Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet.

The most extreme environments are the most vulnerable to transformation under a rapidly changing climate. These ecosystems harbor some of the most specialized species, which will likely suffer the highest extinction rates. We document the steepest temperature increase (2010-2021) on record at altitudes of above 4,000 m, triggering a decline of the relictual and highly adapted moss Takakia lepidozioides. Its de-novo-sequenced genome with 27,467 protein-coding genes includes distinct adaptations to abiotic stresses and comprises the largest number of fast-evolving genes under positive selection. The uplift of the study site in the last 65 million years has resulted in life-threatening UV-B radiation and drastically reduced temperatures, and we detected several of the molecular adaptations of Takakia to these environmental changes. Surprisingly, specific morphological features likely occurred earlier than 165 mya in much warmer environments. Following nearly 400 million years of evolution and resilience, this species is now facing extinction.

Milk fat globule membrane protects Bifidobacterium longum ssp. infantis ATCC 15697 against bile stress by modifying global transcriptional responses.

The milk fat globule membrane (MFGM) can protect probiotic bacteria from bile stress. However, its potential mechanism has not been reported. In this study, the viability, morphology and gene transcriptional response of Bifidobacterium longum ssp. infantis ATCC 15697 (BI_15697) stressed by bile salts with or without MFGM were investigated. It was shown that MFGM alleviated the reduction in BI_15697 population induced by 0.2% porcine bile stress and restored the population to the control levels. MFGM ameliorated the shrunken, fragmented appearance and irregular morphology of BI_15697 and maintained cell integrity disrupted by bile stress. RNA-sequencing results showed that MFGM increased transport of glucose and raffinose and decreased that of branched-chain amino acids (BCAA) in the presence of bile salts. MFGM stimulated the expression of genes involved in the synthesis of raffinose in galactose metabolism and the metabolism of BCAA, suggesting that MFGM stimulated the accumulation of raffinose and BCAA in the presence of bile. In addition, MFGM stimulated the expression of 2 bile efflux transporters under bile stress. Together, the multifactorial response helps BI_15697 excrete bile salts and maintain cellular integrity in response to bile stress. This study proposes a mechanism for the protection of BI_15697 against bile salt stress by MFGM, thereby providing a molecular basis for its application in incorporation of probiotics.

First report of Colletotrichum plurivorum causing anthracnose on pecan (Carya illinoinensis) in China.

Pecan (Carya illinoinensis) is an economically important nut crop worldwide (Xiao et al 2021). Anthracnose symptoms were found on pecan fruits and leaves in plantations in Anhui and Jiangsu provinces, China in August 2019. Irregular, dark brown or black spotted lesions firstly appeared on the surface and inside of fruits, and spread to all leaves. The symptoms resulted in 30% to 50% leaf drop and nearly a half of fruit decay in almost all trees of the susceptible cv. Wichita. The causal agent were isolated from fruits with target symptoms following the steps: surface disinfected with 75% ethanol (2×, 30 s), rinsed with sterile deionized water (3×), ~ 0.5 cm small fragments of the fruits excised and plated on potato dextrose agar (PDA) medium and incubated at 28 °C in dark for 3-d. Mycelium of each colony was picked and incubated on fresh PDA at 25 °C with a 12-hour light/dark cycle for 6-d to induce conidia formation. One 5-mm hyphal plug produced from each single spore isolate was transferred onto fresh PDA to obtain the pure cultures. Koch's postulates was employed for pathogenicity determination of the isolates. Non-wounded healthy leaves from seedlings of the disease susceptible cv. Pawnee were disinfected with 1% NaClO and inoculated with 5-mm 5-d hyphal of each isolate at 25 ℃. Tiny lesion spots were visible on the leaves after 2 days post inoculation (DPI) with isolate W-6 (the only pathogenic one among all isolates), and expanded over time until to the leaves withered, while the control leaves and leaves inoculated with other isolates remained asymptomatic. The pathogenicity of W-6 were confirmed using leaves and fruits of living Pawnee trees growing in Linglong Mountain Plantation, Lin'an, Hangzhou, China (119°38'51″E, 30°12'39″N, elevation: 119m). Three experimental replicates were conducted separately with three bio-replicates for all pathogenetic testing. The same symptoms were observed on both detached leaves and leaves and fruits of living trees.. The colony of W-6 have round cottony mycelium with complete edges and showed the fastest growth rate 3 - 4 DPI. After 7 DPI, white aerial mycelium turned yellowish brown and formed Acervulus in the mycelium. Conidia (n=50) one-celled, 12.0 - 20.0 µm × 3.5 to 6.0 µm width. Hyaline cylindrical with slightly rounded ends and two or three large guttulate at the centre. Most Acervulus dark brown and slightly irregular in shape, 12.70 × 18.79 µm (n=10). Setae were dark brown in color with average length around 34.10 µm (n=10). These characteristics matched previous descriptions of Colletotrichum orchidearum species complex, including C. plurivorum (Damm et al 2019). The identity of W-6 was confirmed by multi-locus phylogenetic analysis using the internal transcribed spacer (ITS) rDNA region and partial sequences of the conserved genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), beta-tubulin 2 (TUB2), and chitin synthase (CHS). The sequences of W-6 were used for Basic Local Alignment Search Tool (BLAST) against NCBI GenBank and the sequences with 100% identity to that of W-6 were achieved, respectively. The concatenated sequences of the ACT-CHS-GAPDH-ITS-TUB2 was used for building a phylogenetic tree. The molecular analyses allowed the identification of the pathogen as C. plurivorum. It was known that 9 of the 11 Colletotrichum species causing pecan anthrax worldwide were reported in southern China (Brenneman 1989; Oh et al 2021). This is the first report of C. plurivorum as causal agent of pecan in China.

