Evaluating the risk of data loss due to particle radiation damage in a DNA data storage system.

DNA data storage is a potential alternative to magnetic tape for archival storage purposes, promising substantial gains in information density. Critical to the success of DNA as a storage media is an understanding of the role of environmental factors on the longevity of the stored information. In this paper, we evaluate the effect of exposure to ionizing particle radiation, a cause of data loss in traditional magnetic media, on the longevity of data in DNA data storage pools. We develop a mass action kinetics model to estimate the rate of damage accumulation in DNA strands due to neutron interactions with both nucleotides and residual water molecules, then utilize the model to evaluate the effect several design parameters of a typical DNA data storage scheme have on expected data longevity. Finally, we experimentally validate our model by exposing dried DNA samples to different levels of neutron irradiation and analyzing the resulting error profile. Our results show that particle radiation is not a significant contributor to data loss in DNA data storage pools under typical storage conditions.

Ultrafast Au(III)-Mediated Arylation of Cysteine.

Through mechanistic work and rational design, we have developed the fastest organometallic abiotic Cys bioconjugation. As a result, the developed organometallic Au(III) bioconjugation reagents enable selective labeling of Cys moieties down to picomolar concentrations and allow for the rapid construction of complex heterostructures from peptides, proteins, and oligonucleotides. This work showcases how organometallic chemistry can be interfaced with biomolecules and lead to a range of reactivities that are largely unmatched by classical organic chemistry tools.

Polyethylene Glycol Fusion Restores Axonal Continuity and Improves Return of Function in a Rat Median Nerve Denervation Model.

BACKGROUND: Polyethylene glycol (PEG) can fuse severed closely-apposed axolemmas and restore axonal continuity. We evaluated the effects of PEG-fusion on functional recovery in a rodent forelimb model of peripheral nerve injury. METHODS: The median nerves of male Lewis rats (n=5 per group) were transected and repaired with standard suture repair (SR), SR with PEG (PEG), or SR with PEG and 1% methylene blue (PEG+MB); a sham surgery group was also included. Proximal stimulation produced compound nerve (CAPS) and muscle (CMAPs) action potentials recorded distally. The contralateral limb of each animal acted as an internal control for grip strength measurements. RESULTS: CAPs and CMAPs immediately returned in all PEG and PEG+MB animals, but not in SR animals. PEG and PEG+MB groups demonstrated earlier return of function by post-operative day (POD) 7 (62.6 ±7.3% and 50.9 ±6.7% of contralateral limb grip strength, respectively) compared to SR group, in which minimal return of function was not measurable until POD 21. At POD 98, the PEG group grip strength recovered to 77.2 ±2.8% while the PEG+MB grip strength recovered to 79.9 ±4.4%, compared to 34.9 ±1.8% recovery in the SR group (p<0.05). The PEG and PEG+MB groups reached 50% of the Sham group grip strength on POD 3.8 and 6.3, respectively, whereas the SR group did not reach 50% grip strength recovery of the Sham group throughout the study period. CONCLUSION: PEG-fusion plus neurorrhaphy with or without methylene blue re-established axonal continuity, shortened recovery time, and augmented functional recovery compared to suture neurorrhaphy alone.

Multiple mechanisms contribute to isolation by environment in the redheaded pine sawfly, Neodiprion lecontei.

Isolation by environment (IBE) is a population genomic pattern that arises when ecological barriers reduce gene flow between populations. Although current evidence suggests IBE is common in nature, few studies have evaluated the underlying mechanisms that generate IBE patterns. In this study, we evaluate five proposed mechanisms of IBE (natural selection against immigrants, sexual selection against immigrants, selection against hybrids, biased dispersal, and environment-based phenological differences) that may give rise to host-associated differentiation within a sympatric population of the redheaded pine sawfly, Neodiprion lecontei, a species for which IBE has previously been detected. We first characterize the three pine species used by N. lecontei at the site, finding morphological and chemical differences among the hosts that could generate divergent selection on sawfly host-use traits. Next, using morphometrics and ddRAD sequencing, we detect modest phenotypic and genetic differentiation among sawflies originating from different pines that is consistent with recent, in situ divergence. Finally, via a series of laboratory assays-including assessments of larval performance on different hosts, adult mate and host preferences, hybrid fitness, and adult eclosion timing-we find evidence that multiple mechanisms contribute to IBE in N. lecontei. Overall, our results suggest IBE can emerge quickly, possibly due to multiple mechanisms acting in concert to reduce migration between different environments.

