Next-generation marker-free transplastomic plants: engineering the chloroplast genome without integration of marker genes in Solanum tuberosum (potato).

This study describes an optimized plastid genetic engineering platform to produce full marker-free transplastomic plants with transgene integrated at homoplasmy in one step in tissue culture. Plastid engineering is attractive for both biotechnology and crop improvement due to natural bio-confinement from maternal inheritance, the absence of transgene positional effects and silencing, the ability to express transgenes in operons, and unparalleled production of heterologous proteins. While plastid engineering has had numerous successes in the production of high-value compounds, no transplastomic plants have been approved for use in agriculture.

Bifunctional degraders of cyclin dependent kinase 9 (CDK9): Probing the relationship between linker length, properties, and selective protein degradation.

Cyclin-dependent kinase 9 (CDK9) is a promising therapeutic target in multiple cancer types, including acute myeloid leukemia (AML). Protein degraders, also known as proteolysis targeting chimeras (PROTACs), have emerged as tools for the selective degradation of cancer targets, including CDK9, complementing the activity of traditional small-molecule inhibitors. These compounds typically incorporate previously reported inhibitors and a known E3 ligase ligand to induce ubiquitination and subsequent degradation of the target protein.

Interlocking activities of DNA polymerase β in the base excision repair pathway.

SignificanceBase excision repair (BER) is one of the major DNA repair pathways used to fix a myriad of cellular DNA lesions. The enzymes involved in BER, including DNA polymerase β (Polβ), have been identified and characterized, but how they act together to efficiently perform BER has not been fully understood. Through gel electrophoresis, mass spectrometry, and kinetic analysis, we discovered that the two enzymatic activities of Polβ can be interlocked, rather than functioning independently from each other, when processing DNA intermediates formed in BER.

Optimization of proteomics sample preparation for forensic analysis of skin samples.

We present an efficient protein extraction and in-solution enzymatic digestion protocol optimized for mass spectrometry-based proteomics studies of human skin samples. Human skin cells are a proteinaceous matrix that can enable forensic identification of individuals. We performed a systematic optimization of proteomic sample preparation for a protein-based human forensic identification application.

Fractionation of DNA and protein from individual latent fingerprints for forensic analysis.

Human touch samples represent a significant portion of forensic DNA casework. Yet, the generally low abundance of genetic material combined with the predominantly extracellular nature of DNA in these samples makes DNA-based forensic analysis exceptionally challenging. Human proteins present in these same touch samples offer an abundant and environmentally-robust alternative.

An algorithm for random match probability calculation from peptide sequences.

For the past three decades, forensic genetic investigations have focused on elucidating DNA signatures. While DNA has a number of desirable properties (e.g.

A New Normal.

A badly injured young man and his family take an important step toward acceptance.

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species ( and ) living in sympatry.

Microbiota inhabiting the gastrointestinal (GI) tract of animals has important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut micro-organismal community, few comparative studies have considered how differences in diet influence community composition across the length of the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's () and fox squirrels () living in the same habitat.

Temporal Dynamics of the Soil Metabolome and Microbiome During Simulated Anaerobic Soil Disinfestation.

Significant interest exists in engineering the soil microbiome to attain suppression of soil-borne plant diseases. Anaerobic soil disinfestation (ASD) has potential as a biologically regulated disease control method; however, the role of specific metabolites and microbial community dynamics contributing to ASD mediated disease control is mostly uncharacterized. Understanding the trajectory of co-evolutionary processes leading to syntrophic generation of functional metabolites during ASD is a necessary prelude to the predictive utilization of this disease management approach.

Time may heal wounds: Aging and life regrets.

Psychological research on regret has focused mostly on the negative emotions associated with troubling past decisions. Because aging is associated with a preference for positive information in attention and memory, investigation into positive emotions elicited by regrets may provide insights into adult developmental changes in subjective experience. The present study investigated age differences in regret-related affect in a survey of adults (n = 629) aged 18-92 years.

The Safety of Bypass to Percutaneous Coronary Intervention Facility by Basic Life Support Providers in Patients with ST-Elevation Myocardial Infarction in Prehospital Setting.

Background: Most patients transferred from a non-percutaneous coronary intervention (PCI) facility for primary PCI do not meet target reperfusion times. Direct transportation of patients with ST-elevation myocardial infarction (STEMI) from the scene by advanced life support (ALS) paramedics has been shown to improve reperfusion times and outcomes.

Objective: The aim of this study was to determine whether it is safe to bypass the closest hospital and transport by basic life support (BLS) provider to a PCI facility.

Kinetic Mechanism of DNA Polymerases: Contributions of Conformational Dynamics and a Third Divalent Metal Ion.

Faithful transmission and maintenance of genetic material is primarily fulfilled by DNA polymerases. During DNA replication, these enzymes catalyze incorporation of deoxynucleotides into a DNA primer strand based on Watson-Crick complementarity to the DNA template strand. Through the years, research on DNA polymerases from every family and reverse transcriptases has revealed structural and functional similarities, including a conserved domain architecture and purported two-metal-ion mechanism for nucleotidyltransfer.

Barriers to Self-Reporting Patient Safety Incidents by Paramedics: A Mixed Methods Study.

