The response of LncRNAs associated with photosynthesis-and pigment synthesis-related genes to green light in Chlamydomonas reinhardtii.

The quality of light is an important abiotic factor that affects the growth and development of green plants. Ultraviolet, red, blue, and far-red light all have demonstrated roles in regulating green plant growth and development, as well as light morphogenesis. However, the mechanism underlying photosynthetic organism responses to green light throughout the life of them are not clear. In this study, we exposed the unicellular green alga Chlamydomonas reinhardtii to green light and analyzed the dynamics of transcriptome changes. Based on the whole transcriptome data from C. reinhardtii, a total of 9974 differentially expressed genes (DEGs) were identified under green light. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were mainly related to "carboxylic acid metabolic process," "enzyme activity," "carbon metabolism," and "photosynthesis and other processes." At the same time, 253 differentially expressed long non-coding RNAs (DELs) were characterized as green light responsive. We also made a detailed analysis of the responses of photosynthesis- and pigment synthesis-related genes in C. reinhardtii to green light and found that these genes exhibited obvious dynamic expression. Lastly, we constructed a co-expression regulatory network, comprising 49 long non-coding RNAs (lncRNAs) and 20 photosynthesis and pigment related genes, of which 9 mRNAs were also the predicted trans/cis-targets of 8 lncRNAs, these results suggested that lncRNAs may affect the expression of mRNAs related to photosynthesis and pigment synthesis. Our findings give a preliminary explanation of the response mechanism of C. reinhardtii to green light at the transcriptional level.

[Clinical appraisal of laparoscopic inguinal lymphadenectomy with preservation of the great saphenous vein through subcutaneous approach via umbilical cord for the treatment of penile carcinoma: Report of 27 cases].

OBJECTIVE: To explore the clinical efficacy and advantages of laparoscopic inguinal lymphadenectomy (IL) with preservation of the great saphenous vein through subcutaneous approach via umbilical cord for the treatment of penile carcinoma patients. METHODS: The data of 27 patients with penile cancer underwent the laparoscopic inguinal lymph adenectomy with preservation of the great saphenous vein through subcutaneous via umbilical cord approach in the General Hospital of Eastern Theater Command from 2014 May to 2022 May were analyzed retrospectively.All patients underwent partial penile resection, with a pathological diagnosis of squamous cell carcinoma and 20 cases were highly differentiated, 7 cases were moderately differentiated, with the average age was 54 ± 7.5 years old. All patients were in supine position, and a subcutaneous space was established under visualization to establish a laparoscopic operation channel. The scope of cleaning included the superficial and deep inguinal lymph nodes, while the key aspects of the procedure was the preservation of the main trunk of the great saphenous vein. The external boundary of bilateral inguinal lymph node dissection was the line between the anterior superior iliac spine and 20cm lower, the inner boundary was pubic tubercle and its 15cm medical lower measurement, and the line between the inner boundary and the external lower edge was the lower boundary. RESULT: All the 27 patients were successfully completed without transfer to open surgery. The average operation time was (115 ± 26) minutes, the average blood loss during operation was (40 ± 8) ml, postoperative hospital stays was (6.8 ± 1.5) days, and postoperative drainage tube removal time was (6.4 ± 1.2) days. The average number of lymph nodes was 12.5 (5-21) on the left side, and 11.4 (2-19) on the right side. No skin necrosis and subcutaneous hematoma was occurred in all patients. Three patients had postoperative lymphatic leakage and two patients had lymphatic cysts. All patients were cured by conservation treatment. No recurrence and metastasis were occurred during 14-28 months follow up postoperatively. Conclusion： Laparoscopic inguinal lymphadenectomy with preservation of the great saphenous vein through subcutaneous approach via umbilical cord can achieve the expected surgical outcome. It has some advantages of shorter operation time, less blood loss，low incidence of complication ,especially avoid skin flap necrosis and subcutaneous hematoma．.

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers.

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus.

