In adult tobacco smokers, adding e-cigarettes to standard smoking cessation counseling increased abstinence at 6 mo.

SOURCE CITATION: Auer R, Schoeni A, Humair JP, et al. Electronic nicotine-delivery systems for smoking cessation. N Engl J Med. 2024;390:601-610. 38354139.

Soil microbial sensitivity to temperature remains unchanged despite community compositional shifts along geothermal gradients.

Climate warming may be exacerbated if rising temperatures stimulate losses of soil carbon to the atmosphere. The direction and magnitude of this carbon-climate feedback are uncertain, largely due to lack of knowledge of the thermal adaptation of the physiology and composition of soil microbial communities. Here, we applied the macromolecular rate theory (MMRT) to describe the temperature response of the microbial decomposition of soil organic matter (SOM) in a natural long-term warming experiment in a geothermally active area in New Zealand. Our objective was to test whether microbial communities adapt to long-term warming with a shift in their composition and their temperature response that are consistent with evolutionary theory of trade-offs between enzyme structure and function. We characterized the microbial community composition (using metabarcoding) and the temperature response of microbial decomposition of SOM (using MMRT) of soils sampled along transects of increasing distance from a geothermally active zone comprising two biomes (a shrubland and a grassland) and sampled at two depths (0-50 and 50-100 mm), such that ambient soil temperature and soil carbon concentration varied widely and independently. We found that the different environments were hosting microbial communities with distinct compositions, with thermophile and thermotolerant genera increasing in relative abundance with increasing ambient temperature. However, the ambient temperature had no detectable influence on the MMRT parameters or the relative temperature sensitivity of decomposition (Q10 ). MMRT parameters were, however, strongly correlated with soil carbon concentration and carbon:nitrogen ratio. Our findings suggest that, while long-term warming selects for warm-adapted taxa, substrate quality and quantity exert a stronger influence than temperature in selecting for distinct thermal traits. The results have major implications for our understanding of the role of soil microbial processes in the long-term effects of climate warming on soil carbon dynamics and will help increase confidence in carbon-climate feedback projections.

Specificity of MYB interactions relies on motifs in ordered and disordered contexts.

Physical interactions between members of the MYB and bHLH transcription factor (TF) families regulate many important biological processes in plants. Not all reported MYB-bHLH interactions can be explained by the known binding sites in the R3 repeat of the MYB DNA-binding domain. Noteworthy, most of the sequence diversity of MYB TFs lies in their non-MYB regions, which contain orphan small subgroup-defining motifs not yet linked to molecular functions. Here, we identified the motif mediating interaction between MYB TFs from subgroup 12 and their bHLH partners. Unlike other known MYB-bHLH interactions, the motif locates to the centre of the predicted disordered non-MYB region. We characterised the core motif, which enabled accurate prediction of previously unknown bHLH-interacting MYB TFs in Arabidopsis thaliana, and we confirmed its functional importance in planta. Our results indicate a correlation between the MYB-bHLH interaction affinity and the phenotypic output controlled by the TF complex. The identification of an interaction motif outside R3 indicates that MYB-bHLH interactions must have arisen multiple times, independently and suggests many more motifs of functional relevance to be harvested from subgroup-specific studies.

Evolution of A bHLH Interaction Motif.

Intrinsically disordered proteins and regions with their associated short linear motifs play key roles in transcriptional regulation. The disordered MYC-interaction motif (MIM) mediates interactions between MYC and MYB transcription factors in Arabidopsis thaliana that are critical for constitutive and induced glucosinolate (GLS) biosynthesis. GLSs comprise a class of plant defense compounds that evolved in the ancestor of the Brassicales order. We used a diverse set of search strategies to discover additional occurrences of the MIM in other proteins and in other organisms and evaluate the findings by means of structural predictions, interaction assays, and biophysical experiments. Our search revealed numerous MIM instances spread throughout the angiosperm lineage. Experiments verify that several of the newly discovered MIM-containing proteins interact with MYC TFs. Only hits found within the same transcription factor family and having similar characteristics could be validated, indicating that structural predictions and sequence similarity are good indicators of whether the presence of a MIM mediates interaction. The experimentally validated MIMs are found in organisms outside the Brassicales order, showing that MIM function is broader than regulating GLS biosynthesis.

Emergence of methicillin resistance and Panton-Valentine leukocidin positivity in hospital- and community-acquired Staphylococcus aureus infections in Beira, Mozambique.

