The extensive mC epitranscriptome of Thermococcus kodakarensis is generated by a suite of RNA methyltransferases that support thermophily.

RNAs are often modified to invoke new activities. While many modifications are limited in frequency, restricted to non-coding RNAs, or present only in select organisms, 5-methylcytidine (mC) is abundant across diverse RNAs and fitness-relevant across Domains of life, but the synthesis and impacts of mC have yet to be fully investigated. Here, we map mC in the model hyperthermophile, Thermococcus kodakarensis.

Enhancing robotic telesurgery with sensorless haptic feedback.

Purpose: This paper evaluates user performance in telesurgical tasks with the da Vinci Research Kit (dVRK), comparing unilateral teleoperation, bilateral teleoperation with force sensors and sensorless force estimation.

Methods: A four-channel teleoperation system with disturbance observers and sensorless force estimation with learning-based dynamic compensation was developed. Palpation experiments were conducted with 12 users who tried to locate tumors hidden in tissue phantoms with their fingers or through handheld or teleoperated laparoscopic instruments with visual, force sensor, or sensorless force estimation feedback.

Modeling Nicotine-Induced Chlorine Loss in Drinking Water Using Updated EPANET-MSX.

Multispecies water quality modeling is critical for simulating complex chemical reactions in drinking water distribution systems. An updated EPANET 2.2-compatible version of EPANET multi-species eXtension (EPANET-MSX) was used, which included dispersion and improved mass balance reporting, to simulate an experimental study.

Archaeal histone-based chromatin structures regulate transcription elongation rates.

Many archaea encode and express histone proteins to compact their genomes. Archaeal and eukaryotic histones share a near-identical fold that permits DNA wrapping through select histone-DNA contacts to generate chromatin-structures that must be traversed by RNA polymerase (RNAP) to generate transcripts. As archaeal histones can spontaneously assemble with a single histone isoform, single-histone chromatin variants provide an idealized platform to detail the impacts of distinct histone-DNA contacts on transcription efficiencies and to detail the role of the conserved cleavage stimulatory factor, Transcription Factor S (TFS), in assisting RNAP through chromatin landscapes.

Thermococcus kodakarensis TK0353 is a novel AP lyase with a new fold.

Hyperthermophilic organisms thrive in extreme environments prone to high levels of DNA damage. Growth at high temperature stimulates DNA base hydrolysis resulting in apurinic/apyrimidinic (AP) sites that destabilize the genome. Organisms across all domains have evolved enzymes to recognize and repair AP sites to maintain genome stability.

The Hyperthermophilic Restriction-Modification Systems of Protect Genome Integrity.

(), a hyperthermophilic, genetically accessible model archaeon, encodes two putative restriction modification (R-M) defense systems, TkoI and TkoII. TkoI is encoded by TK1460 while TkoII is encoded by TK1158. Bioinformative analysis suggests both R-M enzymes are large, fused methyltransferase (MTase)-endonuclease polypeptides that contain both restriction endonuclease (REase) activity to degrade foreign invading DNA and MTase activity to methylate host genomic DNA at specific recognition sites.

Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in .

Histone proteins compact and organize DNA resulting in a dynamic chromatin architecture impacting DNA accessibility and ultimately gene expression. Eukaryotic chromatin landscapes are structured through histone protein variants, epigenetic marks, the activities of chromatin-remodeling complexes, and post-translational modification of histone proteins. In most Archaea, histone-based chromatin structure is dominated by the helical polymerization of histone proteins wrapping DNA into a repetitive and closely gyred configuration.

Using Arousal Suppression Exercises to Decrease Inappropriate Sexual Arousal in Detained Adolescent Males: Three Clinical Demonstrations.

Reyes, Vollmer, and Hall (2011) found that 2 arousal suppression strategies, 1 of which involved counting backward from 100 to 0, decreased sexual arousal for 2 male sex offenders with intellectual disabilities. In the current clinical study, we taught 3 adolescent males who had been adjudicated for illegal sexual behavior to self-report arousal when they were presented with sexually arousing visual stimuli. Based on the procedures in the Reyes et al.

Archaeosine Modification of Archaeal tRNA: Role in Structural Stabilization.

Archaeosine (G) is a structurally complex modified nucleoside found quasi-universally in the tRNA of and located at position 15 in the dihydrouridine loop, a site not modified in any tRNA outside the G is characterized by an unusual 7-deazaguanosine core structure with a formamidine group at the 7-position. The location of G at position 15, coupled with its novel molecular structure, led to a hypothesis that G stabilizes tRNA tertiary structure through several distinct mechanisms. To test whether G contributes to tRNA stability and define the biological role of G, we investigated the consequences of introducing targeted mutations that disrupt the biosynthesis of G into the genome of the hyperthermophilic archaeon and the mesophilic archaeon , resulting in modification of the tRNA with the G precursor 7-cyano-7-deazaguansine (preQ) (deletion of ) or no modification at position 15 (deletion of ).

Biochemical reconstitution and genetic characterization of the major oxidative damage base excision DNA repair pathway in Thermococcus kodakarensis.

Reactive oxygen species drive the oxidation of guanine to 8-oxoguanine (8oxoG), which threatens genome integrity. The repair of 8oxoG is carried out by base excision repair enzymes in Bacteria and Eukarya, however, little is known about archaeal 8oxoG repair. This study identifies a member of the Ogg-subfamily archaeal GO glycosylase (AGOG) in Thermococcus kodakarensis, an anaerobic, hyperthermophilic archaeon, and delineates its mechanism, kinetics, and substrate specificity.

