Author Report for: Tu HNo contact information in database for Tu H
Zuo L, Cao L, Ding C, Tu H, Wei C, Yuan L, Wang H, Zhang B Ref: BMC Surg, 22:183, 2022 : PubMed ESTHER: Zuo_2022_BMC.Surg_22_183 PubMedSearch: Zuo 2022 BMC.Surg 22 183 PubMedID: 35568851 Abstract BACKGROUND: Previous studies reported that transnasal ileus tube was a new and useful method for rapid relief of small intestinal obstruction. However, no study reported the impacts of the transnasal ileus tube for Crohn's disease combined with intestinal obstruction. We aimed to describe the strategy to the small intestine obstruction caused by Crohn's disease on the basis of transnasal ileus tube insertion. METHODS: From November 2019 to November 2021, the data of 6 hospitalized patients with CD, diagnosed and conservatively treated in The Second Hospital of Nanjing, were not relived and retrospectively collected. After the insertion of transnasal ileus tube, demographic information, clinical features and treatment data were extracted from medical records. RESULTS: Six Crohn's disease patients with intestinal obstruction were included. Half of them were male. The patients aged from 29 to 70 years. Five patients had chronic intestinal obstruction more than one year. Three patients had intestinal surgery history. One patient had colonic abdominal fistula and anastomotic fistula, when she took intermittent usage of sulfsalazine and steroid. On admission, all the patients had abdominal pain, distention and mass. Five patients had anemia, low albumin and cholinesterase. All CDAI scores were more than 400. Compared to 19 patients with incomplete intestinal obstruction improved by nasogastric decompression tube, 6 patients with intestinal obstruction catheter had significant difference in time for relieving abdominal pain and distension (p = 0.003), time for alleviating abnormal mass (p >= 0.01), drainage volume (p = 0.004), and preoperative CDAI score (p = 0.001). Compared with X-ray image before insertion, complete remission of obstruction of 5 patients were observed in intestinal cavity after insertion. After 1-2 months nutrition, all the patients had small intestine resection and ileostomy, half of them underwent colectomy and fistula repair, and 4 patients were performed enterolysis at the same time, the residual small intestine length ranging from 250 to 400 cm. 1 patient had permanent ileostomy;1 patient had abdominal infection after operation. The typical manifestations of acute and chronic inflammation, transmural inflammation, pseudopolyps and serous fiber hyperplasia could be seen in pathological findings of patients 1 to 5. All the patients continued enteral nutrition after surgery. Four patients were treated with infliximab or vedolizumab. CONCLUSION: The current intestinal obstruction catheter which is used to treat patients with Crohn's combined obstruction can afford quick clinical remission, longer nutrition time, and suitable preoperative CDAI score for operation, which is worthy of wildly being used. Title: The Ig-like domain of Punctin/MADD-4 is the primary determinant for interaction with the ectodomain of neuroligin NLG-1 Platsaki S, Zhou X, Pinan-Lucarre B, Delauzun V, Tu H, Mansuelle P, Fourquet P, Bourne Y, Bessereau JL, Marchot P Ref: Journal of Biological Chemistry, 295:16267, 2020 : PubMed ESTHER: Platsaki_2020_J.Biol.Chem_295_16267 PubMedSearch: Platsaki 2020 J.Biol.Chem 295 16267 PubMedID: 32928959 Abstract Punctin/MADD-4, a member of the ADAMTSL extracellular matrix protein family, was identified as an anterograde synaptic organizer in the nematode Caenorhabditis elegans. At GABAergic neuromuscular junctions, the short isoform MADD-4B binds the ectodomain of neuroligin NLG-1, itself a postsynaptic organizer of inhibitory synapses. To identify