An immunogenic cell death-related lncRNA signature correlates with prognosis and tumor immune microenvironment in bladder cancer.

Immunogenic cell death (ICD) is a newly discovered form of cellular demise that triggers adaptive immune responses mediated by T cells. However, the immunogenic cell death-related lncRNAs (ICDRLs) involved in bladder cancer (BC) development and progression remain to be further elucidated. Molecular profiling data and clinicopathological information for BC patients were obtained from TCGA, and the ICDRGs list was obtained from published literature. For the identification of ICDRLs, Pearson co-expression analysis was performed, and a prognostic signature based on 13 ICDRLs was constructed by univariate assays and LASSO assays. Herein, an ICDRLSig consisting of 13 ICDRLs was constructed. KM curves and ROC curves demonstrated that the constructed signature in the TCGA training, testing, entire and external sets have good predictive performance. Multivariate assays illuminated that the signature is an independent predictor for BC patients' OS, exhibiting greater predictive power for the survival than traditional clinicopathological features. Additionally, patients in the high-ICDRLSig risk subgroup had more abundant immune infiltration, higher immune checkpoint gene expression, lower TMB and poorer response to immunotherapy. We have developed a novel ICDRLSig that can be exploited for survival prediction and provide a reference for further individualized treatment.

Superfast Lombard response in free-flying, echolocating bats.

Acoustic cues are crucial to communication, navigation, and foraging in many animals, which hence face the problem of detecting and discriminating these cues in fluctuating noise levels from natural or anthropogenic sources. Such auditory dynamics are perhaps most extreme for echolocating bats that navigate and hunt prey on the wing in darkness by listening for weak echo returns from their powerful calls in complex, self-generated umwelts.1,2 Due to high absorption of ultrasound in air and fast flight speeds, bats operate with short prey detection ranges and dynamic sensory volumes,3 leading us to hypothesize that bats employ superfast vocal-motor adjustments to rapidly changing sensory scenes. To test this hypothesis, we investigated the onset and offset times and magnitude of the Lombard response in free-flying echolocating greater mouse-eared bats exposed to onsets of intense constant or duty-cycled masking noise during a landing task. We found that the bats invoked a bandwidth-dependent Lombard response of 0.1-0.2 dB per dB increase in noise, with very short delay and relapse times of 20 ms in response to onsets and termination of duty-cycled noise. In concert with the absence call time-locking to noise-free periods, these results show that free-flying bats exhibit a superfast, but hard-wired, vocal-motor response to increased noise levels. We posit that this reflex is mediated by simple closed-loop audio-motor feedback circuits that operate independently of wingbeat and respiration cycles to allow for rapid adjustments to the highly dynamic auditory scenes encountered by these small predators.

Effects of insect pursuit on the Doppler shift compensation in a hipposiderid bat.

Doppler shift compensation (DSC) is a unique feature observed in certain species of echolocating bats and is hypothesized to be an adaptation to detecting fluttering insects. However, current research on DSC has primarily focused on bats that are not engaged in foraging activities. In this study, we investigated the DSC performance of Pratt's roundleaf bat, Hipposideros pratti, which was trained to pursue insects in various motion states within a laboratory setting. Our study yielded three main results. First, H. pratti demonstrated highly precise DSC during insect pursuit, aligning with previous findings of other flutter-detecting foragers during orientation or landing tasks. Second, we found that the motion state of the insect prey had little effect on the DSC performance of H. pratti. Third, we observed variations in the DSC performance of H. pratti throughout the course of insect pursuit. The bats exhibited the highest DSC performance during the phase of maximum flight speed but decreased performance during the phase of insect capture. These findings of high precision overall and the time-dependent performance of DSC during insect pursuit support the hypothesis that DSC is an adaptation to detecting fluttering insects.

Regulating the spatial arrangement of CuO and MgO within activated carbon matrix to maximize their room temperature H2S removal.

Adsorbents with dual-component active phases have attracted much attention owing to their potential application in synergistic H2S removal. The influence of spatial arrangements of two components within a support matrix on their desulfurization performance was investigated through regulating the mutual arrangements of CuO and MgO on an activated carbon surface. Their spatial locations were found to remarkably affect interfacial interactions, local pH, the conductivity of adsorbents, and electronic structure of copper oxide. A close contact of CuO with the carbon surface led to strong interactions of both components, inhibiting the reduction of CuO and decreasing its reactivity with H2S. On the other hand, a proximity of MgO to the carbon surface increased local pH, promoting the oxidation of H2S into elemental S, instead of sulfates. Cu+ in the copper oxide phase increased the desulfurization performance due to its ability to activate oxygen and to accelerate a lattice diffusion. Enhanced surface conductivity due to the interfacial interactions improved the desulfurization efficiency and favored the formation of elemental S through promoting an electron transfer in redox reactions.