Lignin provides structural support in perennial woody plants and is a complex phenolic polymer derived from phenylpropanoid pathway. Lignin biosynthesis is regulated by coordinated networks involving transcription factors (TFs), microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). However, the genetic networks underlying the lignin biosynthesis pathway for tree growth and wood properties remain unknown. Here, we used association genetics (additive, dominant and epistasis) and expression quantitative trait nucleotide (eQTN) mapping to decipher the genetic networks for tree growth and wood properties in 435 unrelated individuals of Populus tomentosa. We detected 124 significant associations (P ≤ 6.89E-05) for 10 growth and wood property traits using 30 265 single nucleotide polymorphisms from 203 lignin biosynthetic genes, 81 TF genes, 36 miRNA genes and 71 lncRNA loci, implying their common roles in wood formation. Epistasis analysis uncovered 745 significant pairwise interactions, which helped to construct proposed genetic networks of lignin biosynthesis pathway and found that these regulators might affect phenotypes by linking two lignin biosynthetic genes. eQTNs were used to interpret how causal genes contributed to phenotypes. Lastly, we investigated the possible functions of the genes encoding 4-coumarate: CoA ligase and cinnamate-4-hydroxylase in wood traits using epistasis, eQTN mapping and enzymatic activity assays. Our study provides new insights into the lignin biosynthesis pathway in poplar and enables the novel genetic factors as biomarkers for facilitating genetic improvement of trees.

Crosstalk between long non-coding RNAs and Wnt/ß-catenin signalling in cancer.

Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts in the human genome which perform crucial functions in diverse biological processes. The abnormal expression of some lncRNAs has been found in tumorigenesis, development and therapy resistance of cancers. They may act as oncogenes or tumour suppressors and can be used as diagnostic or prognostic markers, prompting their therapeutic potentials in cancer treatments. Studies have indicated that many lncRNAs are involved in the regulation of several signal pathways, including Wnt/ß-catenin signalling pathway, which has been reported to play a significant role in regulating embryogenesis, cell proliferation and controlling tumour biology. Emerging evidences have suggested that lncRNAs can interact with several components of the Wnt/ß-catenin signalling pathway to regulate the expression of Wnt target genes in cancer. Moreover, the expression of lncRNAs can also be influenced by the pathway. Nevertheless, Wnt/ß-catenin signalling pathway-related lncRNAs and their interactions in cancer are not systematically analysed before. Considering these, this review emphasized the associations between lncRNAs and Wnt/ß-catenin signalling pathway in cancer initiation, progression and their therapeutic influence. We also provided an overview on characteristics of lncRNAs and Wnt/ß-catenin signalling pathway and discussed their functions in tumour biology. Finally, targeting lncRNAs or/and molecules associated with the Wnt/ß-catenin signalling pathway may be a feasible therapeutic method in the future.

Genetic variants in microRNA biogenesis genes as novel indicators for secondary growth in Populus.

MicroRNAs (miRNAs) function as key regulators of complex traits, but how genetic alterations in miRNA biogenesis genes (miRBGs) affect quantitative variation has not been elucidated. We conducted transcript analyses and association genetics to investigate how miRBGs, miRNA genes (MIRNAs) and their respective targets contribute to secondary growth in a natural population of 435 Populus tomentosa individuals. This analysis identified 29 843 common single-nucleotide polymorphisms (SNPs; frequency > 0.10) within 682 genes (80 miRBGs, 152 MIRNAs, and 457 miRNA targets). Single-SNP association analysis found SNPs in 234 candidate genes exhibited significant additive/dominant effects on phenotypes. Among these, specific candidates that associated with the same traits produced 791 miRBG-MIRNA-target combinations, suggesting possible genetic miRBG-MIRNA and MIRNA-target interactions, providing an important clue for the regulatory mechanisms of miRBGs. Multi-SNP association found 4672 epistatic pairs involving 578 genes that showed significant associations with traits and identified 106 miRBG-MIRNA-target combinations. Two multi-hierarchical networks were constructed based on correlations of miRBG-miRNA and miRNA-target expression to further probe the mechanisms of trait diversity underlying changes in miRBGs. Our study opens avenues for the investigation of miRNA function in perennial plants and underscored miRBGs as potentially modulating quantitative variation in traits.