OBJECTIVES: The objective of this study was to investigate the antibiotic resistance patterns, including methicillin resistance, inducible macrolide-lincosamide-streptogramin B (MLSB ) resistance and Panton-Valentine leukocidin (PVL) toxin gene carriage among hospital-acquired Staphylococcus aureus (HA-SA) and community-acquired S. aureus (CA-SA), in Beira, Mozambique. METHODS: In 2010-2011, two prospective surveillance studies were conducted on post-operative and burn wound infections at the Central Hospital of Beira and on skin and soft tissue abscesses at the São Lucas Health Centre. We cultured pus samples, identified suspected S. aureus isolates and performed antimicrobial susceptibility testing, including detection of MLSB resistance. Real-time polymerase chain reaction was used to detect mecA, Martineau and PVL genes. RESULTS: The prevalence of hospital-acquired methicillin-resistant S. aureus (HA-MRSA) infection among 53 inpatients was 15.1%; the prevalence of community-acquired methicillin-resistant S. aureus (CA-MRSA) infection among 100 outpatients was 1.0%. Inducible MLSB resistance was present in 41.7% and 10.7% of HA-SA and CA-SA isolates, respectively. PVL toxin gene was detected in 81.1% of methicillin-susceptible S. aureus (MSSA) compared with 11.1% of methicillin-resistant S. aureus. CONCLUSIONS: Our study shows, for the first time in Mozambique, the emergence of HA-MRSA. The prevalence of CA-MRSA was low, whereas the rate of PVL toxin gene carriage in MSSA was high. The high rate of inducible MLSB resistance indicates the importance of performing routine D-tests. Overall, our results show the need of strengthening laboratory facilities to provide microbiological data for both directed therapy and surveillance.

Evidence of microbial regulation of biogeochemical cycles from a study on methane flux and land use change.

Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles.

Phosphorylation of Schizosaccharomyces pombe Dss1 mediates direct binding to the ubiquitin-ligase Dma1 in vitro.

Intrinsically disordered proteins (IDPs) are often multifunctional and frequently posttranslationally modified. Deleted in split hand/split foot 1 (Dss1-Sem1 in budding yeast) is a highly multifunctional IDP associated with a range of protein complexes. However, it remains unknown if the different functions relate to different modified states. In this work, we show that Schizosaccharomyces pombe Dss1 is a substrate for casein kinase 2 in vitro, and we identify three phosphorylated threonines in its linker region separating two known disordered ubiquitin-binding motifs. Phosphorylations of the threonines had no effect on ubiquitin-binding but caused a slight destabilization of the C-terminal α-helix and mediated a direct interaction with the forkhead-associated (FHA) domain of the RING-FHA E3-ubiquitin ligase defective in mitosis 1 (Dma1). The phosphorylation sites are not conserved and are absent in human Dss1. Sequence analyses revealed that the Txx(E/D) motif, which is important for phosphorylation and Dma1 binding, is not linked to certain branches of the evolutionary tree. Instead, we find that the motif appears randomly, supporting the mechanism of ex nihilo evolution of novel motifs. In support of this, other threonine-based motifs, although frequent, are nonconserved in the linker, pointing to additional functions connected to this region. We suggest that Dss1 acts as an adaptor protein that docks to Dma1 via the phosphorylated FHA-binding motifs, while the C-terminal α-helix is free to bind mitotic septins, thereby stabilizing the complex. The presence of Txx(D/E) motifs in the disordered regions of certain septin subunits may be of further relevance to the formation and stabilization of these complexes.

Roots affect the response of heterotrophic soil respiration to temperature in tussock grass microcosms.

AIMS AND BACKGROUND: While the temperature response of soil respiration (R(S)) has been well studied, the partitioning of heterotrophic respiration (R(H)) by soil microbes from autotrophic respiration (R(A)) by roots, known to have distinct temperature sensitivities, has been problematic. Further complexity stems from the presence of roots affecting R(H), the rhizosphere priming effect. In this study the short-term temperature responses of R(A) and R(H) in relation to rhizosphere priming are investigated. METHODS: Temperature responses of R(A), R(H) and rhizosphere priming were assessed in microcosms of Poa cita using a natural abundance δ(13)C discrimination approach. RESULTS: The temperature response of R(S) was found to be regulated primarily by R(A), which accounted for 70 % of total soil respiration. Heterotrophic respiration was less sensitive to temperature in the presence of plant roots, resulting in negative priming effects with increasing temperature. CONCLUSIONS: The results emphasize the importance of roots in regulating the temperature response of R(S), and a framework is presented for further investigation into temperature effects on heterotrophic respiration and rhizosphere priming, which could be applied to other soil and vegetation types to improve models of soil carbon turnover.

Challenges in measuring the δ13C of the soil surface CO2 efflux.

