A document by Katherine Whitehouse. Click on the document to view its contents.

Mycobacterium abscessus (Mab) is highly drug resistant, and understanding regulation of antibiotic resistance is critical to future antibiotic development. Regulatory mechanisms controlling Mab’s β-lactamase (Bla Mab) that mediates β-lactam resistance remain unknown. S. aureus encodes a prototypical protease-mediated two-component system BlaRI regulating the β-lactamase BlaZ. BlaR binds extracellular β-lactams, activating an intracellular peptidase domain which cleaves BlaI to derepress blaZ. Mtb encodes homologs of BlaRI, that regulate the Mtb β-lactamase, blaC, but also additional genes related to respiration. We identified orthologs of blaRIMtb in Mab and hypothesized that they regulate blaMab. Surprisingly, neither deletion of blaRIMab nor overexpression of only blaIMab altered blaMab expression or β-lactam susceptibility. However, BlaI Mab did bind to conserved motifs upstream of several Mab genes involved in respiration, yielding a putative regulon that partially overlapped with BlaI Mtb. Prompted by evidence that respiration inhibitors including clofazimine (CFZ) induce the BlaI regulon in Mtb, we found that CFZ triggers induction of blaIRMab and its downstream regulon. Highlighting an important role for BlaRI Mab in adapting to disruptions in energy metabolism, constitutive repression of the BlaI Mab regulon rendered Mab highly susceptible to CFZ. In addition to our unexpected findings that BlaIR Mab does not regulate β-lactam resistance, this study highlights the novel role for mycobacterial BlaRI-type regulators in regulating electron transport and respiration.

There is an urgent need for woodland expansion to help mitigate climate change and biodiversity loss. However, the process of natural regeneration of forest ecosystems is often slow, requiring active reforestation approaches. Factors limiting regeneration are complex, but there is increasing evidence that natural expansion of woodlands onto sites that have been treeless for a long period of time may be limited by the loss of microbial woodland-soil properties. This study explored the potential role of mycorrhizal associations in facilitating obligate ectomycorrhizal (ECM) tree establishment. We determined the spatial distribution patterns of ECM tree seedlings – Pinus sylvestris and Betula spp. - outwith the existing woodlands, in relation to established dual-mycorrhizal Salix. There was very strong evidence that ECM tree seedlings were more likely to be found growing within groups around dual-mycorrhizal Salix than as isolated individuals, supporting the view that Salix drives the current spatial distribution patterns by supporting tree establishment. We suggest that the ability of Salix to form dual-mycorrhizal associations with both arbuscular (AM) and ECM fungi allows these plants to become established across the open AM dominated vegetation. Over time these plants can become colonised by ECM fungi via aerial spores and then act as a source of inoculum for obligate ECM tree seedlings, which land as seeds in the vicinity of Salix. This study highlights the potential role of dual-mycorrhizal Salix as a nurse plant in supporting secondary forest succession of obligate ECM boreal/temperate woodland species onto adjacent open areas through nucleation. Overall, we concluded that there is potential for existing ECM networks to aid tree establishment and propose a nature-based approach to maximize reforestation efforts by targeting existing symbiotic fungal networks as nucleation points for tree planting. Our findings contribute to understanding the ecological dynamics involved in woodland expansion and restoration.

Juvenile growth rate is a critical demographic parameter, as it shortens time to maturity and often dictates how long individuals remain vulnerable to predation. However, developing a mechanistic understanding of the factors determining growth rates can be difficult for wild populations. The gopher tortoise (Gopherus polyphemus) is an ecosystem engineer threatened by habitat loss and deficient management of pinelands in the southeastern United States. We investigated the factors governing immature gopher tortoise growth and explored use of drone-based imagery for habitat assessment by comparing predictive models based on ground-based plant surveys versus drone-derived data. From 2021-2022, we tracked and measured immature tortoises in native sandhill and human-modified, ruderal habitat in south-central Florida. Using quarterly, high-resolution drone imagery, we quantified plant cover types and vegetation indices at each occupied burrow, and measured frequency of occurrence of forage species by hand. Annual growth rates of immature tortoises in ruderal habitat were higher than those in sandhill and were the highest published for this species. Models based on drone-derived data were able to explain similar proportions of variation in growth as ground-collected measures of forage, especially during the late dry season when both types of models were most predictive. Habitat differences in forage nitrogen content were also more pronounced during this season, when dominant ground cover in ruderal habitat (bahiagrass) had much higher nitrogen content than dominant ground cover in sandhill (wiregrass). Despite concerns about potential growth-survival trade-offs, tortoises in ruderal habitat did not exhibit lower apparent survival. Our findings indicate that habitat dominated by nutritious non-native grass can provide a valuable supplement to native sandhill through the mechanism of increased growth rates due to higher forage quality. Finally, our study demonstrates that drone technology may facilitate management by providing less labor-intensive ways to assess habitat quality for this and other imperiled herbivores.

