Profiling of molecular interactions in real time using acoustic detection

Acoustic sensors that exploit resonating quartz crystals to directly detect the binding of an analyte to a receptor are finding increasing utility in the quantification of clinically relevant analytes. We have developed a novel acoustic detection technology, which we term resonant acoustic profiling (RAP). This technology builds on the fundamental basics of the "quartz crystal microbalance" or "QCM" with several key additional features including two- or four-channel automated sample delivery, in-line referencing and microfluidic sensor 'cassettes' that are pre-coated with easy-to-use surface chemistries. Example applications are described for the quantification of myoglobin concentration and its interaction kinetics, and for the ranking of enzyme-cofactor specificities.     

EHD1 interacts with retromer to stabilize SNX1 tubules and facilitate endosome-to-Golgi retrieval

Endosome-to-Golgi retrieval of the cation-independent mannose 6-phosphate receptor (CIMPR) requires the function of the retromer complex. Retromer is localized to endosomes and comprises two distinct sub complexes: the vacuolar protein sorting 35/29/26 sub complex that binds cargo and the sorting nexin (SNX)1/2 sub complex that tubulates endosomal membranes. To identify up- or down-stream regulatory factors of retromer, a comparative proteomic strategy was employed. Protein profiles of endosomally enriched membranes, from either wild-type or retromer-deficient mouse cells, were compared to identify proteins with either elevated or reduced expression levels. Eps15 homology domain-containing protein-1 (EHD1) was identified in endosomally enriched membrane fractions from retromer-deficient cells and was found to be approximately threefold upregulated in the absence of retromer. EHD1 is localized to tubular and vesicular endosomes, partially colocalizes with retromer and is associated with retromer in vivo. Mutation of the nucleotide-binding P-loop of EHD1 results in a dominant-negative effect upon retromer localization and endosome-to-Golgi retrieval, while loss of EHD1 expression by RNA interference destabilizes SNX1-positive tubules and inhibits endosome-to-Golgi retrieval. The interaction between EHD1 and retromer and the requirement for EHD1 to stabilize SNX1-tubules establish EHD1 as a novel facilitating component of endosome-to-Golgi retrieval.     

Viral manipulation of DNA repair and cell cycle checkpoints

Recognition and repair of DNA damage is critical for maintaining genomic integrity and suppressing tumorigenesis. In eukaryotic cells, the sensing and repair of DNA damage are coordinated with cell cycle progression and checkpoints, in order to prevent the propagation of damaged DNA. The carefully maintained cellular response to DNA damage is challenged by viruses, which produce a large amount of exogenous DNA during infection. Viruses also express proteins that perturb cellular DNA repair and cell cycle pathways, promoting tumorigenesis in their quest for cellular domination. This review presents an overview of strategies employed by viruses to manipulate DNA damage responses and cell cycle checkpoints as they commandeer the cell to maximize their own viral replication. Studies of viruses have identified key cellular regulators and revealed insights into molecular mechanisms governing DNA repair, cell cycle checkpoints, and transformation.     

Protostylid expression at the enamel-dentine junction and enamel surface of mandibular molars of Paranthropus robustus and Australopithecus africanus

Distinctive expressions and incidences of discrete dental traits at the outer enamel surface (OES) contribute to the diagnoses of many early hominin taxa. Examination of the enamel-dentine junction (EDJ), imaged non-destructively using micro-computed tomography, has elucidated the morphological development of dental traits and improved interpretations of their variability within and among taxa. The OES expressions of one of these dental traits, the protostylid, have been found to differ among African Plio-Pleistocene fossil hominin taxa. In this study protostylid expression is examined at the OES and at the EDJ of Paranthropus robustus (n = 23) and Australopithecus africanus (n = 28) mandibular molars, with the goals of incorporating EDJ morphology into the definition of the protostylid and assessing the relative contribution of the EDJ and enamel cap to its expression in these taxa. The results provide evidence a) of statistically significant taxon-specific patterns of protostylid morphology at the EDJ that are not evident at the OES; b) that in P. robustus, thick enamel reduces the morphological correspondence between the form of the protostylid seen at the EDJ and the OES, and c) that if EDJ images can be obtained, then the protostylid retains its taxonomic value even in worn teeth.     

Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport

Several bacterial solute transport mechanisms involve members of the periplasmic binding protein (PBP) superfamily that bind and deliver ligand to integral membrane transport proteins in the ATP-binding cassette, tripartite tricarboxylate transporter, or tripartite ATP-independent (TRAP) families. PBPs involved in ATP-binding cassette transport systems have been well characterized, but only a few PBPs involved in TRAP transport have been studied. We have measured the thermal stability, determined the oligomerization state by small angle x-ray scattering, and solved the x-ray crystal structure to 1.9 A resolution of a TRAP-PBP (open reading frame tm0322) from the hyperthermophilic bacterium Thermotoga maritima (TM0322). The overall fold of TM0322 is similar to other TRAP transport related PBPs, although the structural similarity of backbone atoms (2.5-3.1 A root mean square deviation) is unusually low for PBPs within the same group. Individual monomers within the tetrameric asymmetric unit of TM0322 exhibit high root mean square deviation (0.9 A) to each other as a consequence of conformational heterogeneity in their binding pockets. The gel filtration elution profile and the small angle x-ray scattering analysis indicate that TM0322 assembles as dimers in solution that in turn assemble into a dimer of dimers in the crystallographic asymmetric unit. Tetramerization has been previously observed in another TRAP-PBP (the Rhodobacter sphaeroides alpha-keto acid-binding protein) where quaternary structure formation is postulated to be an important requisite for the transmembrane transport process.     

Mutating the tight-dimer interface of dihydrodipicolinate synthase disrupts the enzyme quaternary structure: toward a monomeric enzyme

Dihydrodipicolinate synthase (DHDPS) is a tetrameric enzyme that is the first enzyme unique to the ( S)-lysine biosynthetic pathway in plants and bacteria. Previous studies have looked at the important role of Tyr107, an amino acid residue located at the tight-dimer interface between two monomers, in participating in a catalytic triad of residues during catalysis. In this study, we examine the importance of this residue in determining the quaternary structure of the DHDPS enzyme. The Tyr107 residue was mutated to tryptophan, and structural, biophysical, and kinetic studies were carried out on the mutant enzyme. These revealed that while the solid-state structure of the mutant enzyme was largely unchanged, as judged by X-ray crystallography, it exists as a mixture of primarily monomer and tetramer in solution, as determined by analytical ultracentrifugation, size-exclusion chromatography, and mass spectrometry. The catalytic ability of the DHDPS enzyme was reduced by the mutation, which also allowed the adventitious binding of alpha-ketoglutarate to the active site. A reduction in the apparent melting temperature of the mutant enzyme was observed. Thus, the tetrameric quaternary structure of DHDPS is critical to controlling specificity, heat stability, and intrinsic activity.     

Successful elimination of a lethal wildlife infectious disease in nature

Methods to mitigate the impacts of emerging infectious diseases affecting wildlife are urgently needed to combat loss of biodiversity. However, the successful mitigation of wildlife pathogens in situ has rarely occurred. Indeed, most strategies for combating wildlife diseases remain theoretical, despite the wealth of information available for combating infections in livestock and crops. Here, we report the outcome of a 5-year effort to eliminate infection with Batrachochytrium dendrobatidis affecting an island system with a single amphibian host. Our initial efforts to eliminate infection in the larval reservoir using a direct application of an antifungal were successful ex situ but infection returned to previous levels when tadpoles with cleared infections were returned to their natal sites. We subsequently combined antifungal treatment of tadpoles with environmental chemical disinfection. Infection at four of the five pools where infection had previously been recorded was eradicated, and remained so for 2 years post-application.     