Overlaps and trade-offs in the diversity and inducibility of volatile chemical profiles among diverse sympatric neotropical canopy trees.

A central goal in ecology is to understand the mechanisms by which biological diversity is maintained. The diversity of plant chemical defences and the strategies by which they are deployed in nature may influence biological diversity. Trees in neotropical forests are subject to relatively high herbivore pressure. Such consistent pressure is thought to select for constitutive, non-flexible defence-related phytochemistry with limited capacity for inducible phytochemical responses. However, this has not been explored for volatile organic compounds (VOCs) that have a relatively low ratio of production costs to ecological benefits. To test this, I sampled VOCs emitted from canopy leaves of 10 phylogenetically diverse tree species (3 Magnoliids and 7 Rosids) in the Peruvian Amazon before and after induction with the phytohormone methyl jasmonate (MeJA). There was no phylogenetic signal in induction or magnitude of MeJA-induced VOC emissions from intact leaves: all trees induced VOC profiles dominated by ß-ocimene, linalool, and α-farnesene of varying ratios. Moreover, overall inducibility of VOCs from intact leaves was unrelated to phytochemical diversity or richness. In contrast, experimentally wounded leaves showed considerable phylogeny-based and MeJA-independent variation the richness and diversity of constitutive wound-emitted VOCs. Moreover, VOC inducibility from wounded leaves correlated negatively with phytochemical richness and diversity, potentially indicating a tradeoff in constitutive and inducible defence strategies for non-volatile specialised metabolites but not for inducible VOCs. Importantly, there was no correlation between any chemical profile and either natural herbivory or leaf toughness. The coexistence of multiple phytochemical strategies in a hyper-diverse forest has broad implications for competitive and multitrophic interactions, and the evolutionary forces that maintain the exceptional plant biodiversity in neotropical forests.

Effects of ß-caryophyllene and oxygen availability on cholesterol and fatty acids in breast cancer cells.

Hypoxia is a common feature of most solid tumors, one that favors tumor progression and limits treatment effectiveness. Targeting hypoxia has long been a goal in cancer therapy, by identifying factors that reverse or ameliorate the effects of hypoxia on cancer cells. We, and others, have shown that ß-caryophyllene (BCP) exhibits anti-proliferative properties in cancer cells. We have further shown that non-cytotoxic concentrations of BCP affect cholesterol and lipid biosynthesis in hypoxic hBrC cells at both transcriptional and translational levels. This led us to hypothesize that BCP may reverse the hypoxic phenotype in hBrC cells. To test this, we determined the effect of BCP on hypoxic sensitive pathways, including oxygen consumption, glycolysis, oxidative stress, cholesterol and fatty acid biosynthesis, and ERK activation. While each of these studies revealed new information on the regulation by hypoxia and BCP, only the lipidomic studies showed reversal of hypoxic-dependent effects by BCP. These later studies showed that hypoxia-treated samples lowered monounsaturated fatty acid levels, shifting the saturation ratios of the fatty acid pools. This signature was ameliorated by sub-lethal concentrations of BCP, possibly through an effect on the C:16 fatty acid saturation ratios. This is consistent with BCP-induced upregulation of the stearoyl-CoA desaturase (SCD) gene, observed previously. This suggests that BCP may interfere with the lipid signature modulated by hypoxia which could have consequences for membrane biosynthesis or composition, both of which are important for cell replication.

Selective Thumb Carpometacarpal Joint Denervation for Painful Arthritis: Follow-Up of Long-Term Clinical Outcomes.

