Simultaneous precise editing of multiple genes in human cells

Abstract. When double-strand breaks are introduced in a genome by CRISPR they are repaired either by non-homologous end joining (NHEJ), which often results i

FSK Demodulator- Case Study of PLL Application

FSK Demodulator, one of the applications of PLL has been implemented using both hardware and software. Results are found to be similar and based on these results it is believed that this will contribute for the improvement in performance and reliability for future communication systems. Hence this will also contribute to the development of higher reliability of the systems

A Systematic Study of Projection Biases in Weak Lensing Analysis

We present a systematic study of projection biases in the weak lensing analysis of the first year of data from the Dark Energy Survey (DES) experiment. In the analysis we used a $\Lambda$CDM model and three two-point correlation functions. We show that these biases are a consequence of projecting, or marginalizing, over parameters like $h$, $\Omega_b$, $n_s$ and $\Omega_\nu h^2$ that are both poorly constrained and correlated with the parameters of interest like $\Omega_m$, $\sigma_8$ and $S_8$. Covering the relevant parameter space we show that the projection biases are a function of where the true values of the poorly constrained parameters lie with respect to the parameter priors. For example, biases in the position of the posteriors can exceed the 1.5$\sigma$ level if the true values of $h$ and $n_s$ are close to the top of the prior's range and the true values of $\Omega_b$ and $\Omega_\nu h^2$ are close to the bottom of the range of their priors. We also show that in some cases the 1D credible intervals can be over-specified by as much as 30% and coverage can be as low as 27%. Finally we estimate these projection biases for the analysis of three and six years worth of DES data

Some like it cold: understanding the survival strategies of psychrophiles

Much of the Earth's surface, both marine and terrestrial, is either periodically or permanently cold. Although habitats that are largely or continuously frozen are generally considered to be inhospitable to life, psychrophilic organisms have managed to survive in these environments. This is attributed to their innate adaptive capacity to cope with cold and its associated stresses. Here, we review the various environmental, physiological and molecular adaptations that psychrophilic microorganisms use to thrive under adverse conditions. We also discuss the impact of modern “omic” technologies in developing an improved understanding of these adaptations, highlighting recent work in this growing field.http://embor.embopress.org/content/15/5/508hb201

CADD: predicting the deleteriousness of variants throughout the human genome

Combined Annotation-Dependent Depletion (CADD) is a widely used measure of variant deleteriousness that can effectively prioritize causal variants in genetic analyses, particularly highly penetrant contributors to severe Mendelian disorders. CADD is an integrative annotation built from more than 60 genomic features, and can score human single nucleotide variants and short insertion and deletions anywhere in the reference assembly. CADD uses a machine learning model trained on a binary distinction between simulated de novo variants and variants that have arisen and become fixed in human populations since the split between humans and chimpanzees; the former are free of selective pressure and may thus include both neutral and deleterious alleles, while the latter are overwhelmingly neutral (or, at most, weakly deleterious) by virtue of having survived millions of years of purifying selection. Here we review the latest updates to CADD, including the most recent version, 1.4, which supports the human genome build GRCh38. We also present updates to our website that include simplified variant lookup, extended documentation, an Application Program Interface and improved mechanisms for integrating CADD scores into other tools or applications. CADD scores, software and documentation are available at https://cadd.gs.washington.edu

Complement C3d Conjugation to Anthrax Protective Antigen Promotes a Rapid, Sustained, and Protective Antibody Response

B. anthracis is the causative agent of anthrax. Pathogenesis is primarily mediated through the exotoxins lethal factor and edema factor, which bind protective antigen (PA) to gain entry into the host cell. The current anthrax vaccine (AVA, Biothrax™) consists of aluminum-adsorbed cell-free filtrates of unencapsulated B. anthracis, wherein PA is thought to be the principle target of neutralization. In this study, we evaluated the efficacy of the natural adjuvant, C3d, versus alum in eliciting an anti-PA humoral response and found that C3d conjugation to PA and emulsion in incomplete Freund's adjuvant (IFA) imparted superior protection from anthrax challenge relative to PA in IFA or PA adsorbed to alum. Relative to alum-PA, immunization of mice with C3d-PA/IFA augmented both the onset and sustained production of PA-specific antibodies, including neutralizing antibodies to the receptor-binding portion (domain 4) of PA. C3d-PA/IFA was efficacious when administered either i.p. or s.c., and in adolescent mice lacking a fully mature B cell compartment. Induction of PA-specific antibodies by C3d-PA/IFA correlated with increased efficiency of germinal center formation and plasma cell generation. Importantly, C3d-PA immunization effectively protected mice from intranasal challenge with B. anthracis spores, and was approximately 10-fold more effective than alum-PA immunization or PA/IFA based on dose challenge. These data suggest that incorporation of C3d as an adjuvant may overcome shortcomings of the currently licensed aluminum-based vaccine, and may confer protection in the early days following acute anthrax exposure

Dark Energy Survey year 3 results: Constraints on cosmological parameters and galaxy-bias models from galaxy clustering and galaxy-galaxy lensing using the redMaGiC sample