MSH7 confers quantitative variation in pollen fertility and boosts grain yield in maize.

Fertile pollen is critical for the survival, fitness, and dispersal of flowering plants, and directly contributes to crop productivity. Extensive mutational screening studies have been carried out to dissect the genetic regulatory network determining pollen fertility, but we still lack fundamental knowledge about whether and how pollen fertility is controlled in natural populations. We used a genome-wide association study (GWAS) to show that ZmGEN1A and ZmMSH7, two DNA repair-related genes, confer natural variation in maize pollen fertility. Mutants defective in these genes exhibited abnormalities in meiotic or post-meiotic DNA repair, leading to reduced pollen fertility. More importantly, ZmMSH7 showed evidence of selection during maize domestication, and its disruption resulted in a substantial increase in grain yield for both inbred and hybrid. Overall, our study describes the first systematic examination of natural genetic effects on pollen fertility in plants, providing valuable genetic resources for optimizing male fertility. In addition, we find that ZmMSH7 represents a candidate for improvement of grain yield.

RNA m6A modification facilitates DNA methylation during maize kernel development.

N6-methyladenosine (m6A) in mRNA and 5-methylcytosine (5mC) in DNA have critical functions for regulating gene expression and modulating plant growth and development. However, the interplay between m6A and 5mC is an elusive territory and remains unclear mechanistically in plants. We reported an occurrence of crosstalk between m6A and 5mC in maize (Zea mays) via the interaction between mRNA adenosine methylase (ZmMTA), the core component of the m6A methyltransferase complex, and decrease in DNA methylation 1 (ZmDDM1), a key chromatin-remodeling factor that regulates DNA methylation. Genes with m6A modification were coordinated with a much higher level of DNA methylation than genes without m6A modification. Dysfunction of ZmMTA caused severe arrest during maize embryogenesis and endosperm development, leading to a significant decrease in CHH methylation in the 5' region of m6A-modified genes. Instead, loss of function of ZmDDM1 had no noteworthy effects on ZmMTA-related activity. This study establishes a direct link between m6A and 5mC during maize kernel development and provides insights into the interplay between RNA modification and DNA methylation.

Distribution characteristics, risk assessment, and relevance with surrounding soil of heavy metals in coking solid wastes from coking plants in Shanxi, China.

Heavy metal concentrations represent important pollution evaluation indices, and it is necessary to assess the potential environmental and health risks from heavy metals associated with coking wastes from coking plants. In this study, coking sludge (CS), tar residue (TR), coke powder (CP), and sulfur paste (SP) from three coking plants (Plant A, Plant B, and Plant C) in central, western, and southern Shanxi Province and from soils surrounding Plant A were selected as the research objects, and the distributions of Cu, Ni, Pb, Zn, Mn, Cd, and Cr were determined. The results showed that Cd in the four solid wastes far exceeded the soil background value by a factor of 16~195, and the contents of Pb in TR (three plants) and CS (Plant C) exceeded the soil background values 19.70-, 23.57-, 14.46-, and 12.56-fold, respectively. Similarly, the concentrations of Cu, Ni, Pb, Zn, and Cd in soils were higher than the background values by factors of 31.18, 8.35, 34.79, 29.48, and 3.43, respectively. In addition, the Cu, Ni, Pb, and Cr in the four solid wastes and soils mainly existed in the residual state. As depth increased, the overall Ni, Pb, Mn, and Cd concentrations in soils increased. The high ecological risks associated with the four solid wastes were mainly due to the enrichment of Cd. Workers in coking plants face certain Cr health risks. This study provides theoretical support for the coking industry with respect to the treatment, disposal, and management of solid wastes.

Contrasting laboratory and field outcomes of bat-moth interactions.

Predator-prey interactions are important but difficult to study in the field. Therefore, laboratory studies are often used to examine the outcomes of predator-prey interactions. Previous laboratory studies have shown that moth hearing and ultrasound production can help prey avoid being eaten by bats. We report here that laboratory behavioural outcomes may not accurately reflect the outcomes of field bat-moth interactions. We tested the success rates of two bat species capturing moths with distinct anti-bat tactics using behavioural experiments. We compared the results with the dietary composition of field bats using next-generation DNA sequencing. Rhinolophus episcopus and Rhinolophus osgoodi had a lower rate of capture success when hunting for moths that produce anti-bat clicks than for silent eared moths and earless moths. Unexpectedly, the success rates of the bats capturing silent eared moths and earless moths did not differ significantly from each other. However, the field bats had a higher proportion of silent eared moths than that of earless moths and that of clicking moths in their diets. The difference between the proportions of silent eared moths and earless moths in the bat diets can be explained by the difference between their abundance in bat foraging habitats. These findings suggest that moth defensive tactics, bat countertactics and moth availability collectively shape the diets of insectivorous bats. This study illustrates the importance of using a combination of behavioural experiments and molecular genetic techniques to reveal the complex interactions between predators and prey in nature.

