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Radish (Raphanus sativus L.) is one of the most vital root vegetable crops worldwide. Cadmium (Cd), a non-essential and toxic heavy metal, can dramatically restrict radish taproot quality and safety. Although the Peiotrpic Drug Resistance (PDR) genes play crucial roles in heavy metal accumulation and transport in plants, the systematic identification and functional characterization of RsPDRs remain largely unexplored in radish. Herein, a total of 19 RsPDR genes were identified from the radish genome. A few RsPDRs , including RsPDR1 , RsPDR8 and RsPDR12 , showed significant differential expression under Cd and lead (Pb) stress in the 'NAU-YH' genotype. Interestingly, the plasma membrane-localized RsPDR8 exhibited significantly up-regulated expression and enhanced promoter activity under Cd exposure. Ectopic expression of RsPDR8 conferred Cd tolerance via reducing Cd accumulation in yeast cells. Moreover, the transient transformation of RsPDR8 revealed that it positively regulated Cd tolerance by promoting ROS scavenging and enhancing membrane permeability in radish. In addition, overexpression of RsPDR8 increased root elongation but deceased Cd accumulation compared with the WT plants in Arabidopsis , demonstrating that it could play a positive role in mediating Cd efflux and tolerance in plants. Together, these results would facilitate deciphering the molecular mechanism underlying RsPDR8 -mediated Cd tolerance and detoxification in radish. • In total, 19 RsPDR genes are globally identified from the radish genome. • RsPDR8 exhibited dramatic Cd-induced expression and promoter activity in radish. • RsPDR8 is localized to plasma membrane and has Cd transport activity in yeast. • Overexpression of RsPDR8 promotes Cd efflux and ROS scavenging in plants. [ABSTRACT FROM AUTHOR]

Cyanophages are abundant in the oceanic environment and directly impact cyanobacterial distributions, physiological processes and evolution. Two samples collected from coastal Maine in July and September 2009 were enriched for S ynechococcus cells using flow cytometry and examined through metagenomic sequencing. Homology-based sequence prediction indicated cyanophages, largely myoviruses, accounted for almost half the reads and provided insights into environmental infection events. T4-phage core-gene phylogenetic reconstruction revealed unique diversity among uncultured cyanophages and reference isolates resulting in identification of a new phylogenetic cluster. Genomic comparison of reference cyanophage strains S- SM2 and Syn1 with putative homologous contigs recovered from metagenomes provided evidence that gene insertion, deletion and recombination have occurred among, and are likely important for diversification of, natural populations. Identification of putative genetic exchange between cyanophage and non-cyanophage viruses, i.e. M icromonas virus and P elagibacter phage, supports hypotheses related to a significant role for viruses in mediating transfer of genetic material between taxonomically diverse organisms with overlapping ecological niches. [ABSTRACT FROM AUTHOR]

Summary Plasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry-sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment. [ABSTRACT FROM AUTHOR]

Unilateral biportal endoscopic decompression (UBED) offers the advantages of minimal tissue damage, operational flexibility, and clear visualization, positioning it as an innovative and minimally invasive endoscopic technique. Nevertheless, the clinical evidence supporting the use of UBED in the treatment of degenerative lumbar diseases is limited and conflicting. As of October 1, 2023, a comprehensive search was conducted across databases including Web of Science, PubMed, Embase, and the Cochrane Library to identify all published studies on minimally invasive UBED for the treatment of degenerative lumbar diseases. Data pertaining to patient demographics, fluoroscopy time, operative duration, intraoperative hemorrhage, hospitalization length, visual analog scale (VAS) score for back and leg pain, MacNab criteria, Oswestry Disability Index (ODI), and complication rates were extracted. The Newcastle-Ottawa scale was utilized to assess the quality. Twelve articles were included, involving 816 patients. The back VAS score (95% confidence interval [CI]: −0.09–0.07, P = 0.75), MacNab criteria (95% CI: 0.52–2.3, P = 0.82), fluoroscopy time (95% CI: −7.03 to –0.4, P = 0.08), and the incidence of complications (95% CI: 0.5–1.73, P = 0.82) were not significantly different, while the leg VAS score (95% CI: 0.01–0.18, P = 0.03), ODI score (95% CI: −1.03 to –0.09, P = 0.02), operation time (95% CI: 5.76–20.62, P = 0.0005), hospitalization length (95% CI: 0.41–2.76, P = 0.008), and intraoperative hemorrhage (95% CI: 21.92–72.44, P = 0.0003) were significantly different. UBED offers superiority in ODI, flexibility, and visual field clarity. Conversely, percutaneous endoscopic lumbar decompression presents advantages in terms of operation duration, blood loss, hospitalization length, and leg VAS score. These factors should be thoroughly considered when selecting a surgical approach. [ABSTRACT FROM AUTHOR]