The δ13C of the soil surface efflux of carbon dioxide (δ13CRS) has emerged as a powerful tool enabling investigation of a wide range of soil processes from characterising entire ecosystem respiration to detailed compound-specific isotope studies. δ13CRS can be used to trace assimilated carbon transfer below ground and to partition the overall surface efflux into heterotrophic and autotrophic components. Despite this wide range of applications no consensus currently exists on the most appropriate method of sampling this surface efflux of CO2 in order to measure δ13CRS. Here we consider and compare the methods which have been used, and examine the pitfalls. We also consider a number of analysis options, isotope ratio mass spectrometry (IRMS), tuneable diode laser spectroscopy (TDLS) and cavity ring-down laser spectroscopy (CRDS). δ13CRS is typically measured using chamber systems, which fall into three types: closed, open and dynamic. All are imperfect. Closed chambers often rely on Keeling plots to estimate δ13CRS, which may not be appropriate without free turbulent air mixing. Open chambers have the advantage of being able to maintain steady-state conditions but analytical errors may become limiting with low efflux rates. Dynamic chambers like open chambers are complex, and controlling pressure fluctuations caused by air movement is a key concern. Both open and dynamic chambers in conjunction with field portable TDLS and CRDS analysis systems have opened up the possibility of measuring δ13CRS in real time permitting new research opportunities and are on balance the most suited to this type of measurement.

Measuring and modelling occupancy time in NHS continuing healthcare.

BACKGROUND: Due to increasing demand and financial constraints, NHS continuing healthcare systems seek to find better ways of forecasting demand and budgeting for care. This paper investigates two areas of concern, namely, how long existing patients stay in service and the number of patients that are likely to be still in care after a period of time. METHODS: An anonymised dataset containing information for all funded admissions to placement and home care in the NHS continuing healthcare system was provided by 26 (out of 31) London primary care trusts. The data related to 11289 patients staying in placement and home care between 1 April 2005 and 31 May 2008 were first analysed. Using a methodology based on length of stay (LoS) modelling, we captured the distribution of LoS of patients to estimate the probability of a patient staying in care over a period of time. Using the estimated probabilities we forecasted the number of patients that are likely to be still in care after a period of time (e.g. monthly). RESULTS: We noticed that within the NHS continuing healthcare system there are three main categories of patients. Some patients are discharged after a short stay (few days), some others staying for few months and the third category of patients staying for a long period of time (years). Some variations in proportions of discharge and transition between types of care as well as between care groups (e.g. palliative, functional mental health) were observed. A close agreement of the observed and the expected numbers of patients suggests a good prediction model. CONCLUSIONS: The model was tested for care groups within the NHS continuing healthcare system in London to support Primary Care Trusts in budget planning and improve their responsiveness to meet the increasing demand under limited availability of resources. Its applicability can be extended to other types of care, such as hospital care and re-ablement. Further work will be geared towards updating the dataset and refining the results.

Nitrogen storage and remobilization by trees: ecophysiological relevance in a changing world.

The role of carbon (C) and nitrogen (N) storage by trees will be discussed in terms of uncoupling their growth from resource acquisition. There are profound differences between the physiology of C and N storage. C storage acts as a short-term, temporary buffer when photosynthesis cannot meet current sink demand and remobilization is sink driven. However, the majority of C allocated to non-structural carbohydrates such as starch is not reused so is in fact sequestered, not stored. In contrast, N storage is seasonally programmed, closely linked to tree phenology and operates at temporal scales of months to years, with remobilization being source driven. We examine the ecological significance of N storage and remobilization in terms of regulating plant N use efficiency, allowing trees to uncouple seasonal growth from N uptake by roots and allowing recovery from disturbances such as browsing damage. We also briefly consider the importance of N storage and remobilization in regulating how trees will likely respond to rising atmospheric carbon dioxide concentrations. Most studies of N storage and remobilization have been restricted to small trees growing in a controlled environment where (15)N can be used easily as a tracer for mineral N. We highlight the need to describe and quantify these processes for adult trees in situ where most root N uptake occurs via ectomycorrhizal partners, an approach that now appears feasible for deciduous trees through quantification of the flux of remobilized N in their xylem. This opens new possibilities for studying interactions between N and C allocation in trees and associated mycorrhizal partners, which are likely to be crucial in regulating the response of trees to many aspects of global environmental change.

Remobilization of acorn nitrogen for seedling growth in holm oak (Quercus ilex), cultivated with contrasting nutrient availability.