Allelic variation in PtoPsbW associated with photosynthesis, growth, and wood properties in Populus tomentosa.

Photosynthesis is one of the most important reactions on earth. PsbW, a nuclear-encoded subunit of photosystem II (PSII), stabilizes PSII structure and plays an important role in photosynthesis. Here, we used candidate gene-based linkage disequilibrium (LD) mapping to detect significant associations between allelic variations of PtoPsbW and traits related to photosynthesis, growth, and wood properties in Populus tomentosa. PtoPsbW showed the highest expression in leaves and it increased during the development of these leaves, suggesting that PtoPsbW may play an important role in plant growth and development. Analysis of nucleotide diversity and LD revealed that PtoPsbW has low single-nucleotide polymorphism (SNP) diversity (π tot = 0.0048 and θ w = 0.0050) and relatively low average value of LD (0.1500), indicating that PtoPsbW is conserved due to its indispensable function. Using single-SNP associations in an association population of 435 individuals, we identified five significant associations at the threshold of P ≤ 0.05, explaining 3.28-15.98 % of the phenotypic variation. Haplotype-based association analyses indicated that 13 haplotypes (P ≤ 0.05) from six blocks were associated with photosynthesis, growth, and wood properties. Our work shows that identifying allelic variation and LD can help to decipher the genetic basis of photosynthesis and could potentially be applied for molecular marker-assisted selection in Populus.

Enzymatic synthesis of pyridine heterocyclic compounds and their thermal stability.

An efficient method was discovered for catalyzing the esterification under air using Novozym 435 to obtain pyridine esters. The following conditions were found to be optimal: 60 mg of Novozyme 435, 5.0 mL of n-hexane, a molar ratio of 2:1 for nicotinic acids (0.4 mmol) to alcohols (0.2 mmol), 0.25 g of molecular sieve 3A, a revolution speed of 150 rpm, a reaction temperature of 50 °C, and reaction time of 48 h. Under nine cycles of Novozym 435, the 80 % yield was consistently obtained. Optimum conditions were used to synthesize 23 pyridine esters, including five novel compounds. Among them, gas chromatography-mass spectrometry-olfactometry (GC-MS-O) showed phenethyl nicotinate (3g), (E)-hex-4-en-1-yl nicotinate (3m), and octyl nicotinate (3n) possessed strong aromas. Thermogravimetric analysis (TG) revealed that the compounds 3g, 3m and 3n exhibited stability at the specified temperature. This finding provides theoretical support for adding pyridine esters fragrance to high-temperature processed food.

Construction of chitosan-derived porous nest-like C/SnO2 materials for microwave absorption.

Electromagnetic waves have an irreplaceable role as information carriers in civil and radar stealth fields, but they also lead to electromagnetic pollution and electromagnetic leakage. Therefore, electromagnetic wave absorbing materials that can reduce electromagnetic radiation have come into being. Especially, SnO2 has made a wave among many wave-absorbing materials as an easily tunable dielectric material, but it hardly has both broadband and powerful absorption properties. Here, the nested porous C/SnO2 composites derived from nitrogen-doped chitosan is obtained by freeze-drying and supplemented with carbonization treatment. The chitosan creates a nested cross-linked conductive network that can make part of the contribution to conduction loss. The amino groups contained in the molecule either help promote in situ nitrogen doping and trigger dipole polarization. The multiphase dissimilar interface between the nested carbon layer and the inner clad SnO2 formation is the major inducer of interfacial polarization. It reached intense absorption of -48.8 dB and bandwidth of 5.2 GHz at 3.46 mm. The interfacial polarization is confirmed to be the main force of dielectric loss by simulating the electromagnetic field distribution. In addition, the RCS simulation data assure the prospect of enticing applications of C/SnO2 composites in the field of radar stealth.

