Publications by authors named "Xiaofei Song"

69 Publications

Genes: Genome-Wide Identification, Evolution, and Their Contribution to Lignin Biosynthesis in Pear ().

Plants (Basel) 2021 Jul 15;10(7). Epub 2021 Jul 15.

Pear Engineering Research Centre, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China.

The synthetic enzyme cinnamyl alcohol dehydrogenase (CAD) is involved in responses to various stresses during plant growth. It regulates the monolignol biosynthesis and catalyzes hydroxyl cinnamaldehyde reduction to the corresponding alcohols. Although the CAD gene families have been explored in some species, little known is in Rosaceae. In this study, we identified 149 genes in (), (), () and (). They were phylogenetically clustered into six subgroups. All CAD genes contained ADH-N and ADH-zinc-N domains and were distributed on chromosomes unevenly. Dispersed and WGD/segmental duplications accounted the highest number of evolutionary events. Eight collinear gene pairs were identified among the four Rosaceae species, and the highest number was recorded in pear as five pairs. The five gene pairs had undergone purifying selection under Ka/Ks analysis. Furthermore, nine genes were identified based on transcriptomic and stone cell content in pear fruit. In qRT-PCR, the expression patterns of , , , and were consistent with variation in stone cell content during pear fruit development. These results will provide valuable information for understanding the relationship between gene expressions and stone cell number in fruit.
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http://dx.doi.org/10.3390/plants10071444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8309377PMC
July 2021

Down-regulation of long non-coding RNA XIST aggravates sepsis-induced lung injury by regulating miR-16-5p.

Hum Cell 2021 Sep 12;34(5):1335-1345. Epub 2021 May 12.

Department of Gastrointestinal Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Medical College of Henan University, Weiwu Road No. 7, Zhengzhou, 450003, Henan Province, China.

This study aims to explain the role and related mechanisms of long non-coding RNA (lncRNA) X inactive specific transcript (XIST) in sepsis-induced acute lung injury (ALI). The in vivo septic models and in vitro septic model were established. In animal models, the lung injury of the rats was evaluated after XIST was overexpressed. In cell models, the effects of XIST and microRNA (miR)-16-5p on ALI was detected by MTT assay, Western blot and ELISA. The interaction between XIST and miR-16-5p was investigated by bioinformatics analysis, dual-luciferase reporter assay, RIP assay and RNA pull-down assay. We found that XIST expression was down-regulated in lung tissues of septic rats and lipopolysaccharide-stimulated cells, while the expression of miR-16-5p was up-regulated. Down-regulation of XIST significantly promoted pulmonary edema, increased the levels of TNF-α, IL-1β and malondialdehyde, inhibited the cell viability and decreased the level of superoxide dismutase. Mechanistically, it was confirmed that XIST could sponge miR-16-5p, and thus repress its expression, and the transfection of miR-16-5p mimics could reverse the effects of XIST over-expression in the cell model. Collectively, it is concluded that XIST reduces sepsis-induced ALI via regulating miR-16-5p.
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http://dx.doi.org/10.1007/s13577-021-00542-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8114023PMC
September 2021

Pilot Clinical Trial of Perioperative Durvalumab and Tremelimumab in the Treatment of Resectable Colorectal Cancer Liver Metastases.

Clin Cancer Res 2021 Jun 2;27(11):3039-3049. Epub 2021 Apr 2.

Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.

Purpose: Despite the prognostic importance of immune infiltrate in colorectal cancer, immunotherapy has demonstrated limited clinical activity in refractory metastatic proficient mismatch-repair (pMMR) colorectal cancer. This study explores combining anti-CTLA-4 and an anti-PD-L1 therapy in the preoperative management of resectable colorectal cancer liver metastases with the intent to improve immune responses in this disease setting.

Patients And Methods: Patients with resectable colorectal cancer liver-only metastases received one dose of tremelimumab and durvalumab preoperatively followed by single-agent durvalumab postoperatively. Primary objectives were to determine feasibility and safety.

Results: A total of 24 patients were enrolled between November 2016 and November 2019. Twenty-three patients received treatment [21 pMMR and 2 deficient mismatch-repair (dMMR)] and subsequently 17 (74%; 95% CI: 53%-88%) underwent surgical resection. Grade 3/4 treatment-related immune toxicity and postoperative grade 3/4 toxicity were seen in 5/23 (22%; 95% CI: 10%-44%) and 2/17 (12%; 95% CI: 2%-38%) patients. The median relapse-free survival (RFS) was 9.7 (95% CI: 8.1-17.8) months, and overall survival was 24.5 (95% CI: 16.5-28.4) months. Four patients demonstrated complete pathologic response, two dMMR patients and two POLE mutation patients. Pre- and post-tumor tissue analysis by flow cytometry, immunofluorescence, and RNA sequencing revealed similar levels of T-cell infiltration, but did demonstrate evidence of CD8 and CD4 activation posttreatment. An increase in B-cell transcriptome signature and B-cell density was present in posttreatment samples from patients with prolonged RFS.