The relative contribution of nitrogen (N) reserves from seeds or uptake by the roots to the growth and N content of young seedlings has received little attention. In this study, we investigated the contribution of N from the acorn or uptake by the roots to the N content of holm oak (Quercus ilex L.) seedlings and determined if remobilization of acorn N was affected by nutrient availability in the growing media. Q. ilex seedlings were cultivated for 3 months, until the end of the second shoot flush of growth, with three N fertilization rates: 8.6 mM N, 1.4 mM N or no fertilization. Fertilizer N was enriched in (15)N. Between 62 and 75% of the N contained in high and low fertilized seedlings, respectively, at the end of the second flush of growth was derived from the acorn. However, the dependence on acorn N was greater during the early root growth and first shoot flush of growth and decreased during the second shoot flush of growth, with root uptake contributing 32-54% of plant new N in this latter developmental stage in high and low fertilized plants, respectively. Fertilization rate did not affect the amount of N taken up during the earliest developmental stages, but it increased it during the second shoot flush of growth. Fertilization increased the mass of the shoot segment formed during the second shoot flush of growth and reduced the root mass, with no effect on whole plant growth. Remobilization of acorn N was faster in unfertilized plants than in fertilized plants. It is concluded that the holm oak seedlings depend greatly upon acorn N until the end of the second shoot flush of growth, that significant root N uptake starts at the beginning of the second shoot flush of growth and that acorn N remobilization is a plastic process that is accelerated under extremely low substratum nutrient content.

Minimally invasive, sutureless, adolescent male circumcision with topical anesthetic: a field trial of Unicirc, a single-use surgical instrument.

BACKGROUND: Circumcision has been shown to reduce the rate of HIV transmission in Africa. It is most cost effective if performed in younger men. Surgical assist devices can increase the efficiency and potentially reduce the cost of performing circumcisions. METHODS: We used the Unicirc disposable instrument to perform circumcisions in an outpatient primary care clinic. The trial was non-blinded. Circumcisions were performed under topical anaesthetic and the wound was sealed with cyanoacrylate tissue adhesive. The primary outcome was intraoperative duration; secondary outcomes were intraoperative and postoperative pain; adverse events (AEs); time to healing and patient satisfaction; and, cosmetic result. RESULTS: A total of 82 adolescent boys (aged 10-15 years) were circumcised. The median intraoperative time was 10 minutes and the median blood loss was 1 mL. All wounds were healed by 4 weeks and cosmetic results were excellent. There were no AEs. CONCLUSIONS: Adolescent circumcision with Unicirc under topical anesthetic and wound sealing with cyanoacrylate tissue adhesive is safe, rapid, and heals by primary intention with excellent cosmetic results. It is cost effective and can be used for large scale programs.

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors.

Protein domains constitute regions of distinct structural properties and molecular functions that are retained when removed from the rest of the protein. However, due to the lack of tertiary structure, the identification of domains has been largely neglected for long (>50 residues) intrinsically disordered regions. Here we present a sequence-based approach to assess and visualize domain organization in long intrinsically disordered regions based on compositional sequence biases. An online tool to find putative intrinsically disordered domains (IDDomainSpotter) in any protein sequence or sequence alignment using any particular sequence trait is available at http://www.bio.ku.dk/sbinlab/IDDomainSpotter. Using this tool, we have identified a putative domain enriched in hydrophilic and disorder-promoting residues (Pro, Ser, and Thr) and depleted in positive charges (Arg and Lys) bordering the folded DNA-binding domains of several transcription factors (p53, GCR, NAC46, MYB28, and MYB29). This domain, from two different MYB transcription factors, was characterized biophysically to determine its properties. Our analyses show the domain to be extended, dynamic and highly disordered. It connects the DNA-binding domain to other disordered domains and is present and conserved in several transcription factors from different families and domains of life. This example illustrates the potential of IDDomainSpotter to predict, from sequence alone, putative domains of functional interest in otherwise uncharacterized disordered proteins.

No preferential carbon-allocation to storage over growth in clipped birch and oak saplings.

