Antitumor progenitor exhausted CD8+ T cells are sustained by TCR engagement.

The durability of an antitumor immune response is mediated in part by the persistence of progenitor exhausted CD8+ T cells (Tpex). Tpex serve as a resource for replenishing effector T cells and preserve their quantity through self-renewal. However, it is unknown how T cell receptor (TCR) engagement affects the self-renewal capacity of Tpex in settings of continued antigen exposure. Here we use a Lewis lung carcinoma model that elicits either optimal or attenuated TCR signaling in CD8+ T cells to show that formation of Tpex in tumor-draining lymph nodes and their intratumoral persistence is dependent on optimal TCR engagement. Notably, attenuated TCR stimulation accelerates the terminal differentiation of optimally primed Tpex. This TCR-reinforced Tpex development and self-renewal is coupled to proximal positioning to dendritic cells and epigenetic imprinting involving increased chromatin accessibility at Egr2 and Tcf1 target loci. Collectively, this study highlights the critical function of TCR engagement in sustaining Tpex during tumor progression.

Wetland emission and atmospheric sink changes explain methane growth in 2020.

Atmospheric methane growth reached an exceptionally high rate of 15.1 ± 0.4 parts per billion per year in 2020 despite a probable decrease in anthropogenic methane emissions during COVID-19 lockdowns1. Here we quantify changes in methane sources and in its atmospheric sink in 2020 compared with 2019. We find that, globally, total anthropogenic emissions decreased by 1.2 ± 0.1 teragrams of methane per year (Tg CH4 yr-1), fire emissions decreased by 6.5 ± 0.1 Tg CH4 yr-1 and wetland emissions increased by 6.0 ± 2.3 Tg CH4 yr-1. Tropospheric OH concentration decreased by 1.6 ± 0.2 per cent relative to 2019, mainly as a result of lower anthropogenic nitrogen oxide (NOx) emissions and associated lower free tropospheric ozone during pandemic lockdowns2. From atmospheric inversions, we also infer that global net emissions increased by 6.9 ± 2.1 Tg CH4 yr-1 in 2020 relative to 2019, and global methane removal from reaction with OH decreased by 7.5 ± 0.8 Tg CH4 yr-1. Therefore, we attribute the methane growth rate anomaly in 2020 relative to 2019 to lower OH sink (53 ± 10 per cent) and higher natural emissions (47 ± 16 per cent), mostly from wetlands. In line with previous findings3,4, our results imply that wetland methane emissions are sensitive to a warmer and wetter climate and could act as a positive feedback mechanism in the future. Our study also suggests that nitrogen oxide emission trends need to be taken into account when implementing the global anthropogenic methane emissions reduction pledge5.

The highest-elevation frog provides insights into mechanisms and evolution of defenses against high UV radiation.

Defense against ultraviolet (UV) radiation exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV defense mechanisms remains largely unexplored. Herein, we used integrated approaches to analyze UV responses in the highest-elevation frog, Nanorana parkeri. We show less damage and more efficient antioxidant activity in skin of this frog than those of its lower-elevation relatives after UV exposure. We also reveal genes related to UV defense and a corresponding temporal expression pattern in N. parkeri. Genomic and metabolomic analysis along with large-scale transcriptomic profiling revealed a time-dependent coordinated defense mechanism in N. parkeri. We also identified several microRNAs that play important regulatory roles, especially in decreasing the expression levels of cell cycle genes. Moreover, multiple defense genes (i.e., TYR for melanogenesis) exhibit positive selection with function-enhancing substitutions. Thus, both expression shifts and gene mutations contribute to UV adaptation in N. parkeri. Our work demonstrates a genetic framework for evolution of UV defense in a natural environment.

Epigenetic regulation of T cell adaptive immunity.

The conceptualization of adaptive immunity, founded on the observation of immunological memory, has served as the basis for modern vaccination and immunotherapy approaches. This fundamental concept has allowed immunologists to explore mechanisms that enable humoral and cellular lymphocytes to tailor immune response functions to a wide array of environmental insults and remain poised for future pathogenic encounters. Until recently, for T cells it has remained unclear how memory differentiation acquires and sustains a gene expression program that grants a cell with a capacity for a heightened recall response. Recent investigations into this critical question have identified epigenetic programs as a causal molecular mechanism governing T cell subset specification and immunological memory. Here, we outline the studies that have illustrated this concept and posit on how insights into T cell adaptive immunity can be applied to improve upon existing immunotherapies.

