Comprehensive effects of salinity, dissolved organic carbon and copper on mortality, osmotic regulation and bioaccumulation of copper in Oryzias melastigma.

Cu, as an essential and toxic element, has gained widespread attention. Both salinity and dissolved organic carbon (DOC) are known to influence Cu toxicity in marine organisms. However, the intricate interplay between these factors and their specific influence on Cu toxicity remains ambiguous. So, this study conducted toxicity tests of Cu on Oryzias melastigma. The experiments involved three salinity levels (10, 20, and 30 ppt) and three DOC levels (0, 1, and 5 mg/L) to comprehensively investigate the underlying mechanisms of toxicity. The complex toxic effects were analyzed by mortality, NKA activity, net Na+ flux and Cu bioaccumulation in O. melastigma. The results indicate that Cu toxicity is notably influenced by both DOC and salinity. Interestingly, the discernible variation in Cu toxicity across different DOC levels diminishes as salinity levels increase. The presence of DOC enhances the impact of salinity on Cu toxicity, especially at higher Cu concentrations. Additionally, Visual MINTEQ was utilized to elucidate the chemical composition of Cu, revealing that DOC had a significant impact on Cu forms. Furthermore, we observed that fluctuations in salinity lead to the inhibition of Na+/K+-ATPase (NKA) activity, subsequently hindering the inflow of Na+. The effects of salinity and DOC on the bioaccumulation of copper were not significant. The influence of salinity on Cu toxicity is mainly through its effect on the osmotic regulation and biophysiology of O. melastigma. Additionally, DOC plays a crucial role in the different forms of Cu. Moreover, DOC-Cu complexes can be utilized by organisms. This study contributes to understanding the mechanism of copper's biological toxicity in intricate marine environments and serves as a valuable reference for developing marine water quality criteria for Cu.

Comprehensive assessment of copper's effect on marine organisms under ocean acidification and warming in the 21st century.

Copper (Cu) has sparked widespread global concern as one of the most hazardous metals to aquatic animals. Ocean acidification (OA) and warming (OW) are expected to alter copper's bioavailability based on pH and temperature-sensitive effects; research on their effects on copper on marine organisms is still in its infancy. Therefore, under representative concentration pathways (RCP) 2.6, 4.5, and 8.5, we used the multiple linear regression-water quality criteria (MLR-WQC) method to assess the effects of OA and OW on the ecological risk posed by copper in the Ocean of East China (OEC), which includes the Bohai Sea, Yellow Sea, and East China Sea. The results showed that there was a positive correlation between temperature and copper toxicity, while there was a negative correlation between pH and copper toxicity. The short-term water quality criteria (WQC) values were 1.53, 1.41, 1.30 and 1.13 µg·L-1, while the long-term WQC values were 0.58, 0.48, 0.40 and 0.29 µg·L-1 for 2020, 2099-RCP2.6, 2099-RCP4.5 and 2099-RCP8.5, respectively. Cu in the OEC poses a moderate ecological risk. Under the current copper exposure situation, strict intervention (RCP2.6) only increases the ecological risk of copper exposure by 20 %, and no intervention (RCP8.5) will increase the ecological risk of copper exposure by nearly double. The results indicate that intervention on carbon emissions can slow down the rate at which OA and OW worsen the damage copper poses to marine creatures. This study can provide valuable information for a comprehensive understanding of the combined impacts of climate change and copper on marine organisms.

Comparison of nitrification performance in SBR and SBBR with response to NaCl salinity shock: microbial structure and functional genes.

Ammonia removal by nitrifiers at the extremely high salinity poses a great challenge for saline wastewater treatment. Sequencing batch reactor (SBR) was conducted with a stepwise increase of salinity from 10 to 40 g-NaCl·L-1, while sequencing batch biofilm reactor (SBBR) with one-step salinity enhancement, their nitrification performance, microbial structure and interaction were evaluated. Both SBR and SBBR can achieve high-efficiency nitrification (98% ammonia removal) at 40 g-NaCl·L-1. However, SBBR showed more stable nitrification performance than SBR at 40 g-NaCl·L-1 after a shorter adaptation period of 4-15 d compared to previous studies. High-throughput sequencing and metagenomic analysis demonstrated that the abundance and capability of conventional ammonia-oxidizing bacteria (Nitrosomonas) were suppressed in SBBR relative to SBR. Gelidibacter, Anaerolineales were the predominant genus in SBBR, which were not found in SBR. NorB and nosZ responsible for reducing NO to N2O and reducing N2O to N2 respectively had s strong synergistic effect in SBBR. This study will provide a valuable reference for the startup of nitrification process within a short period of time under the extremely high NaCl salinity.

