Author Report for: Cai ZNo contact information in database for Cai Z
Cai Z, Li M, Zhu Z, Wang X, Huang Y, Li T, Gong H, Yan M Ref: Microorganisms, 11:, 2023 : PubMed ESTHER: Cai_2023_Microorganisms_11_ PubMedSearch: Cai 2023 Microorganisms 11 PubMedID: 37512834 Abstract Plastic and microplastic pollution has caused a great deal of ecological problems because of its persistence and potential adverse effects on human health. The degradation of plastics through biological processes is of great significance for ecological health, therefore, the feasibility of plastic degradation by microorganisms has attracted a lot of attention. This study comprises a preliminary discussion on the biodegradation mechanism and the advantages and roles of different bacterial enzymes, such as PET hydrolase and PCL-cutinase, in the degradation of different polymers, such as PET and PCL, respectively. With a particular focus on their modes of action and potential enzymatic mechanisms, this review sums up studies on the biological degradation of plastics and microplastics related to mechanisms and influencing factors, along with their enzymes in enhancing the degradation of synthetic plastics in the process. In addition, biodegradation of plastic is also affected by plastic additives and plasticizers. Plasticizers and additives in the composition of plastics can cause harmful impacts. To further improve the degradation efficiency of polymers, various pretreatments to improve the efficiency of biodegradation, which can cause a significant reduction in toxic plastic pollution, were also preliminarily discussed here. The existing research and data show a large number of microorganisms involved in plastic biodegradation, though their specific mechanisms have not been thoroughly explored yet. Therefore, there is a significant potential for employing various bacterial strains for efficient degradation of plastics to improve human health and safety. Title: Alteration of myoepithelial cells during botulinum toxin type A-inhibited salivary secretion Xu H, Ge H, Shan X, Cai Z Ref: Oral Dis, :, 2023 : PubMed ESTHER: Xu_2023_Oral.Dis__ PubMedSearch: Xu 2023 Oral.Dis PubMedID: 36971615 Abstract OBJECTIVE: Intraglandular injection of botulinum toxin type A (BoNT/A) effectively treats sialorrhea. Myoepithelial cells (MECs) are essential for salivary secretion. The role of MECs in BoNT/A-inhibited salivary secretion and its underlying mechanisms remain unknown. MATERIALS AND METHODS: BoNT/A was injected into rat submandibular glands (SMGs). At 1, 2, 4, 8, and 12 weeks postinjection, salivary flow rate of SMGs was measured. Electron microscopy, immunohistochemistry, immunofluorescence, and western blot analysis were used to detect morphological and functional changes of MECs and chemical denervation in SMGs. RESULTS: BoNT/A temporarily decreased salivary secretion in rat SMGs and this inhibitory effect lasted 4 weeks. During the inhibitory period, MECs atrophied and expressed reduced alpha-smooth muscle actin (alpha-SMA), vimentin, and phosphorylated myosin light chain 2 (p-MLC2), suggesting that BoNT/A attenuated MEC contractility. Furthermore, BoNT/A cleaved synaptosome-associated protein 25 (SNAP-25) and decreased the expression and activity of acetylcholinesterase (AChE), indicating that BoNT/A induced chemical parasympathetic denervation of SMGs by cleaving SNAP-25. CONCLUSIONS: BoNT/A temporarily caused MEC atrophy and decreased MEC contractility in rat SMGs, which contributed to reversible inhibition of salivary secretion. The underlying mechanisms involved temporary parasympathetic denervation caused by SNAP-25 cleavage. These findings provide new insights into the mechanisms of BoNT/A-inhibited salivary secretion. Title: Acquisition of T6SS Effector TseL Contributes to the Emerging of Novel Epidemic Strains of Pseudomonas aeruginosa Ren A, Jia M, Liu J, Zhou T, Wu L, Dong T, Cai Z, Qu J, Liu Y and Zhang Y <1 more author(s)> Ren A, Jia M, Liu J, Zhou T, Wu L, Dong T, Cai Z, Qu J, Liu Y, Yang L, Zhang Y (- 1) Ref: Microbiol Spectr, :e0330822, 2022 : PubMed ESTHER: Ren_2022_Microbiol.Spectr__e0330822 PubMedSearch: Ren 2022 Microbiol.Spectr e0330822 PubMedID: 36546869 Gene_locus related to this paper: pseae-T6SSTseL Abstract Pseudomonas aeruginosa is an opportunistic pathogen with