Bacterial lifestyle shapes pangenomes.

Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes. Two main hypotheses have been suggested to explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies have not been able to test between these hypotheses because the different features of lifestyle and effective population size are highly correlated with each other, and phylogenetically conserved, making it hard to disentangle their relative importance. We used phylogeny-based analyses, across 126 bacterial species, to tease apart the causal role of different factors. We found that pangenome fluidity was lower in i) host-associated compared with free-living species and ii) host-associated species that are obligately dependent on a host, live inside cells, and are more pathogenic and less motile. In contrast, we found no support for the competing hypothesis that larger effective population sizes lead to more fluid pangenomes. Effective population size appears to correlate with pangenome variation because it is also driven by bacterial lifestyle, rather than because of a causal relationship.

PaMYB11 promotes suberin deposition in Norway spruce embryogenic tissue during cryopreservation: A novel resistance mechanism against osmosis.

The osmotic resistance mechanism has been extensively studied in whole plants or plant tissues. However, little is known about it in embryogenic tissue (ET) which is widely used in plant-based biotechnological systems. Suberin, a cell wall aliphatic and aromatic heteropolymer, plays a critical role in plant cells against osmosis stress. The suberin regulatory biosynthesis has rarely been studied in gymnosperms. Here, PaMYB11, a subgroup 11 R2R3-MYB transcription factor, plays a key role in the osmotic resistance of Norway spruce (Picea abies) ETs during cryoprotectant pretreatment. Thus, RNA-seq, histological, and analytical chemical analyses are performed on the stable transformations of PaMYB11-OE and PaMYB11-SRDX in Norway spruce ETs. DAP-seq, Y1H, and LUC are further combined to explore the PaMYB11 targets. Activation of PaMYB11 is necessary and sufficient for suberin lamellae deposition on Norway spruce embryogenic cell walls, which plays a decisive role in ET survival under osmotic stress. Transcriptome analysis shows that PaMYB11 enhances suberin lamellae monomer synthesis by promoting very long-chain fatty acid (VLCFA) synthesis. PaPOP, PaADH1, and PaTET8L, the first two (PaADH1 and PaPOP, included) involved in VLCFA synthesis, are proved to be the direct targets of PaMYB11. Our study identified a novel osmotic response directed by PaMYB11 in Norway spruce ET, which provides a new understanding of the resistance mechanism against osmosis in gymnosperms.

Climate of origin shapes variations in wood anatomical properties of 17 Picea species.

BACKGROUND: Variations in hydraulic conductivity may arise from species-specific differences in the anatomical structure and function of the xylem, reflecting a spectrum of plant strategies along a slow-fast resource economy continuum. Spruce (Picea spp.), a widely distributed and highly adaptable tree species, is crucial in preventing soil erosion and enabling climate regulation. However, a comprehensive understanding of the variability in anatomical traits of stems and their underlying drivers in the Picea genus is currently lacking especially in a common garden. RESULTS: We assessed 19 stem economic properties and hydraulic characteristics of 17 Picea species grown in a common garden in Tianshui, Gansu Province, China. Significant interspecific differences in growth and anatomical characteristics were observed among the species. Specifically, xylem hydraulic conductivity (Ks) and hydraulic diameter exhibited a significant negative correlation with the thickness to span ratio (TSR), cell wall ratio, and tracheid density and a significant positive correlation with fiber length, and size of the radial tracheid. PCA revealed that the first two axes accounted for 64.40% of the variance, with PC1 reflecting the trade-off between hydraulic efficiency and mechanical support and PC2 representing the trade-off between high embolism resistance and strong pit flexibility. Regression analysis and structural equation modelling further confirmed that tracheid size positively influenced Ks, whereas the traits DWT, D_r, and TSR have influenced Ks indirectly. All traits failed to show significant phylogenetic associations. Pearson's correlation analysis demonstrated strong correlations between most traits and longitude, with the notable influence of the mean temperature during the driest quarter, annual precipitation, precipitation during the wettest quarter, and aridity index. CONCLUSIONS: Our results showed that xylem anatomical traits demonstrated considerable variability across phylogenies, consistent with the pattern of parallel sympatric radiation evolution and global diversity in spruce. By integrating the anatomical structure of the stem xylem as well as environmental factors of origin and evolutionary relationships, our findings provide novel insights into the ecological adaptations of the Picea genus.