Conclusions: This study demonstrates the safety of neoadjuvant combination tremelimumab and durvalumab prior to colorectal cancer liver resection. Evidence for T- and B-cell activation following this therapy was seen in pMMR metastatic colorectal cancer.
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http://dx.doi.org/10.1158/1078-0432.CCR-21-0163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8172528PMC
June 2021

Heavy Metal Exposure Leads to Rapid Changes in Cellular Biophysical Properties.

ACS Biomater Sci Eng 2020 04 24;6(4):1965-1976. Epub 2020 Mar 24.

School of Environment and Energy, South China University of Technology, Guangzhou 510006, China.

Biophysical properties of cells, such as cell mechanics, cell shape, and cell migration, are emerging hallmarks for characterizing various cell functions. Conversely, disruptions to these biophysical properties may be used as reliable indicators of disruptions to cell homeostasis, such as in the case of chemical-induced toxicity. In this study, we demonstrate that treatment of lead(II) nitrate and cadmium nitrate leads to dosage-dependent changes in a collection of biophysical properties, including cellular traction forces, focal adhesions, mechanical stiffness, cell shape, migration speed, permeability, and wound-healing efficacy in mammalian cells. As those changes appear within a few hours after the treatment with a trace amount of lead/cadmium, our results highlight the promise of using biophysical properties to screen environmental chemicals to identify potential toxicants and establish dose response curves. Our systematic and quantitative characterization of the rapid changes in cytoskeletal structure and cell functions upon heavy metal treatment may inspire new research on the mechanisms of toxicity.
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http://dx.doi.org/10.1021/acsbiomaterials.9b01640DOI Listing
April 2020

Roles of CsBRC1-like in leaf and lateral branch development in cucumber.

Plant Sci 2021 Jan 9;302:110681. Epub 2020 Oct 9.

State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China.

TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family genes, as plant-specific transcription factors, play vital roles in flower pattern, leaf development and plant architecture. Our recent study shows that the TCP gene BRANCHED1 (CsBRC1) specifically regulates shoot branching in cucumber. Here, we found CsBRC1 had a closely related paralogous gene CsBRC1-like. The synteny analysis revealed that these two genes originated from a segmental duplication. CsBRC1-like displayed different expression patterns in cucumber compared with CsBRC1, indicating that they may have functional differentiation. Ectopic expression of CsBRC1-like in Arabidopsis brc1-1 mutant resulted in reduced rosette branches and rosette leaves, whereas silencing CsBRC1-like in cucumber only led to a deformed true leaf of seedling rather than affecting the shoot branching. RNA-seq analysis of wild-type and CsBRC1-like-RNAi plants implicated that CsBRC1-like might regulate early leaf development through affecting the transcripts of auxin and cytokinin related genes in cucumber. Moreover, CsBRC1-like directly interacts with CsTCP10a and CsBRC1 in vivo. Our results demonstrated that CsBRC1-like has a specific role in regulating leaf development, and CsBRC1-like and CsBRC1 may have overlapping roles in shoot branching.
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http://dx.doi.org/10.1016/j.plantsci.2020.110681DOI Listing
January 2021

A highly efficient recombinant canarypox virus-based vaccine against canine distemper virus constructed using the CRISPR/Cas9 gene editing method.

Vet Microbiol 2020 Dec 5;251:108920. Epub 2020 Nov 5.

College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, 130122, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, China. Electronic address:

Canine distemper virus (CDV) is the causative agent of canine distemper (CD), which is one of the most important infectious diseases affecting wild and domestic carnivores. Vaccination represents an effective approach to prevent CDV infection among domestic carnivores. Canarypox-vectored recombinant CD vaccines (such as Recombitek CDV, PureVax Ferret Distemper, and Merial) with the CDV hemagglutinin (H) and fusion (F) genes can induce a potent immune response in dogs and ferrets. However, the vaccine's effectiveness varies with the species. In the current study, we developed a highly efficient recombinant canarypox virus termed as "ALVAC-CDV-M-F-H/C5" that contained CDV virus-like particles (VLPs) by using the CRISPR/Cas9 gene editing method, which enabled concurrent expression of the matrix (M), H, and F genes. The recombinant strain provided faster seroconversion than the parent strain among minks as well as provided higher rates of antibody positivity than the parent strain among foxes and minks even before the administration of a second booster vaccination. We demonstrated, for the first time, that the CRISPR/Cas9 system can be applied for the rapid and efficient modification of the ALVAC-CDV-F-H genome and also that a high-dose new recombinant strain that produces CDV VLPs may present good outcomes in the prevention of CD among foxes and minks.
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http://dx.doi.org/10.1016/j.vetmic.2020.108920DOI Listing
December 2020

Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease.

Neurol Genet 2020 Oct 28;6(5):e498. Epub 2020 Jul 28.

Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston.

Objective: To determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms.

Methods: We performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and further characterized CNVs with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing.

Results: Using ES, we discovered individuals with known pathogenic SNVs in (p.Glu365Lys, p.Thr408Met, p.Asn409Ser, and p.Leu483Pro) and (p.Arg1441Gly and p.Gly2019Ser). Two subjects were each double heterozygotes for variants in and . Based on aCGH, we additionally discovered cases with an duplication and heterozygous intragenic deletion. Five additional subjects harbored both SNVs (p.Asn52Metfs*29, p.Thr240Met, p.Pro437Leu, and p.Trp453*) and likely disrupting CNVs at the locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors.