Development and validation of a nomogram for predicting sepsis in patients with pyogenic liver abscess.

Pyogenic liver abscess (PLA) is a severe condition that significantly increases the risk of sepsis. However, there is a notable dearth of research regarding the prediction of sepsis in PLA patients. The objective of this study was to develop and validate a prognostic nomogram for predicting sepsis in PLA patients. A total of 206 PLA patients were enrolled in our study, out of which 60 individuals (29.1%) met the Sepsis-3 criteria. Independent risk factors for sepsis were identified through univariate and multivariate logistic regression analyses. Subsequently, a nomogram was developed based on age, positive blood culture, procalcitonin, alanine aminotransferase, blood urea nitrogen, and D-dimer. The nomogram demonstrated excellent calibration and discrimination, as evidenced by the area under the receiver operating characteristic curve (AUC) values of 0.946 (95% confidence interval [CI], 0.912-0.979) and 0.980 (95%CI 0.951-1.000) in the derivation and validation cohorts, respectively. Furthermore, decision-curve analysis confirmed the clinical utility of the nomogram. This study provides valuable insights for the prevention of sepsis in PLA patients and underscores the potential application of the prognostic nomogram in clinical practice.

ZmRPN1 confers quantitative variation in pollen number and boosts hybrid seed production in maize.

The number of pollen grains is a critical determinant of reproductive success in seed plants and varies among species and individuals. However, in contrast with many mutant-screening studies relevant to anther and pollen development, the natural genetic basis for variations in pollen number remains largely unexplored. To address this issue, we carried out a genome-wide association study in maize, ultimately revealing that a large presence/absence variation in the promoter region of ZmRPN1 alters its expression level and thereby contributes to pollen number variation. Molecular analyses showed that ZmRPN1 interacts with ZmMSP1, which is known as a germline cell number regulator, and facilitates ZmMSP1 localization to the plasma membrane. Importantly, ZmRPN1 dysfunction resulted in a substantial increase in pollen number, consequently boosting seed production by increasing female-male planting ratio. Together, our findings uncover a key gene controlling pollen number, and therefore, modulation of ZmRPN1 expression could be efficiently used to develop elite pollinators for modern hybrid maize breeding.

Echo feedback mediates noise-induced vocal modifications in flying bats.

Diverse animal taxa are capable of rapidly modifying vocalizations to mitigate interference from environmental noise. Echolocating bats, for example, must frequently perform sonar tasks in the presence of interfering sounds. Numerous studies have documented sound production flexibility in echolocating bats; however, it remains unknown whether noise-induced vocal modifications (NIVMs) mitigate interference effects on echoes or calls. In this study, we leverage echo level compensation behavior of echolocating bats to answer this question. Using a microphone array, we recorded echolocation calls of Hipposideros pratti trained to approach and land on a perch in the laboratory under quiet and noise conditions. We found that H. pratti exhibited echo level compensation behavior during approaching flights, which depended critically on distance to the landing perch. Broadcast noise delayed and affected the rate of echo level compensation in H. pratti. Moreover, H. pratti increased vocalization amplitude, i.e., exhibited the Lombard effect, while also adjusting call duration and bandwidth with increasing noise levels. Quantitative analyses of the data show that H. pratti relies on echo feedback, not vocal feedback, to adjust signals in the presence of noise. These findings provide compelling evidence that NIVMs in echolocating animals and non-echolocating animals operate through different mechanisms.

ZmCCT10-relayed photoperiod sensitivity regulates natural variation in the arithmetical formation of male germinal cells in maize.

