proteins likely facilitates their ability to copolymerize during amyloid fibril assembly

Kalsium Silikat sebagai Bahan Komposit Biosemen Gigi dengan Penyiapan Silika dari Sekam Padi melalui Metode Sol-Gel

Rice husk has the content of organic and inorganic compounds that have not been utilized maximally, one of them is silica. High silica content in rice husks can be used as an alternative source of potential silica for the synthesis of calcium silicate as a base material of Trioxide Aggregate mineral composites in tooth biocement. In this study, calcium silicate was obtained through two stages of the process, namely silica isolation from rice husk ash by sol-gel method, and reacting between silica and calcium oxide. Silica and calcium oxide are reacted to the mole ratio between silica to calcium oxide of 7:3, 6:4, 4:6, and 3:7. The isolated silica is characterized by the distribution of the size and composition of each element with Particle Size Analyzer (PSA) and EDS. The formation of calcium silicate and its size distribution from the synthesis stage is determined by XRD and PSA. The result showed that silica isolation from rice husk ash with sol-gel method obtained silica with content and particle size of 71.6% and 52.82 mm. While the optimum condition of calcium silicate synthesis was achieved at the mole ratio of silica to calcium oxide by 4:6. In the mole ratios obtained calcium silicate type b-dicalcium silicate with an average particle size of 102.2 mm.Sekam padi memiliki kandungan senyawa organik maupun anorganik yang belum termanfaatkan secara maksimal, salah satunya adalah silika. Kandungan silika yang tinggi pada sekam padi dapat digunakan sebagai alternatif sumber silika yang potensial untuk sintesis kalsium silikat sebagai bahan dasar komposit Mineral Trioxide Aggregate pada biosemen gigi. Pada penelitian ini, kalsium silikat diperoleh melalui dua tahap proses, yaitu isolasi silika dari abu sekam padi dengan metode sol-gel, dan pereaksian antara silika dan kalsium oksida. Silika dan kalsium oksida direaksikan pada rasio mol antara silika terhadap kalsium oksida sebesar 7:3, 6:4, 4:6, dan 3:7. Silika hasil isolasi dikarakterisasi distribusi ukuran dan komposisi unsurnya masing-masing dengan Particle Size Analyzer (PSA) dan EDS. Pembentukan kalsium silikat dan distribusi ukurannya dari tahap sintesis ditentukan dengan XRD dan PSA. Hasil penelitian menunjukkan bahwa pada tahap isolasi silika dari abu sekam padi dengan metode sol-gel diperoleh silika dengan kadar dan ukuran partikel rata-rata berturut-turut sebesar 71,6% dan 52,82 mm. Sedangkan kondisi optimum dari sintesis kalsium silikat dicapai pada rasio mol silika terhadap kalsium oksida sebesar 4:6. Pada rasio mol tersebut diperoleh kalsium silikat jenis b-dikalsium silikat dengan ukuran partikel rata-rata 102,2 mm

Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1

Peer reviewedPublisher PD

Coding by Choice: A Transitional Analysis of Social Participation Patterns and Programming Contributions in the Online Scratch Community

While massive online communities have drawn the attention of researchers and educators on their potential to support active collaborative work, knowledge sharing, and user-generated content, few studies examine participation in these communities at scale. The little research that does exist attends almost solely to adults rather than communities to support youths’ learning and identity development. In this chapter, we tackle two challenges related to understanding social practices that support learning in massive social networking forums where users engage in design. We examined a youth programmer community, called Scratch.mit.edu, that garners the voluntary participation of millions of young people worldwide. We report on site-wide distributions and patterns of participation that illuminate the relevance of different online social practices to ongoing involvement in the online community. Drawing on a random sample of more than 5000 active users of Scratch.mit.edu over a 3-month time period in early 2012, we examine log files that captured the frequency of three types of social practices that contribute to enduring participation: DIY participatory activities, socially supportive actions, and socially engaging interactions. Using latent transition analysis, we found (1) distinct patterns of participation (classes) across three time points (e.g., high networkers who are generally active, commenters who focus mainly on social participation, downloaders engaging in DIY participatory activities), (2) unique migration changes in class membership across time, (3) relatively equal gender representation across these classes, and (4) importance of membership length (or age) in terms of class memberships. In the discussion, we review our approach to analysis and outline implications for the design and study of online communities and tools for youth