Application of Polymeric CO2 Thickener Polymer-Viscosity-Enhance in Extraction of Low-Permeability Tight Sandstone.

The conventional production technique employed for low-permeability tight reservoirs exhibits limited productivity. To solve the problem, an acetate-type supercritical carbon dioxide (scCO2) thickener, PVE, which contains a large number of microporous structures, was prepared using the atom transfer radical polymerization (ATRP) method. The product exhibited an ability to decrease the minimum miscibility pressure of scCO2 during a solubility test and demonstrated a favorable extraction efficiency in a low-permeability tight core displacement test. At 15 MPa and 70 °C, PVE-scCO2 at a concentration of 0.2% exhibits effective oil recovery rates of 5.61% for the 0.25 mD core and 2.65% for the 5 mD core. The result demonstrates that the incorporation of the thickener PVE can effectively mitigate gas channeling, further improve oil displacement efficiency, and inflict minimal damage to crude oil. The mechanism of thickening was analyzed through molecular simulation. The calculated trend of thickening exhibited excellent agreement with the experimental measurement rule. The simulation results demonstrate that the contact area between the polymer and CO2 increases in direct proportion to both the number of thickener molecules and the viscosity of the system. The study presents an effective strategy for mitigating gas channeling during scCO2 flooding and has a wide application prospect.

Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis).

The Quercus variabilis, a deciduous broadleaved tree species, holds significant ecological and economical value. While a chromosome-level genome for this species has been made available, it remains riddled with unanchored sequences and gaps. In this study, we present a nearly complete comprehensive telomere-to-telomere (T2T) and haplotype-resolved reference genome for Q. variabilis. This was achieved through the integration of ONT ultra-long reads, PacBio HiFi long reads, and Hi-C data. The resultant two haplotype genomes measure 789 Mb and 768 Mb in length, with a contig N50 of 65 Mb and 56 Mb, and were anchored to 12 allelic chromosomes. Within this T2T haplotype-resolved assembly, we predicted 36,830 and 36,370 protein-coding genes, with 95.9% and 96.0% functional annotation for each haplotype genome. The availability of the T2T and haplotype-resolved reference genome lays a solid foundation, not only for illustrating genome structure and functional genomics studies but also to inform and facilitate genetic breeding and improvement of cultivated Quercus species.

A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis).

Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lacking. Here, we present a high-quality Q. variabilis genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used ab initio, RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that Q. variabilis was more closely related to Q. suber than to Q. lobata or Q. robur. We found no evidence for species-specific whole genome duplications in Quercus after the species had diverged. This study provides the first genome assembly and the first gene annotation data for Q. variabilis. These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.

Erythropoietin Preconditioning Mobilizes Endothelial Progenitor Cells to Attenuate Nephron-Sparing Surgery-Induced Ischemia-Reperfusion Injury.

The purpose of this study was to examine the role of endothelial progenitor cells (EPCs) in protection against ischemic-reperfusion injury (IRI) in a nephron-sparing surgery (NSS) rat model using erythropoietin (EPO) preconditioning. Fifty-four male Sprague-Dawley rats were randomly divided into 3 groups for right kidney nephrectomy treatment: sham group (exposure without clamp treatment), NSS group (3 days of peritoneal phosphate buffered saline [PBS] injection before renal blood vessels were clamped for 40 mins and NSS was performed), and EPO group (3 days of EPO abdomen injections prior to renal blood vessel clamping for 40 min before NSS was performed). After 12, 24, and 72 hours, inferior vena cava blood and renal tissues were harvested. The extent of renal injury was assessed, along with EPC number, cell proliferation, angiogenesis, and vascular growth factor expression. EPO preconditioning significantly improved renal function and histologic morphology, indicated by reduced blood urea nitrogen (BUN) ([33.12 ± 1.88] vs [16.03 ± 0.91], P < .05) and serum creatinine (Scr) ([190.2 ± 20.23] vs [77.23 ± 5.82], P < .05) levels and histologic injury scores ([3.20 ± 0.78] vs [1.70 ± 0.67], P < .05). Angiogenesis in peritubular capillaries markedly increased in the EPO group. EPC numbers increased in the kidneys at 24 hours following reperfusion in the EPO group, compared to the NSS group. Furthermore, EPO preconditioning also increased SDF-1α and CXCR7 expression at 24 hours following reperfusion relative to the NSS group. These findings suggest that EPO pretreatment can reduce renal injury in rats caused by IRI. Mechanistically, this may be related to EPC mobilization and recruitment to injured renal tissues by SDF-1α and CXCR7.

