Mental Health In College Students: Disclosure & Seeking Support

A study was conducted through Bridgewater State University in order to better understand the mental health and help seeking behaviors of college students. The data collected served to provide information regarding what specific types of mental health difficulties are reported by college students

Discovery and characterization of Cas13b, a differentially regulated RNA-targeting CRISPR system

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 129-144).RNA plays a significant role in human biology and disease, not only as messenger RNA encoding proteins but also as noncoding RNA regulating DNA, proteins, and other RNA species. Until recently, it has been challenging to target RNA in a simple, efficient manner. CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) systems, which confer adaptive immunity to prokaryotes, have revolutionized DNA targeting through the engineering of RNA-programmable Cas9-based tools. Effective RNA-programmable RNA-targeting tools would likewise transform RNA biology and biotechnology. Class 2 CRISPR-Cas systems, which rely only on a single effector protein and programmable CRISPR RNA (crRNA) to target nucleic acids, represent the most promising tool to target RNA. Building on previous research, a biocomputational pipeline was developed to discover novel functional class 2 CRISPR systems lacking the canonical adaptive machinery of Cas1 and Cas2 at their genomic loci. Out of this pipeline emerged the class 2 CRISPR-Cas RNA-targeting system, VI-B (Cas13b with accessory Csx27/Csx28). Cas13b was characterized both biochemically and genetically, and found to be differentially regulated--inhibited by Csx27 in VI-B1 systems and enhanced by Csx28 in VI-B2 systems. RNA-targeting rules are critical to tool development, and so an E. coli essential gene screen was conducted and analyzed to assess the RNA sequence and structure requirements for targeting. The completion of this work advances both knowledge in the CRISPR field and possibilities in the RNA-targeting toolkit.by Aaron Andrew Smargon.Ph. D

Detection of intrinsic cluster alignments to 100 Mpc/h in the SDSS

We measure the large-scale intrinsic alignments of galaxy clusters in the Sloan Digital Sky Survey (SDSS) using subsets of two cluster catalogues: 6625 clusters with 0.1<z<0.3 from the maxBCG cluster catalogue (Koester et al. 2007, 7500 sq. deg.), and 8081 clusters with 0.08<z<0.44 from the Adaptive Matched Filter catalogue (Dong et al. 2008, 6500 sq. deg.). We search for two types of cluster alignments using pairs of clusters: the alignment between the projected major axes of the clusters (`correlation' alignment), and the alignment between one cluster major axis and the line connecting it to the other cluster in the pair (`pointing' alignment). In each case, we use the cluster member galaxy distribution as a tracer of the cluster shape. All measurements are carried out with each catalogue separately, to check for dependence on cluster selection procedure. We find a strong detection of the pointing alignment on scales up to 100 Mpc/h, at the 6 or 10-sigma level depending on the cluster selection algorithm used. The correlation alignment is only marginally detected up to ~20 Mpc/h, at the 2 or 2.5-sigma level. These results support our current theoretical understanding of galaxy cluster intrinsic alignments in the LCDM paradigm, although further work will be needed to understand the impact of cluster selection effects and observational measurement errors on the amplitude of the detection.Comment: 6 pages, 2 figures, submitted to MNRAS; minor revisions to address referee comments primarily in section 5, no changes to result

On the anisotropic density distribution on large scales

Motivated by the recent detection of an enhanced clustering signal along the major axis of haloes in N-body simulations, we derive a formula for the anisotropic density distribution around haloes and voids on large scales. Our model, which assumes linear theory and that the formation and orientation of nonlinear structures are strongly correlated with the Lagrangian shear, is in good agreement with measurements. We also show that the measured amplitude is inconsistent with a model in which the alignment is produced by the initial inertia rather than shear tensor.Comment: 6 pages, 3 figures; With a moderate revision of the original version, as published in MNRA