Gene transferability and sociality do not correlate with gene connectivity.

The connectivity of a gene, defined as the number of interactions a gene's product has with other genes' products, is a key characteristic of a gene. In prokaryotes, the complexity hypothesis predicts that genes which undergo more frequent horizontal transfer will be less connected than genes which are only very rarely transferred. We tested the role of horizontal gene transfer, and other potentially important factors, by examining the connectivity of chromosomal and plasmid genes, across 134 diverse prokaryotic species. We found that (i) genes on plasmids were less connected than genes on chromosomes; (ii) connectivity of plasmid genes was not correlated with plasmid mobility; and (iii) the sociality of genes (cooperative or private) was not correlated with gene connectivity.

First Report of Collar Rot in Purple Passion Fruit (Passiflora edulis) Caused by Neocosmospora solani in Yunnan province, China.

Purple passion fruit (Passiflora edulis Sims) is a perennial climbing vine native to South America that is grown worldwide as an edible tropical fruit with excellent nutritional value and high economic value (Zibadi et al. 2007). With the increasing expansion of the plantation area in China, considerable economic loss caused by collar rot has attracted wide attention. From 2018-2020, collar rot resulted in the death of many plants of P. edulis 'Mantianxing', a commercial cultivar in China, in southwest China's Yunnan province. The disease spread quickly, and field incidence reached more than 50%. Stem rot symptoms were observed at the base of the stem, about 5-10 cm from the ground, resulting in wilting, defoliation, and death of plants. Representative symptomatic samples were collected from the base of five plants, surface disinfested for 30 seconds with 75% ethanol and 15 min with 10% hypochlorite, washed three times with sterile distilled water, then transferred to potato dextrose agar (PDA) dishes. After 2 days in the dark at 28℃, emerging fungal colonies were purified on new PDA dishes cultured at 28℃ for 7 days. The mycelia were flocculent. The color of the surface and the reverse colony was white and cream, respectively. On synthetic nutrient agar (SNA) medium, microconidia were oval, ellipsoidal or reniform, 0- or 1-septate, and 6.7-23.1 µm in length (n>30); macroconidia were straight to slightly curved, 3- or 5-septate, and 30.8-53.9 µm in length (n>30). Genomic DNA, extracted from six isolates, was amplified with three pairs of primers, ITS1 and ITS4 (White et al. 1990) , EF1-728F and EF1-986R (Carbone and Kohn 1999), and fRPB2-5F and fRPB2-7cR (Liu et al. 1999). The amplicons from all six isolates were sequenced and identical sequences obtained. The sequence of one representative isolate was uploaded to NCBI (National Center for Biotechnology Information) and analyzed with BLASTn in the Fusarium MLST database (https://fusarium.mycobank.org). The sequence of the internal transcribed spacer 1 (ITS1) region (GenBank MN944550) showed 99.1% (449/453 bp) identity to Fusarium solani strain NRRL 53667 (syn: Neocosmospora solani, GenBank MH582405). The sequence of the translation elongation factor-1 (EF-1) gene (GenBank MN938933) showed 97.8% identity (263/269 bp) to F. solani strain NRRL 32828 (GenBank DQ247135). The sequence of the second largest subunit of RNA polymerase Ⅱ (RPB2) gene (GenBank MW002686) showed 98.7% identity (810/821 bp) to F. solani strain NRRL 43441 (GenBank MH582407). Based on a multilocus phylogenetic analysis of the ITS1, EF-1 and RPB2 sequences, coupled with the morphological characteristics, the isolate (designated as NsPed1) was considered to be Neocosmospora solani (syn: Fusarium solani) (Crespo et al. 2019). Subsequently, three-month-old healthy seedlings and 45-day-old cuttings of P. edulis 'Mantianxing' plants were inoculated with the isolate NsPed1 to test its pathogenicity. Stems were wounded, approximately 1-2 mm deep, in the collar region of plants at 2 cm above the soil. A disk (9 mm in diameter) of NsPed1-colonized PDA was placed on the wound. Sterile PDA served as controls. All plants were kept in a growth chamber with 28-30°C, 60% relative humidity, and 16/8-h light/dark photoperiod. Fifteen plants were used for each treatment and replicated three times. Two weeks after inoculation, the stems of the inoculated plants turned brown with a lesion, 2-5 cm in length, and the leaves wilted. These symptoms were similar to those of the diseased plants in the field. The control plants were asymptomatic. N. solani NsPed1 was re-isolated from the infected plants, satisfying Koch's postulates. Taken together, N. solani NsPed1 was identified as the causal pathogen of collar rot in P. edulis 'Mantianxing'. Knowledge of the causal organism of collar rot in purple passion fruit will lead to improved measures to prevent and control the disease in China and other countries.

