The rockefeller university

Since their discovery more than two decades ago, animal long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes. Recently, a large number of lncRNAs have also been identified in higher plants, and here, we review their identification, classification and known regulatory functions in various developmental events and stress responses. Knowledge gained from a deeper understanding of this special group of noncoding RNAs may lead to biotechnological improvement of crops. Some possible examples in this direction are discussed.

Proteins are acylated by a variety of metabolites that regulates many important cellular pathways in all kingdoms of life. Acyl groups in cells can vary in structure from the smallest unit, acetate, to modified long-chain fatty acids, all of which can be activated and covalently attached to diverse amino acid side chains and consequently modulate protein function. For example, acetylation of Lys residues can alter the charge state of proteins and generate new recognition elements for protein-protein interactions. Alternatively, long-chain fatty-acylation targets proteins to membranes and enables spatial control of cell signalling. To facilitate the analysis of protein acylation in biology, acyl analogues bearing alkyne or azide tags have been developed that enable fluorescent imaging and proteomic profiling of modified proteins using bioorthogonal ligation methods. Herein, we summarize the currently available acylation chemical reporters and highlight their utility to discover and quantify the roles of protein acylation in biology.

One of the most striking properties of the adult central nervous system is its ability to undergo changes in function and/or structure. In mammals, learning is a major inducer of adaptive plasticity. Sensorimotor adaptation is a type of proceduralmotorlearning that allows maintaining accurate movements in the presence of environmental or internal perturbations by adjusting motor output. In this work, we will review experimental evidence gathered from rodents and human and nonhuman primates pointing to possible sites of adaptation-related plasticity at different levels of organization of the nervous system.

Next-generation sequencing is transforming our understanding of human genetic variation but assessing the functional impact of novel variants presents challenges. We analyzed missense variants in the integrin alpha IIb beta 3 receptor subunit genes ITGA2B and ITGB3 identified by whole-exome or -genome sequencing in the Thrombo-Genomics project, comprising similar to 32,000 alleles from 16,108 individuals. We analyzed the results in comparison with 111 missense variants in these genes previously reported as being associated with Glanzmann thrombasthenia (GT), 20 associated with alloimmune thrombocytopenia, and 5 associated with aniso/macrothrombocytopenia. We identified 114 novel missense variants in ITGA2B (affecting similar to 11% of the amino acids) and 68 novel missense variants in ITGB3 (affecting similar to 9% of the amino acids). Of the variants, 96% had minor allele frequencies (MAF) < 0.1%, indicating their rarity. Based on sequence conservation, MAF, and location on a complete model of alpha IIb beta 3, we selected three novel variants that affect amino acids previously associated with GT for expression in HEK293 cells. alpha IIb P176H and beta 3 C547G severely reduced alpha IIb beta 3 expression, whereas aIIb P943A partially reduced alpha IIb beta 3 expression and had no effect on fibrinogen binding. We used receiver operating characteristic curves of combined annotation-dependent depletion, Polyphen 2-HDIV, and sorting intolerant from tolerant to estimate the percentage of novel variants likely to be deleterious. At optimal cut-off values, which had 69-98% sensitivity in detecting GT mutations, between 27% and 71% of the novel aIIb or beta 3 missense variants were predicted to be deleterious. Our data have implications for understanding the evolutionary pressure on alpha IIb beta 3 and highlight the challenges in predicting the clinical significance of novel missense variants.

The mosquito Aedes aegypti is a potent vector of the chikungunya, yellow fever, and dengue viruses, responsible for hundreds of millions of infections and over 50,000 human deaths per year. Mutagenesis in Ae. aegypti has been established with TALENs, ZFNs, and homing endonucleases, which require the engineering of DNA-binding protein domains to provide genomic target sequence specificity. Here, we describe the use of the CRISPRCas9 system to generate site-specific mutations in Ae. aegypti. This system relies on RNA-DNA basepairing to generate targeting specificity, resulting in efficient and flexible genome-editing reagents. We investigate the efficiency of injection mix compositions, demonstrate the ability of CRISPR-Cas9 to generate different types of mutations via disparate repair mechanisms, and report stable germline mutations in several genomic loci. This work offers a detailed exploration into the use of CRISPR-Cas9 in Ae. aegypti that should be applicable to nonmodel organisms previously out of reach of genetic modification.

Multidrug-resistant (MDR) HIV-1 viruses are thought to be less pathogenic than wild-type viruses because of the fitness costs of drug-resistance mutations. However, we identified an individual infected with MDR virus associated with rapid disease progression referred to as MDR-1. To study the contribution of virologic factors to rapid disease progression, we constructed molecular clones that demonstrated high replication fitness and cytopathicity. To dissect determinants of enhanced fitness of a cytopathic clone, pMDR-1c, we divided its genome into 2 parts: the envelope (gp160) and the remaining backbone genome, and constructed mutual chimeric viruses with a reference, wildtype virus clone, pNL4-3. The growth competition assay indicated that pMDR-1c has high fitness (1.62), although its envelope confers remarkably enhanced fitness (2.29) and its backbone confers reduced fitness (0.56) as compared with pNL4-3. We also performed a similar study with a less cytopathic pMDR-5a, a molecular clone derived from another subject MDR-5, infected with MDR HIV-1, and associated with slower clinical progression. The results indicated that pMDR-5a has reduced fitness (0.82), although its envelope confers enhanced fitness (1.64) and its backbone confers reduced fitness (0.49), a fitness pattern compatible with envelope-mediated fitness compensation. These results suggest that the viral envelope may be a major determinant of the enhanced fitness of the MDR HIV-1 variant isolated from a patient with rapid disease progression. Furthermore, we speculate that compensation conferred by envelope may be a mechanism by which MDR HIV-1 maintains overall fitness despite the presence of changes in pol, which reduce replication capacity.