Aromatic and magnetic properties in a series of heavy rare earth-doped Ge6 cluster anions.

A series of pentagonal bipyramidal anionic germanium clusters doped with heavy rare earth elements, REGe 6 - (RE = Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu), have been identified at the PBE0/def2-TZVP level using density functional theory (DFT). Our findings reveal that the centrally doped pentagonal ring structure demonstrates enhanced stability and heightened aromaticity due to its uniform bonding characteristics and a larger charge transfer region. Through natural population analysis and spin density diagrams, we observed a monotonic decrease in the magnetic moment from Gd to Yb. This is attributed to the decreasing number of unpaired electrons in the 4f orbitals of the heavy rare earth atoms. Interestingly, the system doped with Er atoms showed lower stability and anti-aromaticity, likely due to the involvement of the 4f orbitals in bonding. Conversely, the systems doped with Gd and Tb atoms stood out for their high magnetism and stability, making them potential building blocks for rare earth-doped semiconductor materials.

PRMT inhibition induces a viral mimicry response in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with the worst prognosis and few effective therapies. Here we identified MS023, an inhibitor of type I protein arginine methyltransferases (PRMTs), which has antitumor growth activity in TNBC. Pathway analysis of TNBC cell lines indicates that the activation of interferon responses before and after MS023 treatment is a functional biomarker and determinant of response, and these observations extend to a panel of human-derived organoids. Inhibition of type I PRMT triggers an interferon response through the antiviral defense pathway with the induction of double-stranded RNA, which is derived, at least in part, from inverted repeat Alu elements. Together, our results represent a shift in understanding the antitumor mechanism of type I PRMT inhibitors and provide a rationale and biomarker approach for the clinical development of type I PRMT inhibitors.

Effect of Esketamine on Postoperative Delirium in Patients Undergoing Cardiac Valve Replacement with Cardiopulmonary Bypass: A Randomized Controlled Trial.

BACKGROUND: The aim of this study was to investigate the effects of esketamine on the risk of postoperative delirium (POD) in adults undergoing on-pump cardiac valve surgery. METHODS: In this randomized, triple-blind, controlled trial, 116 adult patients with an American Society of Anesthesiologists (ASA) grade Ⅱ or Ⅲ and a New York Heart Association (NYHA) grade Ⅱ or Ⅲ who underwent cardiac valve surgery with cardiopulmonary bypass were included. Esketamine (0.25 mg/kg) or normal saline was administered intravenously before anesthesia induction. The primary outcome was POD, defined as a positive delirium assessment according to the 3-minute confusion assessment method (CAM) or the confusion assessment method for the intensive care unit (CAM-ICU) on a twice-daily basis for 7 days after surgery. Delirium duration and the delirium subtype were also recorded. The cognitive status of patients was measured according to the Mini-Mental State Examination at baseline, discharge, 30 days postoperatively and 3 months postoperatively. RESULTS: A total of 112 patients (mean age, 52 years; 53.6% female) were enrolled; 56 were assigned to receive esketamine, and 56 were assigned to receive placebo. POD occurred in 13 (23.2%) patients in the esketamine group and in 25 (44.6%) patients in the placebo group (relative risk [RR], 0.52, 95% confidence interval [CI], 0.28-0.91; P = .018). Thirteen patients (23.2%) in the esketamine group and 24 (42.9%) patients in the placebo group had multiple episodes of delirium (RR, 0.54, 95% CI, 0.28-0.92), and 13 (23.2%) vs 22 (39.3%) patients exhibited the hyperactive subtype. CONCLUSIONS: A single dose of esketamine (0.25 mg/kg) injected intravenously before anesthesia induction reduced the incidence of delirium in relatively young patients with ASA grade Ⅱ or Ⅲ who underwent on-pump cardiac surgery.

The role of TGF-ß signaling in muscle atrophy, sarcopenia and cancer cachexia.