Signatures of kin selection in a natural population of the bacteria Bacillus subtilis.

Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.

SOCfinder: a genomic tool for identifying social genes in bacteria.

Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial social traits, particularly in natural environments. To address this gap, we can use bioinformatic tools to identify genes that control cooperative or otherwise social traits. Existing tools address this challenge through two approaches. One approach is to identify genes that encode extracellular proteins, which can provide benefits to neighbouring cells. An alternative approach is to predict gene function using annotation tools. However, these tools have several limitations. Not all extracellular proteins are cooperative, and not all cooperative behaviours are controlled by extracellular proteins. Furthermore, existing functional annotation methods frequently miss known cooperative genes. We introduce SOCfinder as a new tool to find bacterial genes that control cooperative or otherwise social traits. SOCfinder combines information from several methods, considering if a gene is likely to [1] code for an extracellular protein [2], have a cooperative functional annotation, or [3] be part of the biosynthesis of a cooperative secondary metabolite. We use data on two extensively-studied species (P. aeruginosa and B. subtilis) to show that SOCfinder is better at finding known cooperative genes than existing tools. We also use theory from population genetics to identify a signature of kin selection in SOCfinder cooperative genes, which is lacking in genes identified by existing tools. SOCfinder opens up a number of exciting directions for future research, and is available to download from https://github.com/lauriebelch/SOCfinder.

Graphene/MoS2-xOx/graphene photomemristor with tunable non-volatile responsivities for neuromorphic vision processing.

Conventional artificial intelligence (AI) machine vision technology, based on the von Neumann architecture, uses separate sensing, computing, and storage units to process huge amounts of vision data generated in sensory terminals. The frequent movement of redundant data between sensors, processors and memory, however, results in high-power consumption and latency. A more efficient approach is to offload some of the memory and computational tasks to sensor elements that can perceive and process the optical signal simultaneously. Here, we proposed a non-volatile photomemristor, in which the reconfigurable responsivity can be modulated by the charge and/or photon flux through it and further stored in the device. The non-volatile photomemristor has a simple two-terminal architecture, in which photoexcited carriers and oxygen-related ions are coupled, leading to a displaced and pinched hysteresis in the current-voltage characteristics. For the first time, non-volatile photomemristors implement computationally complete logic with photoresponse-stateful operations, for which the same photomemristor serves as both a logic gate and memory, using photoresponse as a physical state variable instead of light, voltage and memresistance. The polarity reversal of photomemristors shows great potential for in-memory sensing and computing with feature extraction and image recognition for neuromorphic vision.

[Detection of the viable but nonculturable Escherichia coli O157:H7 in aquatic microcosm].