Purpose: Thumb carpometacarpal (CMC) joint osteoarthritis is a common problem affecting up to 85% of patients over the age of 70. The most common presenting symptom for patients with CMC arthritis is pain with joint loading. Loss of function due to subluxation or joint destruction is comparatively rare. Carpometacarpal joint denervation is a relatively novel method for managing CMC arthritis, treating the most impactful symptom: pain. Methods: In this paper, we present a 4- to 6-year follow-up case series on patients who underwent CMC denervation between 2015 and 2017. Results: Denervation was safe, with less downtime than trapeziectomy with ligament reconstruction with tendon interposition and provided durable complete or partial relief of pain after 5 years in 5 of 9 patients. Four of 9 patients had recurrence of pain by 5 years. Of those with recurrent pain, 3 of 5 eventually underwent trapeziectomy with ligament reconstruction and tendon interposition; the secondary surgery occurred between 17 and 66 months after denervation. Conclusion: Thumb CMC denervation provides effective relief of arthritis pain that was durable at 5+ years after surgery in more than half of our initial cohort of patients treated. Prospective studies with validated patient-reported and objective outcome measures between distinct treatment arms, such as denervation versus ligament reconstruction with tendon interposition, are needed to firmly establish the role of CMC denervation for patients with symptomatic thumb CMC osteoarthritis. Type of study/level of evidence: Therapeutic/Level IV.

Therapies for Long COVID in non-hospitalised individuals: from symptoms, patient-reported outcomes and immunology to targeted therapies (The TLC Study).

INTRODUCTION: Individuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. METHODS AND ANALYSIS: A cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink, and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability and patient-reported outcome measures. Data will be collected monthly for 1 year.Statistical clustering methods will be used to identify distinct Long COVID-19 symptom clusters. Individuals from the four most prevalent clusters and two control groups will be invited to participate in the BioWear substudy which will further phenotype Long COVID symptom clusters by measurement of immunological parameters and actigraphy.We will review existing evidence on interventions for postviral syndromes and Long COVID to map and prioritise interventions for each newly characterised Long COVID syndrome. Recommendations will be made using the cumulative evidence in an expert consensus workshop. A virtual supportive intervention will be coproduced with patients and health service providers for future evaluation.Individuals with lived experience of Long COVID will be involved throughout this programme through a patient and public involvement group. ETHICS AND DISSEMINATION: Ethical approval was obtained from the Solihull Research Ethics Committee, West Midlands (21/WM/0203). Research findings will be presented at international conferences, in peer-reviewed journals, to Long COVID patient support groups and to policymakers. TRIAL REGISTRATION NUMBER: 1567490.

Priming Seeds with Indole and (Z)-3-Hexenyl Acetate Enhances Resistance Against Herbivores and Stimulates Growth.

A striking feature of plant ecology is the ability of plants to detect and respond to environmental cues such as herbivore-induced plant volatiles (HIPVs) by priming or directly activating defenses against future herbivores. However, whether seeds also respond to compounds that are common constituents of HIPV blends and initiate future plant resistance is unknown. Considering that seeds depend on other environmental cues to determine basic survival traits such as germination timing, we predicted that seeds exposed to synthetic constituents of HIPV blends would generate well-defended plants. We investigated the effect of seed exposure to common volatiles on growth, reproduction, and resistance characteristics in the model plants Arabidopsis thaliana and Medicago truncatula using herbivores from two feeding guilds. After seed scarification and vernalization, we treated seeds with one of seven different plant-derived volatile compounds for 24 h. Seeds were then germinated and the resulting plants were assayed for growth, herbivore resistance, and expression of inducible defense genes. Of all the synthetic volatiles tested, indole specifically reduced both beet armyworm growth on A. thaliana and pea aphid fecundity on M. truncatula. The induction of defense genes was not affected by seed exposure to indole in either plant species, indicating that activation of direct resistance rather than inducible resistance is the mechanism by which seed priming operates. Moreover, neither plant species showed any negative effect of seed exposure to any synthetic volatile on vegetative and reproductive growth. Rather, M. truncatula plants derived from seeds exposed to (Z)-3-hexanol and (Z)-3-hexenyl acetate grew larger compared to controls. Our results indicate that seeds are sensitive to specific volatiles in ways that enhance resistance profiles with no apparent costs in terms of growth. Seed priming by HIPVs may represent a novel ecological mechanism of plant-to-plant interactions, with broad potential applications in agriculture and seed conservation.

Stimuli responsive asymmetric catalysis by triggered pseudo-enantiomeric proligand release.