Background: A minimal amount of research exists examining the extent to which patient safety events occur within paramedicine and even fewer studies investigating patient safety systems for self-reporting by paramedics. The purpose of this study was to identify barriers to paramedic self-reporting of patient safety incidents (PSIs).

Methods: We randomly distributed paper-based surveys among 1,153 paramedics in an Ontario region in Canada.

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.

The oxidative DNA lesion 7,8-dihydro-2'-deoxyguanine (8-oxoG) often occurs in double-stranded DNA and poses a threat to genomic integrity due to the ability of 8-oxoG to form stable Watson-Crick base pairs with deoxycytidine (8-oxoG:dC) and Hoogsteen base pairs with deoxyadenosine (8-oxoG:dA). In humans, short-patch base excision repair of 8-oxoG:dA base pairs requires human DNA polymerase β (hPolβ) to bypass 8-oxoG. Previously, we have shown hPolβ-catalyzed 8-oxoG bypass to exhibit low fidelity and identified a unique stacking interaction between the newly incorporated nucleotide (dCMP or dAMP) and the templating 8-oxoG.

Structural basis for the D-stereoselectivity of human DNA polymerase β.

Nucleoside reverse transcriptase inhibitors (NRTIs) with L-stereochemistry have long been an effective treatment for viral infections because of the strong D-stereoselectivity exhibited by human DNA polymerases relative to viral reverse transcriptases. The D-stereoselectivity of DNA polymerases has only recently been explored structurally and all three DNA polymerases studied to date have demonstrated unique stereochemical selection mechanisms. Here, we have solved structures of human DNA polymerase β (hPolβ), in complex with single-nucleotide gapped DNA and L-nucleotides and performed pre-steady-state kinetic analysis to determine the D-stereoselectivity mechanism of hPolβ.

Advances in Structural and Single-Molecule Methods for Investigating DNA Lesion Bypass and Repair Polymerases.

Innovative advances in X-ray crystallography and single-molecule biophysics have yielded unprecedented insight into the mechanisms of DNA lesion bypass and damage repair. Time-dependent X-ray crystallography has been successfully applied to view the bypass of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), a major oxidative DNA lesion, and the incorporation of the triphosphate form, 8-oxo-dGTP, catalyzed by human DNA polymerase β. Significant findings of these studies are highlighted here, and their contributions to the current mechanistic understanding of mutagenic translesion DNA synthesis (TLS) and base excision repair are discussed.

Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase.

DNA polymerases are essential enzymes that faithfully and efficiently replicate genomic information.1-3 The mechanism of nucleotide incorporation by DNA polymerases has been extensively studied structurally and kinetically, but several key steps following phosphodiester bond formation remain structurally uncharacterized due to utilization of natural nucleotides. It is thought that the release of pyrophosphate (PP) triggers reverse conformational changes in a polymerase in order to complete a full catalytic cycle as well as prepare for DNA translocation and subsequent incorporation events.

Information and Communication Technology Use Is Related to Higher Well-Being Among the Oldest-Old.

Objectives: Older adults often prioritize socially meaningful goals over informational goals. Thus, we predicted that using information and communication technology (ICT) in service of socially meaningful versus informational goals relates to higher well-being among the oldest-old.

Method: We surveyed 445 adults aged 80+ (mean = 84, range = 80-93; 64% female; 26% non-White) online or via telephone.

Rat and poultry feeding studies with soybean meal produced from imidazolinone-tolerant (CV127) soybeans.

The safety and nutritional properties of CV127 soybeans were evaluated in rat and broiler feeding studies. Some episodic differences were observed between rats fed CV127, Conquista, and the standard diet for the endpoints examined. None of these differences were considered treatment related, adverse, or biologically meaningful.

Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.

One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction.

Meta-analysis of the age-related positivity effect: age differences in preferences for positive over negative information.

In contrast to long-held axioms of old age as a time of "doom and gloom," mounting evidence indicates an age-related positivity effect in attention and memory. However, several studies report inconsistent findings that raise critical questions about the effect's reliability, robustness, and potential moderators. To address these questions, we conducted a systematic meta-analysis of 100 empirical studies of the positivity effect (N = 7,129).

Preferences for choice across adulthood: age trajectories and potential mechanisms.

Across a variety of decision domains, older adults were found to desire fewer choice options than younger adults, but the age trajectory and underlying mechanisms of these effects remain unknown. The present study examined the pattern and correlates of age differences in choice set size preferences using self-report and behavioral measures. Self-reported choice set size preferences were assessed in a large-scale survey using an adult life span sample (N = 318, ages 18-90 years).

The theory behind the age-related positivity effect.

The "positivity effect" refers to an age-related trend that favors positive over negative stimuli in cognitive processing. Relative to their younger counterparts, older people attend to and remember more positive than negative information. Since the effect was initially identified and the conceptual basis articulated (Mather and Carstensen, 2005) scores of independent replications and related findings have appeared in the literature.

Who saves the best for last? Age differences in preferences for affective sequences.

We examined age differences in preferences for the temporal sequence of emotional events. In 2 studies, participants were asked to select the order in which they would like to view a series of emotionally salient images. Study 1 (N = 87; aged 21-88 years) elicited sequence preferences both directly (via a sequence construction task) and indirectly (via a temporal discounting task).