Large language models (LLMs) have been touted to enable increased productivity in many areas of today’s work life. Scientific research as an area of work is no exception: the potential of LLM-based tools to assist in the daily work of scientists has become a highly discussed topic across disciplines. However, we are only at the very onset of this subject of study. It is still unclear how the potential of LLMs will materialise in research practice. With this study, we give first empirical evidence on the use of LLMs in the research process. We have investigated a set of use cases for LLM-based tools in scientific research, and conducted a first study to assess to which degree current tools are helpful. In this paper we report specifically on use cases related to software engineering; specifically, on generating application code and developing scripts for data analytics and visualisation. While we studied seemingly simple use cases, results across tools differ significantly. Our results highlight the promise of LLM-based tools in general, yet we also observe various issues, particularly regarding the integrity of the output these tools provide.

Pediatric primary myelofibrosis (PMF) is an extremely rare entity which differs from adult disease in both etiology and outcome.[[1, 2]](https://paperpile.com/c/kO3nmc/v7ZT+LtZX) We report a case of aggressive primary pediatric myelofibrosis driven by somatic trisomy 8, JAK2 and SETBP1 mutations. Disease relapsed +45 days post hematopoietic stem cell transplant. Fortunately, our patient responded to weaning immunosuppression and donor lymphocyte infusion (DLI) and remains in remission with only mild liver and skin graft-versus-host-disease (GVHD). This case is unique not only in its similarity to adult disease but in the response to DLI as salvage therapy.

Readers of Chinese characters need to recognize how they are formed in order to identify them correctly. However, our understanding of the cognitive processing of characters in working memory is limited. In Experiment 1, using the character N-back task paradigm, electrophysiological data were recorded from 26 participants to investigate the effects of the visual feature of radicals on neural activity during the character recognition, updating, and maintenance in the N-back task. Results showed that compound characters required longer response times than single-component characters. For the ERPs, the compound character condition had more negative N2pc and lower P300 amplitudes than the single-component character condition. In Experiment 2, data from 26 participants were used to analyze the effect of the phonological feature of radicals on neural activity during the character recognition, updating, and maintenance in the N-back task. Results showed that there was a larger P200 in the irregular character condition than in the regular character condition, but there was no difference between the regular and the irregular characters in the N2pc, P300, and SW components. The visual feature and the phonological feature of the radicals may have different effects on the character processing. This study reveals the neural effects of Chinese character radicals on cognitive processing in a working memory task and provides behavioral and electrophysiological evidence for a theoretical model of verbal working memory subprocesses.

In this case study we present the course of the psychotherapy of Myriam, a 19-year old female with a severe personality disorder and comorbid eating disorder. During the initial assessment she reported high levels of neuroticism that parallel the diagnosis of obsessive-compulsive personality disorder, borderline personality disorder, and anorexia nervosa. Myriam showed a severely impaired personality functioning defined by perfectionism, self-criticism, interpersonal guilt and overcontrol. Her daily experience was shaped by a self-recriminative inner dialogue associated with maladaptive patterns in the form of food, water and sleep restrictions, self-harm behaviors, and suicidal ideation. She accessed an integrative treatment based on individual (Evolutionary Systems Therapy) and group psychotherapy (Mindful Compassion for Perfectionism). At the end of 14-month intervention she remitted from all the categorical diagnoses and showed reliable changes in several measures. These outcomes were maintained at 3-month follow-up. We describe the integrative conceptualization based on Myriam’s perfectionistic self-recrimination patterns, and the consequent treatment that targeted these patterns rather than focusing on symptom reduction exclusively.

Li/Mn-rich layered oxide (LMR) cathode active materials offer remarkably high specific discharge capacity (>250 mAh g-1) stemming from both cationic and anionic redox. The latter necessitates harsh charging conditions to high cathode potentials (>4.5 V vs. Li|Li+), which is accompanied by lattice oxygen release, phase transformation, voltage fade, and transition metal (TM) dissolution. In cells with graphite anode, TM dissolution is particularly detrimental as it initiates electrode crosstalk. Lithium difluorophosphate (LiDFP) is known for its pivotal role in suppressing electrode crosstalk through TM scavenging. In LMR || graphite cells charged to an upper cut-off voltage (UCV) of 4.5 V, effective TM scavenging effects of LiDFP is observed. In contrast, in cells with an UCV of 4.7 V, the scavenging effects is limited due to more severe TM dissolution compared an UCV of 4.5 V. Worth noting, the low solubility limit of the TM scavenging agents, e.g., PO43- and PO3F2-, which are the decomposition products of LiDFP, cannot scavenge additional TMs, even when higher LiDFP concentration are added to the electrolyte and can even worsen the performance.

Achieving successful blinding is a persistent challenge for clinical trials involving transcranial direct current stimulation. Studies involving populations with increased sensory sensitivity, such as children, could be at risk for increased bias from inadequate blinding due to unique sensation of stimulation relative to adults. The objectives of this study were 1) To examine differences in transcranial stimulation blinding between children and young adults and its relationship to sensory sensitivity. 2) To test the efficacy of an ActiSham protocol for participant blinding, compared to a traditional sham protocol. Typically developing right-handed children (N=11, 5-14 yr) and young adults (N=14, 15-25 yr) completed a single-session study to test transcranial stimulation blinding after three conditions counterbalanced across participants: Active, Sham, and ActiSham. Stimulation was paired with a motor learning task to simulate a combinatory neurorehabilitation intervention. After each condition, participants reported if they received real or fake stimulation and their response confidence. To quantify sensory sensitivity, participants completed the Sensory Profile (2nd edition). Compared to a chance level, 1) children and young adults correctly identified Active stimulation, 2) children incorrectly identified Sham and ActiSham stimulation, 3) young adults identified Sham and ActiSham stimulation at chance-level. Blinding accuracy was not related to sensory sensitivity. Children report stimulation as real stimulation with higher confidence for almost all conditions, indicating unsuccessful blinding compared to young adults. Future studies should consider alternative sham protocols or methods to improve blinding in child participants.

Habitat fragmentation reduces gene flow, causing genetic differentiation and diversity loss in endangered species through genetic drift and inbreeding. However, the impact of habitat fragmentation on ectomycorrhizal (ECM) fungi remains unexplored, despite their critical roles in forest ecosystems. Here, we investigated the population genetic structure and the demographic history of Rhizopogon togasawarius, the ECM fungus specifically colonizing the host tree Pseudotsuga japonica, across its entire distribution range (>200 km). These two species are designated as endangered species on the IUCN Red List since they are found only in small, fragmented forests in Japan. We analyzed 236 R. togasawarius individuals from five remaining populations across the Kii Peninsula and the Shikoku Island, separated by a sea channel. Simple sequence repeat (SSR) analyses using 20 loci revealed strong genetic differentiation among populations (FST = 0.255), even significant in the nearest population pair separated by a distance of only 8 km (FST = 0.075), indicating extremely limited gene flow between populations. DIYABC-RF analyses implied that population divergence occurred approximately 6000 generations ago between the two regions, and nearly 1500 generations ago between the nearest populations within Shikoku Island, related to past climate events. Because of prolonged genetic isolation, significant inbreeding was confirmed in four of five populations, where effective population sizes became very small (Ne = 9.0–58.0). Although evaluation of extinction risks for microorganisms is challenging, our conservation genetic results indicated that habitat fragmentation increases extinction risk through population genetic mechanisms, and therefore should not be overlooked in biodiversity conservation efforts.

A document by Aykut Toplama. Click on the document to view its contents.

How to obtain organic electro-optic materials with large electro-optic coefficients, high glass transition temperature, and good optical transparency remains a challenge in this field. To solve this problem, we introduce groups that can undergo Huisgen cycloaddition reactions into the donor and electron bridge of chromophores with large hyperpolarizability using tetrahydroquinoline as the donor. Binary cross-linkable chromophores TLD1-2 with CF3-TCF as the acceptor and chromophores TLD3-4 with 5Fph-TCF as the acceptor were synthesized. After poling and crosslinking, the Tg of TLD1/TLD2 and TLD3/TLD4 were raised to 152 and 174 °C, respectively. The electro-optical coefficients of chromophores TLD1/TLD2 and TLD3/TLD4 were as high as 312 pm/V and 287 pm/V, respectively. The long-term alignment stability test showed that after being left at 85 °C for 500 hours, the cross-linked film TLD3/TLD4 can still maintain more than 98% of the original electro-optical coefficient value, which is higher than that of TLD1/TLD2 (93%). The chromophore TLD3-4 exhibited much blue-shifted maximum absorption wavelengths (~40nm) compared to TLD1-2 which was beneficial for reducing optical loss in the device. The combination of high electro-optic coefficient, strong stability, and excellent optical transparency makes the TLD series of binary cross-linked materials very promising for practical high-performance electro-optic devices.

Understanding the molecular mechanisms of thermal adaptation is crucial to predict the impacts of global warming. However, there is still a lack of research on the effects of rising temperatures over time, and of studies involving different populations from the same species. The present study focuses on these two aspects, which have been shown to be of great importance in understanding how organisms cope and adapt to ongoing changes in their environment. This study investigates the impact of global warming on the gene expression patterns of Drosophila subobscura populations from two different latitudinal locations after 23 generations of thermal evolution. Our results indicate that transcriptomic changes due to selection are contingent on the genetic background of the populations, with the high-latitude population exhibiting more pronounced changes. We found an interplay between plasticity and selection, with the high latitude population showing fewer initial plastic genes and lower levels of adaptive plasticity, but a greater magnitude of change in both plastic and selective responses during evolution under warming conditions compared to its low latitude counterpart. A substantial proportion of the transcriptome was observed to be subject to selection, despite the lack of observable response at the higher level of organisation. The interplay between plasticity and selection may prove to be an essential component in shaping species' evolutionary responses to climate change. Furthermore, the value of conducting studies on multiple populations of the same species is emphasised, given the identification of differences between populations with different backgrounds in several contexts.

A document by Zulin Xiao. Click on the document to view its contents.

Rapid dynamics and remarkable proton conduction induced by confined water in nanospaces have attracted much attentions from researchers, which is crucial for advancing the development of innovative proton conductors and deepening comprehension of proton and water transport mechanisms within biological systems. In this aspect, carbon nanotubes (CNTs) are frequently employed as a research platform. However, they possess certain limitations, such as their inherent electronic conductivity and extreme hydrophobicity, which can impede the accurate assessment and precise regulation of proton conduction. We herein prepared two 2D COFs with different hydrophilic fragment, and obtains maximum acid-free proton conductivity of 3.04×10-4 S cm-1 at 70 °C and 100% RH with Grotthuss type activation energy of 0.14 eV. This is mainly due to that the water molecules in the center of channel form strong hydrogen bonds, enhancing proton dissociation and guiding fast directional diffusion.

Four polycyclic ten-membered lactones possessing unprecedented 10/6/5 tricyclic ring skeleton, named eutypetides A−D (1−4), and an intriguing polyketide containing a hexahydroisobenzofuran-1(3H)-one motif, named eutypetide E (5) were isolated from the ma-rine-derived fungus Eutypella sp. F0219, together with three new related biosynthetic polyketides eutypetides F−H (6−8). The abso-lute configurations of 1−5 were unequivocally determined by single-crystal X-ray diffraction analyses (Cu Kα), and electronic circular dichroism (ECD) calculations. Eutypetides G (7) showed remarkable anti-inflammatory activity and could reduce the mRNA expres-sion of proinflammatory cytokines IL-1β, IL-6, TNF-α, and iNOS induced by LPS. Most notably, compounds 1, 2, and 5 were formed bi-ogenetically from 6−8 via the key intramolecular [4+2] cycloaddition, respectively.

Yeasts in the subphylum Saccharomycotina are found across the globe in disparate ecosystems. A major aim of yeast research is to understand the diversity and evolution of ecological traits, such as carbon metabolic breadth, insect association, and cactophily. This includes studying aspects of ecological traits like genetic architecture or association with other phenotypic traits. Genomic resources in the Saccharomycotina have grown rapidly. Ecological data, however, are still limited for many species, especially those only known from species descriptions where usually only a limited number of strains are studied. Moreover, ecological information is recorded in natural language format limiting high throughput computational analysis. To address these limitations, we developed an ontological framework for the analysis of yeast ecology. A total of 1,088 yeast strains were added to the Ontology of Yeast Environments (OYE) and analyzed in a machine-learning framework to connect genotype to ecology. This framework is flexible and can be extended to additional isolates, species, or environmental sequencing data. Widespread adoption of OYE would greatly aid the study of macroecology in the Saccharomycotina subphylum.