the molecular bases of their partnership, we generated recombinant forms of the two proteins and carried out a comprehensive biochemical and biophysical study of their interaction, complemented by an in vivo localization study. We show that spontaneous proteolysis of MADD-4B first generates a shorter N-MADD-4B form, which comprises four thrombospondin (TSP) domains and one Ig-like domain and binds NLG-1. A second processing event eliminates the C-terminal Ig-like domain along with the ability of N-MADD-4B to bind NLG-1. These data identify the Ig-like domain as the primary determinant for N-MADD-4B interaction with NLG-1 in vitro We further demonstrate in vivo that this Ig-like domain is essential, albeit not sufficient per se, for efficient recruitment of GABA(A) receptors at GABAergic synapses in C. elegans The interaction of N-MADD-4B with NLG-1 is also disrupted by heparin, used as a surrogate for the extracellular matrix component, heparan sulfate. High-affinity binding of heparin/heparan sulfate to the Ig-like domain may proceed from surface charge complementarity, as suggested by homology three-dimensional modeling. These data point to N-MADD-4B processing and cell-surface proteoglycan binding as two possible mechanisms to regulate the interaction between MADD-4B and NLG-1 at GABAergic synapses. Title: Collagen XIII secures pre- and postsynaptic integrity of the neuromuscular synapse Haronen H, Zainul Z, Tu H, Naumenko N, Sormunen R, Miinalainen I, Shakirzyanova A, Oikarainen T, Abdullin A and Pihlajaniemi T <7 more author(s)> Haronen H, Zainul Z, Tu H, Naumenko N, Sormunen R, Miinalainen I, Shakirzyanova A, Oikarainen T, Abdullin A, Martin P, Santoleri S, Koistinaho J, Silman I, Giniatullin R, Fox MA, Heikkinen A, Pihlajaniemi T (- 7) Ref: Hum Mol Genet, 26:2076, 2017 : PubMed ESTHER: Haronen_2017_Hum.Mol.Genet_26_2076 PubMedSearch: Haronen 2017 Hum.Mol.Genet 26 2076 PubMedID: 28369367 Abstract Both transmembrane and extracellular cues, one of which is collagen XIII, regulate the formation and function of the neuromuscular synapse, and their absence results in myasthenia. We show that the phenotypical changes in collagen XIII knock-out mice are milder than symptoms in human patients, but the Col13a1-/- mice recapitulate major muscle findings of congenital myasthenic syndrome type 19 and serve as a disease model. In the lack of collagen XIII neuromuscular synapses do not reach full size, alignment, complexity and function resulting in reduced muscle strength. Collagen XIII is particularly important for the preterminal integrity, and when absent, destabilization of the motor nerves results in muscle regeneration and in atrophy especially in the case of slow muscle fibers. Collagen XIII was found to affect synaptic integrity through binding the ColQ tail of acetylcholine esterase. Although collagen XIII is a muscle-bound transmembrane molecule, it also undergoes ectodomain shedding to become a synaptic basal lamina component. We investigated the two forms' roles by novel Col13a1tm/tm mice in which ectodomain shedding is impaired. While postsynaptic maturation, terminal branching and neurotransmission was exaggerated in the Col13a1tm/tm mice, the transmembrane form's presence sufficed to prevent defects in transsynaptic adhesion, Schwann cell invagination/retraction, vesicle accumulation and acetylcholine receptor clustering and acetylcholinesterase dispersion seen in the Col13a1-/- mice, pointing to the transmembrane form as the major conductor of collagen XIII effects. Altogether, collagen XIII secures postsynaptic, synaptic and presynaptic integrity, and it is required for gaining and maintaining normal size, complexity and functional capacity of the neuromuscular synapse. Title: Tumor cell migration is inhibited by a