The rockefeller university

The Agrobacterium Ti plasmid (T-DNA) 6b proteins interact with many different host proteins implicated in plant cell proliferation. Here, we show that Arabidopsis plants overexpressing 6b display microRNA (miRNA) deficiency by directly targeting SERRATE and AGO1 via a specific loop fragment (residues 40-55). In addition, we report the crystal structures of Agrobacterium tumefaciens AK6b at 2.1 angstrom, Agrobacterium vitis AB6b at 1.65 angstrom, and Arabidopsis ADP ribosylation factor (ARF) at 1.8 angstrom. The 6b structure adopts an ADP-ribosylating toxin fold closely related to cholera toxin. In vitro ADP ribosylation analysis demonstrates that 6b represents a new toxin family, with Tyr 66, Thr 93, and Tyr 153 as the ADP ribosylation catalytic residues in the presence of Arabidopsis ARF and GTP. Our work provides molecular insights, suggesting that 6b regulates plant cell growth by the disturbance of the miRNA pathway through its ADP ribosylation activity.

The results of the first search for long-lived gluinos produced in 7 TeV pp collisions at the CERN Large Hadron Collider are presented. The search looks for evidence of long-lived particles that stop in the CMS detector and decay in the quiescent periods between beam crossings. In a dataset with a peak instantaneous luminosity of 1 x 10(32) cm(-2) s(-1), an integrated luminosity of 10 pb(-1), and a search interval corresponding to 62 hours of LHC operation, no significant excess above background was observed. Limits at the 95% confidence level on gluino pair production over 13 orders of magnitude of gluino lifetime are set. For a mass difference m((g) over tilde) - m((chi) over tilde1)(0) >100 GeV/c(2), and assuming BR((g) over tilde -> g<(chi over bar>(0)(1)) = 100%, m((g) over tilde) < 370 GeV/c(2) are excluded for lifetimes from 10 mu s to 1000 s.

The Division of Birds, National Museum of Natural History, Smithsonian Institution in Washington, DC, has obtained and released DNA barcodes for 2,808 frozen tissue samples. Of the 1,403 species represented by these samples, 1,147 species have not been barcoded previously. This data release increases the number of bird species with standard barcodes by 91%. These records meet the data standard of the Consortium for the Barcode of Life and they have the reserved keyword BARCODE in GenBank. The data are now available on GenBank and the Barcode of Life Data Systems.

Pathologic rheumatoid factor (RF) levels are hallmarks of several human diseases. Production of monoclonal RF in vitro is essential for studies of the antigenic specificities of RF, as well as for a dissection of the mechanisms of aberrant RF+ B cell activation. We have expanded upon previous methods to develop a flow cytometry-based method to efficiently clone monoclonal antibodies (mAbs) from humans with expansions of RF-like, immunoglobulin heavy chain variable region (IgVH) 1-69 gene segment-containing B cells. The cloned variable regions are expressed as IgM and produced during culture at concentrations between 5 and 20 mu g/ml. Using this system, we show that clonal Igs from patients with HCV-related mixed cryoglobulinemia, when expressed as IgM, have RF activity. We anticipate that this system will be useful for the cloning and expression of mAbs partially encoded by VH1-69 and for determination of the reactivity patterns of polyspecific, low-affinity IgMs of human pathogenic importance. (C) 2010 Elsevier B.V. All rights reserved.

Background: Comparing a patient's bleeding symptoms with those of healthy individuals is an important component of the diagnosis of bleeding disorders, but little is known about whether bleeding symptoms in healthy individuals vary by sex, race, ethnicity, age, or aspirin use. Objectives, Patients/Methods: We developed a comprehensive, ontology-backed, Web-based questionnaire to collect bleeding histories from 500 healthy adults. The mean age was 43 years (range 19-86 years), 63% were female, 19% were Hispanic, 37% were African-American, 43% were Caucasian, 8% were Asian, and 4% were multiracial. Results: 18 of the 36 symptoms captured occurred with < 5% frequency, and 26% of participants reported no bleeding symptoms (range 0-19 symptoms). Differences in sex, race, ethnicity, aspirin use and age accounted for only 6-13% of the variability in symptoms. Although men reported fewer symptoms than women (median 1 vs. 2, P < 0.01), there was no difference when sex-specific questions were excluded (median 1 for both men and women, P = 0.50). However, women reported more easy bruising (24% vs. 7%, P < 0.01) and venipuncture-related bruising (10% vs. 3%, P = 0.02). The number of symptoms did not vary by race or age, but epistaxis was reported more frequently by Caucasians than by African-Americans (29% vs. 18%, P = 0.02), and epistaxis frequency decreased with age (odds ratio 0.97 per year, P < 0.01). Paradoxically, infrequent aspirin users reported more bruising and heavy menses than frequent users (21% vs. 8%, P = 0.01, and 56% vs. 38%, P = 0.03, respectively). Conclusions: Our findings provide a contemporaneous and comprehensive description of bleeding symptoms in a diverse group of healthy individuals. Our Web-based system is freely available to other investigators.