Skeletal muscle, comprising a significant proportion (40 to 50 percent) of total body weight in humans, plays a critical role in maintaining normal physiological conditions. Muscle atrophy occurs when the rate of protein degradation exceeds protein synthesis. Sarcopenia refers to age-related muscle atrophy, while cachexia represents a more complex form of muscle wasting associated with various diseases such as cancer, heart failure, and AIDS. Recent research has highlighted the involvement of signaling pathways, including IGF1-Akt-mTOR, MuRF1-MAFbx, and FOXO, in regulating the delicate balance between muscle protein synthesis and breakdown. Myostatin, a member of the TGF-ß superfamily, negatively regulates muscle growth and promotes muscle atrophy by activating Smad2 and Smad3. It also interacts with other signaling pathways in cachexia and sarcopenia. Inhibition of myostatin has emerged as a promising therapeutic approach for sarcopenia and cachexia. Additionally, other TGF-ß family members, such as TGF-ß1, activin A, and GDF11, have been implicated in the regulation of skeletal muscle mass. Furthermore, myostatin cooperates with these family members to impair muscle differentiation and contribute to muscle loss. This review provides an overview of the significance of myostatin and other TGF-ß signaling pathway members in muscular dystrophy, sarcopenia, and cachexia. It also discusses potential novel therapeutic strategies targeting myostatin and TGF-ß signaling for the treatment of muscle atrophy.

Laser acupuncture and photobiomodulation therapy in Bell's palsy with a duration of greater than 8 weeks: a randomized controlled trial.

To investigate the efficacy of laser acupuncture and photobiomodulation therapy in alleviating symptoms among patients diagnosed with Bell's palsy with duration of greater than 8 weeks. The randomized controlled trial has been performed from May 2021 to April 2023. Patients were eligible who had Bell's palsy with duration of greater than 8 weeks on out-patient Department of Otorhinolaryngology in Beijing Tongren Hospital. The laser acupuncture group received class IV laser treatment for 3 times per weeks, a total of 72 times. The control group received the same treatment procedure except the laser parameter. The primary outcome measures comprised House-Brackmann facial nerve grading system and electroneurography. Secondary outcome measures comprised Sunnybrook facial grading system, electromyography, and the blink reflex. A total of 84 participants were included (42 control group, 42 laser acupuncture group). After treatment, House-Brackmann facial nerve grading system (OR, 0.11; 95% CI, 0.04-0.30; P < 0.001), and the pathologic numbers of electroneuronography were statistically different between the laser acupuncture group and control group, including orbicularis oculi (OR,0.08; 95% CI, 0.02-0.21; P < 0.001), Frontalis muscle (OR,0.14; 95% CI, 0.05-0.39; P < 0.001), Orbicularis oris (OR,0.13; 95% CI, 0.04-0.36; P < 0.001), Ala nasi muscle (OR,0.06; 95% CI, 0.02-0.18; P < 0.001). In secondary outcomes, Sunnybrook facial grading system, has significant difference between the two groups (20.26; 95% CI, 14.69 to 25.83; P < 0.01). Latency by ENoG, include orbicularis oculi (-0.61; 95% CI, -0.43 to -0.09; P < 0.001), frontalis muscle (-0.12; 95% CI, -0.21 to -0.03; P < 0.01), orbicularis oris (-0.28; 95% CI, -0.41 to -0.16; P < 0.001), and ala nasi muscle (-0.26; 95% CI, -0.38 to -0.16; P < 0.001). All amplitudes of MUAPs and durations by electromyography (EMG) showed statistically significant differences compared with the control group after treatment. For the frontalis muscle, the amplitude of MUAPs was -64.23 (95% CI, -80.89 to -47.56; P < 0.001) and duration was -1.18 (95% CI, -1.49 to -0.87; P < 0.001). For orbicularis oris, amplitude of MUAPs was -29.82 (95% CI, -55.03 to -4.62; P = 0.02) and duration was -0.57 (95% CI, -0.94 to -0.20; P < 0.001). For depressor angulli oris, amplitude of MUAPs was -47.06 (95% CI, -62.15 to -31.97; P < 0.001) and duration was -2.21 (95% CI, -2.69 to -1.72; P < 0.001). Blink reflex, including R1 (OR, 0.03; 95% CI, 0.01-0.16; P < .001), R2 (OR, 0.04; 95% CI, 0.004-0.29; P < .001), and R2 latency differences (OR, 0.15; 95% CI, 0.05-0.51; P < .001), have significant difference between the two groups, respectively. The findings suggest that laser acupuncture relieve symptoms for patients with Bell's palsy with a duration of greater than 8 weeks.Trial registration: ClinicalTrials.gov Identifier: NCT05846217.

Experimental Investigation and Damage Identification of High-Pile Wharf Framed Bents under Horizontal Impact Loads.