Complex stimuli responsive systems are the basis for molecular machines and computing. A dual psuedo-enantiomer system was conceived, where the combination of two 'switch-on' asymmetric catalytic cycles could be selectively triggered to afford an enantioenriched product. Two pseudo-enantiomeric proligands were designed and synthesised for selective activation by fluoride and alkaline phosphatase. The proligands were firstly incorporated into single proligand systems, and then into a dual proligand system, where enantioselectivity of up to 98 : 2 was achieved in the reduction of prochiral ketone following external stimulation.

A visual technique used by citizen scientists shows higher herbivory in understory vs. canopy leaves of a tropical forest.

Citizen science (CS) initiatives can transform how some ecological data are collected. Herbivory is a fundamental ecological interaction, but herbivory rates in many natural systems are unknown due in part to lack of personnel for monitoring efforts. This limits our ability to understand broad ecological patterns relevant to herbivory. Fortunately, accurate and reliable visual estimation techniques for assessing herbivory could be amenable to CS approaches. In 2008, I developed a CS training initiative (the Million Leaf Project, MLP) to measure herbivory based on a seven-category visual assessment of leaf area removed (LAR). From 2010 to 2018, 394 citizen scientists assessed damage on 175,421 leaves to test the hypothesis that herbivory varies between understory and canopy leaves in a Peruvian tropical forest. In support of this hypothesis, the longitudinal CS data reveal that understory leaves consistently experience more herbivory than do canopy leaves on average (18.3% vs. 12.3%, P < 0.001), a difference that was consistent regardless of CS observer age. Furthermore, data integrity was high, even though younger participants showed some leaf selection bias. The MLP is based on a simple technique, intended to broaden public participation in ecological science, and applicable to any ecological system in which herbivory or leaf damage occurs.

Special Considerations for Secondary Surgery After Upper Extremity Transplantation.

BACKGROUND: Upper extremity (UE) transplantation is a complex undertaking that may require emergent or elective secondary surgery (SS) days to years following transplant. Various patient and transplantation may help determine what SS is needed. In this study, we characterize the SS needed by our UE transplant patients. METHODS: We retrospectively reviewed 6 patients who underwent hand and UE transplantation by one of the authors. Transplantation and SS details were obtained from medical records. Hand and arm function was quantified both subjectively (patient-reports) and objectively (Disabilities of the Arm, Shoulder, and Hand Score; Carroll test; Action Research Arm Tests; Box and Block test). RESULTS: Six patients underwent transplantation for a total of 10 transplanted limbs. Five transplants were performed below and 5 above the elbow. Mean time post-transplantation at last follow-up was 5 years (range: 1-9 years). In all, 66.7% of the patients required SS: total 7 surgeries comprising 13 procedures. The most common procedures were to improve hand function-nerve decompressions and tendon transfer, both in above-elbow transplant. Both patients showed a mean improvement of 15 points on Carroll scores. One above-elbow transplant had a brachioplasty for excess skin and another had a hematoma evacuation immediately after transplantation. Procedures in the below-elbow transplants included multiple incision and drainages for a septic wrist and an open reduction and internal fixation for a forearm fracture. CONCLUSION: Patients receiving UE transplantation often require one or more secondary procedures which may vary with level of transplantation. Secondary surgery should be an important aspect of pretransplant planning and cost-effectiveness determinations. LEVEL OF EVIDENCE: Level IV.

Pd(II)-Mediated C-H Activation for Cysteine Bioconjugation.

Selective bioconjugation remains a significant challenge for the synthetic chemist due to the stringent reaction conditions required by biomolecules coupled with their high degree of functionality. The current trailblazer of transition-metal mediated bioconjugation chemistry involves the use of Pd(II) complexes prepared via an oxidative addition process. Herein, the preparation of Pd(II) complexes for cysteine bioconjugation via a facile C-H activation process is reported. These complexes show bioconjugation efficiency competitive with what is seen in the current literature, with a user-friendly synthesis, common Pd(II) sources, and a more cost-effective ligand. Furthermore, these complexes need not be isolated, and still achieve high conversion efficiency and selectivity of a model peptide. These complexes also demonstrate the ability to selectively arylate a single surface cysteine residue on a model protein substrate, further demonstrating their utility.