Conclusions: Integrated ES and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for and CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.
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http://dx.doi.org/10.1212/NXG.0000000000000498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7413630PMC
October 2020

Kidney manifestations of mild, moderate and severe coronavirus disease 2019: a retrospective cohort study.

Clin Kidney J 2020 Jun 9;13(3):340-346. Epub 2020 May 9.

Renal Department and Nephrology Institute, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.

Background: Coronavirus disease 2019 (COVID-19) is a pandemic that has affected more than 3 million patients globally. Previous data from Wuhan city showed that acute kidney injury (AKI), proteinuria and hematuria occurred frequently in patients with severe COVID-19. However, the prevalence of kidney injury in milder cases remains unclear.

Methods: This retrospective study included two major consecutive cohorts of COVID-19 patients in Sichuan Province. Baseline characteristics, laboratory data including renal function, proteinuria and dipstick hematuria, and other laboratory parameters were collected. A subgroup of patients was followed up for 2-4 weeks to evaluate the short-term outcome of renal impairment.

Results: Overall, 168 COVID-19-positive patients were included in the study. The majority of patients (79.7%) were diagnosed with mild or moderate disease. Half of patients presented with fever; however, in The Tibetan cohort, fever only occurred in 13.4% of patients. On hospital admission, proteinuria and dipstick hematuria were noted in 18.4% and 17.4% of patients, respectively, while AKI only occurred in one patient. Further analysis showed that severe or critical COVID-19 was associated with higher risk of proteinuria [relative risk (RR) 7.37, 95% confidence interval (CI) 2.45-22.18, P = 3.8 × 10] and dipstick hematuria (RR 8.30, 95% CI 2.69-25.56, P = 2.3 × 10). Proteinuria, dipstick hematuria, or the combination of proteinuria and hematuria could significantly predict severe or critical severe COVID-19.

Conclusions: Proteinuria and dipstick hematuria are not uncommon in patients with COVID-19 infection, especially in severe or critical cases.
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http://dx.doi.org/10.1093/ckj/sfaa083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239220PMC
June 2020

Optimization of the l-tyrosine metabolic pathway in by analyzing -coumaric acid production.

3 Biotech 2020 Jun 18;10(6):258. Epub 2020 May 18.

The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, 300071 People's Republic of China.

In this study, we applied a series of genetic modifications to wild-type strain BY4741 to address the bottlenecks in the l-tyrosine pathway. A tyrosine ammonia-lyase (TAL) gene from , which can catalyze conversion of l-tyrosine into -coumaric acid, was overexpressed to facilitate the analysis of l-tyrosine and test the strain's capability to synthesize heterologous derivatives. First, we enhanced the supply of precursors by overexpressing transaldolase gene , enolase II gene , and pentafunctional enzyme gene resulting in a 1.55-fold increase in -coumaric acid production. Second, feedback inhibition of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase and chorismate mutase was relieved by overexpressing the mutated feedback-resistant and , and a 3.61-fold improvement of -coumaric acid production was obtained. Finally, formation of byproducts was decreased by deleting pyruvate decarboxylase gene and phenylpyruvate decarboxylase gene , and -coumaric acid production was increased 2.52-fold. The best producer-when , , , , , and were overexpressed, and and were deleted-increased -coumaric acid production by 14.08-fold (from 1.4 to 19.71 mg L). Our study provided a valuable insight into the optimization of l-tyrosine metabolic pathway.
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http://dx.doi.org/10.1007/s13205-020-02223-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275107PMC
June 2020

Long Noncoding RNA SOX2-OT Knockdown Inhibits Proliferation and Metastasis of Prostate Cancer Cells Through Modulating the miR-452-5p/HMGB3 Axis and Inactivating Wnt/β-Catenin Pathway.

Cancer Biother Radiopharm 2020 Nov 14;35(9):682-695. Epub 2020 May 14.

Department of Urology, Fudan University, Minhang Hospital, Shanghai, China.