novel therapeutic strategy antagonizing the alpha-7 receptor Pepper C, Tu H, Morrill P, Garcia-Rates S, Fegan C, Greenfield SA Ref: Oncotarget, 8:11414, 2017 : PubMed ESTHER: Pepper_2017_Oncotarget_8_11414 PubMedSearch: Pepper 2017 Oncotarget 8 11414 PubMedID: 28077796 Abstract A 14mer peptide (T14) derived from the C-terminus of acetylcholinesterase (AChE) selectively activates metastatic breast cancer cells via the alpha-7 nicotinic receptor (alpha7 nAChR). This naturally occurring peptide is also present in brain, is elevated in Alzheimer's disease, and is antagonised by a cyclized variant (NBP-14). Here we investigated the effects of NBP-14 in six different cancer cell lines, primary leukemia B-cells and normal B-cells. All cells tested expressed alpha7 nAChR, intracellular and extracellular T14. However, NBP-14 showed low toxicity and weak anti-proliferative effects in the majority of the cell lines and was even less toxic in normal B-cells when compared to primary chronic lymphocytic leukemia cells (P < 0.001). Given the potential role of T14 peptide in metastasis, we next investigated the effects of NBP-14 on tumor cell migration, where it caused a dose-dependent reduction. The extent of NBP-14 inhibition positively correlated with the migration of the cells (r2 = 0.45; P = 0.06). Furthermore, NBP-14 preferentially inhibited the migration of primary leukemia cells when compared with normal B-cells (P = 0.0002); when the normal B-cell data was excluded, this correlation was strengthened (r2 = 0.80; P = 0.006). Importantly, the constitutive alpha7 nAChR expression positively correlated with intracellular T14 levels (r2 = 0.91; P = 0.0003) and inversely correlated with extracellular T14 levels in the cell culture supernatants (r2 = -0.79; P = 0.034). However, in the presence of NBP-14, alpha7 nAChR expression was reduced (P = 0.04) and the most migratory cells showed the largest reduction in expression. In conclusion, NBP-14-mediated antagonism of the alpha7 nAChR offers a novel therapeutic strategy with the potential to inhibit tumor cell migration. Title: (I) Pharmacological profiling of a novel modulator of the alpha7 nicotinic receptor: Blockade of a toxic acetylcholinesterase-derived peptide increased in Alzheimer brains Garcia-Rates S, Morrill P, Tu H, Pottiez G, Badin AS, Tormo-Garcia C, Heffner C, Coen CW, Greenfield SA Ref: Neuropharmacology, 105:487, 2016 : PubMed ESTHER: Garcia-Rates_2016_Neuropharmacol_105_487 PubMedSearch: Garcia-Rates 2016 Neuropharmacol 105 487 PubMedID: 26867503 Abstract The primary cause of Alzheimer's disease is unlikely to be the much studied markers amyloid beta or tau. Their widespread distribution throughout the brain does not account for the specific identity and deep subcortical location of the primarily vulnerable neurons. Moreover an unusual and intriguing feature of these neurons is that, despite their diverse transmitters, they all contain acetylcholinesterase. Here we show for the first time that (1) a peptide derived from acetylcholinesterase, with independent trophic functions that turn toxic in maturity, is significantly raised in the Alzheimer midbrain and cerebrospinal fluid; (2) a synthetic version of this peptide enhances calcium influx and eventual production of amyloid beta and tau phosphorylation via an allosteric site on the alpha7 nicotinic receptor; (3) a synthetic cyclic version of this peptide is neuroprotective against the toxicity not only of its linear counterpart but also of amyloid beta, thereby opening up the prospect of a novel therapeutic approach. Title: C. elegans Punctin Clusters GABA Receptors via Neuroligin Binding and UNC-40/DCC Recruitment Tu H, Pinan-Lucarre B, Ji T, Jospin M, Bessereau JL Ref: Neuron, 86:1407, 2015 : PubMed ESTHER: Tu_2015_Neuron_86_1407 