Drawing upon the American Pragmatic tradition in philosophy and the more recent work of philosopher Karen Barad, this paper examines how scientific problems are both obscured, and resolved by our use of language describing the natural world. Using the example of the immune response engendered by neural implants inserted in the brain, the author explains how this discourse has been altered by the advent of nanotechnology methods and devices which offer putative remedies that might temper the immune response in the central nervous system. This emergent nanotechnology has altered this problem space and catalyzed one scientific community to acknowledge a material reality that was always present, if not fully acknowledged.

Background: Immunoglobulin class-switch recombination defects (CSR-D) are rare primary immunodeficiencies characterized by impaired production of switched immunoglobulin isotypes and normal or elevated IgM levels. They are caused by impaired T:B cooperation or intrinsic B cell defects. However, many immunoglobulin CSR-Ds are still undefined at the molecular level. Objective: This study's objective was to delineate new causes of immunoglobulin CSR-Ds and thus gain further insights into the process of immunoglobulin class-switch recombination (CSR). Methods: Exome sequencing in 2 immunoglobulin CSR-D patients identified variations in the INO80 gene. Functional experiments were performed to assess the function of INO80 on immunoglobulin CSR. Results: We identified recessive, nonsynonymous coding variations in the INO80 gene in 2 patients affected by defective immunoglobulin CSR. Expression of wild-type INO80 in patients' fibroblastic cells corrected their hypersensitivity to high doses of gamma-irradiation. In murine CH12-F3 cells, the INO80 complex accumulates at Sa and Em regions of the IgH locus, and downregulation of INO80 as well as its partners Reptin and Pontin impaired CSR. In addition, Reptin and Pontin were shown to interact with activation-induced cytidine deaminase. Finally, an abnormal separation of sister chromatids was observed upon INO80 downregulation in CH12-F3 cells, pinpointing its role in cohesin activity. Conclusion: INO80 deficiency appears to be associated with defective immunoglobulin CSR. We propose that the INO80 complex modulates cohesin function that may be required during immunoglobulin switch region synapsis.

A search is performed for long-lived particles that decay into final states that include a pair of electrons or a pair of muons. The experimental signature is a distinctive topology consisting of a pair of charged leptons originating from a displaced secondary vertex. Events corresponding to an integrated luminosity of 19.6 (20.5) fb(-1) in the electron (muon) channel were collected with the CMS detector at the CERN LHC in proton-proton collisions at root s TeV. No significant excess is observed above standard model expectations. Upper limits on the product of the cross section and branching fraction of such a signal are presented as a function of the long-lived particle's mean proper decay length. The limits are presented in an approximately model-independent way, allowing them to be applied to a wide class of models yielding the above topology. Over much of the investigated parameter space, the limits obtained are the most stringent to date. In the specific case of a model in which a Higgs boson in the mass range 125-1000 GeV/c(2) decays into a pair of long-lived neutral bosons in the mass range 20-350 GeV= c(2), each of which can then decay to dileptons, the upper limits obtained are typically in the range 0.2-10 fb for mean proper decay lengths of the long-lived particles in the range 0.01-100 cm. In the case of the lowest Higgs mass considered (125 GeV/c(2)), the limits are in the range 2-50 fb. These limits are sensitive to Higgs boson branching fractions as low as 10(-1).

Kinetochore (KT) localization of mitotic checkpoint proteins is essential for their function during mitosis. hSpindly KT localization is dependent on the RZZ complex and hSpindly recruits the dynein-dynactin complex to KTs during mitosis, but the mechanism of hSpindly KT recruitment is unknown. Through domain-mapping studies we characterized the KT localization domain of hSpindly and discovered it undergoes farnesylation at the C-terminal cysteine residue. The N-terminal 293 residues of hSpindly are dispensable for its KT localization. Inhibition of farnesylation using a farnesyl transferase inhibitor (FTI) abrogated hSpindly KT localization without affecting RZZ complex, CENP-E, and CENP-F KT localization. We showed that hSpindly is farnesylated in vivo and farnesylation is essential for its interaction with the RZZ complex and hence KT localization. FTI treatment and hSpindly knockdown displayed the same mitotic phenotypes, indicating that hSpindly is a key FTI target in mitosis. Our data show a novel role of lipidation in targeting a checkpoint protein to KTs through protein-protein interaction.