Recent studies have proven that abnormal expression of long noncoding RNAs (lncRNAs) often contributes to growth and invasion of cancer cells. The purpose of this study was to investigate the biological function and regulatory mechanism of lncRNA SOX2 overlapping transcript (SOX2-OT) in prostate cancer (PCa) progression. The expression of SOX2-OT, microRNA-452-5p (miR-452-5p), and high mobility group box 3 (HMGB3) was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Flow cytometry was performed to determine the cell cycle distribution. Western blot assay was conducted to measure the protein levels of cyclin D1, p21, p27, -cadherin, vimentin, and -cadherin. The interaction between miR-452-5p and SOX2-OT or HMGB3 was predicted by bioinformatics analysis and verified by dual-luciferase reporter assay and RNA immunoprecipitation assay. The mice xenograft model was established to investigate the role of SOX2-OT . SOX2-OT and HMGB3 were upregulated, whereas miR-452-5p was downregulated in PCa tissues and cells. Knockdown of SOX2-OT inhibited PCa cell growth and metastasis. MiR-452-5p could directly bind to SOX2-OT and its knockdown reversed the inhibitory effects of SOX2-OT interference on growth and metastasis of PCa cells. HMGB3 was a direct target of miR-452-5p and its knockdown weakened the promotive effects of miR-452-5p silence on growth and metastasis of PCa cells. Moreover, HMGB3 expression was inversely regulated by miR-452-5p and positively modulated by SOX2-OT. Furthermore, SOX2-OT activated the Wnt/β-catenin signaling pathway through increasing HMGB3 expression. Finally, SOX2-OT knockdown hindered tumor growth by regulating miR-452-5p/HMGB3 axis. SOX2-OT downregulation limited PCa cell growth and metastasis by regulating miR-452-5p/HMGB3 axis and inactivating Wnt/β-catenin signaling pathway, which might offer lncRNA-directed diagnosis and therapy for PCa.
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http://dx.doi.org/10.1089/cbr.2019.3479DOI Listing
November 2020

The behaviors of Microcystis aeruginosa and microcystins during the Fe/persulfate (PS) preoxidation-coagulation and flocs storage period.

Environ Res 2020 07 18;186:109549. Epub 2020 Apr 18.

School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China.

The frequent occurrence of toxin-producing cyanobacteria blooms driven by anthropogenic eutrophication has become a major threat to aquaculture ecosystems worldwide. In this study, the behavior of M. aeruginosa cells during flocs storage period of 6 days was first investigated after pre-oxidation and coagulation of Fe/PS. Fe/PS achieved a superior removal efficiency of 90.7% for OD and 90.4% for chl-a. The contents of extracellular MCs in the pre-oxidation and coagulation system were significantly (P < 0.05) lower than those in the control. A significant (P < 0.05) difference in intracellular protein between the control and the coagulated systems was observed. Three-dimensional fluorescence excitation emission matrix (EEM) was employed to investigate the variations in extracellular organic matter (EOM) during flocs storage. The results indicated the presence of four peaks, representing protein-like substances, intermediate dissolved microbial metabolites, fulvic and humic-like compounds in the Fe/PS process. And the intensities of four peaks were all decreased in the Fe/PS system compared to those in the control. A low level of accumulated residual Fe of 0.28 mg/L was observed without posing potential environmental risk. The results showed that the M. aeruginosa cells were under stressful conditions after 3-d storage due to the decomposition of extracellular polymeric substances (EPSs) and the insufficient supply of nutrients. However, SEM results indicated that no significant alteration in cell morphology was observed. Therefore, with high removal of M. aeruginosa, low MCs concentrations, and trivial cell damage, the Fe/PS preoxidation-coagulation was proved to be an environmental-friendly method for cyanobacteria removal without yielding serious secondary pollution. This work will contribute to better understanding and managing the cyanobacteria-laden aquaculture water after pre-oxidation and coagulation.
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http://dx.doi.org/10.1016/j.envres.2020.109549DOI Listing
July 2020

Up-Regulation of GATA4 Regulates Human Lens Epithelial Cell Function in Age-Related Cataract.

Ophthalmic Res 2020 20;63(6):564-571. Epub 2020 Apr 20.

Department of Ophthalmology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China.

Purpose: GATA4 has emerged as a novel regulator that plays a critical role in mediating senescence. However, the role of GATA4 in age-related cataract (ARC), the leading cause of visual impairment, requires further elucidation.

Methods: GATA4 expression was measured by quantitative RT-PCR and capillary Western immunoassay (WES). The MTT assay, EdU assay, and rhodamine-123/Hoechst and calcein-AM/propidium iodide double staining were used to investigate the role of GATA4 in the viability, proliferation, and apoptosis of cultured human lens epithelial cells (HLECs).

Results: HLECs were subjected to 3 different treatment models, including prolonged exposure to low-dose H2O2, UVB irradiation, and mild heating, to simulate senescence and apoptosis. GATA4 expression was significantly increased in these models in a time- and dose-dependent manner. Overexpression of GATA4 reduced cell viability, accelerated apoptosis development, and reduced the proliferation of HLECs. Furthermore, the expression of GATA4 from ARC was up-regulated at both mRNA and at protein level compared with clear lenses.

Conclusion: GATA4 is up-regulated in all 3 models of HLECs in vitro and the cells from ARC lenses in vivo. Up-regulation of GATA4 mediates HLEC dysfunction. GATA4-mediated effects in HLECs would provide a novel insight into the pathogenesis of ARC.
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http://dx.doi.org/10.1159/000507962DOI Listing
August 2021

Porous Organic Polymer-Derived [email protected],P-Codoped Porous Carbon as Efficient Electrocatalysts for pH Universal ORR.

ACS Omega 2020 Apr 24;5(13):7225-7234. Epub 2020 Mar 24.

College of Pharmacy, Weifang Medical University, Weifang 261053, Shandong, P. R. China.