Background: Accurate genetic maps are required for successful and efficient linkage mapping of disease genes. However, most available genome-wide genetic maps were built using only small collections of pedigrees, and therefore have large sampling errors. A large set of genetic studies genotyped by the NHLBI Mammalian Genotyping Service (MGS) provide appropriate data for generating more accurate maps. Results: We collected a large sample of uncleaned genotype data for 461 markers generated by the MGS using the Weber screening sets 9 and 10. This collection includes genotypes for over 4,400 pedigrees containing over 17,000 genotyped individuals from different populations. We identified and cleaned numerous relationship and genotyping errors, as well as verified the marker orders. We used this dataset to test for population-specific genetic maps, and to re-estimate the genetic map distances with greater precision; standard errors for all intervals are provided. The map-interval sizes from the European (or European descent), Chinese, and Hispanic samples are in quite good agreement with each other. We found one map interval on chromosome 8p with a statistically significant size difference between the European and Chinese samples, and several map intervals with significant size differences between the African American and Chinese samples. When comparing Palauan with European samples, a statistically significant difference was detected at the telomeric region of chromosome 11p. Several significant differences were also identified between populations in chromosomal and genome lengths. Conclusions: Our new population-specific screening set maps can be used to improve the accuracy of disease-mapping studies. As a result of the large sample size, the average length of the 95% confidence interval (CI) for a 10 cM map interval is only 2.4 cM, which is considerably smaller than on previously published maps.

Background: MicroRNAs are short (similar to 22 nt) non-coding regulatory RNAs that control gene expression at the post-transcriptional level. Here the functional impact of microRNAs on cell cycle arrest during neuronal lineage differentiation of unrestricted somatic stem cells from human cord blood (USSC) was analyzed. Methodology/Principal Findings: Expression profiling revealed downregulation of microRNAs miR-17, -20a, and -106b in USSC differentiated into neuronal lineage but not in USSC differentiated into osteogenic lineage. Transfection experiments followed by Ki67 immunostainings demonstrated that each of these microRNAs was able to promote proliferation of native USSC and to prevent in part cell cycle arrest during neuronal lineage differentiation of USSC. Bioinformatic target gene predictions followed by experimental target gene validations revealed that miR-17, -20a, and -106b act in a common manner by downregulating an overlapping set of target genes mostly involved in regulation and execution of G(1)/S transition. Pro-proliferative target genes cyclinD1 (CCND1) and E2F1 as well as anti-proliferative targets CDKN1A (p21), PTEN, RB1, RBL1 (p107), RBL2 (p130) were shown as common targets for miR-17, -20a, and -106b. Furthermore, these microRNAs also downregulate WEE1 which is involved in G(2)/M transition. Most strikingly, miR-17, -20a, and -106b were found to promote cell proliferation by increasing the intracellular activity of E2F transcription factors, despite the fact that miR-17, 20a, and -106b directly target the transcripts that encode for this protein family. Conclusions/Significance: Mir-17, -20a, and -106b downregulate a common set of pro-and anti-proliferative target genes to impact cell cycle progression of USSC and increase intracellular activity of E2F transcription factors to govern G(1)/S transition.

Multiple levels of control are in play to regulate pluripotency and differentiation in human embryonic stem cells (hESCs). At the transcriptional level, the core factors OCT4, NANOG and SOX2 form a positive autoregulatory loop that is pivotal for maintaining the undifferentiated state. At the post-transcriptional level, microRNAs (miRNAs) belonging to the miR-302 family are emerging as key players in the control of proliferation and cell fate determination during differentiation. Here, we show that the transcriptional factors OCT4 and NR2F2 (COUP-TFII) and the miRNA miR-302 are linked in a regulatory circuitry that critically regulate both pluripotency and differentiation in hESCs. In the undifferentiated state, both OCT4 and the OCT4-induced miR-302 directly repress NR2F2 at the transcriptional and post-transcriptional level, respectively. Conversely, NR2F2 directly inhibits OCT4 during differentiation, triggering a positive feedback loop for its own expression. In addition, we show that regulation of NR2F2 activity itself relies on alternative splicing and transcriptional start site choice to generate a full-length transcriptionally active isoform and shorter variants, which enhance the activity of the long isoform. During hESC differentiation, NR2F2 is first detected at the earliest steps of neural induction and thus is among the earliest human embryonic neural markers. Finally, our functional analysis points to a crucial role for NR2F2 in the activation of neural genes during early differentiation in humans. These findings introduce a new molecular player in the context of early embryonic stem cell state and cell fate determination in humans. The EMBO Journal (2011) 30, 237-248. doi:10.1038/emboj.2010.319; Published online 10 December 2010