• Flower-like microspheres with cavity-in-cavity structure and radical openings. • Firstly reported bramble-knitted microspheres prepared with NiSO 4 as nickel source. • Multiple roles of HMT in hydrothermal fabrications of porous Ni(OH) 2 microspheres. • Effects of chloride, nitrate and sulfate ions on the structures and morphologies. Hierarchical nickel hydroxide nanostructures have been hydrothermally synthesized with only hexamethylenetetramine (HMT) as alkaline source and NiCl 2 , Ni(NO 3) 2 and NiSO 4 as nickel source, respectively. All samples were verified to be of α-Ni(OH) 2 phase. The samples produced with NiCl 2 or Ni(NO 3) 2 resembled each other in structure and morphology: the flower-like porous microspheres with an interesting cavity-in-cavity structural characteristic. The product prepared with NiSO 4 , however, showed two kinds of structures with distinctly different characteristics. One was the flower-like porous microsphere; the other was like a microsphere of knitted brambles, which was probably first reported. The formation mechanisms were explored and attributed to the multiple roles of HMT and the effects of anions. Different from chloride and nitrate ions, sulfate ions could be adsorbed strongly on the surface of nickel hydroxide, which resulted in the formation of bramble-like structure units. This work suggested that combining the selections of alkaline source and anion could be helpful for controlling the structures and morphologies of transition metal hydroxides. [ABSTRACT FROM AUTHOR]

Radish is one of the most economical root vegetable crops worldwide. Cold stress dramatically impedes radish taproot formation and development as well as reduces its yield and quality. Although the Cycling Dof Factors (CDFs) play crucial roles in plant growth, development and abiotic stress responses, how CDF TFs mediate the regulatory network of cold stress response remains largely unexplored in radish. Herein, a total of nine RsCDF genes were identified from the radish genome. Among them, the RsCDF3 exhibited obviously up-regulated expression under cold stress, especially at 12 h and 24 h. RsCDF3 was localized to the nucleus and displayed dramatic cold-induced promoter activity in tobacco leaves. Moreover, overexpression of RsCDF3 significantly enhanced cold tolerance of radish plants, whereas its knock-down plants exhibited the opposite phenotype. Interestingly, both in vitro and in vivo assays indicated that the RsCDF3 repressed the transcription of RsRbohA and RsRbohC via directly binding to their promoters, which contributed to maintaining the cellular homeostasis of reactive oxygen species (ROS) production and scavenging in radish. In addition, the RsCDF3 bound to its own promoter to mediate its transcription, thereby forming an autoregulatory feedback loop to cooperatively trigger RsRbohs -dependent cold tolerance. Together, we revealed a novel RsCDF3- RsRbohs module to promote the cold tolerance in radish plants. These findings would facilitate unveiling the molecular mechanism governing RsCDF3-mediated cold stress response in radish. • In all, nine RsCDF genes are systematically identified from the radish genome. • RsCDF3 exhibited dramatic cold-induced expression and promoter activity in radish. • RsCDF3 positively regulates cold tolerance via repressing two RsRbohs transcription. • RsCDF3 regulates its own expression and forms a feedback loop to mediate cold tolerance. [ABSTRACT FROM AUTHOR]

The aim of this study was to carry out a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing. We recruited 50 OC-SCC cases which were then matched with a control patient by age, gender, race, smoking status and alcohol status. DNA was extracted from oral wash samples from all patients and whole genome shotgun sequencing performed. The raw sequence data was cleaned, reads aligned with the human genome (GRCH38), nonhuman reads identified and then HPV genotypes identified using HPViewer. In the 50 patients with OC-SCC, the most common subsite was tongue in 26 (52%). All patients were treated with primary resection and neck dissection. All but 2 tumors were negative on p16 immunohistochemistry. There were no statistically significant differences between the cases and controls in terms of gender, age, race/ethnicity, alcohol drinking, and cigarette smoking. There was no statistically significant difference between the cancer samples and control samples in the nonhuman DNA reads (medians 4,228,072 vs. 5,719,715, P value = 0.324). HPV was detected in 5 cases (10%) of OC-SCC (genotypes 10, 16, 98) but only 1 tumor sample (genotype 16) yielded a high number of reads to suggest a role in the etiology of OC-SCC. HPV was detected in 4 control patients (genotypes 16, 22, 76, 200) but all had only 1–2 HPV reads per human genome. Genotypes of HPV are rarely found in patients with oral cancer. [ABSTRACT FROM AUTHOR]