PubMedSearch: Tu 2015 Neuron 86 1407 PubMedID: 26028575 Gene_locus related to this paper: caeel-NLGN1 Abstract Positioning type A GABA receptors (GABAARs) in front of GABA release sites sets the strength of inhibitory synapses. The evolutionarily conserved Ce-Punctin/MADD-4 is an anterograde synaptic organizer that specifies GABAergic versus cholinergic identity of postsynaptic domains at the C. elegans neuromuscular junctions (NMJs). Here we show that the Ce-Punctin secreted by GABAergic motor neurons controls the clustering of GABAARs through the synaptic adhesion molecule neuroligin (NLG-1) and the netrin receptor UNC-40/DCC. The short isoform of Ce-Punctin binds and clusters NLG-1 postsynaptically at GABAergic NMJs. NLG-1 disruption causes a strong reduction of GABAAR content at GABAergic synapses. Ce-Punctin also binds and localizes UNC-40 receptors in the postsynaptic membrane of NMJs, which promotes the recruitment of GABAARs by NLG-1. Since the mammalian orthologs of these genes are expressed in the central nervous system and their mutations are implicated in neuropsychiatric diseases, this molecular pathway might have been evolutionarily conserved. Title: C. elegans Punctin specifies cholinergic versus GABAergic identity of postsynaptic domains Pinan-Lucarre B, Tu H, Pierron M, Cruceyra PI, Zhan H, Stigloher C, Richmond JE, Bessereau JL Ref: Nature, 511:466, 2014 : PubMed ESTHER: Pinan-Lucarre_2014_Nature_511_466 PubMedSearch: Pinan-Lucarre 2014 Nature 511 466 PubMedID: 24896188 Gene_locus related to this paper: caeel-NLGN1 Abstract Because most neurons receive thousands of synaptic inputs, the neuronal membrane is a mosaic of specialized microdomains where neurotransmitter receptors cluster in register with the corresponding presynaptic neurotransmitter release sites. In many cases the coordinated differentiation of presynaptic and postsynaptic domains implicates trans-synaptic interactions between membrane-associated proteins such as neurexins and neuroligins. The Caenorhabditis elegans neuromuscular junction (NMJ) provides a genetically tractable system in which to analyse the segregation of neurotransmitter receptors, because muscle cells receive excitatory innervation from cholinergic neurons and inhibitory innervation from GABAergic neurons. Here we show that Ce-Punctin/madd-4 (ref. 5), the C. elegans orthologue of mammalian punctin-1 and punctin-2, encodes neurally secreted isoforms that specify the excitatory or inhibitory identity of postsynaptic NMJ domains. These proteins belong to the ADAMTS (a disintegrin and metalloprotease with thrombospondin repeats)-like family, a class of extracellular matrix proteins related to the ADAM proteases but devoid of proteolytic activity. Ce-Punctin deletion causes the redistribution of synaptic acetylcholine and GABAA (gamma-aminobutyric acid type A) receptors into extrasynaptic clusters, whereas neuronal presynaptic boutons remain unaltered. Alternative promoters generate different Ce-Punctin isoforms with distinct functions. A short isoform is expressed by cholinergic and GABAergic motoneurons and localizes to excitatory and inhibitory NMJs, whereas long isoforms are expressed exclusively by cholinergic motoneurons and are confined to cholinergic NMJs. The differential expression of these isoforms controls the congruence between presynaptic and postsynaptic domains: specific disruption of the short isoform relocalizes GABAA receptors from GABAergic to cholinergic synapses, whereas expression of a long isoform in GABAergic neurons recruits acetylcholine receptors to GABAergic NMJs. These results identify Ce-Punctin as a previously unknown synaptic organizer and show that presynaptic and postsynaptic domain identities can be genetically uncoupled in vivo. Because human