Alignment facility and software for single-crystal time-of-flight neutron spectroscopy.

An instrument and software algorithm are described for the purpose of characterization of large single crystals at the Alignment Facility of the ISIS spallation neutron source. A method for both characterizing the quality of the sample and aligning it in a particular scattering plane is introduced. A software package written for this instrument is presented, and its utility is demonstrated by way of an example of the structural characterization of large single crystals of Pb(Mg1/3Nb2/3)O3. Extensions and modifications of characterization instruments for future improved beamlines are suggested. It is hoped that this software will be used by the neutron community for pre-characterizing large single crystals for spectroscopy experiments and that in the future such a facility will be included as part of the spectroscopy suite at other spallation neutron sources.

Ratiometric Electrochemistry: Improving the Robustness, Reproducibility and Reliability of Biosensors.

Electrochemical biosensors are an increasingly attractive option for the development of a novel analyte detection method, especially when integration within a point-of-use device is the overall objective. In this context, accuracy and sensitivity are not compromised when working with opaque samples as the electrical readout signal can be directly read by a device without the need for any signal transduction. However, electrochemical detection can be susceptible to substantial signal drift and increased signal error. This is most apparent when analysing complex mixtures and when using small, single-use, screen-printed electrodes. Over recent years, analytical scientists have taken inspiration from self-referencing ratiometric fluorescence methods to counteract these problems and have begun to develop ratiometric electrochemical protocols to improve sensor accuracy and reliability. This review will provide coverage of key developments in ratiometric electrochemical (bio)sensors, highlighting innovative assay design, and the experiments performed that challenge assay robustness and reliability.

Latissimus Dorsi Myocutaneous Flap Procedure in a Swine Model.

BACKGROUND: As surgical research expands in both breadth and scope, translational models become increasingly important. The accessibility, reproducibility, and clinical applicability of translational models is of vital importance to ensure adequate and accurate research. Though different flap models have been described, the literature lacks an in-depth, technical description of an easy large-animal preclinical model. We here describe the procedure for elevation of a latissimus dorsi flap in a swine. This flap contains muscle and skin that can be isolated on a vascular pedicle, transferred as a free flap, perfused, or innervated/denervated as dictated by the needs of the experiment. METHODS: Five different latissimus dorsi flaps were elevated in miniature swine. Careful attention was paid to anatomical landmarks and optimal placement of incision, dissection, and retraction. Temporary ischemia with vascular clamping was performed along with serial digital and infrared imaging both intra- and postoperatively. In three of the flaps with induced ischemia, the animal was observed for a 30-day follow up with daily photodocumentation and intermittent biopsy. RESULTS: A reproducible latissimus flap model was designed with optimized conditions. In the animals in which flaps were followed postoperatively, complete healing was seen within 30 days without evidence of procedure-related ischemia or loss of motor function. CONCLUSION: We have identified and described a pre-clinical large animal flap model that can be easily reproduced for translational studies of multiple scientific areas including flap-based repair, ischemia, ischemia reperfusion, and operative technique. This provides an important model for ready replication in preclinical studies of many varieties.

Defoliation-induced compensatory transpiration is compromised in SUT4-RNAi Populus.

The tonoplast sucrose transporter PtaSUT4 is well expressed in leaves of Populus tremula × Populus alba (INRA 717-IB4), and its inhibition by RNA-interference (RNAi) alters leaf sucrose homeostasis. Whether sucrose partitioning between the vacuole and the cytosol is modulated by PtaSUT4 for specific physiological outcomes in Populus remains unexplored. In this study, partial defoliation was used to elicit compensatory increases in photosynthesis and transpiration by the remaining leaves in greenhouse-grown poplar. Water uptake, leaf gas exchange properties, growth and nonstructural carbohydrate abundance in source and sink organs were then compared between wild-type and SUT4-RNAi lines. Partial defoliation increased maximum photosynthesis rates similarly in all lines. There was no indication that source leaf sugar levels changed differently between wild-type and RNAi plants following partial defoliation. Sink levels of hexose (glucose and fructose) and starch decreased similarly in all lines. Interestingly, plant water uptake after partial defoliation was not as well sustained in RNAi as in wild-type plants. While the compensatory increase in photosynthesis was similar between genotypes, leaf transpiration increased less robustly in RNAi than wild-type plants. SUT4-RNAi and wild-type source leaves differed constitutively in their bulk modulus of elasticity, a measure of leaf turgor, and storage water capacitance. The data demonstrate that reduced sucrose partitioning due to PtaSUT4-RNAi altered turgor control and compensatory transpiration capacity more strikingly than photosynthesis and sugar export. The results are consistent with the interpretation that SUT4 may control vacuolar turgor independently of sink carbon provisioning.