Variation in monthly and seasonal elevation use impacts behavioral and dietary flexibility in Rhinopithecus bieti.

Black-and-white snub-nosed monkeys (Rhinopithecus bieti) rely on behavioral and dietary flexibility to survive in temperate latitudes at high-elevation habitats characterized by climate and resource seasonality. However, little is known about how elevation influences their behavioral and dietary flexibility at monthly or seasonal scales. We studied an isolated R. bieti population at Mt. Lasha in the Yunling Provincial Nature Reserve, Yunnan, China, between May 2008 and August 2016 to assess the impacts of elevation on feeding behavior and diet. Across our sample, R. bieti occupied elevations between 3031 and 3637 m above mean sea level (amsl), with a 315.1 m amsl range across months and a 247.3 m amsl range across seasons. Contrary to expectations, individuals spent less time feeding when ranging across higher elevations. Lichen consumption correlated with elevation use across months and seasons, with individuals spending more time feeding on this important resource at higher elevations. Leaf consumption only correlated with elevation use during the spring. Our results suggest that R. bieti do not maximize their food intake at higher elevations and that monthly and seasonal changes in lichen and leaf consumption largely explain variation in elevation use. These findings shed light on the responses of R. bieti to environmental change and offer insight into strategies for conserving their habitats in the face of anthropogenic disturbance.

ROS-induced translational regulation-through spatiotemporal differences in codon recognition-is a key driver of brown adipogenesis.

The role of translational regulation in brown adipogenesis is relatively unknown. Localized translation of mRNAs encoding mitochondrial components enables swift mitochondrial responses, but whether this occurs during brown adipogenesis, which involves massive mitochondrial biogenesis, has not been explored. Here, we used ribosome profiling and RNA-Seq, coupled with cellular fractionation, to obtain spatiotemporal insights into translational regulation. During brown adipogenesis, a translation bias towards G/C-ending codons is triggered first in the mitochondrial vicinity by reactive oxygen species (ROS), which later spreads to the rest of the cell. This translation bias is induced through ROS modulating the activity of the tRNA modification enzyme, ELP3. Intriguingly, functionally relevant mRNAs, including those encoding ROS scavengers, benefit from this bias; in so doing, ROS-induced translation bias both fuels differentiation and concurrently minimizes oxidative damage. These ROS-induced changes could enable sustained mitochondrial biogenesis during brown adipogenesis, and explain in part, the molecular basis for ROS hormesis.

Evaluation study of single-anastomosis duodenal-ileal bypass with sleeve gastrectomy in the treatment of Chinese obese patients based on efficacy and nutrition.