multiple strategies to interact with other microbes and host cells, gaining fitness in complicated infection sites. The contact-dependent type VI secretion system (T6SS) is one critical secretion apparatus involved in both interbacterial competition and pathogenesis. To date, only limited numbers of T6SS-effectors have been clearly characterized in P. aeruginosa laboratory strains, and the importance of T6SS diversity in the evolution of clinical P. aeruginosa remains unclear. Recently, we characterized a P. aeruginosa clinical strain LYSZa7 from a COVID-19 patient, which adopted complex genetic adaptations toward chronic infections. Bioinformatic analysis has revealed a putative type VI secretion system (T6SS) dependent lipase effector in LYSZa7, which is a homologue of TseL in Vibrio cholerae and is widely distributed in pathogens. We experimentally validated that this TseL homologue belongs to the Tle2, a subfamily of T6SS-lipase effectors; thereby, we name this effector TseL (TseL(PA) in this work). Further, we showed the lipase-dependent bacterial toxicity of TseL(PA), which primarily targets bacterial periplasm. The toxicity of TseL(PA) can be neutralized by two immunity proteins, TsiP1 and TsiP2, which are encoded upstream of tseL. In addition, we proved this TseL(PA) contributes to bacterial pathogenesis by promoting bacterial internalization into host cells. Our study suggests that clinical bacterial strains employ a diversified group of T6SS effectors for interbacterial competition and might contribute to emerging of new epidemic clonal lineages. IMPORTANCE Pseudomonas aeruginosa is one predominant pathogen that causes hospital-acquired infections and is one of the commonest coinfecting bacteria in immunocompromised patients and chronic wounds. This bacterium harbors a diverse accessory genome with a high frequency of gene recombination, rendering its population highly heterogeneous. Numerous Pa lineages coexist in the biofilm, where successful epidemic clonal lineage or strain-specific type commonly acquires genes to increase its fitness over the other organisms. Current studies of Pa genomic diversity commonly focused on antibiotic resistant genes and novel phages, overlooking the contribution of type VI secretion system (T6SS). We characterized a Pa clinical strain LYSZa7 from a COVID-19 patient, which adopted complex genetic adaptations toward chronic infections. We report, in this study, a novel T6SS-lipase effector that is broadly distributed in Pa clinical isolates and other predominant pathogens. The study suggests that hospital transmission may raise the emergence of new epidemic clonal lineages with specified T6SS effectors. Title: Functional Characterization and Crystal Structure of the Bifunctional Thioesterase Catalyzing Epimerization and Cyclization in Skyllamycin Biosynthesis Yu J, Juan S, Chi C, Liu T, Geng T, Cai Z, Dong W, Shi C, Ma X and Ma M <6 more author(s)> Yu J, Juan S, Chi C, Liu T, Geng T, Cai Z, Dong W, Shi C, Ma X, Zhang Z, Xing B, Jin H, Zhang L, Dong S, Yang D, Ma M (- 6) Ref: ACS Catal, 11:11733, 2021 : PubMed ESTHER: Yu_2021_ACS.Catalysis_11_11733 PubMedSearch: Yu 2021 ACS.Catalysis 11 11733 Gene_locus related to this paper: strsq-a0a1j0r317 Abstract The d-amino acid residues are hallmark building blocks of nonribosomal peptides. Here, we report the bifunctional thioesterase domain (TE domain) Skyxy-TE that catalyzes both epimerization and cyclization in skyllamycin biosynthesis. Skyxy-TE specifically catalyzes the epimerization of the C-terminal l-amino acid residue of the linear substrate, then catalyzes regioselective intramolecular cyclization. The crystal structure of Skyxy-TE was solved at 2.25 and site-directed mutagenesis was performed, revealing key residues involved in the epimerization and cyclization. This study expands the understanding of the versatile TE domains and facilitates chemoenzymatic synthesis or combinatorial biosynthesis in the future. Title: Synthesis, physicochemical properties, and health aspects of structured lipids: A review Guo Y, Cai Z, Xie Y, Ma A, Zhang H, Rao P, Wang Q Ref: Compr Rev Food Sci Food Saf, 19:759, 2020 : PubMed ESTHER: Guo_2020_Compr.Rev.Food.Sci.Food.Saf_19_759 PubMedSearch: Guo 2020 Compr.Rev.Food.Sci.Food.Saf 19 759 PubMedID: 33325163 Abstract Structured lipids (SLs) refer to a new type of functional lipids obtained by chemically, enzymatically, or genetically modifying the composition and/or distribution of fatty acids in the glycerol backbone. Due to the unique physicochemical characteristics and health benefits of SLs (for example, calorie reduction, immune function improvement, and reduction in serum triacylglycerols), there is increasing interest in the research and application of novel SLs in the food industry. The chemical structures and molecular architectures of SLs define mainly their physicochemical properties and nutritional values, which are also affected by the processing conditions. In this regard, this holistic review provides coverage of the latest developments and applications of SLs in terms of synthesis strategies, physicochemical properties, health aspects, and potential food applications. Enzymatic synthesis of SLs particularly with immobilized lipases is presented with a short introduction to the genetic engineering approach. Some physical features such as solid fat content, crystallization and melting behavior, rheology and interfacial properties, as well as oxidative stability are discussed as influenced by chemical structures and processing conditions. Health-related considerations of SLs including their metabolic characteristics, biopolymer-based lipid digestion modulation, and oleogelation of liquid oils are also explored. Finally, potential food applications of SLs are shortly introduced. Major challenges and future trends in the industrial production of SLs, physicochemical properties, and digestion behavior of SLs in complex food systems, as well as further exploration of SL-based oleogels and their food application are also discussed. Title: Paeoniflorin Alleviates Abnormalities in Rats with Functional Dyspepsia by Stimulating the Release of Acetylcholine Zou X, Wang Y, Yang J, Guo H, Cai Z Ref: Drug Des Devel Ther, 14:5623, 2020 : PubMed ESTHER: Zou_2020_Drug.Des.Devel.Ther_14_5623 PubMedSearch: Zou 2020 Drug.Des.Devel.Ther 14 5623 PubMedID: 33376306 Abstract INTRODUCTION: Paeoniflorin is a main active component in traditional Chinese medicine. Paeoniae alba radix is widely used as a spasmolytic and pain-relieving agent for abdominal spasmodic pain. Functional dyspepsia (FD) is characterized by pain or burning in the epigastrium, fullness, bloating and nausea. However, limited information is available about the effect of paeoniflorin on FD. MATERIALS AND METHODS: In this study, iodoacetamide or clonidine-induced FD rat models were established to investigate the impacts of paeoniflorin on FD induced by different pathophysiologic disturbances. RESULTS: We found the therapeutic effect of paeoniflorin through assessing the gastric emptying, gastric accommodation and visceral hypersensitivity. This function of paeoniflorin was related to the release of acetylcholine (ACh), which was accompanied by reduced acetylcholinesterase (AchE) activity in stomach and hypothalamus. Paeoniflorin administration inhibited the cyclo-oxygenase-2 (COX-2) expression and increased the level of ghrelin in the stomach. Besides, the levels of occludin and ZO-1 were elevated in the duodenum from paeoniflorin-treated rats, suggesting the impaired duodenal barrier was ameliorated. DISCUSSION: These results indicate that paeoniflorin possesses the ability to alleviate functional dyspepsia. Title: Small Molecule Natural Products and Alzheimer's Disease Wu X, Cai H, Pan L, Cui G, Qin F, Li Y, Cai Z Ref: Curr Top Med Chem, 19:187, 2019 : PubMed ESTHER: Wu_2019_Curr.Top.Med.Chem_19_187 PubMedSearch: Wu 2019 Curr.Top.Med.Chem 19 187 PubMedID: 30714527 Abstract Alzheimer's disease (AD) is a progressive and deadly neurodegenerative disease that is characterized by memory loss, cognitive impairment and dementia. Several hypotheses have been proposed for the pathogenesis based on the pathological changes in the brain of AD patients during the last few decades. Unfortunately, there is no effective agents/therapies to prevent or control AD at present. Currently, only a few drugs, which function as acetylcholinesterase (AChE) inhibitors or N-methyl-Daspartate (NMDA) receptor antagonists, are available to alleviate symptoms. Since many small molecule natural products have shown their functions as agonists or