First report of Fusarium concentricum as a causal agent of Fusarium leaf blotch on pecan (Carya illinoinensis) in Southeast China.

The economically important nut crop pecan (Carya illinoinensis (Wangenh.) K. Koch) is seriously affected by increasing incidence of fungal disease worldwide (Xiao et al 2021). The top leaves of the pecan variety 'Pawnee' in the orchard of Zhejiang A&F University, Zhejiang, China were damaged by massive dark brown plaques in summer to autumn 2021. The causal agent was isolated from leaves with target plaques following the steps: sterilized with 70% alcohol (30 s × 2), rinsed with sterilized water (3 ×) before and after 5% sodium hypochlorite (30 s), excised the plaques, and placed on PDA medium at 28℃ in a dark incubator for 3-d. The mycelium on the edge of each colony was transferred to fresh SNA medium in dark for 2 weeks to induce conidia formation. A few conidia-germinated mycelia were transferredand inoculated on new plates containing fresh PDA medium to obtain the purified cultures. Koch's postulates were applied to validate the pathogenicity of the purified isolates. Non-woundedly healthy leaves (disinfected with 5% sodium hypochlorite) of 'Pawnee' seedlings were inoculated with 5 mm 7-d old purified cultures. Dark-brown spots appeared on the leaves 2 days post inoculation at 25℃. The spots became larger accompanied by partially cracking and slight deformation of inoculated leaves from day 2 to day 4, while the control leaves remained asymptomatic. A re-isolated strain ZJ-6 from these infected leaves was identified as the pathogenic isolate with the same symptom as the previous one. Morphologically, aerial mycelia of the pathogenic isolate ZJ-6 cashmere and white. The reverse of colony orange. The edge of the colony appeared gradually thinner, the aerial mycelia loose and flocky, and the matrix mycelium whitened. Hyphae were septate, translucent with smooth wall and 1.47-7.14 µm in width. Microconidia (n = 20) obovoid to fusoid, mainly with 0-septate, 4.45-7.78×4.79-16.25 µm. Macroconidia (n = 20) sickle, mainly with 3-5 septa, 5.56-10.28×56.67-114.54 µm. Simultaneous of monophialidic and polyphialidic conidiophores. Conidiophore width 1.47-3.68 µm, slightly smaller than vegetative hyphae. The morphological characteristics matched with previous descriptions of Fusarium species (Nirenberg and O'Donnell 1998; Wang et al 2013). The identity of ZJ-6 was confirmed by phylogenetic reconstruction using the concatenated sequences of the ATP citrate lyase (ACL1), Calmodulin (CaM), the internal transcribed spacer (ITS) rDNA region, ribosomal RNA gene (LSU), the largest subunit of DNA-dependent RNA polymerase II (RPB1), partial translation elongation factor-1 alpha (TEF) and ß-Tubulin (TUB). To this end, the genomic DNA of ZJ-6 was extracted by the M5 hipermix-MF859 (Mei5 Biotechnology) and submitted to GenBank under the accession numbers OP933646, OP933647, OP925890, OP925889, OP933396, OP933648, and OP933397, respectively. The obtained sequences of ZJ-6 were used for nucleotide BLAST against thetandard databases, respectively, and the strains with sequence identification values above 98% were selected to construct multiple alignment for building a phylogenetic tree. This analyses allowed the identification of ZJ-6 as Fusarium concentricum Nirenberg & O'Donnell, a species with few reports that can cause serious damage to the fruits and branches of other hosts (Hasan et al 2020; Huda-Shakirah et al 2020; Wang et al 2013). This is the first report of pathogenic F. concentricum on pecan in Southeast China that caused no harvest of infected plants.