OBJECTIVES: This study is to monitor the survival of E. coli O157:H7 in the aquatic microcosm from Han River and explore the feasibility of fluorescence staining, heterotrophic plate count and ELISA in detection of viable but nonculturable E. coli O157:H7. METHODS: E. coli O157:H7 were added into aquatic microcosm from Han River and cultured with low temperature and oligo-nutrition. Then the survival of E. coli O157:H7 were real-time monitored by acridine orange direct count (AODC), direct viable count (DVC)-CTC staining, DVC-nalidixic acid (NA) staining, heterotrophic plate count (HPC) and ELISA. RESULTS: E. coli O157:H7 can be converted to a viable but nonculturable state in the aquatic microcosm from Han River 58 days after cultured at 4°C with oligo-nutrition. The amount of viable E. coli O157:H7 was measured as 1.2 × 10(5) CFU/ml by DVC-CTC and 9.0 × 10(4) CFU/ml by DVC-NA, whereas the amount of culturable bacterial determined by HPC is 0. The amounts of bacteria determined by ELISA are basically stable within 58 days around 10(6) CFU/ml. CONCLUSION: E. coli O157:H7 can be converted into a viable but nonculturable state in Han River water at 4°C with oligo-nutrition, and ELISA combined with fluorescence staining and heterotrophic plate count can be used in quantitative detection of the viable but nonculturable E. coli O157:H7.

Simulation of English Speech Recognition Based on Improved Extreme Random Forest Classification.

Existing speech recognition systems are only for mainstream audio types; there is little research on language types; the system is subject to relatively large restrictions; and the recognition rate is not high. Therefore, how to use an efficient classifier to make a speech recognition system with a high recognition rate is one of the current research focuses. Based on the idea of machine learning, this study combines the computational random forest classification method to improve the algorithm and builds an English speech recognition model based on machine learning. Moreover, this study uses a lightweight model and its improved model to recognize speech signals and directly performs adaptive wavelet threshold shrinkage and denoising on the generated time-frequency images. In addition, this study uses the EI strong classifier to replace the softmax of the lightweight AlexNet model, which further improves the recognition accuracy under a low signal-to-noise ratio. Finally, this study designs experiments to verify the model effect. The research results show that the effect of the model constructed in this study is good.

The complete chloroplast genome of Bauhinia racemosa Lam. (Fabaceae): a versatile tropical medicinal plant.

Bauhinia racemosa Lam. (1783), a versatile medicinal plant, belongs to the family Fabaceae (subfamily Cercidoideae). In this study, we analyzed the complete chloroplast genome to facilitate its use in genetic research. The complete chloroplast genome of B. racemosa was found to be 155,501 bp long, including two inverted repeat (IR) regions of 25,446 bp, which are separated by a small single-copy (SSC) region of 18,295 bp and a large single-copy (LSC) region of 86,314 bp. The overall GC content is 36.4%. The genome of B. racemosa contains 129 genes, including 83 protein-coding genes, 37 tRNAs, 8 rRNAs, and 1 pseudogene (rps19). Phylogenetic analysis suggests that B. racemosa forms a monophyletic clade with the other four Bauhinia species (B. brachycarpa, B. purpurea, B. blakeana and B. variegata var. variegata).

Metabolomic and transcriptomic exploration of the uric acid-reducing flavonoids biosynthetic pathways in the fruit of Actinidia arguta Sieb. Zucc.

Flavonoids from Actinidia arguta Sieb. Zucc. can reduce uric acid in mice. However, the molecular basis of its biosynthesis is still unclear. In this paper, we used a combination of extensively targeted metabolomics and transcriptomics analysis to determine the types and differences of flavonoids in the fruit ripening period (August to September) of two main cultivated varieties in northern China. The ethanol extract was prepared, and the potential flavonoids of Chrysin (Flavone1), Rutin (Flavone2), and Daidzein (Flavone3) in Actinidia arguta Sieb. Zucc. were separated and purified by HPD600 macroporous adsorption resin and preparative liquid chromatography. The structure was identified by MS-HPLC, and the serum uric acid index of male Kunming mice was determined by an animal model test.125 flavonoids and 50 differentially regulated genes were identified. The contents of UA (uric acid), BUN (urea nitrogen), Cr (creatinine), and GAPDH in mouse serum and mouse liver glycogen decreased or increased in varying degrees. This paper reveals the biosynthetic pathway of uric acid-reducing flavonoids in the fruit of Actinidia arguta Sieb. Zucc., a major cultivar in northern China, provides valuable information for the development of food and drug homologous functional foods.