This study investigates damage characteristics, dynamic structural performance changes, and quantitative damage assessment of high-pile wharf framed bents exposed to horizontal impact loads. Through extensive testing of wharf framed bents under such loads, a damage identification approach based on stiffness, natural vibration period, and acceleration data derived from experiments is presented. The findings reveal that under horizontal impact loads, framed bents initially exhibit tensile damage and leaning piles, followed by short straight piles. Additionally, structural damage results in a reduced self-oscillation frequency and an increased amplitude decay rate. Both stiffness-based and cycle-based damage indicators effectively track the cumulative damage progression of the structure. However, the cycle-based damage indicators demonstrate superior stability and accuracy, while acceleration-based indicators precisely identify the moment of damage mutation. This research contributes to enhancing local components, implementing damage identification methods, and advancing health monitoring practices in high-pile wharf projects, aligning with the standards of scientific publications in the field.

Investigation of Structures, Stabilities, and Electronic and Magnetic Properties of Niobium Carbon Clusters Nb7Cn (n = 1-7).

The geometrical structures, relative stabilities, and electronic and magnetic properties of niobium carbon clusters, Nb7Cn (n = 1-7), are investigated in this study. Density functional theory (DFT) calculations, coupled with the Saunders Kick global search, are conducted to explore the structural properties of Nb7Cn (n = 1-7). The results regarding the average binding energy, second-order difference energy, dissociation energy, HOMO-LUMO gap, and chemical hardness highlight the robust stability of Nb7C3. Analysis of the density of states suggests that the molecular orbitals of Nb7Cn primarily consist of orbitals from the transition metal Nb, with minimal involvement of C atoms. Spin density and natural population analysis reveal that the total magnetic moment of Nb7Cn predominantly resides on the Nb atoms. The contribution of Nb atoms to the total magnetic moment stems mainly from the 4d orbital, followed by the 5p, 5s, and 6s orbitals.

PSMC5 regulates microglial polarization and activation in LPS-induced cognitive deficits and motor impairments by interacting with TLR4.

Luteolin is a flavonoid found in high concentrations in celery and green pepper, and acts as a neuroprotectant. PSMC5 (proteasome 26S subunit, ATPase 5) protein levels were reduced after luteolin stimulation in activated microglia. We aimed to determine whether regulating PSMC5 expression could inhibit neuroinflammation, and investigate the underlying mechanisms.BV2 microglia were transfected with siRNA PSMC5 before the addition of LPS (lipopolysaccharide, 1.0 µg/ml) for 24 h in serum free DMEM. A mouse model of LPS-induced cognitive and motor impairment was established to evaluate the neuroprotective effects of shRNA PSMC5. Intracerebroventricular administration of shRNA PSMC5 was commenced 7 days prior to i.p. injection of LPS (750 µg/kg). Treatments and behavioral experiments were performed once daily for 7 consecutive days. Behavioral tests and pathological/biochemical assays were performed to evaluate LPS-induced hippocampal damage. Molecular dynamics simulation was used to confirm the interaction between PSMC5 and TLR4 (Toll-like receptor 4) in LPS-stimulated BV2 microglia. SiRNA PSMC5 inhibited BV2 microglial activation, and suppressed the release of inflammatory factors (IL-1ß, COX-2, PGE2, TNF-α, and iNOS) upon after LPS stimulation in BV2 microglia. LPS increased IκB-α and p65 phosphorylation, which was attenuated by siRNA PSMC5. Behavioral tests and pathological/biochemical assays showed that shRNA PSMC5 attenuated LPS-induced cognitive and motor impairments, and restored synaptic ultrastructure and protein levels in mice. ShRNA PSMC5 reduced pro-inflammatory cytokine (TNF-α, IL-1ß, PGE2, and NO) levels in the serum and brain, and relevant protein factors (iNOS and COX-2) in the brain. Furthermore, shRNA PSMC5 upregulated the anti-inflammatory mediators interleukin IL-4 and IL-10 in the serum and brain, and promoted a pro-inflammation-to-anti-inflammation phenotype shift in microglial polarization. Mechanistically, shRNA PSMC5 significantly alleviated LPS-induced TLR4 expression. The polarization of LPS-induced microglial pro-inflammation phenotype was abolished by TLR4 inhibitor and in the TLR-4-/- mouse, as in shRNA PSMC5 treatment. PSMC5 interacted with TLR4 via the amino sites Glu284, Met139, Leu127, and Phe283. PSMC5 site mutations attenuated neuroinflammation and reduced pro-inflammatory factors by reducing TLR4-related effects, thereby reducing TLR4-mediated MyD88 (myeloid differentiation factor 88)-dependent activation of NF-κB. PSMC5 could be an important therapeutic target for treatment of neurodegenerative diseases involving neuroinflammation-associated cognitive deficits and motor impairments induced by microglial activation.