Pseudomonas phages PaGz-1 and PaZq-1, two new phages infecting Pseudomonas aeruginosa, were isolated from fresh water in Guangdong province, China. The genomes of these two phages consist of 93,975 bp and 94,315 bp and contain 175 and 172 open reading frames (ORFs), respectively. The genome sequences of PaGz-1 and PaZq-1 share 95.8% identity with a query coverage of 94%, suggesting that these two phages belong to two different species. Based on results of nucleotide sequence alignment, gene annotation, and phylogenetic analysis, we propose PaGz-1 and PaZq-1 as representative isolates of two species in the genus Pakpunavirus within the family Myoviridae. [ABSTRACT FROM AUTHOR]

Emerging evidence suggests that the gut microbiome actively regulates cognitive functions and that gut microbiome imbalance is associated with Alzheimer's disease (AD), the most prevalent neurodegenerative disorder. However, the changes in gut microbiome composition in AD and their association with disease pathology, especially in the early stages, are unclear. Here, we compared the profiles of gut microbiota between APP/PS1 transgenic mice (an AD mouse model) and their wild-type littermates at different ages by amplicon-based sequencing of 16S ribosomal RNA genes. Microbiota composition started diverging between the APP/PS1 and wild-type mice at young ages (i.e., 1–3 months), before obvious amyloid deposition and plaque-localized microglial activation in the cerebral cortex in APP/PS1 mice. At later ages (i.e., 6 and 9 months), there were distinct changes in the abundance of inflammation-related bacterial taxa including Escherichia-Shigella, Desulfovibrio, Akkermansia, and Blautia in APP/PS1 mice. These findings suggest that gut microbiota alterations precede the development of key pathological features of AD, including amyloidosis and plaque-localized neuroinflammation. Thus, the investigation of gut microbiota might provide new avenues for developing diagnostic biomarkers and therapeutic targets for AD. [ABSTRACT FROM AUTHOR]

Recent studies have shown that microorganisms may be associated with the onset and development of bladder cancer. The purpose of this study is to identify the common core bacteria associated with bladder cancer. We characterized the urinary microbial profile of the individuals with bladder cancer by 16S rRNA gene sequencing, and the results of 24 bladder cancer samples collected in our laboratory reveal 31 common core bacteria at genera level. In addition, the abundance of four common core bacteria is significantly higher in bladder cancer samples than in samples from nondiseased people analyzed by LEfSe, based on two previous datasets. In particular, the abundance of Acinetobacter is much higher in bladder cancer samples. It has been reported that Acinetobacter is involved not only in biofilm formation but also in the adhesion and invasion of epithelial cells, the spread of bacteria caused by the degradation of phospholipids in the mucosal barrier, and the escape of the host immune response. Thus, Acinetobacter may be related to bladder cancer and is a potential microbial marker of bladder cancer. However, due to the limited number of participants, further studies are needed to better understand the role of microorganisms in bladder cancer to provide novel biomarkers for diagnosis, prognosis, and therapy. [ABSTRACT FROM AUTHOR]

Salmonella phages SenALZ1 and SenASZ3, two novel phages infecting Salmonella enterica, were isolated and analyzed. The genomes of these two phages consist of 154,811 and 157,630 base pairs (bp), with G+C contents of 44.56% and 44.74%, respectively. Fifty-nine of 199 open reading frames (ORFs) in the SenALZ1 genome, and 60 of the 204 in the SenASZ3 genome show similarity to reference sequences in the NCBI nr database that encode putative phage proteins with predicted functions. Based on the results of transmission electron microscopy (TEM) examination, complete genome sequence alignment, phylogenetic analysis, and gene annotation, we propose that these two phages are representative isolates of two new species of the genus Cba120virus, subfamily Cvivirinae, family Ackermannviridae. [ABSTRACT FROM AUTHOR]