A 14-Year Follow-Up of a Combined Liver-Pancreas-Kidney Transplantation: Case Report and Literature Review.

Objective: To investigate the long-term effect of triple organ transplantation (liver, kidney, and pancreas) in a patient with end-stage liver disease, post chronic hepatitis B, cirrhosis, chronic renal failure, and insulin-dependent diabetes mellitus caused by chronic pancreatitis and to explore the optimal surgical procedure. Case: A 43-year-old man with progressive emaciation and hypourocrinia for 2 months. Results indicated exocrine pancreatic insufficiency and insulin-dependent diabetes related to chronic pancreatitis (CP) after developing end-stage hepatic and renal failure. Simultaneous piggyback orthotopic liver and heterotopic pancreas-duodenum and renal transplantation was performed in 2005. Pancreatic exocrine secretions were drained enterically to the jejunum, and the donor kidney was placed in the left iliac fossa. Patient was prescribed with prednisone, tacrolimus, mycophenolate mofetil, Rabbit Anti-human Thymocyte Immunoglobulin, and simulect for immunosuppression. Results: Satisfactory hepatic and pancreatic functional recovery was achieved within 7 days post-surgery. The kidney was not functional, and continuous renal replacement therapy was used. However, the donor kidney was removed at day 16 post-surgery due to acute rejection reaction. A new renal transplantation at the same position was performed, and satisfactory kidney function from the new graft was achieved 3 days later. In 14 years of follow-up, patient has not had any rejection reactions or other complications such as pancreatitis, thrombosis, and localized infections. The patient is insulin independent with normal liver and renal functions. FK506+Pred was used for immunosuppression, and the tac tough level maintained 3.0-4.5 ng/ml. Lamivudine was prescribed for long-term use to inhibit HBV virus duplication. Conclusion: Simultaneous piggyback orthotopic liver and heterotopic pancreas-duodenum and renal transplantation is a good therapeutic option for patients with exocrine pancreatic insufficiency and insulin-dependent diabetes combined with hepatic and renal failure.

Cytokine responses following laparoscopic or open pyeloplasty in children.

BACKGROUND: The present study evaluated the cytokine response in children following laparoscopic pyeloplasty (LP) or open pyeloplasty (OP). A series of cytokines were measured postoperatively, including interkin1-beta (IL-1beta), interleukin-6 (IL-6), interleukin-8 (IL-8), interleukin-10 (IL-10), tumor necrosis factor-alpha (TNF-alpha), and C-reactive protein (CRP). METHODS: A total of 31 patients, with an average age of 9.1 +/- 3.0 years (range 2.5-14 years) were studied. Fourteen patients underwent LP and 17 underwent OP. Blood serum concentrations of IL-1beta, IL-6, IL-8, IL-10, TNF-alpha, and CRP were measured via enzyme-linked immunosorbent assay (ELISA) before surgery as well as 4, 24, and 48 h following the operation. In addition, the procedure duration, hospital stay, incidence of wound infection, and the recurrence rate of stenosis in both groups were compared. RESULTS: Serum IL-6 and CRP concentrations were significantly elevated in both groups at 4, 24, and 48 h relative to preoperative levels. However, the rise in IL-6 and CRP in OP group was significantly more robust than in LP group. No significant changes were observed in serum levels of IL-1beta, IL-8, IL-10, or TNF-alpha in either group. The procedure duration was significantly longer for LP (193.6 +/- 74.7 min, range 120-360 min) versus OP (120.1 +/- 27.5 min, range 90-165 min, p < 0.05), but the hospital stay following LP was shorter (LP group: 5.3 +/- 1.1 days versus OP group: 9.3 +/- 2.1 days, p < 0.05). No severe complications were noted in either group, however, one child experienced wound infection following OP procedure. An incident of recurrent stenosis following the operation occurred in both groups. There was no postoperative morbidity or severe implications at 12 month follow-up in either group. CONCLUSIONS: Both OP and LP are safe and effective procedures for the treatment of ureteropelvic junction obstruction in the pediatric population. However, the shorter hospital stay and decreased cytokine response following LP indicates potential benefits over traditional invasive procedures.