Dioscorea composita WRKY5 positively regulates AtSOD1 and AtABF2 to enhance drought and salt tolerances.

KEY MESSAGE: DcWRKY5 increases the antioxidant enzyme activity and proline accumulation, oppositely, reduces the accumulation of ROS and MDA, through directly activating the genes expression, finally enhances the salt and drought tolerance. Drought and salinity are two main environmental factors that limit the large-scale cultivation of the medicinal plant Dioscorea composita (D. composita). WRKY transcription factors (TFs) play vital roles in regulating drought and salt tolerance in plants. Nevertheless, the molecular mechanism of WRKY TF mediates drought and salt resistance of D. composita remains largely unknown. Here, we isolated and characterized a WRKY TF from D. composita, namely DcWRKY5, which was localized to the nucleus and bound to the W-box cis-acting elements. Expression pattern analysis showed that it was highly expressed in root and significantly up-regulated in the presence of salt, polyethylene glycol-6000 (PEG-6000) and abscisic acid (ABA). Heterologous expression of DcWRKY5 increased salt and drought tolerance in Arabidopsis, but was insensitive to ABA. In addition, compared with the wild type, the DcWRKY5 overexpressing transgenic lines had more proline, higher antioxidant enzyme (POD, SOD, and CAT) activities, less reactive oxygen species (ROS) and malondialdehyde (MDA). Correspondingly, the overexpression of DcWRKY5 modulated the expression of genes related to salt and drought stresses, such as AtSS1, AtP5CS1, AtCAT, AtSOD1, AtRD22, and AtABF2. Dual luciferase assay and Y1H were further confirmed that DcWRKY5 activate the promoter of AtSOD1 and AtABF2 through directly binding to the enrichment region of the W-box cis-acting elements. These results suggest that DcWRKY5 is a positive regulator of the drought and salt tolerance in D. composita and has potential applications in transgenic breeding.

An Anti-Noise Fast Circle Detection Method Using Five-Quadrant Segmentation.

Extracting circle information from images has always been a basic problem in computer vision. Common circle detection algorithms have some defects, such as poor noise resistance and slow computation speed. In this paper, we propose an anti-noise fast circle detection algorithm. In order to improve the anti-noise of the algorithm, we first perform curve thinning and connection on the image after edge extraction, then suppress noise interference by the irregularity of noise edges and extract circular arcs by directional filtering. In order to reduce the invalid fitting and speed up the running speed, we propose a circle fitting algorithm with five quadrants, and improve the efficiency of the algorithm by the idea of "divide and conquer". We compare the algorithm with RCD, CACD, WANG and AS on two open datasets. The results show that we have the best performance under noise while keeping the speed of the algorithm.

Making Sense of the Growth Behavior of Ultra-High Magnetic Gd2-Doped Silicon Clusters.

The growth behavior, stability, electronic and magnetic properties of the Gd2Sin- (n = 3-12) clusters are reported, which are investigated using density functional theory calculations combined with the Saunders 'Kick' and the Artificial Bee Colony algorithm. The lowest-lying structures of Gd2Sin- (n = 3-12) are all exohedral structures with two Gd atoms face-capping the Sin frameworks. Results show that the pentagonal bipyramid (PB) shape is the basic framework for the nascent growth process of the present clusters, and forming the PB structure begins with n = 5. The Gd2Si5- is the potential magic cluster due to significantly higher average binding energies and second order difference energies, which can also be further verified by localized orbital locator and adaptive natural density partitioning methods. Moreover, the localized f-electron can be observed by natural atomic orbital analysis, implying that these electrons are not affected by the pure silicon atoms and scarcely participate in bonding. Hence, the implantation of these elements into a silicon substrate could present a potential alternative strategy for designing and synthesizing rare earth magnetic silicon-based materials.

Effects of season and slope orientation on stable isotopes of different water bodies in the subalpine shrub zone of the eastern Qilian Mountains in China.

The subalpine shrub zone of the Qilian Mountains is an important water-retaining area, and it is crucial to clarify the processes of its hydrological cycle. Therefore, based on the stable isotope values of different water bodies in the subalpine shrub zone of the eastern Qilian Mountains from May to October 2019, the characteristics of δD and δ18O of different water bodies and their hydraulic relationships with each other were studied. The results showed that the stable isotope values of precipitation exhibited the largest fluctuations, while they were the most stable for groundwater. Plant transpiration was stronger than the evaporation of other water bodies. The stable isotope of precipitation was enriched in high temperature and low humidity environments. Isotopic values of plant and soil water were higher and more stable on the semi-sunny slope than on the semi-shady slope. According to the stable isotopes, there was a strong hydraulic relationship between the different water bodies in the study area, and precipitation was the ultimate source of all of them. Precipitation replenished soil water through infiltration. Part of the soil water was absorbed by plants, while the rest continued to infiltrate to replenish groundwater. Groundwater and precipitation replenished the river water.