Modeling the Alignment Profile of Satellite Galaxies in Clusters

Analyzing the halo and galaxy catalogs from the Millennium simulations at redshifts $z=0,\ 0.5,\ 1$, we determine the alignment profiles of cluster galaxies by measuring the average alignments between the major axes of the pseudo inertia tensors from all satellites within cluster's virial radius and from only those satellites within some smaller radius as a function of the top-hat scale difference. The alignment profiles quantify how well the satellite galaxies retain the memory of the external tidal fields after merging into their host clusters and how fast they lose the initial alignment tendency as the cluster's relaxation proceeds. It is found that the alignment profile drops faster at higher redshifts and on smaller mass scales. This result is consistent with the picture that the faster merging of the satellites and earlier onset of the nonlinear effect inside clusters tend to break the preferential alignments of the satellites with the external tidal fields. Modeling the alignment profile of cluster galaxies as a power-law of the density correlation coefficient that is independent of the power spectrum normalization ($\sigma_{8}$) and demonstrating that the density correlation coefficient varies sensitively with the density parameter ($\Omega_{m}$) and neutrino mass fraction ($f_{\nu}$), we suggest that the alignment profile of cluster galaxies might be useful for breaking the $\Omega_{m}$-$\sigma_{8}$ and $f_{\nu}$-$\sigma_{8}$ degeneracies.Comment: accepted for publication in ApJ, Introduction and Conclusion sections improved, mistakes in plotting the figures corrected, detailed explanations for the dependence of the alignment profiles on the mass and redshift provided, 7 figures, 3 table

Remarks on the methods of investigations of alignment of galaxies

In the 1975 Hawley and Peebles gave the proposal to use three statistical tests for investigations of the galaxies orientation in the large structures. Nowadays, it has been considered as the standard method of searching for galactic alignments. In the present paper we analyzed the tests in details and proposed a few improvements. Basing on the improvements, the new method of analysis of the alignment of galaxies in clusters is proposed. The power of this method is demonstrated on the sample of 247 Abell clusters with at least 100 objects in each. The distributions of the position angles for galaxies in each cluster are analyzed using statistical tests: $\chi^2$, Fourier, autocorrelation and Kolmogorow test. The mean value of analyzed statistics is compared with theoretical predictions as well as with results obtained from numerical simulations. We performed 1000 simulations of 247 fictious clusters, each with numbers of galaxies the same as the real ones. We found that orientations of galaxies in analyzed clusters are not random i.e. that there exists an alignment of galaxies in rich Abell galaxy clusters.Comment: APJ accepted, Some references are missing in arXive and ADS - see PDF fil

Expanded search for ribonucleic acid-programmable genomic engineering effectors

Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2016.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 31-33).A biocomputational pipeline was designed and implemented to mine through metagenomic datasets for novel Class 2 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) single effectors, akin to the revolutionary genome-engineering tools Cas9 and Cpf1. Whereas previous search strategies relied on protein proximity to CRISPR-associated spacer acquisition proteins Cas1 and Cas2, this approach was seeded on CRISPR arrays alone. What resulted was the discovery of a potential new Class 2 CRISPR system, with two subtypes as characterized by distinct putative accessory proteins. Follow-up experimental work is required to assess the system's activity: first, in the presence and absence of the accessory protein; and second, as a single effector protein capable of precise genome engineering in prokaryotic and eukaryotic cells.by Aaron Andrew Smargon.S.M

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity. Using an E. coli essential gene screen, we demonstrate that Cas13b has a double-sided protospacer-flanking sequence and elucidate RNA secondary structure requirements for targeting. We also find that Csx27 represses, whereas Csx28 enhances, Cas13b-mediated RNA interference. Characterization of these CRISPR systems creates opportunities to develop tools to manipulate and monitor cellular transcripts.National Institute of General Medical Sciences (U.S.) (Award T32GM007753)National Institute of Mental Health (U.S.) (Award 5DP1-MH100706)National Institute of Mental Health (U.S.) (Award 1R01-MH110049

Diversity and evolution of class 2 CRISPR–Cas systems

Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas. Keywords: Bacterial evolution; Bacterial genetics; CRISPR-Cas systemsUS National Institute of Mental Health (Grant 5DP1-MH100706)US National Institute of Mental Health (Grant 1R01-MH110049