Cardioprotection by Guanxin II in rats with acute myocardial infarction is related to its three compounds.

AIM: We tested the hypothesis that cardioprotection afforded by traditional Chinese Guanxin II (GXII) formula is related to absorbed bioactive compounds (ABCs). METHODS: Sprague-Dawley rats with acute myocardial infarction (AMI) were induced by coronary occlusion. ABCs including ferulic acid (F), hydroxyl safflor yellow A (A), tanshinol (T), protocatechualdehyde (P) and paeoniflorin (E) were measured in blood after oral GXII. The effects of GXII and FATPE, alone and in combination, and of some components of FATPE on infarct size, myocardial apoptosis and caspase-3 activity were determined. Myocardial blood flow (MBF) in AMI rat was detected 2h after oral GXII and FAT. RESULTS: FATPE was found in rat blood. FAT was similar to FATPE and GXII in decreasing infarct size, myocardial apoptosis and caspase-3 activity of AMI. Both FAT and GXII were similar in increasing of MBF. CONCLUSION: GXII and FAT protect the heart from ischemic injury by increasing MBF, and decrease infarct size by inhibiting myocardial apoptosis and caspase-3 activity. These findings provide a potential cardioprotective cocktail.

Transcription factors involved in the regulatory networks governing the Calvin-Benson-Bassham cycle.

Transcription factors (TFs) play crucial roles in the regulation of photosynthesis; elucidating these roles will facilitate our understanding of photosynthesis and thus accelerate its improvement for enhancing crop yield. Promoter analysis of 52 nuclear-encoded Populus tomentosa Carr. genes involved in the Calvin-Benson-Bassham (CBB) cycle revealed 706 motifs and 326 potentially interacting TFs. A backward elimination random forest (BWERF) algorithm reduced the number of TFs to 40, involved in a three-layer gene regulatory network (GRN) including 46 photosynthesis genes (bottom layer), 25 TFs (second layer) and 15 TFs (top layer). Phenotype-genotype association identified 248 single-nucleotide polymorphisms (SNPs) within 72 genes associated with 11 photosynthesis traits. Of the regulatory pairs identified by the BWERF (202 pairs), 77 TF-target combinations harbored SNPs associated with the same trait, supporting similar mechanisms of phenotype modulation. We used expression quantitative trait nucleotide (eQTN) analysis to identify causal SNPs affecting gene expression, identifying 1851 eQTN signals for 50 eGenes (genes whose expressions are regulated by eQTNs). Distribution patterns identified 14 eQTNs from seven TFs associated with eight expression levels of their downstream targets (defined in the GRN), whereas seven TF-target pairs were also identified by phenotype-genotype associations. To further validate the roles of TFs at the metabolic level, we selected 6764 SNPs from 55 genes (identified by GRN-association or GRN-eQTN pairs or both) for metabolic association, identifying variants within 10 TFs affecting metabolic processes underlying the CBB cycle. Our study provides new insights into the photosynthesis pathway in poplar and may facilitate understanding of processes underlying photosynthesis improvement.