First report of Curvularia muehlenbeckiae, the causal agent of Curvularia leaf spot on pecan (Carya illinoinensis) in China.

The pecan (Carya illinoinensis) industry is largely affected by the increased incidence of diseases (Xiao et al 2021). Leaf spot symptoms were identified in an orchard of cultivar Pawnee pecan trees at Zhejiang A&F University, Zhejiang, China in August 2020. Small black spots occurred on the veins and edges of the leaves and nearby tissues turned yellow and slightly deformed (May to July). The spots (0.5-1.5cm) spread to all leaves with 25% to 40% leaf drop occurring in almost all trees between August and October. The causal pathogen was isolated from leaves with target symptoms using the following method: surface sterilized with 70% alcohol (2×, 30 s), rinsed with sterilized water (3×), leaf spots excised and placed on PCA media, and left to incubate at 28℃ in the dark for 3-d. Mycelium on the edge of each clone was excised and incubated on fresh oatmeal agar medium with a 12-hour light/dark cycle for 7-d to obtain conidia. Single spore isolates were germinated on PDA medium under the same conditions as previously described, one 5-mm hyphal plug was transferred to fresh PCA media to obtain the pure cultures. The pathogenicity of the isolates were verified using Koch's postulates. Non-wounded healthy leaves (disinfected with 1% NaClO) of cv. Pawnee (disease susceptible) were obtained from seedlings grown in green-house at 26 ℃ and inoculated with 5-mm hyphal plugs and a conidia-hyphae suspension (~106/mL) containing one-week old purified cultures. After 3-15 days post-inoculation, small black spots appeared on the leaves inoculated with isolate P-6 (the only pathogenic isolate from the leaf spots in the orchard) and grew larger until the whole leaf wilted while the control leaves remained asymptomatic. The experiment was repeated two times with two bio-replicates each run. Finally, the pathogen was re-isolated from infected leaves, which showed the same symptoms as the previous isolate. Aerial mycelia of P-6 turned from white to gray and substrate mycelia from brown to black. Colonies had a fimbriate margin before mycelia filled the medium. Hyphae were septate, branched, brown or black, smooth wall and 1.4-10 µm in width. Conidiophore single-branch, dark brown, curved or straight, 1.93-5.51×44.12-104.41 µm width, conidiogenous cells 6.66-16.67 µm (terminal) and 8.82-23.33 µm (intercalary) length, mono- to polytretic, proliferating sympodially. Conidia (n=20) four cells, 15.7 - 25.7 µm × 7.1 - 11.4 µm wdth, swelling and curving from the basal cell to the third. The bending angle was 5° to 80°. The middle two cells were brown and usually verruculose, the basal and apical cells paler and less ornamented. No sexual morph observed. The morphological characteristics matched previous descriptions of Curvularia species (Madrid et al 2014). The identity of P-6 was confirmed by phylogenetic reconstruction using the concatenated sequences of ITS rDNA, partial GAPDH, LSU, TEF-1α and RPB2 regions (Raza et al 2019). The genomic DNA of P-6 was extracted by the M5 hipermix-MF859 (Mei5 Biotechnology). The sequences of P-6 were used for nucleotide BLAST against the Standard databases and model strains were selected to construct the concatenated sequences of GAPDH-ITS-LSU-TEF-1α-RPB2 for building a phylogenetic tree. This analysis identified P-6 as a strain of C. muehlenbeckiae, a species with few reports other than in gramineous crops (Raza et al 2019; Chen et al 2021; Cui et al 2020; Ni et al 2016). This is the first report of C. muehlenbeckiae on pecan in China and worldwide.