To evaluate the efficacy and nutrition of single-anastomosis duodenal-ileal bypass with sleeve gastrectomy (SADI-S) in Chinese obese patients in the first postoperative year. Clinical data of 66 obese patients who underwent SADI-S surgery at China-Japan Union Hospital of Jilin University from November 2018 to May 2022 were retrospectively collected. The weight, body mass index (BMI), percentage of excess weight loss (%EWL), and percentage of total weight loss (%TWL) were recorded at 3, 6, and 12 months after surgery. Moreover, metabolic disease remission and nutrient deficiencies were assessed at 1 year postoperatively. Overall, 66 patients (38 males and 28 females) were recruited, with a mean age of 35 (18-61) years and an average preoperative BMI of 42.94 kg/m2. Before surgery, 38 patients had type 2 diabetes mellitus (T2DM), 46 patients had hyperuricemia (HUA), 45 patients had hypertension (HTN), 35 patients had hyperlipidemia, 12 patients had hypercholesterolemia, 12 patients had hyper-low-density lipoproteinemia, and 14 patients had gastroesophageal reflux disease symptoms (GERD). All patients had undergone a DaVinci robotic or laparoscopic SADI-S surgery, and none converted to laparotomy or died. Four patients developed postoperative complications and were cured and discharged after conservative treatment or surgical treatment. At 3, 6 and 12 months, the average %EWL was 62.07 ± 26.56, 85.93 ± 27.92, and 106.65 ± 29.65%, %TWL was 22.67 ± 4.94, 32.10 ± 5.18, and 40.56 ± 7.89%, respectively. Fasting blood glucose (FBG), glycated hemoglobin (HbA1c), uric acid (UA), triglycerides (TG), blood pressure (BP), and other indexes were significantly lower after one year post-surgery compared with the preoperative period (P < 0.05). The remission rates of T2DM, HUA, HTN, hypertriglyceridemia, hypercholesterolemia, and hyper-low-density lipoproteinemia 1 year after surgery were 100, 65.2, 62.2, 94.3, 100, and100%, respectively. One year after surgery, the remission rate of GERD was 71.4% (10/14), the rate of new occurrence of GERD was 12.1% (8/66), and the overall incidence rate was 18.2% (12/66). Except for vitamin B12(vit B12), the other nutrient indexes were significantly decreased after 1 year of surgery relative to levels before surgery (P < 0.05). The deficiency rates for vitamin A (vit A), vitamin E (vit E), zinc ion (Zn), and folic acid (FA) were higher (45.5, 25.8, 24.2, and 16.7%, respectively); however, there were no related clinical symptoms. SADI-S had significant effects on weight loss and metabolic disease remission. The main nutrient deficiencies after SADI-S were vit A, vit E, Zn, and FA deficiencies. The long-term efficacy and safety of SADI-S warrant further follow-up.

A simple and effective method to enrich endogenous DNA from mammalian faeces.

Utilization of faeces has long been a popular approach for genetic and ecological studies of wildlife. However, the success of molecular marker genotyping and genome resequencing is often unpredictable due to insufficient enrichment of endogenous DNA in the total faecal DNA that is dominated by bacterial DNA. Here, we report a simple and cheap method named PEERS to predominantly lyse animal cells over bacteria by using sodium dodecyl sulphate so as to discharge endogenous DNA into liquid phase before bacterial DNA. By brief centrifugation, total DNA with enriched endogenous fraction can be extracted from the supernatant using routine methods. Our assessments showed that the endogenous DNA extracted by PEERS was significantly enriched for various types of faeces from different species, preservation time and conditions. It significantly improves the genotyping correctness and efficiency of genome resequencing with the total additional cost of $ 0.1 and a short incubation step to treat a faecal sample. We also provide methods to assess the enrichment efficiency of mitochondrial and nuclear DNA and models to predict the usability of faecal DNA for genotyping of short tandem repeat, single-nucleotide polymorphism and whole-genome resequencing.

Consensus on rapid screening for prodromal Alzheimer's disease in China.

Alzheimer's disease (AD) is a common cause of dementia, characterised by cerebral amyloid-ß deposition, pathological tau and neurodegeneration. The prodromal stage of AD (pAD) refers to patients with mild cognitive impairment (MCI) and evidence of AD's pathology. At this stage, disease-modifying interventions should be used to prevent the progression to dementia. Given the inherent heterogeneity of MCI, more specific biomarkers are needed to elucidate the underlying AD's pathology. Although the uses of cerebrospinal fluid and positron emission tomography are widely accepted methods for detecting AD's pathology, their clinical applications are limited by their high costs and invasiveness, particularly in low-income areas in China. Therefore, to improve the early detection of Alzheimer's disease (AD) pathology through cost-effective screening methods, a panel of 45 neurologists, psychiatrists and gerontologists was invited to establish a formal consensus on the screening of pAD in China. The supportive evidence and grades of recommendations are based on a systematic literature review and focus group discussion. National meetings were held to allow participants to review, vote and provide their expert opinions to reach a consensus. A majority (two-thirds) decision was used for questions for which consensus could not be reached. Recommended screening methods are presented in this publication, including neuropsychological assessment, peripheral biomarkers and brain imaging. In addition, a general workflow for screening pAD in China is established, which will help clinicians identify individuals at high risk and determine therapeutic targets.