Extensive mutational screening studies have documented genes regulating anther and pollen development. Knowledge concerning how formation of male germinal cell is arithmetically controlled in natural populations, under different environmental conditions, is lacking. We counted pollen number within a single anther and a maize-teosinte BC2 S3 recombinant inbred line population to identify ZmCCT10 as a major determinant of pollen number variation. ZmCCT10 was originally identified as a photoperiod-sensitive negative regulator of flowering. ZmCCT10 inactivation, after transposon insertion within its promoter, is proposed to have accelerated maize spread toward higher latitudes, thus allowing temperate maize to flower under long-day conditions. We showed that the active ZmCCT10 allele decreased pollen formation. As different active and inactive ZmCCT10 alleles have been found in natural maize populations, this represents the first report of a gene controlling pollen number in a crop natural population. These findings suggest that higher pollen number, which provides a competitive advantage in open-pollinated populations, may have been one of the major driving forces for the selection of an inactive ZmCCT10 allele during tropical maize domestication. We provide evidence that ZmCCT10 has opposite effects on cell proliferation of archesporial and tapetum cells and it modulates expression of key regulators during early anther development.

Spatial variability and risk assessment of heavy metals in the soil surrounding solid waste from coking plants in Shanxi, China.

Heavy metal pollution in the soil surrounding solid wastes from coking plants poses potential threats to human health and has attracted widespread attention. This study is the first to assess the spatial variability and risks of heavy metals in the soil surrounding solid waste from coking plants. The results showed that the concentrations of Cu, Ni, Pb, and Cd in the soil were much higher than the background value of the soil. Solid waste had a clear influence on the contents of Ni, Cd, Mn, Pb, and Cr in the soil. The ecological risk assessment of heavy metal pollution demonstrated that the pollution degree of Cu, Pb, and Cd was more serious than others, and the ecological risk of heavy metals was mainly caused by Cd in the soil. The human health risk assessment showed that adults and children near coking plants might face carcinogenic risk from exposure to Cr. This study can provide a theoretical basis for the prevention and management of soil heavy metal pollution surrounding solid waste in coking plants.

Perceptual hearing sensitivity during vocal production.

Vocalization, such as speaking, inevitably generates sensory feedback that can cause self-generated masking. However, perceptual hearing sensitivity during vocal production is poorly understood. Using an adaptive psychophysical method, we measured the perceptual hearing sensitivity of an echolocating bat, Hipposideros pratti, in a passive listening (PL) task to detect pure tones, an active listening (AL) task to detect pure tones triggered by its vocalization, and a phantom echo task. We found that hanging H. pratti had the best hearing sensitivity of approximately 0 dB sound pressure level (SPL) in the PL task but much lower hearing sensitivity (nearly 40 dB worse) in the echo task. In the AL task, all bats gradually increased call frequency by 0.8-1.1 kHz, which improved their hearing sensitivity by 25-29 dB. This study underscores the need for studying the sensory capability of subjects engaged in active behaviors.

Doppler shift compensation performance in Hipposideros pratti across experimental paradigms.

A central aim of neuroethological research is to discover the mechanisms of natural behaviors in controlled laboratory studies. This goal, however, comes with challenges, namely the selection of experimental paradigms that allow full expression of natural behaviors. Here, we explore this problem in echolocating bats that evolved Doppler shift compensation (DSC) of sonar vocalizations to yield close matching between echo frequency and hearing sensitivity. We ask if behavioral tasks influence the precision of DSC in Pratt's roundleaf bat, Hipposideros pratti, in three classic laboratory paradigms evoking audio-vocal adjustments: Stationary bats listening to echo playbacks, bats transported on a moving pendulum, and bats flying freely. We found that experimental conditions had a strong influence on the expression of the audiovocal frequency adjustments in bats. H. pratti exhibited robust DSC in both free-flying and moving-pendulum experiments but did not exhibit consistent audiovocal adjustments in echo playback experiments. H. pratti featured a maximum compensation magnitude of 87% and a compensation precision of 0.27% in the free flight experiment. Interestingly, in the moving pendulum experiment H. pratti displayed surprisingly high-precision DSC, with an 84% maximum compensation magnitude and a 0.27% compensation precision. Such DSC performance places H. pratti among the bat species exhibiting the most precise audio-vocal control of echo frequency. These data support the emerging view that Hipposiderid bats have a high-precision DSC system and highlight the importance of selecting experimental paradigms that yield the expression of robust natural behaviors.

Sensory error drives fine motor adjustment.

Fine audiovocal control is a hallmark of human speech production and depends on precisely coordinated muscle activity guided by sensory feedback. Little is known about shared audiovocal mechanisms between humans and other mammals. We hypothesized that real-time audiovocal control in bat echolocation uses the same computational principles as human speech. To test the prediction of this hypothesis, we applied state feedback control (SFC) theory to the analysis of call frequency adjustments in the echolocating bat, Hipposideros armiger. This model organism exhibits well-developed audiovocal control to sense its surroundings via echolocation. Our experimental paradigm was analogous to one implemented in human subjects. We measured the bats' vocal responses to spectrally altered echolocation calls. Individual bats exhibited highly distinct patterns of vocal compensation to these altered calls. Our findings mirror typical observations of speech control in humans listening to spectrally altered speech. Using mathematical modeling, we determined that the same computational principles of SFC apply to bat echolocation and human speech, confirming the prediction of our hypothesis.