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

Metazoan genomes encode hundreds of RNA-binding proteins (RBPs). These proteins regulate post-transcriptional gene expression and have critical roles in numerous cellular processes including mRNA splicing, export, stability and translation. Despite their ubiquity and importance, the binding preferences for most RBPs are not well characterized. In vitro and in vivo studies, using affinity selection-based approaches, have successfully identified RNA sequence associated with specific RBPs; however, it is difficult to infer RBP sequence and structural preferences without specifically designed motif finding methods. In this study, we introduce a new motif-finding method, RNAcontext, designed to elucidate RBP-specific sequence and structural preferences with greater accuracy than existing approaches. We evaluated RNAcontext on recently published in vitro and in vivo RNA affinity selected data and demonstrate that RNAcontext identifies known binding preferences for several control proteins including HuR, PTB, and Vts1p and predicts new RNA structure preferences for SF2/ASF, RBM4, FUSIP1 and SLM2. The predicted preferences for SF2/ASF are consistent with its recently reported in vivo binding sites. RNAcontext is an accurate and efficient motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures

Search for a Technicolor omega_T Particle in Events with a Photon and a b-quark Jet at CDF

If the Technicolor omega_T particle exists, a likely decay mode is omega_T -> gamma pi_T, followed by pi_T -> bb-bar, yielding the signature gamma bb-bar. We have searched 85 pb^-1 of data collected by the CDF experiment at the Fermilab Tevatron for events with a photon and two jets, where one of the jets must contain a secondary vertex implying the presence of a b quark. We find no excess of events above standard model expectations. We express the result of an exclusion region in the M_omega_T - M_pi_T mass plane.Comment: 14 pages, 2 figures. Available from the CDF server (PS with figs): http://www-cdf.fnal.gov/physics/pub98/cdf4674_omega_t_prl_4.ps FERMILAB-PUB-98/321-

Measurement of the B0 anti-B0 oscillation frequency using l- D*+ pairs and lepton flavor tags

The oscillation frequency Delta-md of B0 anti-B0 mixing is measured using the partially reconstructed semileptonic decay anti-B0 -> l- nubar D*+ X. The data sample was collected with the CDF detector at the Fermilab Tevatron collider during 1992 - 1995 by triggering on the existence of two lepton candidates in an event, and corresponds to about 110 pb-1 of pbar p collisions at sqrt(s) = 1.8 TeV. We estimate the proper decay time of the anti-B0 meson from the measured decay length and reconstructed momentum of the l- D*+ system. The charge of the lepton in the final state identifies the flavor of the anti-B0 meson at its decay. The second lepton in the event is used to infer the flavor of the anti-B0 meson at production. We measure the oscillation frequency to be Delta-md = 0.516 +/- 0.099 +0.029 -0.035 ps-1, where the first uncertainty is statistical and the second is systematic.Comment: 30 pages, 7 figures. Submitted to Physical Review

Search for New Particles Decaying to top-antitop in proton-antiproton collisions at squareroot(s)=1.8 TeV

We use 106 \ipb of data collected with the Collider Detector at Fermilab to search for narrow-width, vector particles decaying to a top and an anti-top quark. Model independent upper limits on the cross section for narrow, vector resonances decaying to \ttbar are presented. At the 95% confidence level, we exclude the existence of a leptophobic \zpr boson in a model of topcolor-assisted technicolor with mass M_{\zpr} $<$ 480 \gev for natural width $\Gamma$ = 0.012 M_{\zpr}, and M_{\zpr} $<$ 780 \gev for $\Gamma$ = 0.04 M_{\zpr}.Comment: The CDF Collaboration, submitted to PRL 25-Feb-200

A Measurement of the Differential Dijet Mass Cross Section in p-pbar Collisions at sqrt{s}=1.8 TeV

We present a measurement of the cross section for production of two or more jets as a function of dijet mass, based on an integrated luminosity of 86 pb^-1 collected with the Collider Detector at Fermilab. Our dijet mass spectrum is described within errors by next-to-leading order QCD predictions using CTEQ4HJ parton distributions, and is in good agreement with a similar measurement from the D0 experiment.Comment: 18 pages including 2 figures and 3 tables. Submitted to Phys. Rev. D Rapid Communication