antagonists of receptors, as well as inhibitors of enzymes and proteins in the brain during the development of central nervous system (CNS) drugs, it is likely that natural products will play an important role in anti-AD drug development. We review recent papers on using small molecule natural products as drug candidates for the treatment of AD. These natural products possess antioxidant, anti-inflammatory, anticholinesterase, anti-amyloidogenic and neuroprotective activities. Moreover, bioactive natural products intended to be used for preventing AD, reducing the symptoms of AD and the new targets for treatment of AD are summarized. Title: Increased lncRNA ABHD11-AS1 represses the malignant phenotypes of bladder cancer Chen M, Li J, Zhuang C, Cai Z Ref: Oncotarget, 8:28176, 2017 : PubMed ESTHER: Chen_2017_Oncotarget_8_28176 PubMedSearch: Chen 2017 Oncotarget 8 28176 PubMedID: 28157695 Gene_locus related to this paper: human-ABHD11 Abstract Bladder cancer is one of the most common urothelial tumors worldwide. While there are some progresses on early bladder cancer detection, patients' mortalities have not been changed significantly. So it is important to get further understanding the mechanism involved in the development and progression of bladder cancer. Long non-coding RNAs play important regulatory roles in a variety of biological processes ranging from gene regulation, cellular differentiation to tumorigenesis. Previous literatures reported that lncRNA ABHD11 Antisense RNA 1 (ABHD11-AS1) (Organism: Homo sapiens) was highly expressed in gastric cancer. Inspired by these observations, we hypothesized that ABHD11-AS1 possibly plays an analogous role in human bladder cancer. We first found that ABHD11-AS1 was up-regulated in bladder cancer tissues and cell lines, and ABHD11-AS1 expression level was positively associated with clinicobiological features. Cell proliferation, cell migration and apoptosis were observed by silencing ABHD11-AS1 and overexpression ABHD11-AS1 caused contrary effects. Taken together, these data suggested that ABHD11-AS1 may be an oncogene and a therapeutic target in bladder cancer. Title: Testosterone Deficiency Induces Changes of the Transcriptomes of Visceral Adipose Tissue in Miniature Pigs Fed a High-Fat and High-Cholesterol Diet Zhang L, Cai Y, Wei S, Ling Y, Zhu L, Li D, Cai Z Ref: Int J Mol Sci, 17:, 2016 : PubMed ESTHER: Zhang_2016_Int.J.Mol.Sci_17_ PubMedSearch: Zhang 2016 Int.J.Mol.Sci 17 PubMedID: 27999286 Abstract Testosterone deficiency causes fat deposition, particularly in visceral fat, and its replacement might reverse fat accumulation, however, the underlying mechanisms of such processes under diet-induced adiposity are largely unknown. To gain insights into the genome-wide role of androgen on visceral adipose tissue (VAT), RNA-Seq was used to investigate testosterone deficiency induced changes of VAT in miniature pigs fed a high-fat and high-cholesterol (HFC) diet among intact male pigs (IM), castrated male pigs (CM), and castrated male pigs with testosterone replacement (CMT) treatments. The results showed that testosterone deficiency significantly increased VAT deposition and serum leptin concentrations. Moreover, a total of 1732 differentially expressed genes (DEGs) were identified between any two groups. Compared with gene expression profiles in IM and CMT pigs, upregulated genes in CM pigs, i.e., LOC100520753 (CD68), LCN2, EMR1, S100A9, NCF1 (p47phox), and LEP, were mainly involved in inflammatory response, oxidation-reduction process, and lipid metabolic process, while downregulated genes in CM pigs, i.e., ABHD5, SPP1, and GAS6, were focused on cell differentiation and cell adhesion. Taken together, our study demonstrates that testosterone deficiency alters the expression of numerous genes involved in key biological processes of VAT accumulation under HFC diet and provides a novel genome-wide view on the role of androgen on VAT deposition under HFC diet, thus improving our understanding of the molecular mechanisms involved in VAT changes induced by testosterone deficiency. Title: The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W and Palsson BO <12 more author(s)> Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO (- 12) Ref: Nat Biotechnol, 29:735, 2011 : PubMed ESTHER: Xu_2011_Nat.Biotechnol_29_735 