Radish is an economical cool-season root vegetable crop worldwide. Heat shock protein 70 (HSP70) plays indispensable roles in plant growth, development and abiotic stress responses. Nevertheless, little information is available regarding the identification and functional characterization of HSP70 gene family in radish. Herein, a total of 34 RsHSP70 genes were identified at the radish genome level, among which nine and 25 RsHSP70s were classified into the HSP110/SSE and DnaK subfamilies, respectively. RNA-seq analysis revealed that some RsHSP70 genes had differential expression profile in radish leaf, root, stamen and pistil. A range of RsHSP70 genes exhibited differential expression under several abiotic stresses such as heat, salt and heavy metals. Intriguingly, the expression of four RsHSP70 genes (RsHSP70-7 , RsHSP70-12 , RsHSP70-20 and RsHSP70-22) was dramatically up-regulated under heat stress (HS). RT-qPCR and transient LUC reporter assay indicated that both the expression and promoter activity of RsHSP70-20 was strongly induced by HS. Notably, overexpression of RsHSP70-20 significantly enhanced thermotolerance by decreasing reactive oxygen species and promoting proline accumulation in radish, whereas its knock-down plants exhibited increased thermosensitivity, indicating that RsHSP70-20 positively regulate HS response in radish. These results would provide valuable information to decipher the molecular basis of RsHSP70 -mediated thermotolerance in radish. [Display omitted] • RsHSP70 gene family was systematically characterized at genome-wide level in radish. • Expression and promoter activity of RsHSP70-20 was markedly induced by heat stress. • Transgenic analysis reveals that RsHSP70-20 enhanced thermotolerance of radish plant. [ABSTRACT FROM AUTHOR]

In this study, two bacteriophage isolates, AhSzq-1 and AhSzw-1 that specifically infect Aeromonas hydrophila strain KT998822, were isolated from seawater and characterized. One-step growth curves showed that the latent period of AhSzq-1 and AhSzw-1 are 50 min and 60 min, respectively. The sequence similarities between AhSzq-1 and AhSzw-1 were 88% at the DNA and 83% at the protein level, suggesting that these two phages are representatives of two different species. The virion morphology, DNA genome size and terminal repeats of these two phages are similar to those of viruses classified as T5virus phages. Both phylogenetic analyses and proteomic comparison show that AhSzq-1 and AhSzw-1 group with members of the T5virus genus. We thus propose these two phages as representative isolates of two new species within the T5virus genus. [ABSTRACT FROM AUTHOR]

The purpose of this paper is to extend the meta-theory of theory of nuclear safety to a new stage. Meta-theory method describes nuclear power plant’s nuclear safety systematically and is devised to analyze and to assist the investigation of the theory of nuclear safety. Different types of “capacity” and “load” via RISMC method were present by meta-theory, which could be found out from the real examples that one of load and capacity is deterministic, while the other is probabilistic. In the current research, the authors intend to develop all four combinations in one single Initial Event, aiming to extend this meta-theory method to a more extensive and practical level. A methodology has been verified by a specific yet simple engineering case, i.e., LOCA. To validate its logic, we present an Event Tree to explain the different responses of different safety systems. Then, RELAP 5 is programmed to establish a traditional LOCA sequence to investigate the changing situations of various parameters in reactor coolant system. Based on these approaches, the “capacity” and “load” should be described and all the four “capacity – load” cases in an Initial Event are determined. [ABSTRACT FROM AUTHOR]

AsXd-1, a bacteriophage that infects Aeromonas salmonicida, was isolated from the wastewater of a seafood market in Shenzhen, China. The 39,014-bp genome of this phage contains 52 open reading frames (ORFs), 30 of which were found to be homologous to reference sequences that putatively encode functional phage proteins. Nine out of the remaining 22 ORFs with unknown functions were unique to AsXd-1. Gene annotation suggests that AsXd-1 has both lysogenic and lytic life cycles. Furthermore, both phylogenetic analysis based on the large subunit of terminase and genome sequence comparisons show that AsXd-1 is closely related to phages belonging to the genus Hk97virus. We thus propose AsXd-1 as a new member of the genus Hk97virus within the family Siphoviridae. [ABSTRACT FROM AUTHOR]