Atypical Mycobacterial Infections After Plastic Surgery Procedures Abroad: A Multidisciplinary Algorithm for Diagnosis and Treatment.

BACKGROUND: The recent rise in medical tourism, especially for cosmetic procedures, has been mirrored by an increase in the incidence of infections with Mycobacterium abscessus, which is an atypical mycobacterium that is ubiquitous in aquatic environments. M. abscessus soft tissue infections arise from the use of improperly sterilized water and surgical equipment during surgical procedures, and these infections have devastating consequences if not promptly treated. M. abscessus infections are notoriously difficult to diagnose and properly treat, and therefore, we illustrate a typical case presentation and provide a comprehensive diagnostic and treatment algorithm. METHODS: Of the patients who have presented to our hospital for treatment of cutaneous M. abscessus infections, a representative patient's story was included to illustrate the typical presentation and treatment timeline. The current literature on M. abscessus infections was reviewed, and this literature and the clinical experience of our plastic surgery and infectious disease teams were used in the creation of a diagnostic and treatment algorithm for M. abscessus infections. RESULTS: M. abscessus infections can have an incubation period of months, and the classic presenting signs include purulent drainage, violaceous nodules, and subcutaneous abscesses at the site of a recent surgery. A key finding is persistence of the infection despite debridement and empiric antibiotic treatment. Cultures grown on mycobacterial-specific growth media are considered the diagnostic criterion standard, but high clinical suspicion is enough to warrant the initiation of treatment. Treatment itself consists of surgical drainage and debridement in combination with multidrug antibiotic regimens that typically include amikacin, a macrolide, and a carbapenem or cephalosporin antibiotic, with the option for macrolide and fluoroquinolone maintenance therapy. CONCLUSIONS: M. abscessus cutaneous infections present with unique history and physical examination findings and often require complex diagnostic workups and treatment plans. Increased provider awareness of the management and potential complications of M. abscessus is crucial to the improvement patient outcomes, as is a multidisciplinary approach that incorporates primary care providers, pathologists, plastic surgeons, and infectious disease specialists.

A non-catalytic function of carbonic anhydrase IX contributes to the glycolytic phenotype and pH regulation in human breast cancer cells.

The most aggressive and invasive tumor cells often reside in hypoxic microenvironments and rely heavily on rapid anaerobic glycolysis for energy production. This switch from oxidative phosphorylation to glycolysis, along with up-regulation of the glucose transport system, significantly increases the release of lactic acid from cells into the tumor microenvironment. Excess lactate and proton excretion exacerbate extracellular acidification to which cancer cells, but not normal cells, adapt. We have hypothesized that carbonic anhydrases (CAs) play a role in stabilizing both intracellular and extracellular pH to favor cancer progression and metastasis. Here, we show that proton efflux (acidification) using the glycolytic rate assay is dependent on both extracellular pH (pHe) and CA IX expression. Yet, isoform-selective sulfonamide-based inhibitors of CA IX did not alter proton flux, which suggests that the catalytic activity of CA IX is not necessary for this regulation. Other investigators have suggested the CA IX co-operates with the MCT transport family to excrete protons. To test this possibility, we examined the expression patterns of selected ion transporters and show that members of this family are differentially expressed within the molecular subtypes of breast cancer. The most aggressive form of breast cancer, triple-negative breast cancer, appears to co-ordinately express the monocarboxylate transporter 4 (MCT4) and carbonic anhydrase IX (CA IX). This supports a possible mechanism that utilizes the intramolecular H+ shuttle system in CA IX to facilitate proton efflux through MCT4.