Genetic variation in transcription factors and photosynthesis light-reaction genes regulates photosynthetic traits.

Transcription factors (TFs) play crucial roles in regulating the production of the components required for photosynthesis; elucidating the mechanisms by which underlying genetic variation in TFs affects complex photosynthesis-related traits may improve our understanding of photosynthesis and identify ways to improve photosynthetic efficiency. Promoter analysis of 96 nuclear-encoded Populus tomentosa Carr. genes within this pathway revealed 47 motifs responsive to light, stress, hormones and organ-specific regulation, as well as 86 TFs that might bind these motifs. Using phenotype-genotype associations, we identified 244 single-nucleotide polymorphisms (SNPs) within 105 genes associated with 12 photosynthesis-related traits. Most (30.33%) of these SNPs were located in intronic regions and these SNPs explained 18.66% of the mean phenotypic variation in the photosynthesis-related traits. Additionally, expression quantitative trait loci (eQTL) mapping identified 216 eQTLs associated with 110 eGenes (genes regulated by eQTLs), explaining 14.12% of the variability of gene expression. The lead SNPs of 12.04% of the eQTLs also contributed to phenotypic variation. Among these, a SNP in zf-Dof 5.6 (G120_9287) affected photosynthesis by modulating the expression of a sub-regulatory network of eight other TFs, which in turn regulate 55 photosynthesis-related genes. Furthermore, epistasis analysis identified a large interacting network representing 732 SNP-SNP pairs, of which 354 were photosynthesis gene-TF pairs, emphasizing the important roles of TFs in affecting photosynthesis-related traits. We combined eQTL and epistasis analysis and found 32 TFs harboring eQTLs being epistatic to their targets (identified by eQTL analysis), of which 15 TFs were also associated with photosynthesis traits. We therefore constructed a schematic model of TFs involved in regulating the photosynthetic light reaction pathway. Taken together, our results provide insight into the genetic regulation of photosynthesis, and may drive progress in the marker-assisted selection of desirable P. tomentosa genotypes with more efficient photosynthesis.

High expression of spindle and kinetochore- associated protein 1 predicts early recurrence and progression of non-muscle invasive bladder cancer.

BACKGROUND: Spindle and kinetochore-associated protein 1 (SKA1) is a component of SKA, which is essential for proper chromosome segregation. Recently, SKA1 was found to be over-expressed in several types of human cancers. However, reports on the relationship between SKA1 expression and the prognosis of bladder cancer, in particular, are lacking. OBJECTIVES: To clarify the clinical significance of SKA1 as a prognostic biomarker for early recurrence and progression of patients with non-muscle invasive bladder cancer (NMIBC). METHODS: The differential expression levels of SKA1 of 148 NMIBC tissues were determined by immunohistochemical staining. Quantitative real-time PCR and western blot analysis were further performed to confirm the immunohistochemistry results. Recurrence and progression free interval were assessed by Kaplan-Meier method and differences between groups calculated by log-rank statistics. The prognostic value of SKA1 for early recurrence and progression was analyzed by multivariate Cox proportional hazard regression models. RESULTS: SKA1 expression was significantly different in various NMIBC tissues. Kaplan-Meier analysis revealed that patients with high SKA1 expression showed high early recurrence (p< 0.001) and progression (p< 0.05) rates. Although univariate Cox regression analysis revealed that several other factors had an impact on recurrence and progression, upon multivariate analysis, high SKA1expression was the only independent predictor for early recurrence (hazards ratio [HR], 0.246; 95% confidence interval [CI], 0.131-0.461; p= 0.000) and progression (HR, 0.194; 95% CI, 0.052-0.715; p= 0.014). CONCLUSIONS: High SKA1 expression is associated with early recurrence and progression in patients with NMIBC, indicating SKA1 may serve as a promising prognostic biomarker for this disease.