Herbivory is one of the most globally distributed disturbances affecting carbon (C)-cycling in trees, yet our understanding of how it alters tree C-allocation to different functions such as storage, growth or rhizodeposition is still limited. Prioritized C-allocation to storage replenishment vs growth could explain the fast recovery of C-storage pools frequently observed in growth-reduced defoliated trees. We performed continuous 13C-labeling coupled to clipping to quantify the effects of simulated browsing on the growth, leaf morphology and relative allocation of stored vs recently assimilated C to the growth (bulk biomass) and non-structural carbohydrate (NSC) stores (soluble sugars and starch) of the different organs of two tree species: diffuse-porous (Betula pubescens Ehrh.) and ring-porous (Quercus petraea [Matt.] Liebl.). Carbon-transfers from plants to bulk and rhizosphere soil were also evaluated. Clipped birch and oak trees shifted their C-allocation patterns above-ground as a means to recover from defoliation. However, such increased allocation to current-year stems and leaves did not entail reductions in the allocation to the rhizosphere, which remained unchanged between clipped and control trees of both species. Betula pubescens and Q. petraea showed differences in their vulnerability and recovery strategies to clipping, the ring-porous species being less affected in terms of growth and architecture by clipping than the diffuse-porous. These contrasting patterns could be partly explained by differences in their C cycling after clipping. Defoliated oaks showed a faster recovery of their canopy biomass, which was supported by increased allocation of new C, but associated with large decreases in their fine root biomass. Following clipping, both species recovered NSC pools to a larger extent than growth, but the allocation of 13C-labeled photo-assimilates into storage compounds was not increased as compared with controls. Despite their different response to clipping, our results indicate no preventative allocation into storage occurred during the first year after clipping in either of the species.

Temperature sensitivity of decomposition decreases with increasing soil organic matter stability.

Evaluation of the temperature sensitivity of soil organic matter (SOM) decomposition is critical for forecasting whether soils in a warming world will lose or gain carbon and, therefore, accelerate or mitigate climate warming. It is usually described, using Arrhenius kinetics, as increasing with the stability of the substrate in laboratory conditions, where substrate availability is non-limiting and where chemical recalcitrance, therefore, predominantly regulates stability. However, conditions of non-limiting subtrate availability are rare in the undisturbed soil, where physicochemical protection of substrates may control their stability. The aim of this study was to assess the temperature sensitivity of decomposition of SOM with contrasting stability in the field. Our conceptual approach was based on in situ measurements of soil CO2 efflux at a range of temperatures from root exclusion plots of increasing age (1 month and three decades) and, therefore, with SOM of increasing stability. From a set of short-term measurements in spring, using diurnal temperature variation, the relative temperature sensitivity of SOM decomposition decreased significantly (p < 0.0001) with increasing SOM stability, and was weak (Q10 < 1.3) in long-term root exclusion plots. This result was confirmed in a similar set of short-term measurements repeated later in the year, in summer, as well as from an analysis perfomed at the seasonal timscale. We provide direct field evidence that the temperature sensitivity of SOM decomposition decreases with increasing stability, in direct contrast with Arrhenius kinetics prediction, and therefore show that stability of SOM in the field cannot be the sole result of chemical recalcitrance. We conclude that the physicochemical protection of SOM, which controls SOM stability in the field, constrains the temperature sensitivity of SOM decomposition under field conditions.

Surplus Carbon Drives Allocation and Plant-Soil Interactions.

Plant growth is usually constrained by the availability of nutrients, water, or temperature, rather than photosynthetic carbon (C) fixation. Under these conditions leaf growth is curtailed more than C fixation, and the surplus photosynthates are exported from the leaf. In plants limited by nitrogen (N) or phosphorus (P), photosynthates are converted into sugars and secondary metabolites. Some surplus C is translocated to roots and released as root exudates or transferred to root-associated microorganisms. Surplus C is also produced under low moisture availability, low temperature, and high atmospheric CO2 concentrations, with similar below-ground effects. Many interactions among above- and below-ground ecosystem components can be parsimoniously explained by the production, distribution, and release of surplus C under conditions that limit plant growth.

Through the eye of the needle: a review of isotope approaches to quantify microbial processes mediating soil carbon balance.

For soils in carbon balance, losses of soil carbon from biological activity are balanced by organic inputs from vegetation. Perturbations, such as climate or land use change, have the potential to disrupt this balance and alter soil-atmosphere carbon exchanges. As the quantification of soil organic matter stocks is an insensitive means of detecting changes, certainly over short timescales, there is a need to apply methods that facilitate a quantitative understanding of the biological processes underlying soil carbon balance. We outline the processes by which plant carbon enters the soil and critically evaluate isotopic methods to quantify them. Then, we consider the balancing CO(2) flux from soil and detail the importance of partitioning the sources of this flux into those from recent plant assimilate and those from native soil organic matter. Finally, we consider the interactions between the inputs of carbon to soil and the losses from soil mediated by biological activity. We emphasize the key functional role of the microbiota in the concurrent processing of carbon from recent plant inputs and native soil organic matter. We conclude that quantitative isotope labelling and partitioning methods, coupled to those for the quantification of microbial community substrate use, offer the potential to resolve the functioning of the microbial control point of soil carbon balance in unprecedented detail.