Behavioral Skills Training to Increase Appropriate Reactions of Adolescent Males in Residential Treatment.

Adolescents in secured residential facilities may engage in excess behavior immediately following verbal directives or corrective statements from staff. Excess behavior may include verbal aggression, indices of disrespect (e.g.

Effect of case study versus video simulation on nursing students' satisfaction, self-confidence, and knowledge: A quasi-experimental study.

Background: Research on simulation in nursing education has demonstrated the positive impact active, experiential learning has on student satisfaction, self-confidence, and knowledge. As a result, simulation laboratories with high-fidelity human patient simulators have become a common adjunct to clinical teaching. It is important to also promote active learning in the classroom setting; however, there is limited evidence on using video simulations in large classrooms.

Bioinformatic Mapping of Radical S-Adenosylmethionine-Dependent Ribosomally Synthesized and Post-Translationally Modified Peptides Identifies New Cα, Cβ, and Cγ-Linked Thioether-Containing Peptides.

Recently developed bioinformatic tools have bolstered the discovery of ribosomally synthesized and post-translationally modified peptides (RiPPs). Using an improved version of Rapid ORF Description and Evaluation Online (RODEO 2.0), a biosynthetic gene cluster mining algorithm, we bioinformatically mapped the sactipeptide RiPP class via the radical S-adenosylmethionine (SAM) enzymes that form the characteristic sactionine (sulfur-to-α carbon) cross-links between cysteine and acceptor residues.

Effects of Rules and Feedback on Classroom Behavior of Adolescents in a Residential Treatment Setting.

Over the past 30 years, researchers have shown that various types of group contingency procedures can decrease problem behavior displayed by young children in academic settings. Recently, researchers have demonstrated that presession rules, within-session feedback, and interdependent group contingencies (i.e.

Distinct Physiological Roles of the Three Ferredoxins Encoded in the Hyperthermophilic Archaeon .

Control of electron flux is critical in both natural and bioengineered systems to maximize energy gains. Both small molecules and proteins shuttle high-energy, low-potential electrons liberated during catabolism through diverse metabolic landscapes. Ferredoxin (Fd) proteins-an abundant class of Fe-S-containing small proteins-are essential in many species for energy conservation and ATP production strategies.

Heterogeneity in Male Adolescents With Illegal Sexual Behavior: A Latent Profile Approach to Classification.

Current research has established that male adolescents with illegal sexual behavior (AISB) are a heterogeneous population. We aimed to explore this within-group heterogeneity to derive clinically relevant groups of AISB using the Millon Adolescent Clinical Inventory (MACI). We then compared these groups on selected covariates (age at intake, minority status, and child maltreatment history) and distal outcomes (general, nonviolent, violent, drug, and sexual recidivism 5 years after release) to identify any differences.

Group Procedures for Decreasing Problem Behavior Displayed by Detained Adolescents.

As one component of providing treatment in a residential facility, Brogan, Falligant, and Rapp decreased problem behavior by two groups of detained adolescents using group contingency procedures. The current series of studies evaluated the extent to which group procedures could be extended to other contexts within a residential facility. In Study 1, fixed-time delivery of attention by dormitory staff decreased problem behavior displayed by a group of five to 11 detained adolescents during free periods.

An Archaeal Fluoride-Responsive Riboswitch Provides an Inducible Expression System for Hyperthermophiles.

Robust genetic systems for the hyperthermophilic have facilitated the overexpression of native genes, enabled the addition of sequences encoding secretion signals, epitope, and affinity tags to coding regions, and aided the introduction of sequences encoding new proteins in these fast-growing fermentative heterotrophs. However, tightly controlled and easily manipulated systems facilitating regulated gene expression are limited for these hosts. Here, we describe an alternative method for regulatory control reliant on a -encoded functional riboswitch in the model archaeon Despite the hyperthermophilic growth temperatures, the proposed structure of the riboswitch conforms to a fluoride-responsive riboswitch encoded in many bacteria and similarly functions to regulate a component-conserved fluoride export pathway.

Genome Replication in Independent of Cdc6 and an Origin of Replication.

The initiation of DNA replication is typically tightly regulated by proteins that form initiation complexes at specific sequences known as replication origins. In Archaea and Eukaryotes, Cdc6, a near-universally conserved protein binds and facilitates the origin-dependent assembly of the replicative apparatus. TK1901 encodes Cdc6 in but, as we report here, TK1901 and the presumed origin of replication can be deleted from the genome of this hyperthermophilic Archaeon without any detectable effects on growth, genetic competence or the ability to support autonomous plasmid replication.

From Family Violence Exposure to Violent Offending: Examining Effects of Race and Mental Health in a Moderated Mediation Model Among Confined Male Juveniles.

Depression, substance use, and impulsivity have been linked to family violence exposure and to the development of violent offending during adolescence. Additionally, the indirect effects associated with these factors may not generalize across different racial/ethnic adolescent populations. The present study tested whether race/ethnicity moderated the mediated relationship between family violence exposure and violent offending, with depression, substance use, and impulsivity as mediators.

Structure of histone-based chromatin in Archaea.

Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome.