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Water resource utilization and future supply–demand scenarios in energy cities of semi-arid regions
The revised elastic field of an edge dislocation
We modify the traditional linear-elastic field of an edge dislocation. The modifications stem from symmetry and energy requirements imposed in terms of embedded (deformed) coordinates. These requirements are satisfied if a line force is added to the dislocation field. The modification to the stress field is expressed by coefficients that are a function only of Poisson’s ratio. Qualitatively, the field of the dislocation is increased in the glide direction and decreased in the climb direction. There are small changes to the field of a screw dislocation that do not entail the addition of a line force. Effects of nonlinearity, anisotropic elasticity, and image forces are briefly considered.
Validation of two swabbing methods to sample DNA for genotyping Atlantic bluefin tuna (Thunnus thynnus)
Abstract In fisheries, genetic based assignment of individuals to their population of origin can benefit efforts aimed at monitoring and managing stocks. Assignment combined with knowledge of the migration history of individuals can provide powerful insights into mechanisms of genetic mixing, for which refined sampling methods are required to minimise any impacts. In this study we tested two minimally invasive swabbing techniques for sampling DNA when attaching electronic satellite tags to Atlantic bluefin tuna (Thunnus thynnus) for migration studies. First, DNA was sampled by skin swabbing (hereafter skin swabs) individuals from which there were corresponding fin clip samples. Second, swabs were taken from the applicator poles used to attach electronic tags (hereafter pole swabs). Quantification of DNA from the different sources revealed decreasing yields moving from fin clips, to skin swabs, to pole swabs. The utility of the DNA obtained by both swabbing methods for individual genotyping was then assessed by sequencing of the mtDNA control region and genotyping of six microsatellite loci. In all cases successful genotyping was achieved. For mtDNA an 868 bp fragment was successfully amplified in all samples with 775 bp aligned across individuals revealing 26 haplotypes (overall haplotype diversity = 0.987). All six microsatellites were successfully amplified including a largest allele size of 291 bp. mtDNA and microsatellite genotypes for the skin swabs matched with the corresponding fin clip samples. Although no tissue replicates were available for the pole swab samples the genotypes obtained were unambiguous, consistent across repeated PCRs, and reported no evidence of PCR issues such as large allele drop out. Overall, the genetic data suggested high variability among individuals sampled, comparable to levels of genetic diversity seen within the species’ Atlantic range. The study demonstrates that non-invasive sampling can be used to obtain DNA for population assignment studies and that valuable material can be sampled from tagging equipment.
Identification of a central regulator of ginkgolide biosynthesis in <i>Ginkgo biloba</i> that integrates jasmonate and light signaling
Ginkgolides are secondary metabolites unique to Ginkgo biloba with the potential to prevent and treat cardiovascular and cerebrovascular diseases. Although the biosynthetic pathways of ginkgolides have been partly uncovered, the mechanism regulating their biosynthesis is still largely unknown. Here, using multiomic and genetic analyses, we report the identification of a transcription factor, named ETHYLENE RESPONSE FACTOR ASSOCIATED WITH GINKGOLIDE BIOSYNTHESIS (GbEAG), as a critical regulator of ginkgolide biosynthesis. GbEAG is highly expressed in the roots of G. biloba, and its expression is significantly induced by methyl jasmonate (MeJA). Ginkgolide content was significantly increased in roots by overexpressing GbEAG using a “cut-dip-regeneration” system. GbEAG positively regulates ginkgolide biosynthesis by directly binding to the GCC-boxes in the promoter regions of genes involved in the biosynthesis of ginkgolides, such as ISOPENTENYL DIPHOSPHATE ISOMERASE ( GbIDI ) and CYTOCHROME P450 7005C3 ( GbCYP7005C3 ). GbEAG mediates the jasmonic acid (JA)-activated ginkgolide synthesis through its direct interaction with the JASMONATE ZINC-FINGER INFLORESCENCE MERISTEM DOMAIN 3 (GbJAZ3) repressor. Importantly, we also found that the central light-response regulator ELONGATED HYPOCOTYL 5 (GbHY5) mediates light induction of ginkgolide biosynthesis by binding to the G-box in the GbEAG promoter. Our findings provide mechanistic insights into the coordinated regulation of ginkgolide biosynthesis via JA and light signals, with GbEAG as a central regulator in G. biloba, and shed light on the potential to develop ginkgolide-rich varieties through molecular breeding and gene editing.
Development and validation of a predictive model for carotid atherosclerosis in postmenopausal women
Biochemical and structural bases for talin ABSs–F-actin interactions
Focal adhesions (FAs) are large intracellular macromolecular assemblies that play a critical role in cell polarization and migration. Talin serves as a direct connection between integrin receptor and actomyosin cytoskeleton within FAs. Talin contains three actin-binding sites (ABS1-3) that engage discreetly during the development of FAs, thus acting as a critical player in FA initiation and maturation. However, the molecular basis of the ABS–F-actin interactions remains unknown. Here, we explore interactions of ABSs with F-actin to understand the multivalent behavior of talin. Particularly, the cryo-EM structure of the F-actin–ABS3 complex at 2.9 Å shows ABS3 spanning through two actin monomers along the filament axis, each occupied by the R13 rod subdomain and the DD domain. The dimerization of ABS3 occurs through the DD domain where both protomers interact on the actin surface, and the dimerization of talin to the actin surface is necessary for the engagement to F-actin. The R13 helical bundle is distorted upon binding to F-actin and releases the H1 helix from the rest of the bundle. This phenomenon has also been observed with other tension-sensing proteins like vinculin and α-catenin, highlighting that unfolding is relevant for its force sensing activity. On the contrary, ABS2 (R4R8 subdomains), which is thought to be critical for the maintenance of mature FAs, had multiple F-actin-binding regions within ABS2 and the binding likely occurred by these subdomains running through the surface of F-actin, thus strengthening the interactions upon the maturation of FAs.
Vibrotactile stimulus duration threshold for perception of pulse to vibration transition
Abstract This study investigates the minimum stimulus duration required to perceive the transition from pulse to vibration sensations, a critical parameter for optimizing information transmission via haptic interfaces such as smartphones, tablets, smartwatches, game consoles, and sensory substitution systems. Efficient transmission relies on minimizing stimulus duration, enabling more information to be conveyed in less time. A preliminary experiment established intensity perception thresholds—the minimum vibration intensities detectable—at 40, 80, 150, 250, 300, and 590 Hz, frequencies primarily activating the Pacinian (Rapid Adapting II) psychophysical channel. Subsequently, 35 participants determined the minimum durations needed to perceive the transition from pulse to vibration sensations across this frequency range. Results revealed a consistent minimum duration of approximately 30 ms, contrasting with findings in audition, where shorter durations suffice at higher frequencies, but aligning with prior studies in tactile perception.
Human MAIT cell response profiles biased toward IL-17 or IL-10 are distinct effector states directed by the cytokine milieu
Mucosal-associated invariant T (MAIT) cells are unconventional T cells that mediate rapid antimicrobial immune responses to antigens derived from microbial riboflavin pathway metabolites presented by the evolutionarily conserved MR1 molecules. MAIT cells represent a large pre-expanded T cell subset in humans and are involved in both protective immunity and inflammatory immunopathology. However, what controls the functional heterogeneity of human MAIT cell responses is still largely unclear. Here, combining functional and transcriptomic analyses, we investigate how MAIT cell response programs are influenced by the cytokine milieu at the time of antigen recognition. Activation by MR1-presented antigen together with IL-12 induces intermediate levels of IFNγ and TNF, as well as a regulatory profile with substantial IL-10 production and elevated expression of TIM-3, LAG-3, and PD-1. Activation by the combination of antigen and IL-12 induces a c-MAF-dependent program required for IL-10 production. The MAIT cell-derived IL-10 mediates both autocrine and paracrine immune regulation. In contrast, coactivation of MAIT cells with IL-18 induces IL-17, GM-CSF, IFNγ, and TNF, without IL-10. Notably, IL-18 dominantly counteracts IL-10 expression. The activation states biased toward IL-10 or IL-17 production are reversible and do not represent stable subsets. Finally, MR1-restricted TCR-mediated activation without cytokine coactivation drives primarily granzyme B cytolytic arming. Altogether, these findings demonstrate that human MAIT cells adapt their functional effector response during antigen recognition to cytokine cues in the microenvironment, and identify programs biased toward either regulatory c-MAF-dependent IL-10 expression, or an inflammatory IL-17 and GM-CSF profile.
Comparative analysis and process optimization for manufacturing CAR-T using the PiggyBac system derived from cryopreserved versus fresh PBMCs
Abstract Chimeric antigen receptor T (CAR-T) therapy holds promise for cancer treatment but faces challenges with using fresh patient cells, including manufacturing failures and logistical hurdles. Cryopreserved peripheral blood mononuclear cells (PBMCs) offer a potential solution, and while lentiviral processes have been reported for generating CAR-T from these cells, few studies have demonstrated successful PiggyBac electroporation methods. Therefore, the objectives of our study were twofold: Firstly, to conduct a comparative study on cryopreserved PBMCs, fresh PBMCs, and their respective preparations of CAR-T. Secondly, to establish a PiggyBac electroporation CAR-T preparation process using cryopreserved PBMCs through process optimization. The results revealed that long-term frozen PBMCs viability in a relatively stable manner. CAR-T generated from cryopreserved PBMCs exhibited comparable expansion potential, cell phenotype, differentiation profiles, exhaustion markers, and cytotoxicity against human ovarian cancer cell line (SKOV-3) cells to those derived from fresh PBMCs. Moreover, through process optimization, we further enhanced the proliferation and toxicity of CAR-T. This approach has the potential to revolutionize the CAR-T production model by utilizing healthy donor cells instead of patient cells. This shift could mitigate issues affecting treatment efficacy, such as suboptimal cell condition following illness or delays in cell preparation.
Creation, stabilization, and investigation at ambient pressure of pressure-induced superconductivity in Bi <sub>0.5</sub> Sb <sub>1.5</sub> Te <sub>3</sub>
In light of breakthroughs in superconductivity under high pressure, and considering that record critical temperatures (T c s) across various systems have been achieved under high pressure, the primary challenge for higher T c should no longer solely be to increase T c under extreme conditions but also to reduce, or ideally eliminate, the need for applied pressure in retaining pressure-induced or -enhanced superconductivity. The topological semiconductor Bi 0.5 Sb 1.5 Te 3 (BST) was chosen to demonstrate our approach to addressing this challenge and exploring its intriguing physics. Under pressures up to ~50 GPa, three superconducting phases (BST-I, -II, and -III) were observed. A superconducting phase in BST-I appears at ~4 GPa, without a structural transition, suggesting the possible topological nature of this phase. Using the pressure-quench protocol (PQP) recently developed by us, we successfully retained this pressure-induced phase at ambient pressure and revealed the bulk nature of the state. Significantly, this demonstrates recovery of a pressure-quenched sample from a diamond anvil cell at room temperature with the pressure-induced phase retained at ambient pressure. Other superconducting phases were retained in BST-II and -III at ambient pressure and subjected to thermal and temporal stability testing. Superconductivity was also found in BST with T c up to 10.2 K, the record for this compound series. While PQP maintains superconducting phases in BST at ambient pressure, both depressurization and PQP enhance its T c , possibly due to microstructures formed during these processes, offering an added avenue to raise T c . These findings are supported by our density-functional theory calculations.
Comparing effects of breathing exercises alone and combined with breathing-stretching exercises on respiratory indices, disease severity and exercise capacity in COPD
Quantifying the impact of air pollution from coal-fired electricity generation on crop productivity in India
Air pollution from coal electricity generation is a major driver of poor air quality in India and its effects on human health have been extensively studied. Despite considerable evidence that the same pollution also reduces crop productivity, we lack similar quantitative assessments of coal electricity’s crop damages. Here, we estimate rice and wheat crop losses from coal generation’s nitrogen dioxide (NO 2 ) emissions using a regression model that combines station-level electricity generation and wind direction, satellite-measured NO 2 , and its association with crop productivity. Coal emissions impact yields up to 100 km away from power stations. In parts of West Bengal, Madhya Pradesh, and Uttar Pradesh heavily exposed to coal-linked NO 2 , annual yield losses exceed 10%, equivalent to approximately 6 y worth of average annual yield growth in both rice and wheat in India between 2011 and 2020. While station-specific crop damages (value of lost output) are almost always lower than mortality damages (monetized value of annual premature PM 2.5 -related deaths), crop damage intensity (crop damage per GWh of electricity generated) is frequently higher than mortality damage intensity (mortality damage/GWh). Rice damage intensity exceeds mortality damage intensity at 58, and wheat damage intensity at 35 of the 144 power stations studied. The stations associated with the largest crop losses differ from those associated with the highest mortality. Co-optimizing for crop gains and mortality reduction slightly increases and meaningfully changes the distribution of social benefits from reducing emissions, highlighting the importance of considering crop losses alongside health impacts when regulating coal electricity emissions in India.
Repeat expansion in a fragile X model is independent of double strand break repair mediated by Pol θ, RAD52, RAD54 or RAD54B
Abstract Microsatellite instability is responsible for the human repeat expansion diseases (REDs). The mutagenic process differs from classical cancer-associated microsatellite instability (MSI) in that it requires the mismatch repair proteins that normally protect against MSI. LIG4, an enzyme essential for non-homologous end-joining (NHEJ), the major pathway for double-strand break repair (DSBR) in mammalian cells, protects against expansion in mouse models. Thus, NHEJ may compete with the expansion pathway for access to a common intermediate. This raises the possibility that expansion involves an NHEJ-independent form of DSBR. Pol θ, a polymerase involved in the theta-mediated end joining (TMEJ) DSBR pathway, has been proposed to play a role in repeat expansion. Here we examine the effect of the loss of Pol θ on expansion in FXD mouse embryonic stem cells (mESCs), along with the effects of mutations in Rad52, Rad54l and Rad54b, genes important for multiple DSBR pathways. None of these mutations significantly affected repeat expansion. These observations put major constraints on what pathways are likely to drive expansion. Together with our previous demonstration of the protective effect of nucleases like EXO1 and FAN1, and the importance of Pol β, they suggest a plausible model for late steps in the expansion process.