Mutations in a subfamily of abscisic acid receptor genes promote rice growth and productivity.

Abscisic acid (ABA) is a key phytohormone that controls plant growth and stress responses. It is sensed by the pyrabactin resistance 1 (PYR1)/PYR1-like (PYL)/regulatory components of the ABA receptor (RCAR) family of proteins. Here, we utilized CRISPR/Cas9 technology to edit group I (PYL1-PYL6 and PYL12) and group II (PYL7-PYL11 and PYL13) PYL genes in rice. Characterization of the combinatorial mutants suggested that genes in group I have more important roles in stomatal movement, seed dormancy, and growth regulation than those in group II. Among all of the single pyl mutants, only pyl1 and pyl12 exhibited significant defects in seed dormancy. Interestingly, high-order group I mutants, but not any group II mutants, displayed enhanced growth. Among group I mutants, pyl1/4/6 exhibited the best growth and improved grain productivity in natural paddy field conditions, while maintaining nearly normal seed dormancy. Our results suggest that a subfamily of rice PYLs has evolved to have particularly important roles in regulating plant growth and reveal a genetic strategy to improve rice productivity.

Desiccation tolerance in Physcomitrella patens: Rate of dehydration and the involvement of endogenous abscisic acid (ABA).

The moss Physcomitrella patens, a model system for basal land plants, tolerates several abiotic stresses, including dehydration. We previously reported that Physcomitrella patens survives equilibrium dehydration to -13 MPa in a closed system at 91% RH. Tolerance of desiccation to water potentials below -100 MPa was only achieved by pretreatment with exogenous abscisic acid (ABA). We report here that gametophores, but not protonemata, can survive desiccation below -100 MPa after a gradual drying regime in an open system, without exogenous ABA. In contrast, faster equilibrium drying at 90% RH for 3-5 days did not induce desiccation tolerance in either tissue. Endogenous ABA accumulated in protonemata and gametophores under both drying regimes, so did not correlate directly with desiccation tolerance. Gametophores of a Ppabi3a/b/c triple knock out transgenic line also survived the gradual dehydration regime, despite impaired ABA signaling. Our results suggest that the initial drying rate, and not the amount of endogenous ABA, may be critical in the acquisition of desiccation tolerance. Results from this work will provide insight into ongoing studies to uncover the role of ABA in the dehydration response and the underlying mechanisms of desiccation tolerance in this bryophyte.

The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration.

"Drying without dying" is an essential trait in land plant evolution. Unraveling how a unique group of angiosperms, the Resurrection Plants, survive desiccation of their leaves and roots has been hampered by the lack of a foundational genome perspective. Here we report the ∼1,691-Mb sequenced genome of Boea hygrometrica, an important resurrection plant model. The sequence revealed evidence for two historical genome-wide duplication events, a compliment of 49,374 protein-coding genes, 29.15% of which are unique (orphan) to Boea and 20% of which (9,888) significantly respond to desiccation at the transcript level. Expansion of early light-inducible protein (ELIP) and 5S rRNA genes highlights the importance of the protection of the photosynthetic apparatus during drying and the rapid resumption of protein synthesis in the resurrection capability of Boea. Transcriptome analysis reveals extensive alternative splicing of transcripts and a focus on cellular protection strategies. The lack of desiccation tolerance-specific genome organizational features suggests the resurrection phenotype evolved mainly by an alteration in the control of dehydration response genes.

Dehydration-responsive features of Atrichum undulatum.