punctin-2 was identified as a candidate gene for schizophrenia, ADAMTS-like proteins may also control synapse organization in the mammalian central nervous system. Title: An Inhibitory Antibody against Dipeptidyl Peptidase IV Improves Glucose Tolerance in Vivo Tang J, Majeti J, Sudom A, Xiong Y, Lu M, Liu Q, Higbee J, Zhang Y, Wang Y and Wang Z <12 more author(s)> Tang J, Majeti J, Sudom A, Xiong Y, Lu M, Liu Q, Higbee J, Zhang Y, Wang Y, Wang W, Cao P, Xia Z, Johnstone S, Min X, Yang X, Shao H, Yu T, Sharkov N, Walker N, Tu H, Shen W, Wang Z (- 12) Ref: Journal of Biological Chemistry, 288:1307, 2013 : PubMed ESTHER: Tang_2013_J.Biol.Chem_288_1307 PubMedSearch: Tang 2013 J.Biol.Chem 288 1307 PubMedID: 23184939 Gene_locus related to this paper: ratno-dpp4 Abstract Dipeptidyl peptidase IV (DPP-IV) degrades the incretin hormone glucagon-like peptide 1 (GLP-1). Small molecule DPP-IV inhibitors have been used as treatments for type 2 diabetes to improve glucose tolerance. However, each of the marketed small molecule drugs has its own limitation in terms of efficacy and side effects. To search for an alternative strategy of inhibiting DPP-IV activity, we generated a panel of tight binding inhibitory mouse monoclonal antibodies (mAbs) against rat DPP-IV. When tested in vitro, these mAbs partially inhibited the GLP-1 cleavage activity of purified enzyme and rat plasma. To understand the partial inhibition, we solved the co-crystal structure of one of the mAb Fabs (Ab1) in complex with rat DPP-IV. Although Ab1 does not bind at the active site, it partially blocks the side opening, which prevents the large substrates such as GLP-1 from accessing the active site, but not small molecules such as sitagliptin. When Ab1 was tested in vivo, it reduced plasma glucose and increased plasma GLP-1 concentration during an oral glucose tolerance test in rats. Together, we demonstrated the feasibility of using mAbs to inhibit DPP-IV activity and to improve glucose tolerance in a diabetic rat model. Title: Changes of calcium channel mRNA, protein and current in NG108-15 cells after cell differentiation Liu J, Tu H, Zhang D, Li YL Ref: Biochemical & Biophysical Research Communications, 423:55, 2012 : PubMed ESTHER: Liu_2012_Biochem.Biophys.Res.Commun_423_55 PubMedSearch: Liu 2012 Biochem.Biophys.Res.Commun 423 55 PubMedID: 22627136 Abstract Based on the characteristics of differentiated NG108-15 cells (cell membrane excitability, acetylcholine release, and activities of choline acetyltransferase and acetylcholinesterase), NG108-15 cells are extensively used to explore neuronal functions as a cholinergic cell line. In the present study, differentiation-induced alterations of voltage-gated Ca(2+) channel mRNA, protein, and current were investigated in the NG108-15 cells. Real-time PCR, Western blot, and whole-cell patch-clamp data showed that differentiation caused mRNA, protein, and ion current changes of all Ca(2+) channel subunits. However, the changes of mRNA, protein, and ion current are inconsistent in all Ca(2+) channel subunits. Especially, P/Q- and R-type Ca(2+) channel proteins do not form the functional P/Q- and R-type Ca(2+) channels even if the mRNA and protein of P/Q- and R-type Ca(2+) channels can be detected in NG108-15 cells. These results indicate that differentiation can modulate gene transcription, protein translation, and post-translation of the Ca(2+) channels to induce the alteration of the Ca(2+) ion currents in NG108-15 cells. From these data, we understand that combining real-time PCR, Western blot, and patch-clamp techniques can comprehensively unveil the modulation of the Ca(2+) channels. Title: The ecoresponsive genome of Daphnia pulex Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ and Boore JL <59 more