Molecular mechanisms of nitrogen dioxide induced epithelial injury in the lung

The lung can be exposed to a variety of reactive nitrogen intermediates through the inhalation of environmental oxidants and those produced during inflammation. Reactive nitrogen species (RNS) include, nitrogen dioxide (.NO2) and peroxynitrite (ONOO-). Classically known as a major component of both indoor and outdoor air pollution, .NO2 is a toxic free radical gas. .NO2 can also be formed during inflammation by the decomposition of ONOO- or through peroxidase-catalyzed reactions. Due to their reactive nature, RNS may play an important role in disease pathology. Depending on the dose and the duration of administration, .NO, has been documented to cause pulmonary injury in both animal and human studies. Injury to the lung epithelial cells following exposure to .NO2 is characterized by airway denudation followed by compensatory proliferation. The persistent injury and repair process may contribute to airway remodeling, including the development of fibrosis. To better understand the signaling pathways involved in epithelial cell death by .NO2 or otherRNS, we routinely expose cells in culture to continuous gas-phase .NO2. Studies using the .NO2 exposure system revealed that lung epithelial cell death occurs in a density dependent manner. In wound healing experiments, .NO2 induced cell death is limited to cells localized in the leading edge of the wound. Importantly, .NO2-induced death does not appear to be dependent on oxidative stress per se. Potential cell signaling mechanisms will be discussed, which include the mitogen activated protein kinase, c-Jun N-terminal Kinase and the Fas/Fas ligand pathways. During periods of epithelial loss and regeneration that occur in diseases such as asthma or during lung development, epithelial cells in the lung may be uniquely susceptible to death. Understanding the molecular mechanisms of epithelial cell death associated with the exposure to .NO2 will be important in designing therapeutics aimed at protecting the lung from persistent injury and repair.     

Is Self‐Grooming by Male Prairie Voles a Predictor of Mate Choice?

Self-grooming by mammals is a form of scent dissemination in which individuals anoint themselves with salivary, anogenital, and other body odours. Self-grooming has been proposed to be a sexually selected trait favoured in reproductive competition and sexual attraction. We tested the hypothesis that females would show a mating preference for males that self-groomed more than a reproductive competitor that groomed less. In mate-choice experiments in which females had a choice of two tethered males, non pair-bonded females did not choose males based on their frequency of self-grooming. In a second experiment in which pair-bonded females in postpartum oestrus had access to their current mate and two strange males, strange males groomed significantly more than pair-bonded mates, yet attained the fewest copulations. Non pair-bonded females and pair-bonded males and females groomed significantly less often than did non pair-bonded males. Self-grooming behaviour was consistent with the sexual attraction hypothesis, but the frequency of self-grooming did not increase a male's mating success. We conclude that the frequency and time spent self grooming are not good predictors of mating success.     

Effects of climbing- and resistance-training on climbing-specific performance: a systematic review and meta-analysis

The objective of this systematic review and meta-analysis was to examine the effects of climbing and climbing-and-resistance-training on climbing performance, and strength and endurance tests. We systematically searched three databases (SPORTDiscus, SCOPUS, and PubMed) for records published until January 2021. The search was limited to randomized-controlled trials using active climbers and measuring climbing performance or performance in climbing-specific tests. Data from the meta-analysis are presented as standardized difference in mean (SDM) with 95% confidence intervals (95% CI). Eleven studies are included in the systematic review and five studies compared training to a control group and could be meta-analyzed. The overall meta-analysis displayed an improvement in climbing-related test performance following climbing-specific resistance training compared to only climbing (SDM = 0.57, 95%CI = 0.24–0.91). Further analyses revealed that finger strength (SDM = 0.41, 95%CI 0.03–0.80), rate of force development (SDM = 0.91, 95%CI = 0.21–1.61), and forearm endurance (SDM = 1.23, 95%CI = 0.69–1.77) were improved by resistance-training of the finger flexors compared to climbing training. The systematic review showed that climbing performance may be improved by specific resistance-training or interval-style bouldering. However, resistance-training of the finger flexors showed no improvements in strength or endurance in climbing-specific tests. The available evidence suggests that resistance-training may be more effective than just climbing-training for improving performance outcomes. Importantly, interventional studies including climbers is limited and more research is needed to confirm these findings.