Drought is an increasingly important limitation on plant productivity worldwide. Understanding the mechanisms of drought tolerance in plants can lead to new strategies for developing drought-tolerant crops. Many moss species are able to survive desiccation-a more severe state of dehydration than drought. Research into the mechanisms and evolution of desiccation tolerance in basal land plants is of particular significance to both biology and agriculture. In this study, we conducted morphological, cytological, and physiological analyses of gametophytes of the highly desiccation-tolerant bryophyte Atrichum undulatum (Hedw.) P. Beauv during dehydration and rehydration. Our results suggested that the mechanisms underlying the dehydration-recovery cycle in A. undulatum gametophytes include maintenance of membrane stability, cellular structure protection, prevention of reactive oxygen species (ROS) generation, elimination of ROS, protection against ROS-induced damage, and repair of ROS-induced damage. Our data also indicate that this dehydration-recovery cycle consists not only of the physical removal and addition of water, but also involves a highly organized series of cytological, physiological, and biochemical changes. These attributes are similar to those reported for other drought- and desiccation-tolerant plant species. Our findings provide major insights into the mechanisms of dehydration-tolerance in the moss A. undulatum.

[Tree-Augmented NaÏve Bayesian network model for predicting prostate cancer].

OBJECTIVE: To evaluate the integrated performance of age, serum PSA, and transrectal ultrasound images in the prediction of prostate cancer using a Tree-Augmented NaÏve (TAN) Bayesian network model. METHODS: We collected such data as age, serum PSA, transrectal ultrasound findings, and pathological diagnoses from 941 male patients who underwent prostate biopsy from January 2008 to September 2011. Using a TAN Bayesian network model, we analyzed the data for predicting prostate cancer, and compared them with the gold standards of pathological diagnosis. RESULTS: The accuracy, sensitivity, specificity, positive prediction rate, and negative prediction rate of the TAN Bayesian network model were 85.11%, 88.37%, 83.67%, 70.37%, and 94.25%, respectively. CONCLUSIONS: Based on age, serum PSA, and transrectal ultrasound images, the TAN Bayesian network model has a high value for the prediction of prostate cancer, and can help improve the clinical screening and diagnosis of the disease.

[Diagnosis Values of Back Propagation Neural Network Integrating Age, Transrectal Ultrasound Characteristics and Serum PSA for Prostate Cancer].

OBJECTIVE: To explore the diagnosis value of back propagation (BP) neural network integrating age, transrectal ultrasound characteristics and serum prostate specific antigen (PSA) for prostate cancer. METHODS: The data of age, PSA, and transrectal ultrasound characteristics were collected from 941 patients who received color doppler transrectal ultrasound scan and systemic biopsies of prostates. A prostate cancer diagnosis system of BP neural network with age, transrectal ultrasound characteristics and serum PSA was developed in MATLAB software, and its diagnostic value for prostate cancer was analyzed based on the pathological results of prostatic biopsy. RESULTS: The biopsy results confirmed 358 cases of prostate cancer (38.04%) and 583 cases noncancerous prostate diseases (61.96%). The sensitivity, specificity, accuracy, positive value and negative predictive value of BP neural networks for prostate cancer diagnosis were 78.57%, 92.94%, 87.23%, 88.00% and 86.81% respectively. CONCLUSION: Back propagation neural network with age, transrectal ultrasound characteristics and PSA shows good diagnosis value for prostate cancer.

Associations of body roundness index with cardiovascular and all-cause mortality: NHANES 2001-2018.

Body roundness index (BRI) was associated with cardiovascular diseases. But the relationship between BRI with cardiovascular disease (CVD) mortality and all-cause mortality remains largely unknown in hypertensive patients. This prospective cohort study included patients with hypertension who participated in the National Health and Nutrition Examination Survey (NHANES) from 2001 through 2018, and aimed to evaluate the association between BRI with CVD mortality and all-cause mortality. A total of 15570 patients were included. Over a median follow-up of 8.0 years (interquartile range, 4.3-12.6 years), 3445 individuals died, including 1166 CVD deaths. Weighted restricted cubic spline regression results showed a nonlinear association between BRI and CVD mortality and all-cause mortality (both P for nonlinear trend <0.001). The weighted multivariate Cox proportional hazards regression showed the hazard ratio (HRs) for CVD mortality were 0.93 (95% CI: 0.84-1.03, P = 0.160) in the low levels of BRI (≤5.9) and 1.11 (95% CI: 1.05-1.19, P < 0.001) in the high levels of BRI (>5.9). Similar associations were observed for all-cause mortality, the HRs were 0.91 (95% CI: 0.87-0.96, P < 0.001) in the low levels of BRI (≤6.3) and 1.09 (95% CI: 1.05-1.13, P < 0.001) in the high levels of BRI (>6.3). This cohort study supported that BRI was nonlinearly associated with CVD mortality and all-cause mortality among patients with hypertension. The thresholds of 5.9 and 6.3 for CVD mortality and all-cause mortality, respectively, may represent intervention targets for lowering the risk of premature death, but this needs to be confirmed in large clinical trials.

