Search for: All records

This study presents a comprehensive benchmarking analysis of the Arm-based AmpereOne A192-32X CPU, a high-performance but low power processor designed for cloud-native workloads characterized by high core occupancy, imperfectly-vectorized or even pure scalar software, limited need for high floating-point performance, and, increasingly, AI inference. These traits also characterize much of academic research computing. Hence a thorough investigation of this novel CPU seeking to characterize its strengths and weaknesses on academic workloads, including traditional HPC codes for which it was not designed, will shed light on its relevance in a research setting. We report comparative analyses with contemporary CPUs (Intel Sapphire Rapids, AMD EPYC, NVIDIA Grace-Grace) and illustrate AmpereOne’s architectural advantages in handling parallel workloads and optimizing power consumption. The CPUs are compared in terms of performance and power consumption using a wide range of applications covering different workloads and disciplines. 

Abstract The canonical non-homologous end joining (c-NHEJ) repair pathway, generally viewed as stochastic, has recently been shown to produce predictable outcomes in CRISPR-Cas9 mutagenesis. This predictability, mainly in 1-bp insertions and small deletions, has led to the development of in-silico prediction programs for various animal species. However, the predictability of CRISPR-induced mutation profiles across species remained elusive. Comparing CRISPR-Cas9 repair outcomes between human and plant species reveals significant differences in 1-bp insertion profiles. The high predictability observed in human cells links to the template-dependent activity of human Polλ. Yet plant Polλ exhibits dual activities, generating 1-bp insertions through both templated and non-templated manners. Polλ knockout in plants leads to deletion-only mutations, while its overexpression enhances 1-bp insertion rates. Two conserved motifs are identified to modulate plant Polλ‘s dual activities. These findings unveil the mechanism behind species-specific CRISPR-Cas9-induced insertion profiles and offer strategies for predictable, precise genome editing through c-NHEJ. 

Abstract Eukaryotic retroelements are generally divided into two classes: long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons. A third class of eukaryotic retroelement, the Penelope-like elements (PLEs), has been well-characterized bioinformatically, but relatively little is known about the transposition mechanism of these elements. PLEs share some features with the R2 retrotransposon fromBombyx mori, which uses a target-primed reverse transcription (TPRT) mechanism, but their distinct phylogeny suggests PLEs may utilize a novel mechanism of mobilization. Using protein purified fromE. coli, we report unique in vitro properties of a PLE from the green anole (Anolis carolinensis), revealing mechanistic aspects not shared by other retrotransposons. We found that reverse transcription is initiated at two adjacent sites within the transposon RNA that is not homologous to the cleaved DNA, a feature that is reflected in the genomic “tail” signature shared between and unique to PLEs. Our results for the first active PLE in vitro provide a starting point for understanding PLE mobilization and biology. 

Abstract Efficient and precise targeted insertion holds great promise but remains challenging in plant genome editing. An efficient nonhomologous end-joining-mediated targeted insertion method was recently developed by combining clustered regularly interspaced short palindromic repeat (CRISPR)/Streptococcus pyogenes CRISPR-associated nuclease 9 (SpCas9) gene editing with phosphorothioate modified double-stranded oligodeoxynucleotides (dsODNs). Yet, this approach often leads to imprecise insertions with no control over the insertion direction. Here, we compared the influence of chemical protection of dsODNs on efficiency of targeted insertion. We observed that CRISPR/SpCas9 frequently induced staggered cleavages with 1-nucleotide 5′ overhangs; we also evaluated the effect of donor end structures on the direction and precision of targeted insertions. We demonstrate that chemically protected dsODNs with 1-nucleotide 5′ overhangs significantly improved the precision and direction control of target insertions in all tested CRISPR targeted sites. We applied this method to endogenous gene tagging in green foxtail (Setaria viridis) and engineering of cis-regulatory elements for disease resistance in rice (Oryza sativa). We directionally inserted 2 distinct transcription activator-like effector binding elements into the promoter region of a recessive rice bacterial blight resistance gene with up to 24.4% efficiency. The resulting rice lines harboring heritable insertions exhibited strong resistance to infection by the pathogen Xanthomonas oryzae pv. oryzae in an inducible and strain-specific manner. 

Graduate students’ mental health and well-being is a prominent concern across various disciplines. However, early predictors of mental health and well-being in graduate education, specifically doctoral education, have rarely been studied. The present study evaluated both the underlying latent classification of individuals’ mental well-being and predictors of those classifications. Results estimated two latent classes of students’ mental health and well-being: one class with generally high levels of mental well-being and one with lower levels of mental well-being. Regression analyses showed that mentoring in the second year of doctoral study, certainty of choice in the third year, and both academic development and sense of belonging in the fourth year were positive predictors of membership in the higher mental well-being class. In contrast to some prior studies, demographic variables were not related to the identified well-being classifications. Regression analyses further showed that mental well-being was negatively related to participants’ number of publications and research self-efficacy, indicating a problematic relationship between scholarly productivity and confidence and well-being. These findings may be used to identify and provide targeted support for students who are at-risk for having or developing lower levels of mental well-being in their graduate programs.