PubMedSearch: Xu 2011 Nat.Biotechnol 29 735 PubMedID: 21804562 Gene_locus related to this paper: crigr-g3hfm0, crigr-g3h894, crigr-a0a061hy43, crigr-g3h3f6, crigr-g3i9k7, crigr-g3i9k8, crigr-g3grm1, crigr-g3in33, crigr-g3i1j5, crigr-a0a061ika1, crigr-g3hqj0, crigr-g3hh02, crigr-g3h083, crigr-a0a3l7ib08, crigr-a0a061ihy9, crigr-g3ifk5, crigr-g3ily8, crigr-g3hvc7, crigr-g3gtp1, crigr-g3h7k6, crigr-g3hkm8 Abstract Chinese hamster ovary (CHO)-derived cell lines are the preferred host cells for the production of therapeutic proteins. Here we present a draft genomic sequence of the CHO-K1 ancestral cell line. The assembly comprises 2.45 Gb of genomic sequence, with 24,383 predicted genes. We associate most of the assembled scaffolds with 21 chromosomes isolated by microfluidics to identify chromosomal locations of genes. Furthermore, we investigate genes involved in glycosylation, which affect therapeutic protein quality, and viral susceptibility genes, which are relevant to cell engineering and regulatory concerns. Homologs of most human glycosylation-associated genes are present in the CHO-K1 genome, although 141 of these homologs are not expressed under exponential growth conditions. Many important viral entry genes are also present in the genome but not expressed, which may explain the unusual viral resistance property of CHO cell lines. We discuss how the availability of this genome sequence may facilitate genome-scale science for the optimization of biopharmaceutical protein production. Title: Morphing activity between structurally similar enzymes: from heme-free bromoperoxidase to lipase Chen B, Cai Z, Wu W, Huang Y, Pleiss J, Lin Z Ref: Biochemistry, 48:11496, 2009 : PubMed ESTHER: Chen_2009_Biochemistry_48_11496 PubMedSearch: Chen 2009 Biochemistry 48 11496 PubMedID: 19883129 Abstract In this study, to explore the plasticity of the alpha/beta-hydrolase fold family, we converted bromoperoxidase A2 (BPO-A2) from Streptomyces aureofaciens to a lipase by structure comparison with lipase A (LipA) from Bacillus subtilis. These two enzymes have similar structures (2.1 A rmsd) and a very low level of sequence identity ( approximately 18%). A variant BL1 was constructed by deleting the caplike domain of BPO-A2 and further fine-tuning the newly formed substrate binding site. The lipase activity was successfully transplanted on BL1, while the halogenation activity was totally lost. BL1 also showed higher hydrolytic activities toward long chain p-nitrophenyl esters, such as p-nitrophenyl caprylate (3.7-fold) and p-nitrophenyl palmitate (7.0-fold), while its activity toward a short chain ester (p-nitrophenyl acetate) decreased dramatically, to only 1.2% of that of BPO-A2. After two rounds of directed evolution and site-directed mutagenesis on selected residues, several mutants with both improved hydrolytic activities and substrate preferences toward long chain substrates were obtained. The highest hydrolytic activity toward p-nitrophenyl palmitate of the best mutant BL1-2-E8-plusI was improved by 40-fold compared with that of BL1. These results demonstrate the possibility of manipulating the caplike domain of alpha/beta-hydrolase fold enzymes and provide further understanding of the structure-function relationship of the alpha/beta-hydrolase fold enzymes. The design strategy used in this study could serve as a useful approach for constructing variants with targeted catalytic properties using the alpha/beta-hydrolase fold. Title: Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing Ren SX, Fu G, Jiang XG, Zeng R, Miao YG, Xu H, Zhang YX, Xiong H, Lu G and Zhao GP <29 more author(s)> Ren SX, Fu G, Jiang XG, Zeng R, Miao YG, Xu H, Zhang YX, Xiong H, Lu G, Lu LF, Jiang HQ, Jia J, Tu YF, Jiang JX, Gu WY, Zhang YQ, Cai Z, Sheng HH, Yin HF, Zhang Y, Zhu GF, Wan M, Huang HL, Qian Z, Wang SY, Ma W, Yao ZJ, Shen Y, Qiang BQ, Xia QC, Guo XK, Danchin A, Saint Girons I, Somerville RL, Wen YM, Shi MH, Chen Z, Xu JG, Zhao GP (- 29) Ref: Nature, 422:888, 2003 : PubMed ESTHER: Ren_2003_Nature_422_888 PubMedSearch: Ren 2003 Nature 422 888 PubMedID: 12712204 Gene_locus related to this paper: lepin-AXEA, lepin-ESTA, lepin-LA0357, lepin-LA0587, lepin-LA0823, lepin-LA0932, lepin-LA1069, lepin-LA1345, lepin-LA1541, lepin-LA1702, lepin-LA1861, lepin-LA1902, lepin-LA1936, lepin-LA1955, lepin-LA2034, lepin-LA2132, lepin-LA2501, lepin-LA2505, lepin-LA2526, lepin-LA2544, lepin-LA2857, lepin-LA2958, lepin-LA3100, lepin-LA3107, lepin-LA3147, lepin-LA3604, lepin-LA3661, lepin-LA3669, lepin-LA3672, lepin-LA3770, lepin-LA3788, lepin-LA3851, lepin-LA3897, lepin-LA3998, lepin-LA4247, lepin-LB147, lepin-LB264, lepin-LB265, lepin-METX, lepin-q8f7a8, lepin-q72tt9 Abstract Leptospirosis is a widely spread disease of global concern. Infection causes flu-like episodes with frequent severe renal and hepatic damage, such as haemorrhage and jaundice. In more severe cases, massive pulmonary haemorrhages, including fatal sudden haemoptysis, can occur. Here we report the complete genomic sequence of a representative virulent serovar type strain (Lai) of Leptospira interrogans serogroup Icterohaemorrhagiae consisting of a 4.33-megabase large chromosome and a 359-kilobase small chromosome, with a total of 4,768 predicted genes. In terms of the genetic determinants of physiological characteristics, the facultatively parasitic L. interrogans differs extensively from two other strictly parasitic pathogenic spirochaetes, Treponema pallidum and Borrelia burgdorferi, although similarities exist in the genes that govern their unique morphological features. A comprehensive analysis of the L. interrogans genes for chemotaxis/motility and lipopolysaccharide synthesis provides a basis for in-depth studies of virulence and pathogenesis. The discovery of a series of genes possibly related to adhesion, invasion and the haematological changes that characterize leptospirosis has provided clues about how an environmental organism might evolve into an important human pathogen. Title: Sequence and analysis of rice chromosome 4 Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y and Han B <61 more author(s)> Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (- 61) Ref: Nature, 420:316, 2002 : PubMed ESTHER: Feng_2002_Nature_420_316 PubMedSearch: Feng 2002 Nature 420 316 PubMedID: 12447439 Gene_locus related to this paper: orysa-Q7XTC5, orysa-Q7F959, orysa-q7f9i3, orysa-q7x7y5, orysa-q7xkj9, orysa-q7xr62, orysa-q7xr63, orysa-q7xr64, orysa-q7xsg1, orysa-q7xsq2, orysa-Q7XTM8, orysa-q7xts6, orysa-q7xue7, orysa-q7xv53, orysa-Q7XVB5, orysa-Q7XVG5, orysj-q0jaf0, orysj-q7f8x1 Abstract Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis. Title: A quantitative histochemistry technique for measuring regional distribution of acetylcholinesterase in the brain using digital scanning densitometry Ma T, Cai Z, Wellman SE, Ho IK Ref: Analytical Biochemistry, 296:18, 2001 : PubMed ESTHER: Ma_2001_Anal.Biochem_296_18 PubMedSearch: Ma 2001 Anal.Biochem 296 18 PubMedID: 11520028 Abstract Studies of brain acetylcholinesterase (AChE) are traditionally based on biochemical assays, immunoreactivity, and histochemistry. Conventional histochemistry yields rich morphological data from tissue sections but yields quantitative results only with great difficulty. Several histochemical methods developed in recent years, including microdensitometry, microphotometry, and video-based histochemistry, are effective in quantitative and detailed study of AChE in tissue sections. However, they are usually time-consuming. As we report here, we adapted digital scanning densitometry to quantitate AChE histochemical staining in brain sections. The AChE and butyrylcholinesterase (BuChE), as measured by the method, were heterogeneously distributed throughout the brain, results that are consistent with those obtained by biochemical methods. The staining intensity is dependent on section thickness, substrate concentration, and reaction time. The cholinesterase inhibitor methyl paraoxon significantly decreased AChE staining intensity. Furthermore, data acquired from densitometry are similar to those obtained by video-based microscopy or by spectrophotometry. The advantage of the densitometric measurements compared to other quantitative histochemical methods is that it is very rapid while collecting data that are equivalent in quality. Because the digital scanning densitometers provide high quality and sensitive imaging, wide dynamic ranges, and convenient image analysis software, they are very useful tools in quantitative histochemistry. | |||||||
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