Huanglian Jiedu plaster ameliorated X-ray-induced radiation dermatitis injury by inhibiting HMGB1-mediated macrophage-inflammatory interaction.

ETHNOPHARMACOLOGICAL RELEVANCE: Huanglian Jiedu plaster (HJP) is a kind of Chinese patent medicine that contains four medicinal plants. It has been clinically proven to be beneficial for the treatment of tumor-associated radiation dermatitis. However, the underlying mechanism of HJP on radiation dermatitis remains unclear. AIM OF THE STUDY: This study aims to investigate the therapeutic effect of HJP on X-ray-induced radiation dermatitis, and how HJP improves the inflammatory response and skin damage of radiation dermatitis. MATERIALS AND METHODS: In this study, We selected a case of esophageal cancer as a clinical demonstration of the efficacy of radiation dermatitis. The patient received a total radiation dose of 7000cGY, and treatment by HJP for 14 days.RD mouse models were established through continuous irradiation with X-ray (800cGY) on the right hind limb of mice for 5 days, and the treatment group mice was applied HJP to the irradiated skin for 15 days from modeling. An inflammatory cellular model was induced through irradiation with X-ray (100cGY) in JB6 cells and a co-culture system of JB6 cell and macrophage was established to examine the effect and mechanism of HJP on the inflammatory interaction of these two cells. The activation of HMGB1-TLR4-NF-κB signaling pathway, and the levels of epidermal injury related factors and inflammatory cytokins were subsequently detected. RESULTS: The results showed that HJP can significantly alleviate X-ray-induced skin injury, inhibiting skin inflammation and reducing the expression of inflammatory cytokins (IL-1ß, IL-6, TNF-α) and epidermal damage related factors (Integrin ß1, CXCL9 and Cytokeratin17), as well as significantly down-regulated the protein level of HMGB1 (a key DAMPs factor) in vivo and in vitro. Cell co-culture experiments demonstrated that HMGB1 released from X-ray-induced JB6 cells can promote inflammatory response of macrophage, which then feedback aggravate epithelial cell damage, notably, HJP can significantly improve radiation skin lesion by inhibiting HMGB1-mediated inflammatory interaction between epithelial cells and macrophages. CONCLUSION: In summary, these findings indicated the role of HJP in the treatment of RD by inhibiting the inflammatory interaction between macrophage and JB6 cells mediated by HMGB1, which may provide a reliable therapeutic method for RD. Furthermore, HMGB1 may be an effective target for HJP to inhibit inflammation and ameliorate skin damage in RD.

Screening of Bifidobacteria with Probiotic Potential from Healthy Infant Feces by Using 2'-Fucosyllactose.

Using 2'-fucosyllactose (2'-FL) as the sole carbon source can be an efficient way to screen bifidobacteria with superior probiotic capabilities since 2'-FL is a key element in promoting the growth of intestinal bifidobacteria in newborns. This approach was used in this work to screen eight bifidobacteria strains, including one strain of Bifidobacterium longum subsp. infantis BI_Y46 and seven strains of Bifidobacterium bifidum (BB_Y10, BB_Y30, BB_Y39, BB_S40, BB_H4, BB_H5 and BB_H22). Studies on their probiotic properties showed that BI_Y46 had a unique morphology with pilus-like structure, a high resistance to bile salt stimulation and a potent inhibitory action on Escherichia coli ATCC 25922. Similarly, BB_H5 and BB_H22 produced more extracellular polysaccharides and had a higher protein content than other strains. In contrast, BB_Y22 displayed considerable auto-aggregation activity and a high resistance to bile salt stimulation. Interestingly, BB_Y39 with weak self-aggregation ability and acid resistance had very excellent bile salt tolerance, extracellular polysaccharides (EPS) production and bacteriostatic ability. In conclusion, 2'-FL was used as sole carbon source to identify eight bifidobacteria with excellent probiotic properties.