Dysfunctions of multiscale dynamic brain functional networks in subjective cognitive decline.

Subjective cognitive decline is potentially the earliest symptom of Alzheimer's disease, whose objective neurological basis remains elusive. To explore the potential biomarkers for subjective cognitive decline, we developed a novel deep learning method based on multiscale dynamical brain functional networks to identify subjective cognitive declines. We retrospectively constructed an internal data set (with 112 subjective cognitive decline and 64 healthy control subjects) to develop and internally validate the deep learning model. Conventional deep learning methods based on static and dynamic brain functional networks are compared. After the model is established, we prospectively collect an external data set (26 subjective cognitive decline and 12 healthy control subjects) for testing. Meanwhile, our method provides monitoring of the transitions between normal and abnormal (subjective cognitive decline-related) dynamical functional network states. The features of abnormal dynamical functional network states are quantified by network and variability metrics and associated with individual cognitions. Our method achieves an area under the receiver operating characteristic curve of 0.807 ± 0.046 in the internal validation data set and of 0.707 (P = 0.007) in the external testing data set, which shows improvements compared to conventional methods. The method further suggests that, at the local level, the abnormal dynamical functional network states are characterized by decreased connectivity strength and increased connectivity variability at different spatial scales. At the network level, the abnormal states are featured by scale-specifically altered modularity and all-scale decreased efficiency. Low tendencies to stay in abnormal states and high state transition variabilities are significantly associated with high general, language and executive functions. Overall, our work supports the deficits in multiscale brain dynamical functional networks detected by the deep learning method as reliable and meaningful neural alternation underpinning subjective cognitive decline.

Analysis of KangDuo-SR-1500 and KangDuo-SR-2000 robotic partial nephrectomy from an operative and ergonomic perspective: a prospective controlled study in porcine models.

The objective of this study is to explore the safety and effectiveness of two new models of KangDuo surgical robots for partial nephrectomy in porcine models, and evaluate the ergonomic characteristics from both subjective and objective perspectives. Twelve porcine models were equally divided for KD-SR-1500 (three-arm) and KD-SR-2000 (four-arm). The perioperative outcomes, and physical and mental workload of the surgeon were compared. Physical workload was evaluated with surface electromyography. Mental workload was evaluated with NASA-TLX. All surgeries were performed successfully. There were no differences in perioperative variables (p > 0.05). There were no perioperative complications. The mental workload in both groups was at a low level. KD-SR-2000 showed advantages in physical workload (p < 0.01). KD-SR-1500 and KD-SR-2000 are technically feasible, valid, and safe for RAPN in porcine models. KD-SR-2000 had ergonomic advantages over KD-SR-1500.

Category Switching Test: A Brief Amyloid-ß-Sensitive Assessment Tool for Mild Cognitive Impairment.

The Category Switching Test (CaST) is a verbal fluency test with active semantic category switching. This study aimed to explore the association between CaST performance and brain amyloid-ß (Aß) burden in patients with mild cognitive impairment (MCI) and the neurofunctional mechanisms. A total of 112 participants with MCI underwent Florbetapir positron emission tomography, resting-state functional magnetic resonance imaging, and a neuropsychological test battery. The high Aß burden group had worse CaST performance than the low-burden group. CaST score and left middle temporal gyrus fractional amplitude of low-frequency fluctuations (fALFF) related inversely to the global Florbetapir standardized uptake value rate. Functional connectivity between the left middle temporal gyrus and frontal lobe decreased widely and correlated with CaST score in the high Aß burden group. Thus, CaST score and left middle temporal gyrus fALFF were valuable in discriminating high Aß burden. CaST might be useful in screening for MCI with high Aß burden.

Spatial distribution, source identification, and transportation paths of plutonium in the Beibu Gulf, South China Sea.