High-throughput discovery of inhibitory protein fragments with AlphaFold
Peptides can bind to specific sites on larger proteins and thereby function as inhibitors and regulatory elements. Peptide fragments of larger proteins are particularly attractive for achieving these functions due to their inherent potential to form native-like binding interactions. Recently developed experimental approaches allow for high-throughput measurement of protein fragment inhibitory activity in living cells. However, it has thus far not been possible to predict de novo which of the many possible protein fragments bind to protein targets, let alone act as inhibitors. We have developed a computational method, FragFold, that employs AlphaFold to predict protein fragment binding to full-length proteins in a high-throughput manner. Applying FragFold to thousands of fragments tiling across diverse proteins revealed peaks of predicted binding along each protein sequence. Comparisons with experimental measurements establish that our approach is a sensitive predictor of fragment function: Evaluating inhibitory fragments from known protein–protein interaction interfaces, we find 87% are predicted by FragFold to bind in a native-like mode. Across full protein sequences, 68% of FragFold-predicted binding peaks match experimentally measured inhibitory peaks. Deep mutational scanning experiments support the predicted binding modes and uncover superior inhibitory peptides in high throughput. Further, FragFold is able to predict previously unknown protein binding modes, explaining prior genetic and biochemical data. The success rate of FragFold demonstrates that this computational approach should be broadly applicable for discovering inhibitory protein fragments across proteomes.
Cortical activity during painful and non-painful stimulation over four lower limb body sites: a functional near-infrared spectroscopy study
Abstract Functional near-infrared spectroscopy (fNIRS) holds potential utility as a measure of neural correlates of pain. However, most studies have focused on upper limb stimulation, with limited investigation into lower limbs. In this study, we utilized fNIRS to observe brain changes in oxyhemoglobin levels during painful and non-painful electrical stimulation of various lower limb sites (bilateral groins and knees) in 16 healthy participants. Additionally, we explored perceptual responses to painful and non-painful electrical stimulation across these lower limb sites. Our findings showed no significant main effect of stimulation across different body sites on oxyhemoglobin activity. However, the interaction between body sites, stimulation modalities, and brain regions significantly influenced oxyhemoglobin activity. Specifically, we found a decrease of neuro-metabolic activity in prefrontal and bilateral primary somatosensory cortices during painful stimulation of the left groin compared to non-painful stimulation, whereas an increase of neuro-metabolic activity was observed during painful stimulation of the right knee. Our findings also revealed that stimulation intensity was notably lower for bilateral knees compared to the left groin. These findings underscore the potential and feasibility of utilizing fNIRS to investigate pain mechanisms related to stimulation across distinct lower limb regions.
Translation elongation defects activate the <i>Caenorhabditis elegans</i> ZIP-2 bZIP transcription factor–mediated toxin defense
The Caenorhabditis elegans bZIP transcription factor ZIP-2 is activated by toxins or mutations that inhibit translational elongation. The zip-2 DNA-binding protein is encoded in a downstream main open reading frame (mORF), but under normal translation elongation conditions only an upstream overlapping oORF -1 frameshifted from mORF is translated. Mutations or toxins that slow translational elongation, but not inhibitors of translational initiation or termination, activate ZIP-2. An mORF initiation codon mutation does not disrupt the normal zip-2 response to translational elongation defects, suggesting that zip-2 activation does not depend on this ATG. An mORF early termination mutant can be activated by strong translation elongation inhibition, suggesting that translation initiated upstream on oORF +1 frameshifts when elongation is inhibited to the mORF reading frame downstream of the stop codon to activate a fused oORF/mORF ZIP-2 transcription factor. The protein and DNA sequences of zip-2 oORF and mORF are conserved across the Caenorhabditis , suggesting selection for particular codons sensitive to translational elongation defects. Mutations that disrupt the oORF initiation codon constitutively activate zip-2 , but not if the mORF initiation codon is also mutant, showing that zip-2 oORF competes with mORF for translational initiation. oORF initiation codon mutation-activated zip-2 slows C. elegans growth, and this slow growth is suppressed by a zip-2 null mutation. A zip-2 null mutant also strongly suppresses the growth arrest caused by translational elongation inhibitors. Thus, ZIP-2 is both a sensor of translational elongation attack, and a defense regulatory output via its activation of response genes.