Nitric oxide restrain root growth by DNA damage induced cell cycle arrest in Arabidopsis thaliana.

Nitric oxide (NO) participates in the regulation of diverse functions in plant cells. However, different NO concentrations may trigger different pathways during the plant development. At basal levels of NO, plants utilize the NO signaling transduction pathway to facilitate plant growth and development, whereas higher concentrations trigger programmed cell death (PCD). Our results show that NO lower than the levels causing PCD, but higher than the basal levels induce DNA damage in root cells in Arabidopsis as witnessed by a reduction in root growth, rather than cell death, since cells retain the capacity to differentiate root hairs. The decrease in meristematic cells and increase in DNA damage signals in roots in responses to NO are in a dose dependent manner. The restraint of root growth is due to cell cycle arrest at G1 phase which is caused by NO induced DNA damage, besides a second arrest at G2/M existed in NO supersensitive mutant cue1. The results indicate that NO restrain root growth via DNA damage induced cell cycle arrest.

Genome-wide characterization of C2H2 zinc-finger gene family provides insight into the mechanisms and evolution of the dehydration-rehydration responses in Physcomitrium and Arabidopsis.

Dehydration tolerance is a vital factor for land plant evolution and world agricultural production. Numerous studies enlightened that the plant-specific C2H2-type zinc-finger proteins (C2H2-ZFPs) as master regulators played pivotal roles in the abiotic stress responses of plants. However, a comprehensive understanding of the evolution of C2H2-ZFPs in terrestrial plants and its regulatory mechanism in dehydration and rehydration response remains a mystery. In this study, the genome-wide identification of C2H2-ZFP genes revealed 549 homologs in the representatives of terrestrial plant lineages from liverwort to angiosperms. Based on the characteristics of the conserved C2H2-ZF domains, four major C2H2-ZF types (M-, Z-, Q-, and D-type) were identified in the C2H2-ZFPs, with the dominants of M-type in all selected species and followed by Z-type in non-seed plants and Q-type in seed plants, respectively. Phylogenetic analyses of the identified C2H2-ZFPs supported four major groups in the land plant representatives, among which the members from the desiccation-tolerant Physcomitrium patens and the dehydration-sensitive Arabidopsis thaliana displayed different topological relationships in the phylogenies reconstructed for a single species. C2H2-ZFPs clustered in the same subclades shared similar features in their conserved domains and gene structures. Approximately, 81% of the C2H2-ZFP promoters of all 549 identified C2H2-ZFPs harbored the conserved ABA-responsive elements (ABREs) and/or dehydration-responsive elements (DREs). Comparative transcriptomic analyses showed that 50 PpZFPs and 56 AtZFPs significantly changed their transcripts abundance. Interestingly, most of the dehydration- and rehydration-responsive PpZPFs and AtZFPs had been predicted to contain the ABRE and DRE elements in their promoter regions and with over half of which phylogenetically belonging to group III. The differences in the expression patterns of C2H2-ZFPs in responses to dehydration and rehydration between P. patens and A. thaliana reflected their different strategies to adapt to dehydration. The identified candidate PpZFPs were specifically induced by moderate dehydration and reached the peak transcript abundance in severe dehydration. Our study lays the foundations for further functional investigation of C2H2-ZFPs in dehydration responses from an evolutionary perspective in land plants. The findings will provide us with genetic resources and potential targets for drought tolerance breeding in crops and beyond.

Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus.

Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.

Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens.