Present and future distribution of bat hosts of sarbecoviruses: implications for conservation and public health.

Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of viral spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological niche modelling pipeline for bat hosts of SARS-like viruses (subgenus Sarbecovirus), given that several closely related viruses have been discovered and sarbecovirus-host interactions have gained attention since SARS-CoV-2 emergence. We assessed sampling biases and modelled current distributions of bats based on climate and landscape relationships and project future scenarios for host hotspots. The most important predictors of species distributions were temperature seasonality and cave availability. We identified concentrated host hotspots in Myanmar and projected range contractions for most species by 2100. Our projections indicate hotspots will shift east in Southeast Asia in locations greater than 2°C hotter in a fossil-fuelled development future. Hotspot shifts have implications for conservation and public health, as loss of population connectivity can lead to local extinctions, and remaining hotspots may concentrate near human populations.

Genome-wide association study reveals the genetic architecture of root hair length in maize.

BACKGROUND: Root hair, a special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stress. Although many genes involved in root hair development have been identified, genetic basis of natural variation in root hair growth has never been explored. RESULTS: Here, we utilized a maize association panel including 281 inbred lines with tropical, subtropical, and temperate origins to decipher the phenotypic diversity and genetic basis of root hair length. We demonstrated significant associations of root hair length with many metabolic pathways and other agronomic traits. Combining root hair phenotypes with 1.25 million single nucleotide polymorphisms (SNPs) via genome-wide association study (GWAS) revealed several candidate genes implicated in cellular signaling, polar growth, disease resistance and various metabolic pathways. CONCLUSIONS: These results illustrate the genetic basis of root hair length in maize, offering a list of candidate genes predictably contributing to root hair growth, which are invaluable resource for the future functional investigation.

Association of exposure to ambient air pollution with ovarian reserve among women in Shanxi province of north China.

Air pollution has been an important risk factor for female reproductive health. However, epidemiological evidence of ambient air pollution on the predictor for ovarian reserve (antral follicle count, AFC) is deficient. We aim to comprehensively evaluate the association of long-term exposure to ambient air pollution with AFC among women of reproductive age in Shanxi of north China. 600 women with spontaneous menstrual cycle, not using controlled ovarian stimulation, were enrolled in the retrospective study. Two distinct periods of antral follicle development were designed as exposure windows. Generalized linear model was employed to estimate the change of AFC associated with exposure of atmospheric pollutants (SO2, NO2, PM10, PM2.5, CO and O3). Stratification analysis based on age (<30, ≥30 years), university degree (yes, no), years of exposure (2013-2016, 2017-2019) and duration of infertility (<2, 2-5, >5 years) along with two pollutants model were employed to further illustrate the association. We found every 10 µg/m3 increase in SO2 concentration level during the entire development stage of antral follicle was associated with a -0.01 change in AFC (95% confidence interval: -0.016, -0.002) adjusting for the confounders including age, BMI, parity and infertility diagnosis factors. The significant association of increased SO2 level with decreased AFC was particularly observed during the early transition from primary follicle to preantral follicle stage by 10 µg/m3 increase in SO2 exposure level with a -0.01 change (95% CI: -0.015, -0.002) in AFC. The negative association was pronounced among women aged ≥30 years old, and also significant in two pollutants model after adjusting the confounders. No significant associations between other air pollutants and AFC were observed. Our finding suggests that long-term exposure to air pollutant SO2 is associated with lower AFC, raising our concern that atmospheric SO2 exposure may have potential adverse impact on women ovarian reserve.

Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize.

Heterosis has been extensively utilized to increase productivity in crops, yet the underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain the contribution of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and distribution of m6A remained unchanged, a greater number of genes had gained an m6A modification in the hybrid. Superior variations were observed at the m6A modification and translational efficiency levels when compared with mRNA abundance between the hybrid and parents. In the hybrid, the vast majority of genes with m6A modification exhibited a non-additive expression pattern, the percentage of which was much higher than that at levels of mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulation of gene expression make distinct contributions to heterosis in hybrid maize. Overall, this integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation of gene expression in hybrid maize, and paves the way for exploring molecular mechanisms underlying hybrid vigor.