To investigate the spatial distribution and source of plutonium isotopes in the Beibu Gulf, surface sediments were collected and analyzed using sector field inductively coupled plasma mass spectrometry (SF-ICP-MS). The activities of 239+240Pu in surface sediments ranged from 0.012 to 0.451 mBq/g (mean: 0.171 ± 0.138 mBq/g, n = 36), indicating a decreasing trend in a counterclockwise direction from the southern bay mouth. The counterclockwise decreasing trend in the south of the bay mouth is similar to the current in the Beibu Gulf. The 240Pu/239Pu atom ratios in surface sediments ranged from 0.156 to 0.283 (mean: 0.236 ± 0.031, n = 36), slightly higher than that of the global fallout value of 0.18. This suggests that the Pu in the Beibu Gulf was a combination of global fallout and Pacific Proving Ground (PPG). The average contribution of the plutonium (Pu) derived from the PPG in the sediment was estimated to be 52 % ± 24 %.

A comprehensive review of the effects of salinity, dissolved organic carbon, pH, and temperature on copper biotoxicity: Implications for setting the copper marine water quality criteria.

In recent years, there has been a growing concern about the ecological hazards associated with copper, which has sparked increased interest in copper water quality criteria (WQC). The crucial factors affecting the bioavailability of copper in seawater are now acknowledged to be salinity, dissolved organic carbon (DOC), pH, and temperature. Research on the influence of these four water quality parameters on copper toxicity is rapidly expanding. However, a comprehensive and clear understanding of the relevant mechanisms is currently lacking, hindering the development of a consistent international method to establish the seawater WQC value for copper. As a response to this knowledge gap, this study presents a comprehensive summary with two key focuses: (1) It meticulously analyzes the effects of salinity, DOC, pH, and temperature on copper toxicity to marine organisms. It takes into account the adaptability of different species to salinity, pH and temperature. (2) Additionally, the study delves into the impact of these four water parameters on the acute toxicity values of copper on marine organisms while also reviewing the methods used in establishing the marine WQC value of copper. The study proposed a two-step process: initially zoning based on the difference of salinity and DOC, followed by the establishment of Cu WQC values for different zones during various seasons, considering the impacts of water quality parameters on copper toxicity. By providing fundamental scientific insights, this research not only enhances our understanding and predictive capabilities concerning water quality parameter-dependent Cu toxicity in marine organisms but also contributes to the development of copper seawater WQC values. Ultimately, this valuable information facilitates more informed decision-making in marine water quality management efforts.

Identification of bladder cancer subtypes and predictive model for prognosis, immune features, and immunotherapy based on neutrophil extracellular trap-related genes.

Bladder cancer is the most common malignant tumor of urinary system, and its morbidity and mortality are increasing rapidly. Although great advances have been made in medical technology in recent years, there is still a lack of effective prognostic and therapeutic methods for bladder cancer. NETs are reticulated DNA structures decorated with various protein substances released extracellularly by neutrophils stimulated by strong signals. Recently, it has been found that NETs are closely related to the growth, metastasis and drug resistance of many types of cancers. However, up to now, the research on the relationship between NETs and bladder cancer is still not enough. In this study, we aimed to conduct a comprehensive analysis of NRGs in bladder cancer tissues to evaluate the relationship between NRGs and prognosis prediction and sensitivity to therapy in patients with bladder cancer. We scored NRGs in each tissue by using ssGSEA, and selected gene sets that were significantly associated with NRGs scores by using the WCGNA algorithm. Based on the expression profiles of NRGs-related genes, NMF clustering analysis was performed to identify different BLCA molecular subtypes. For the differentially expressed genes between subtypes, we used univariate COX regression, LASSO regression and multivariate COX regression to further construct a hierarchical model of BLCA patients containing 10 genes. This model and the nomogram based on this model can accurately predict the prognosis of BLCA patients in multiple datasets. Besides, BLCA patients classified based on this model differ greatly in their sensitivity to immunotherapy and targeted therapies, which providing a reference for individualized treatment of patients with bladder cancer.

Metabolism of glucose activates TORC1 through multiple mechanisms in Saccharomyces cerevisiae.