Factorial structure and measurement invariance of the Chinese version of the Oral Health Impact Profile-14 among clinical populations and non-clinical populations: an evidence for public oral investigations.

OBJECTIVE: Oral health-related quality of life (OHRQoL) is a multidimensional concept that is commonly used to examine the impact of oral health status on quality of life. The purpose of this study was to examine the optimal factor model of the Chinese version of the Oral Health Impact Profile (OHIP-14) questionnaire in clinical populations, measurement invariance across clinical status and gender cohorts. This would ensure equal validity of the Chinese version of OHIP-14 in different populations and further support public oral investigations. METHODS: The Chinese version of OHIP-14 was used to investigate 490 dental patients and 919 college students. Confirmatory factor analysis (CFA), item analysis and reliability, measurement invariance, and the t-test were used for data analyses. RESULTS: We found that the 7-factor structure had the best-fit index in the sample (CFI = 0.970, TLI = 0.952; SRMR = 0.029, RMSEA = 0.052(0.040,0.063)). The reliability of the scales was satisfactory (Cronbach's α = 0.942). The error variance invariance fitted the data adequately in measurement invariance, indicating that measurement invariance is acceptable both across the clinical and non-clinical populations (∆CFI=-0.017, ∆RMSEA = 0.010) and across genders in the clinical population (∆CFI = 0.000, ∆RMSEA=-0.003). T-test for scores showed that the clinical populations scored significantly higher than the non-clinical populations, as did the overall score (t = 7.046, p < 0.001, d = 0.396), in terms of functional limitation (t = 2.178, p = 0.030, d = 0.125), physical pain (t = 7.880, p < 0.001,d = 0.436), psychological discomfort (t = 8.993, p < 0.001, d = 0.514), physical disability (t = 6.343, p < 0.001, d = 0.358), psychological disability (t = 5.592, p < 0.001, d = 0.315), social disability (t = 5.301, p < 0.001,d = 0.304), social handicap (t = 4.452, p < 0.001, d = 0.253), and that in the non-clinical populations, females scored significantly higher than males, as did in terms of physical pain (t = 3.055, p = 0.002, d = 0.280), psychological discomfort (t = 2.478, p = 0.014, d = 0.222), and psychological disability (t = 2.067, p = 0.039, d = 0.188). CONCLUSION: This study found that the Chinese version of OHIP-14 has measurement invariance between the clinical and non-clinical populations and across genders in the clinical populations, and can be widely used in OHRQoL assessment for public oral investigations.

A positive correlation between GC content and growth temperature in prokaryotes.

BACKGROUND: GC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate. RESULTS: With a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation. CONCLUSIONS: This study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.

Hydrocarbon Tracers Suggest Methane Emissions from Fossil Sources Occur Predominately Before Gas Processing and That Petroleum Plays Are a Significant Source.

We use global airborne observations of propane (C3H8) and ethane (C2H6) from the Atmospheric Tomography (ATom) and HIAPER Pole-to-Pole Observations (HIPPO), as well as U.S.-based aircraft and tower observations by NOAA and from the NCAR FRAPPE campaign as tracers for emissions from oil and gas operations. To simulate global mole fraction fields for these gases, we update the default emissions' configuration of C3H8 used by the global chemical transport model, GEOS-Chem v13.0.0, using a scaled C2H6 spatial proxy. With the updated emissions, simulations of both C3H8 and C2H6 using GEOS-Chem are in reasonable agreement with ATom and HIPPO observations, though the updated emission fields underestimate C3H8 accumulation in the arctic wintertime, pointing to additional sources of this gas in the high latitudes (e.g., Europe). Using a Bayesian hierarchical model, we estimate global emissions of C2H6 and C3H8 from fossil fuel production in 2016-2018 to be 13.3 ± 0.7 (95% CI) and 14.7 ± 0.8 (95% CI) Tg/year, respectively. We calculate bottom-up hydrocarbon emission ratios using basin composition measurements weighted by gas production and find their magnitude is higher than expected and is similar to ratios informed by our revised alkane emissions. This suggests that emissions are dominated by pre-processing activities in oil-producing basins.