A new porous organic polymer (CP-CMP) was designed and synthesized via the direct polymerization of pyrrole and hexakis(4-formyl-phenoxy)cyclotriphosphazene, skipping the tedious synthetic procedure of porphyrin-monomers containing special groups. This special porous organic polymer (POP) serves as an "all in one" precursor for C, N, P, and Fe. Direct carbonization of this special POP afforded [email protected],P-codoped porous carbons with hierarchical pore structure and high graphitization. Finally, the optimal catalyst (CP-CMP-900) prepared by carbonization of CP-CMP at 900 °C exhibited high efficiency for oxygen electroreduction. Typically, CP-CMP-900 presented an oxygen reduction reaction half-wave potential ( ) of 0.85, 0.73, and 0.65 V, respectively, in alkaline, neutral, and acidic media, close to those of commercial Pt/C in the same electrolyte (0.843, 0.71, and 0.74 V). Furthermore, it also displayed excellent methanol immunity and long-time stability in various electrolytes better than commercial Pt/C (20%).
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http://dx.doi.org/10.1021/acsomega.9b03851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143406PMC
April 2020

Genome-wide analysis of CsWOX transcription factor gene family in cucumber (Cucumis sativus L.).

Sci Rep 2020 04 10;10(1):6216. Epub 2020 Apr 10.

State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China.

WUSCHEL-related homeobox (WOX) transcription factors are plant-specific members that characterized by the presence of a homeodomain. It has been shown that WOX members regulate several aspects of plant development, but the biological functions of this CsWOX gene family remain largely unknown in cucumber (Cucumis sativus L.). In this study, we identified and characterized 11 putative CsWOX genes in cucumber, which are also divided into three major clades (e.g., the Ancient clade, the Intermediate clade and the WUS clade). Expression pattern analysis revealed tissue-specific expression patterns of CsWOX genes, including that CsWOX9 is mainly expressed in developing fruit and also has lower expression in tip and axillary bud, which was further confirmed by in situ hybridization assay. Moreover, overexpression of CsWOX9 in Arabidopsis led to increased branches and rosette leaves, and shorter siliques. Together, these results indicated that CsWOX members may regulate cucumber growth and development.
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http://dx.doi.org/10.1038/s41598-020-63197-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148364PMC
April 2020

Gene regulatory network controlling carpel number variation in cucumber.

Development 2020 04 6;147(7). Epub 2020 Apr 6.

State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China

The pathway genes play an essential role in shoot apical meristem maintenance and floral organ development, and under intense selection during crop domestication. The carpel number is an important fruit trait that affects fruit shape, size and internal quality in cucumber, but the molecular mechanism remains elusive. Here, we found that expression was negatively correlated with carpel number in cucumber cultivars. led to increased number of petals and carpels, whereas overexpression of resulted in more sepals, petals and carpels, suggesting that and function as a negative and a positive regulator for carpel number variation, respectively. Biochemical analyses indicated that CsWUS directly bound to the promoter of and activated its expression. Overexpression of , a - MADS-box gene, resulted in more petals and carpels. CsFUL1 can directly bind to the promoter to stimulate its expression. Furthermore, we found that auxin participated in carpel number variation in cucumber through interaction of CsARF14 with CsWUS. Therefore, we have identified a gene regulatory pathway involving , , and in determining carpel number variation in an important vegetable crop - cucumber.
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http://dx.doi.org/10.1242/dev.184788DOI Listing
April 2020

Biosynthesis of Caffeic Acid from Glucose by Engineered .

ACS Synth Biol 2020 04 19;9(4):756-765. Epub 2020 Mar 19.

The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China.

Caffeic acid is a plant phenolic compound possessing extensive pharmacological activities. Here, we identified that -coumaric acid 3-hydroxylase from was capable of hydroxylating -coumaric acid to form caffeic acid in . Then, we introduced a combined caffeic acid biosynthetic pathway into and obtained 0.183 mg L caffeic acid from glucose. Next we improved the tyrosine biosynthesis in by blocking the pathway flux to aromatic alcohols and eliminating the tyrosine-induced feedback inhibition resulting in caffeic acid production of 2.780 mg L. Finally, the medium was optimized, and the highest caffeic acid production obtained was 11.432 mg L in YPD medium containing 4% glucose. This study opens a route to produce caffeic acid from glucose in and establishes a platform for the biosynthesis of caffeic acid derived metabolites.
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http://dx.doi.org/10.1021/acssynbio.9b00431DOI Listing
April 2020

A genetic toolbox for metabolic engineering of Issatchenkia orientalis.

Metab Eng 2020 05 31;59:87-97. Epub 2020 Jan 31.

Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States. Electronic address:

The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis, which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.
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http://dx.doi.org/10.1016/j.ymben.2020.01.005DOI Listing
May 2020

Comparative transcriptome analysis of genomic region deletion strain with enhanced L-tyrosine production in Saccharomyces cerevisiae.

Biotechnol Lett 2020 Mar 21;42(3):453-460. Epub 2019 Dec 21.

The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China.

Objective: To determine the effect of large genomic region deletion in a Saccharomyces cerevisiae strain on tyrosine yield and to identify new genetic modification targets through transcriptome analysis.