Target of Rapamycin Complex 1 (TORC1) is a conserved eukaryotic protein complex that links the presence of nutrients with cell growth. In Saccharomyces cerevisiae, TORC1 activity is positively regulated by the presence of amino acids and glucose in the medium. However, the mechanisms underlying nutrient-induced TORC1 activation remain poorly understood. By utilizing an in vivo TORC1 activation assay, we demonstrate that differential metabolism of glucose activates TORC1 through three distinct pathways in yeast. The first "canonical Rag guanosine triphosphatase (GTPase)-dependent pathway" requires conversion of glucose to fructose 1,6-bisphosphate, which activates TORC1 via the Rag GTPase heterodimer Gtr1GTP-Gtr2GDP. The second "non-canonical Rag GTPase-dependent pathway" requires conversion of glucose to glucose 6-phosphate, which activates TORC1 via a process that involves Gtr1GTP-Gtr2GTP and mitochondrial function. The third "Rag GTPase-independent pathway" requires complete glycolysis and vacuolar ATPase reassembly for TORC1 activation. We have established a roadmap to deconstruct the link between glucose metabolism and TORC1 activation.

Verifying and refining early statuses in Alzheimer's disease progression: a possibility from deep feature comparison.

Defining the early status of Alzheimer's disease is challenging. Theoretically, the statuses in the Alzheimer's disease continuum are expected to share common features. Here, we explore to verify and refine candidature early statuses of Alzheimer's disease with features learned from deep learning. We train models on brain functional networks to accurately classify between amnestic and non-amnestic mild cognitive impairments and between healthy controls and mild cognitive impairments. The trained models are applied to Alzheimer's disease and subjective cognitive decline groups to suggest feature similarities among the statuses and identify informative subpopulations. The amnestic mild cognitive impairment vs non-amnestic mild cognitive impairments classifier believes that 71.8% of Alzheimer's disease are amnestic mild cognitive impairment. And 73.5% of subjective cognitive declines are labeled as mild cognitive impairments, 88.8% of which are further suggested as "amnestic mild cognitive impairment." Further multimodal analyses suggest that the amnestic mild cognitive impairment-like Alzheimer's disease, mild cognitive impairment-like subjective cognitive decline, and amnestic mild cognitive impairment-like subjective cognitive decline exhibit more Alzheimer's disease -related pathological changes (elaborated ß-amyloid depositions, reduced glucose metabolism, and gray matter atrophy) than non-amnestic mild cognitive impairments -like Alzheimer's disease, healthy control-like subjective cognitive decline, and non-amnestic mild cognitive impairments -like subjective cognitive decline. The test-retest reliability of the subpopulation identification is fair to good in general. The study indicates overall similarity among subjective cognitive decline, amnestic mild cognitive impairment, and Alzheimer's disease and implies their progression relationships. The results support "deep feature comparison" as a potential beneficial framework to verify and refine early Alzheimer's disease status.

Effects of provisioning on the activity budget and foraging strategies of black-and-white snub-nosed monkeys (Rhinopithecus bieti) in the Baima Snow Mountain Nature Reserve, Yunnan, China.

Provisioning can significantly affect the ranging patterns, foraging strategies, and time budget of wild primates. In this study, we document for the first time, the effects of provisioning on the activity budget and foraging effort in an Asian colobine. Over 3-years, we used an instantaneous scanning method at 10-min intervals to collect data on the activity budget of a semiprovisioned breeding band (SPB) of black-and-white snub-nosed monkeys (Rhinopithecus bieti) (42-70 individuals) at Xiangguqing (Tacheng), Yunnan, China. We then compared the effects of provisioning in our study band with published data on a sympatric wild nonprovisioned breeding band (NPB) of R. bieti (ca. 360 monkeys) at the same field site. The SPB spent 25.6% of their daytime feeding, 17.1% traveling, 46.9% resting, and 10.3% socializing. In comparison, the NPB devoted more time to feeding (34.9%) and socializing (14.1%), less time to resting (31.3%), and was characterized by a greater foraging effort (1.74 versus 0.96, foraging effort = (feeding + traveling)/resting; see Methods). There was no difference between bands in the proportion of their activity budget devoted to traveling (15.7% vs. 17.1%). In addition, the SPB exhibited a more consistent activity budget and foraging effort across all seasons of the year compared to the NPB. These findings suggest that the distribution, availability, and productivity of naturally occurring feeding sites is a major determinant of the behavioral strategies and activity budget of R. bieti. Finally, a comparison of our results with data on six nonprovisioned R. bieti bands indicates that caution must be raised in meta-analyses or intraspecific comparisons of primate behavioral ecology that contain data generated from both provisioned and nonprovisioned groups.