BACKGROUND: Regulation of gene expression plays a pivotal role in controlling the development of multicellular plants. To explore the molecular mechanism of plant developmental-stage transition and cell-fate determination, a genome-wide analysis was undertaken of sequential developmental time-points and individual tissue types in the model moss Physcomitrella patens because of the short life cycle and relative structural simplicity of this plant. RESULTS: Gene expression was analyzed by digital gene expression tag profiling of samples taken from P. patens protonema at 3, 14 and 24 days, and from leafy shoot tissues at 30 days, after protoplast isolation, and from 14-day-old caulonemal and chloronemal tissues. In total, 4333 genes were identified as differentially displayed. Among these genes, 4129 were developmental-stage specific and 423 were preferentially expressed in either chloronemal or caulonemal tissues. Most of the differentially displayed genes were assigned to functions in organic substance and energy metabolism or macromolecule biosynthetic and catabolic processes based on gene ontology descriptions. In addition, some regulatory genes identified as candidates might be involved in controlling the developmental-stage transition and cell differentiation, namely MYB-like, HB-8, AL3, zinc finger family proteins, bHLH superfamily, GATA superfamily, GATA and bZIP transcription factors, protein kinases, genes related to protein/amino acid methylation, and auxin, ethylene, and cytokinin signaling pathways. CONCLUSIONS: These genes that show highly dynamic changes in expression during development in P. patens are potential targets for further functional characterization and evolutionary developmental biology studies.

Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan.

Pecan (Carya illinoinensis) is a tree nut crop of worldwide economic importance that is rich in health-promoting factors. However, pecan production and nut quality are greatly challenged by environmental stresses such as the outbreak of severe fungal diseases. Here, we report a high-quality, chromosome-scale genome assembly of the controlled-cross pecan cultivar 'Pawnee' constructed by integrating Nanopore sequencing and Hi-C technologies. Phylogenetic and evolutionary analyses reveal two whole-genome duplication (WGD) events and two paleo-subgenomes in pecan and walnut. Time estimates suggest that the recent WGD event and considerable genome rearrangements in pecan and walnut account for expansions in genome size and chromosome number after the divergence from bayberry. The two paleo-subgenomes differ in size and protein-coding gene sets. They exhibit uneven ancient gene loss, asymmetrical distribution of transposable elements (especially LTR/Copia and LTR/Gypsy), and expansions in transcription factor families (such as the extreme pecan-specific expansion in the far-red impaired response 1 family), which are likely to reflect the long evolutionary history of species in the Juglandaceae. A whole-genome scan of resequencing data from 86 pecan scab-associated core accessions identified 47 chromosome regions containing 185 putative candidate genes. Significant changes were detected in the expression of candidate genes associated with the chitin response pathway under chitin treatment in the scab-resistant and scab-susceptible cultivars 'Excell' and 'Pawnee'. These findings enable us to identify key genes that may be important susceptibility factors for fungal diseases in pecan. The high-quality sequences are valuable resources for pecan breeders and will provide a foundation for the production and quality improvement of tree nut crops.

Bexarotent Attenuated Chronic Constriction Injury-Induced Spinal Neuroinflammation and Neuropathic Pain by Targeting Mitogen-Activated Protein Kinase Phosphatase-1.

It is widely accepted that neuroinflammation in the spinal cord contributes to the development of central sensitization in neuropathic pain. Mitogen-activated protein kinase (MAPK) activation plays a vital role in the development of neuroinflammation in the spinal cord. In this study, we investigated the effect of bexarotene (bex), a retinoid X receptor agonist, on MAPKs activation in chronic constriction injury (CCI)-induced neuropathic pain. The data showed that daily treatment with bex 50 mg/kg significantly alleviated CCI-induced nociceptive hypersensitivity in rats. Bex 50 mg/kg/day inhibited CCI-induced MAPKs (p38MAPK, ERK1/2, and JNK) activation and upregulation of proinflammatory factors (IL-1ß, tumor necrosis factor-α and IL-6). Bex also reversed CCI-induced microglia activation in the ipsilateral spinal cord. Furthermore, bex treatment significantly upregulated MKP-1 in the spinal cord. These effects were completely abrogated by MKP-1 inhibitor BCI. These results indicated that bex relieved CCI-induced neuroinflammation and neuropathic pain by targeting MKP-1. Therefore, bex might be a potential agent for the treatment of neuropathic pain. PERSPECTIVE: Bex could relieve neuropathic pain behaviors in animals by reversing MKP-1 downregulation and MAPKs activation in the spinal cord. Therapeutic applications of bex may be extended beyond cutaneous T-cell lymphoma.