Results: TAL was used to produce p-coumaric acid (p-CA) from tyrosine to quantity tyrosine yield. S. cerevisiae mutant strain NK14 with deletion of a 23.8 kb genomic region was identified to have p-CA production of 10.3 mg L, while the wild-type strain BY4741 had p-CA production of 1.06 mg L. Analysis of growth patterns and stress tolerance showed that the deletion did not affect the growth phenotype of NK14. Transcriptome analysis suggested that, compared to BY4741, genes related to glycolysis (ENO2, TKL1) and the tyrosine pathway (ARO1, ARO2, ARO4, ARO7, TYR1) were upregulated in NK14 at different levels. Besides genes related to the tyrosine biosynthetic pathway, amino acid transporters (AVT6, VBA5, THI72) and transcription factor (ARO80) also showed changes in transcription levels.

Conclusions: We developed a strain with improved tyrosine yield and identified new genetic modification candidates for tyrosine production.
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http://dx.doi.org/10.1007/s10529-019-02784-1DOI Listing
March 2020

Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants.

Genome Med 2019 12 9;11(1):80. Epub 2019 Dec 9.

Graduate Program in Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Background: We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated.

Methods: Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis.

Results: High-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches).

Conclusions: These data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.
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http://dx.doi.org/10.1186/s13073-019-0676-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6902434PMC
December 2019

Phenotypic expansion of POGZ-related intellectual disability syndrome (White-Sutton syndrome).

Am J Med Genet A 2020 01 29;182(1):38-52. Epub 2019 Nov 29.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.

White-Sutton syndrome (WHSUS) is a recently-identified genetic disorder resulting from de novo heterozygous pathogenic variants in POGZ. Thus far, over 50 individuals have been reported worldwide, however phenotypic characterization and data regarding the natural history are still incomplete. Here we report the clinical features of 22 individuals with 21 unique loss of function POGZ variants. We observed a broad spectrum of intellectual disability and/or developmental delay with or without autism, and speech delay in all individuals. Other common problems included ocular abnormalities, hearing loss and gait abnormalities. A validated sleep disordered breathing questionnaire identified symptoms of obstructive sleep apnea in 4/12 (33%) individuals. A higher-than-expected proportion of cases also had gastrointestinal phenotypes, both functional and anatomical, as well as genitourinary anomalies. In line with previous publications, we observed an increased body mass index (BMI) z-score compared to the general population (mean 0.59, median 0.9; p 0.0253). Common facial features included microcephaly, broad forehead, midface hypoplasia, triangular mouth, broad nasal root and flat nasal bridge. Analysis of the Baylor Genetics clinical laboratory database revealed that POGZ variants were implicated in approximately 0.14% of cases who underwent clinical exome sequencing for neurological indications with or without involvement of other body systems. This study describes a greater allelic series and expands the phenotypic spectrum of this new syndromic form of intellectual disability and autism.
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http://dx.doi.org/10.1002/ajmg.a.61380DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7713511PMC
January 2020

Genetic and molecular mechanism for distinct clinical phenotypes conveyed by allelic truncating mutations implicated in FBN1.

Mol Genet Genomic Med 2020 01 27;8(1):e1023. Epub 2019 Nov 27.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

Background: The molecular and genetic mechanisms by which different single nucleotide variant alleles in specific genes, or at the same genetic locus, cause distinct disease phenotypes often remain unclear. Allelic truncating mutations of FBN1 could cause either classical Marfan syndrome (MFS) or a more complicated phenotype associated with Marfanoid-progeroid-lipodystrophy syndrome (MPLS).

Methods: We investigated a small cohort, encompassing two classical MFS and one MPLS subjects from China, whose clinical presentation included scoliosis potentially requiring surgical intervention. Targeted next generation sequencing was performed on all the participants. We analyzed the molecular diagnosis, clinical features, and the potential molecular mechanism involved in the MPLS subject in our cohort.

Results: We report a novel de novo FBN1 mutation for the first Chinese subject with MPLS, a more complicated fibrillinopathy, and two subjects with more classical MFS. We further predict that the MPLS truncating mutation, and others previously reported, is prone to escape the nonsense-mediated decay (NMD), while MFS mutations are predicted to be subjected to NMD. Also, the MPLS mutation occurs within the glucogenic hormone asprosin domain of FBN1. In vitro experiments showed that the single MPLS mutation p.Glu2759Cysfs*9 appears to perturb proper FBN1 protein aggregation as compared with the classical MFS mutation p.Tyr2596Thrfs*86. Both mutations appear to upregulate SMAD2 phosphorylation in vitro.

Conclusion: We provide direct evidence that a dominant-negative interaction of FBN1 potentially explains the complex MPLS phenotypes through genetic and functional analysis. Our study expands the mutation spectrum of FBN1 and highlights the potential molecular mechanism for MPLS.
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http://dx.doi.org/10.1002/mgg3.1023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978264PMC
January 2020

Association of rare non-coding SNVs in the lung-specific FOXF1 enhancer with a mitigation of the lethal ACDMPV phenotype.