Geometry-asymmetric photodetectors from metal-semiconductor-metal van der Waals heterostructures.

The functional diversities of two-dimensional (2D) material devices with simple architectures are ultimately limited by immature doping techniques. An alternative strategy is to use geometry-asymmetric metal-semiconductor-metal (GA-MSM) structures, which enable the basic functions of semiconductor junctions such as rectification and photovoltaics. Here, the mixed-dimensional van der Waals heterostructures (MDvdWHs) based on the separation and self-assembly of p-type SnS layered nanosheets (NSs) and n-type SnS2 nanoparticles (NPs) are obtained using an aqueous phase exfoliation (APE) method. Due to the surface charge transfer doping, the carrier transport mechanism of devices based on MDvdWHs turns from thermionic field emission (TFE) to thermionic emission (TE), with the rectification factor (Iforward/Ireverse) changing from 0.7 to 3. To further illustrate the experimental results, the generic current transport models of GA-MSM devices have been established based on the TE and TFE mechanisms in which the TE and TFE mechanisms lead to opposite rectification phenomena in good agreement with the experimental results. The GA-MSM devices show a photovoltaic effect with a high responsivity of 35 A W-1 and detectivity of 3.4 × 1011 cm Hz1/2 W-1. This study not only provides a novel strategy to design photovoltaic devices with MDvdWHs, but more importantly, we have established fundamental models for the rectification behavior of GA-MSM devices.

The complete chloroplast genome sequence of Passiflora xishuangbannaensis (Passifloraceae), a vine endemic to Yunnan, China.

Passiflora xishuangbannaensis, Passiflora subgenus Decaloba, is a very rare endemic to the Yunnan, China. Here we report and characterize the complete chloroplast (cp) genome sequence of P. xishuangbannaensis to provide genomic resources useful for promoting its conservation and systematics. The complete genome is 135,742 bp in length and the overall GC content is 37.1%. The cp genome sequence has a typical quadripartite structure, comprising two inverted repeats (IRs: 20,604 bp) regions, which are separated by a small single-copy (SSC: 13,159 bp) region and a large single-copy (LSC: 81,375 bp) region. Moreover, a total of 122 functional genes were annotated, including 77 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis recovered P. xishuangbannaensis as a member of subgenus Decaloba.

Applied analysis of ultrasound-guided ilioinguinal and iliohypogastric nerve blocks in the radical surgery of aged cervical cancer.

In the present study, we evaluated the effects of ultrasound-guided ilioinguinal and iliohypogastric nerve blocks and intratracheal general anesthesia in the radical surgery of aged cervical cancer. From June 2014 to December 2014, 62 patients diagnosed with aged cervical cancer were enrolled in this study. The patients conformed to the indication of cervical cancer radical surgery. Patients were randomly divided into the test group and the control group according to the random number table with 31 individuals in each group. General anesthesia and compound ultrasound-guided ilioinguinal and iliohypogastric nerve blocks were applied in the test group, while intratracheal general anesthesia was used in the control group. The results showed that the operative time, awake time and the total dosage of propofol and sufentanil in the test group were significantly lower than those in the control group. The postoperative VAS score, the times to press the automatic control bump and continuous application time of the automatic control bump in the test group were significantly less than those in the control group. The occurrence rate of anesthesia-related adverse reactions in the test group during the perioperative period was significantly lower than that in the control group. Differences were statistically significant (P<0.05). We concluded that ultrasound-guided ilioinguinal and iliohypogastric nerve blocks significantly improved the analgesic effects during the perioperative and postoperative period in cervical cancer radical surgeries.