We constrain cosmological parameters and galaxy-bias parameters using the combination of galaxy clustering and galaxy-galaxy lensing measurements from the Dark Energy Survey (DES) year-3 data. We describe our modeling framework and choice of scales analyzed, validating their robustness to theoretical uncertainties in small-scale clustering by analyzing simulated data. Using a linear galaxy-bias model and redMaGiC galaxy sample, we obtain 10% constraints on the matter density of the Universe. We also implement a nonlinear galaxy-bias model to probe smaller scales that includes parametrization based on hybrid perturbation theory and find that it leads to a 17% gain in cosmological constraining power. We perform robustness tests of our methodology pipeline and demonstrate stability of the constraints to changes in the theory model. Using the redMaGiC galaxy sample as foreground lens galaxies and adopting the best-fitting cosmological parameters from DES year-1 data, we find the galaxy clustering and galaxy-galaxy lensing measurements to exhibit significant signals akin to decorrelation between galaxies and mass on large scales, which is not expected in any current models. This likely systematic measurement error biases our constraints on galaxy bias and the S8 parameter. We find that a scale-, redshift-and sky-Area-independent phenomenological decorrelation parameter can effectively capture this inconsistency between the galaxy clustering and galaxy-galaxy lensing. We trace the source of this correlation to a color-dependent photometric issue and minimize its impact on our result by changing the selection criteria of redMaGiC galaxies. Using this new sample, our constraints on the S8 parameter are consistent with previous studies and we find a small shift in the ωm constraints compared to the fiducial redMaGiC sample. We infer the constraints on the mean host-halo mass of the redMaGiC galaxies in this new sample from the large-scale bias constraints, finding the galaxies occupy halos of mass approximately 1.6×10 13 M⊙/h

Dark Energy Survey Year 3 results: Cosmology from cosmic shear and robustness to data calibration

This work, together with its companion paper, Secco, Samuroff et al. [Phys. Rev. D 105, 023515 (2022)PRVDAQ2470-001010.1103/PhysRevD.105.023515], present the Dark Energy Survey Year 3 cosmic-shear measurements and cosmological constraints based on an analysis of over 100 million source galaxies. With the data spanning 4143 deg2 on the sky, divided into four redshift bins, we produce a measurement with a signal-to-noise of 40. We conduct a blind analysis in the context of the Lambda-Cold Dark Matter (ΛCDM) model and find a 3% constraint of the clustering amplitude, S8σ8(ωm/0.3)0.5=0.759-0.023+0.025. A ΛCDM-Optimized analysis, which safely includes smaller scale information, yields a 2% precision measurement of S8=0.772-0.017+0.018 that is consistent with the fiducial case. The two low-redshift measurements are statistically consistent with the Planck Cosmic Microwave Background result, however, both recovered S8 values are lower than the high-redshift prediction by 2.3σ and 2.1σ (p-values of 0.02 and 0.05), respectively. The measurements are shown to be internally consistent across redshift bins, angular scales and correlation functions. The analysis is demonstrated to be robust to calibration systematics, with the S8 posterior consistent when varying the choice of redshift calibration sample, the modeling of redshift uncertainty and methodology. Similarly, we find that the corrections included to account for the blending of galaxies shifts our best-fit S8 by 0.5σ without incurring a substantial increase in uncertainty. We examine the limiting factors for the precision of the cosmological constraints and find observational systematics to be subdominant to the modeling of astrophysics. Specifically, we identify the uncertainties in modeling baryonic effects and intrinsic alignments as the limiting systematics

Dark Energy Survey Year 3 Results: Cosmology from Cosmic Shear and Robustness to Modeling Uncertainty

This work and its companion paper, Amon et al. [Phys. Rev. D 105, 023514 (2022)], present cosmic shear measurements and cosmological constraints from over 100 million source galaxies in the Dark Energy Survey (DES) Year 3 data. We constrain the lensing amplitude parameter S 8 ≡ σ 8 √ Ω m / 0.3 at the 3% level in Λ CDM : S 8 = 0.75 9 + 0.025 − 0.023 (68% CL). Our constraint is at the 2% level when using angular scale cuts that are optimized for the Λ CDM analysis: S 8 = 0.77 2 + 0.018 − 0.017 (68% CL). With cosmic shear alone, we find no statistically significant constraint on the dark energy equation-of-state parameter at our present statistical power. We carry out our analysis blind, and compare our measurement with constraints from two other contemporary weak lensing experiments: the Kilo-Degree Survey (KiDS) and Hyper-Suprime Camera Subaru Strategic Program (HSC). We additionally quantify the agreement between our data and external constraints from the Cosmic Microwave Background (CMB). Our DES Y3 result under the assumption of Λ CDM is found to be in statistical agreement with Planck 2018, although favors a lower S 8 than the CMB-inferred value by 2.3 σ (a p -value of 0.02). This paper explores the robustness of these cosmic shear results to modeling of intrinsic alignments, the matter power spectrum and baryonic physics. We additionally explore the statistical preference of our data for intrinsic alignment models of different complexity. The fiducial cosmic shear model is tested using synthetic data, and we report no biases greater than 0.3 σ in the plane of S 8 × Ω m caused by uncertainties in the theoretical models