Hum Genet 2019 Dec 4;138(11-12):1301-1311. Epub 2019 Nov 4.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

Haploinsufficiency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. In one case, the deletion of the maternal allele of the FOXF1 enhancer caused pulmonary hypertension and histopathologically diagnosed MPV without the typical ACD features. In the second case, the deletion of the paternal enhancer resulted in ACDMPV rather than the expected neonatal lethality. In both cases, FOXF1 expression in lung tissue was higher than usually seen or expected in patients with similar deletions, suggesting an increased activity of the remaining allele of the enhancer. Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. Moreover, in a family with three histopathologically-diagnosed ACDMPV siblings whose missense FOXF1 mutation was inherited from the healthy non-mosaic carrier mother, we have identified a rare SNV rs28571077-A within 2-kb of the above-mentioned non-coding SNVs in the FOXF1 enhancer in the mother, that was absent in the affected newborns and 13 unrelated ACDMPV patients with CNV deletions of this genomic region. Based on the low population frequencies of these three variants, their absence in ACDMPV patients, the results of reporter assay, RNAi and EMSA experiments, and in silico predictions, we propose that the described SNVs might have acted on FOXF1 enhancer as hypermorphs.
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http://dx.doi.org/10.1007/s00439-019-02073-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874894PMC
December 2019

A Systematic Literature Review of Cancer Communication with Indigenous Populations in Canada and the United States.

J Cancer Educ 2021 04;36(2):310-324

Indigenous Environmental Studies and Sciences Program, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada.

Cancer is one of the leading causes of death among Indigenous populations. Communication campaigns are an important component of cancer prevention and treatment. However, communication about cancer with Indigenous populations has yet to be fully explored and understood. In this systematic literature review, we examine peer-reviewed research to gain insight into the factors that contribute to effective communication about cancer with Indigenous populations. The review yielded a total of 7313 potential articles and a total of 25 of these manuscripts met the inclusion criteria. Results indicate five primary factors that may increase the effectiveness of communication about cancer with Indigenous populations. Factors include the need to (1) respect traditional knowledge, (2) use appropriate language, (3) involve community members in the communication process, (4) include people from different generations in message design, and (5) engender trust in health communicators. Results also provide insight into communication methods that contribute to effective cancer communication. We identify gaps in the literature and provide recommendations for future cancer communication strategies and research with Indigenous populations.
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http://dx.doi.org/10.1007/s13187-019-01630-2DOI Listing
April 2021

TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease.

Hum Mutat 2020 01 26;41(1):182-195. Epub 2019 Sep 26.

Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas.

Congenital scoliosis (CS) is a birth defect with variable clinical and anatomical manifestations due to spinal malformation. The genetic etiology underlying about 10% of CS cases in the Chinese population is compound inheritance by which the gene dosage is reduced below that of haploinsufficiency. In this genetic model, the trait manifests as a result of the combined effect of a rare variant and common pathogenic variant allele at a locus. From exome sequencing (ES) data of 523 patients in Asia and two patients in Texas, we identified six TBX6 gene-disruptive variants from 11 unrelated CS patients via ES and in vitro functional testing. The in trans mild hypomorphic allele was identified in 10 of the 11 subjects; as anticipated these 10 shared a similar spinal deformity of hemivertebrae. The remaining case has a homozygous variant in TBX6 (c.418C>T) and presents a more severe spinal deformity phenotype. We found decreased transcriptional activity and abnormal cellular localization as the molecular mechanisms for TBX6 missense loss-of-function alleles. Expanding the mutational spectrum of TBX6 pathogenic alleles enabled an increased molecular diagnostic detection rate, provided further evidence for the gene dosage-dependent genetic model underlying CS, and refined clinical classification.
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http://dx.doi.org/10.1002/humu.23907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061259PMC
January 2020

Xq22 deletions and correlation with distinct neurological disease traits in females: Further evidence for a contiguous gene syndrome.

Hum Mutat 2020 01 14;41(1):150-168. Epub 2019 Nov 14.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.

Xq22 deletions that encompass PLP1 (Xq22-PLP1-DEL) are notable for variable expressivity of neurological disease traits in females ranging from a mild late-onset form of spastic paraplegia type 2 (MIM# 312920), sometimes associated with skewed X-inactivation, to an early-onset neurological disease trait (EONDT) of severe developmental delay, intellectual disability, and behavioral abnormalities. Size and gene content of Xq22-PLP1-DEL vary and were proposed as potential molecular etiologies underlying variable expressivity in carrier females where two smallest regions of overlap (SROs) were suggested to influence disease. We ascertained a cohort of eight unrelated patients harboring Xq22-PLP1-DEL and performed high-density array comparative genomic hybridization and breakpoint-junction sequencing. Molecular characterization of Xq22-PLP1-DEL from 17 cases (eight herein and nine published) revealed an overrepresentation of breakpoints that reside within repeats (11/17, ~65%) and the clustering of ~47% of proximal breakpoints in a genomic instability hotspot with characteristic non-B DNA density. These findings implicate a potential role for genomic architecture in stimulating the formation of Xq22-PLP1-DEL. The correlation of Xq22-PLP1-DEL gene content with neurological disease trait in female cases enabled refinement of the associated SROs to a single genomic interval containing six genes. Our data support the hypothesis that genes contiguous to PLP1 contribute to EONDT.
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http://dx.doi.org/10.1002/humu.23902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6953250PMC
January 2020

Development of a CRISPR/Cas9-Based Tool for Gene Deletion in .

mSphere 2019 06 26;4(3). Epub 2019 Jun 26.

Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

The nonconventional yeast has emerged as a potential platform microorganism for production of organic acids due to its ability to grow robustly under highly acidic conditions. However, lack of efficient genetic tools remains a major bottleneck in metabolic engineering of this organism. Here we report that the autonomously replicating sequence (ARS) from (ScARS) was functional for plasmid replication in , and the resulting episomal plasmid enabled efficient genome editing by the CRISPR/Cas9 system. The optimized CRISPR/Cas9-based system employed a fusion ' promoter for single guide RNA (sgRNA) expression and could attain greater than 97% gene disruption efficiency for various gene targets. Additionally, we demonstrated multiplexed gene deletion with disruption efficiencies of 90% and 47% for double gene and triple gene knockouts, respectively. This genome editing tool can be used for rapid strain development and metabolic engineering of this organism for production of biofuels and chemicals. Microbial production of fuels and chemicals from renewable and readily available biomass is a sustainable and economically attractive alternative to petroleum-based production. Because of its unusual tolerance to highly acidic conditions, is a promising potential candidate for the manufacture of valued organic acids. Nevertheless, reliable and efficient genetic engineering tools in are limited. The results outlined in this paper describe a stable episomal ARS-containing plasmid and the first CRISPR/Cas9-based system for gene disruptions in , paving the way for applying genome engineering and metabolic engineering strategies and tools in this microorganism for production of fuels and chemicals.
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http://dx.doi.org/10.1128/mSphere.00345-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6595149PMC
June 2019

Superior Form-Stable Phase Change Material Made with Graphene-Connected Carbon Nanofibers and Fatty Acid Eutectics.

J Nanosci Nanotechnol 2019 11;19(11):7044-7053

Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27401, United States.

A novel form-stable phase change material (FSPCM) with remarkable improvement in thermal properties was fabricated by incorporating ternary fatty acid eutectics with graphene sheetconnected electrospun carbon nanofibers (GCNFs). The GCNFs possessed three-dimensional (3D) porous architecture and large specific surface area while provided mechanical support for FSPCM and effectively prevented flow/leakage of molten fatty acid. The GCNF based FSPCM exhibited desire structural morphology with lauric-myristic-stearic acid (LA-MA-SA) eutectic mixture being well dispersed in a 3D porous architecture. This novel FSPCM demonstrated superior thermal storage/retrieval capability and temperature regulation ability as well as good shape stability and thermal cycling stability. The melting and crystallization enthalpies of the fabricated FSPCMs were up to 120.4 and 120.1 kJ/kg, respectively. The thermal conductivity of the fabricated FSPCMs was 337% and 188% higher than that of LA-MA-SA eutectic mixture and a control sample without graphene, respectively, which ranked the top among the literature about LA-MA-SA eutectic mixture derived composite FSPCMs. Furthermore, the heating/cooling efficiency of the prepared FSPCMs was 45.7/64.9% higher than that of LA-MA-SA eutectic mixture.
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http://dx.doi.org/10.1166/jnn.2019.16711DOI Listing
November 2019

Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri).

BMC Plant Biol 2019 Apr 25;19(1):161. Epub 2019 Apr 25.

College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.

Background: Although the genome of Chinese white pear ('Dangshansuli') has been released, little is known about the functions, evolutionary history and expression patterns of NAC families in this species to date.

Results: In this study, we identified a total of 183 NAC transcription factors (TFs) in the pear genome, among which 146 pear NAC (PbNAC) members were mapped onto 16 chromosomes, and 37 PbNAC genes were located on scaffold contigs. No PbNAC genes were mapped to chromosome 2. Based on gene structure, protein motif analysis, and topology of the phylogenetic tree, the pear PbNAC family was classified into 33 groups. By comparing and analyzing the unique NAC subgroups in Rosaceae, we identified 19 NAC subgroups specific to pear. We also found that whole-genome duplication (WGD)/segmental duplication played critical roles in the expansion of the NAC family in pear, such as the 83 PbNAC duplicated gene pairs dated back to the two WGD events. Further, we found that purifying selection was the primary force driving the evolution of PbNAC family genes. Next, we used transcriptomic data to study responses to drought and cold stresses in pear, and we found that genes in groups C2f, C72b, and C100a were related to drought and cold stress response.

Conclusions: Through the phylogenetic, evolutionary, and expression analyses of the NAC gene family in Chinese white pear, we indentified 11 PbNAC TFs associated with abiotic stress in pear.
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http://dx.doi.org/10.1186/s12870-019-1760-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485137PMC
April 2019

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2.

Cell 2019 03 28;176(6):1310-1324.e10. Epub 2019 Feb 28.

Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX 77030, USA. Electronic address:

DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.
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http://dx.doi.org/10.1016/j.cell.2019.01.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438178PMC
March 2019
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