Prognostic and predictive impact of molecular tumor burden index in non-small cell lung cancer patients.

BACKGROUND: The biomarkers of immune checkpoint inhibitors in the treatment of non-small cell lung cancer (NSCLC) patients have limited predictive performance. In this study we aimed to investigate the feasibility of molecular tumor burden index (mTBI) in circulating tumor DNA (ctDNA) as a predictor for immunotherapy in patients with NSCLC. METHODS: From February 2017 to November 2020, pretreatment and on-treatment (3~6 weeks after first cycle of immunotherapy) dynamic plasma ctDNA samples from NSCLC patients receiving immune monotherapy or combination therapy were analyzed by targeted capture sequencing of 1021 genes. PyClone was used to infer the mTBI. The impact of pretreatment mTBI on survival outcomes was verified in the POPLAR/OAK trials. RESULTS: We found that patients without detectable baseline ctDNA had better survival outcomes (median overall survival [OS]: not reached vs. 12.8 months; hazard ratio [HR], 0.15; p = 0.035]). RB1 and SMARCA4 mutations were remarkably associated with worse survival outcomes. Furthermore, lower pretreatment mTBI was associated with superior OS (median: not reached vs. 8.1 months; HR, 0.22; p = 0.024) and PFS (median: 32.9 vs. 5.4 months; HR, 0.35; p = 0.045), but not objective response, which was validated in the POPLAR/OAK cohort, suggesting that baseline mTBI was a prognostic factor for NSCLC immunotherapy. Early dynamic changes of mTBI (ΔmTBI) significantly distinguished responsive patients, and patients with mTBI decrease to more than 68% at the final tumor evaluation had longer OS (median: 38.2 vs. 4.0 months; HR, 0.18; p = 0.017) and PFS (median: not reached vs. 2.3 months; HR, 0.24; p = 0.030). CONCLUSION: ΔmTBI had a good sensitivity to identify potential beneficial patients based on the best effect CT scans, demonstrating that mTBI dynamics were predictive of benefit from immune checkpoint blockade.

Four additional natural 7-deazaguanine derivatives in phages and how to make them.

Bacteriophages and bacteria are engaged in a constant arms race, continually evolving new molecular tools to survive one another. To protect their genomic DNA from restriction enzymes, the most common bacterial defence systems, double-stranded DNA phages have evolved complex modifications that affect all four bases. This study focuses on modifications at position 7 of guanines. Eight derivatives of 7-deazaguanines were identified, including four previously unknown ones: 2'-deoxy-7-(methylamino)methyl-7-deazaguanine (mdPreQ1), 2'-deoxy-7-(formylamino)methyl-7-deazaguanine (fdPreQ1), 2'-deoxy-7-deazaguanine (dDG) and 2'-deoxy-7-carboxy-7-deazaguanine (dCDG). These modifications are inserted in DNA by a guanine transglycosylase named DpdA. Three subfamilies of DpdA had been previously characterized: bDpdA, DpdA1, and DpdA2. Two additional subfamilies were identified in this work: DpdA3, which allows for complete replacement of the guanines, and DpdA4, which is specific to archaeal viruses. Transglycosylases have now been identified in all phages and viruses carrying 7-deazaguanine modifications, indicating that the insertion of these modifications is a post-replication event. Three enzymes were predicted to be involved in the biosynthesis of these newly identified DNA modifications: 7-carboxy-7-deazaguanine decarboxylase (DpdL), dPreQ1 formyltransferase (DpdN) and dPreQ1 methyltransferase (DpdM), which was experimentally validated and harbors a unique fold not previously observed for nucleic acid methylases.