This paper investigates the time-dependent modeling of the operating behaviors of systems in risk monitoring applications. The approach used focuses on the constructed concept of the risk monitoring time axis and on time-dependent failure probability modeling for dependencies based on this axis. Dependencies among the complex operating behaviors in nuclear power plants (NPPs) are often superimposed on each other. To ensure the safe and reliable operation of the system, a large number of redundant designs are used in NPPs. In this paper, we mainly focus on the dependencies that are common in redundant systems, such as state dependencies, sequential failures and common-cause failure (CCF). Studies are conducted on the rationality and applicability to the risk monitoring model of the model simplification assumptions for ignoring certain dependency problems in traditional static probabilistic safety assessment (PSA) modeling. Time-dependent mathematical models considering these dependencies in risk monitoring are proposed in this paper. Additionally, time-dependent mathematical models considering the superposition of these dependency problems in risk monitoring are developed, and the process of updating the above models with time and configuration changes is also studied in this paper to provide modelers with guidelines for representing such aspects in the risk monitoring application. Moreover, based on the above research results, a second-order redundant system is taken as an example to calculate and compare time-dependent system risk measurements of the model proposed in this paper and the time-independent system risk of the traditional risk monitoring model. These comparative studies demonstrate the effectiveness and benefits of the method proposed in this paper and provide some insightful conclusions. Only by accurately considering the time dependence and system dependencies can we obtain an accurate system risk and then make a reasonable and credible risk-informed decision. [ABSTRACT FROM AUTHOR]

• A Stage 4-living PSA method based on the time-dependent MFT is proposed. • This method enables real-time automatic updating model according to the state signal. • This method can reflect the effect of the cumulative running time on the system risk. • A real-time online risk monitoring (RORM) system is developed based on this method. • The functions and interfaces of the RORM are demonstrated with an application case. This paper presents a living PSA modeling and updating method based on a time-dependent modular fault tree (MFT), which takes into account all the failure modes involved in the whole life cycle of a component for continuous state transition and time-dependent problem analysis. And a Stage 4-Living PSA, characterized by real-time online automatic updating model, is achieved using a combination of the time-dependent MFT method and the state monitoring technology. This method has a remarkable effect in enhancing the updating ability, flexibility of the model and reducing the scale of the model. And using this method cannot only capture the risk fluctuations caused by any configuration change more accurately and timely, but also reflect the effect of the component cumulative running time on the real-time risk of the plant, and provide more valuable data for making operation and maintenance decision. Moreover, A real-time online risk monitoring (RORM) system with a hierarchical modular modeling strategy and computational data structure is also developed to automatically update the living PSA model after receiving configuration change information of the plant, and this system displays graphical risk information that helps users to carry out daily operation risk management more effectively at nuclear power plants (NPPs). Finally, the function and interface of this system applied to RORM are demonstrated by using the living PSA model for the Middle Break Loss of Coolant Accident (MLOCA) in the Fuqing NPP. The achievement of RORM can reduce the burden on the plant personnel, and avoided the fact that the lagged and unreasonable risk information that misleads plant personnel into making decisions, resulting in greater risk or economic loss. [ABSTRACT FROM AUTHOR]

Increasing evidences have revealed a close interaction between the intestinal microbes and host growth performance. The shrimp (Litopenaeus vannamei) gut harbors a diverse microbial community, yet its associations with dietary, body weight and weaning age remain a matter of debate. In this study, we analyzed the effects of different dietary (fishmeal group (NC), krill meal group (KM)) and different growth stages (age from 42 day-old to 98 day-old) of the shrimp on the intestinal microbiota. High throughput sequencing of the 16S rRNA genes of shrimp intestinal microbes determined the novelty of bacteria in the shrimp gut microbiota and a core of 58 Operation Taxonomic Units (OTUs) was present among the shrimp gut samples. Analysis results indicated that the development of the shrimp gut microbiota is a dynamic process with three stages across the age according to the gut microbiota compositions. Furthermore, the dietary of KM group did not significantly change the intestinal microbiota of the shrimps compared with NC group. Intriguingly, compared to NC group, we observed in KM group that a fluctuation of the shrimp gut microbiota coincided with the shrimp body weight gain between weeks 6-7. Six OTUs associated with the microbiota change in KM group were identified. This finding strongly suggests that the shrimp gut microbiota may be correlated with the shrimp body weight likely by influencing nutrient uptake in the gut. The results obtained from this study potentially will be guidelines for manipulation to provide novel shrimp feed management approaches. [ABSTRACT FROM AUTHOR]