author(s)> Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Caceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Frohlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kultz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL (- 59) Ref: Science, 331:555, 2011 : PubMed ESTHER: Colbourne_2011_Science_331_555 PubMedSearch: Colbourne 2011 Science 331 555 PubMedID: 21292972 Gene_locus related to this paper: dappu-e9fut0, dappu-e9fut9, dappu-e9fvw6, dappu-e9fxt4, dappu-e9fyr6, dappu-e9fzg6, dappu-e9g1e2, dappu-e9g1e6, dappu-e9g1e7, dappu-e9g1e8, dappu-e9g1v3, dappu-e9g1z2, dappu-e9gb99, dappu-e9gba0, dappu-e9gcb4, dappu-e9gdv5, dappu-e9gdv7, dappu-e9gi24, dappu-e9gj77, dappu-e9gja7, dappu-e9gmp5, dappu-e9gmr0, dappu-e9gn32, dappu-e9gp76, dappu-e9gp82, dappu-e9gp98, dappu-e9gp99, dappu-e9gvl2, dappu-e9gzn7, dappu-e9h1p4, dappu-e9h2c8, dappu-e9h2c9, dappu-e9h6x9, dappu-e9h6y4, dappu-e9h7w9, dappu-e9h8r4, dappu-e9hd06, dappu-e9hh56, dappu-e9hh57, dappu-e9hh59, dappu-e9hmp4, dappu-e9hp64, dappu-e9hp65, dappu-e9hpy8, dappu-e9htg8, dapul-ACHE1, dapul-ACHE2, dappu-e9gnj1, dappu-e9gu36, dappu-e9hpc4, dappu-e9gb07, dappu-e9glp6, dappu-e9glp5, dappu-e9gjv2, dappu-e9h0c7, dappu-e9g4g2, dappu-e9gw69, dappu-e9h3h9, dappu-e9g545, dappu-e9gw71, dappu-e9gw68, dappu-e9h3e7, dappu-e9gfg9, dappu-e9fvy6, dappu-e9hgt2 Abstract We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges. Title: Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis Goodwin SB, M'Barek S B, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J and Kema GH <47 more author(s)> Goodwin SB, M'Barek S B, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J, Aerts A, Antoniw J, Bailey A, Bluhm B, Bowler J, Bristow J, van der Burgt A, Canto-Canche B, Churchill AC, Conde-Ferraez L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De Wit P, Donzelli B, van de Geest HC, van Ham RC, Hammond-Kosack KE, Henrissat B, Kilian A, Kobayashi AK, Koopmann E, Kourmpetis Y, Kuzniar A, Lindquist E, Lombard V, Maliepaard C, Martins N, Mehrabi R, Nap JP, Ponomarenko A, Rudd JJ, Salamov A, Schmutz J, Schouten HJ, Shapiro H, Stergiopoulos I, Torriani SF, Tu H, de Vries RP, Waalwijk C, Ware SB, Wiebenga A, Zwiers LH, Oliver RP, Grigoriev IV, Kema GH (- 47) Ref: PLoS Genet, 7:e1002070, 2011 : PubMed ESTHER: Goodwin_2011_PLoS.Genet_7_E1002070 PubMedSearch: Goodwin 2011 PLoS.Genet 7 E1002070 PubMedID: 21695235 Gene_locus related to this paper: zymti-f9wzw8, zymti-f9x2y6, zymti-f9x423, zymti-f9x813, zymti-f9xa54, zymti-f9xb42, zymti-f9xbu5, zymti-f9xcr9, zymti-f9xdr7, zymti-f9xer1, zymti-f9xez8, zymti-f9xfz9, zymti-f9xh29, zymti-f9xhe7, zymti-f9xhr4, zymti-f9xk09, zymti-f9xns5, zymti-f9xiu1, zymti-f9xng3, zymti-f9x4f2, zymti-f9x4s7, zymti-f9xdm8, zymti-f9wwy9, zymti-f9xkf2, zymti-f9xlt3, zymti-f9x0i3, zymti-f9wwa6, zymti-f9wyk7, zymti-f9x3z1, zymti-f9xf16, zymtr-a0a1x7rhi5, zymti-f9xfj3, zymti-pks1 Abstract The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors. Title: Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E and Grigoriev IV <31 more author(s)> Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E, Barry K, Lindquist E, Shapiro H, Bruce D, Schmutz J, Salamov A, Fey P, Gaudet P, Anjard C, Babu MM, Basu S, Bushmanova Y, van der Wel H, Katoh-Kurasawa M, Dinh C, Coutinho PM, Saito T, Elias M, Schaap P, Kay RR, Henrissat B, Eichinger L, Rivero F, Putnam NH, West CM, Loomis WF, Chisholm RL, Shaulsky G, Strassmann JE, Queller DC, Kuspa A, Grigoriev IV (- 31) Ref: Genome Biol, 12:R20, 2011 : PubMed ESTHER: Sucgang_2011_Genome.Biol_12_R20.1 PubMedSearch: Sucgang 2011 Genome.Biol 12 R20.1 PubMedID: 21356102 Gene_locus related to this paper: dicpu-f0z7q0, dicpu-f0z822, dicpu-f0zfi0, dicpu-f0zjs1, dicpu-f0zks4, dicpu-f0zmm3, dicpu-f0zmm8, dicpu-f0zmm9, dicpu-f0zni7, dicpu-f0znl3, dicpu-f0zq90, dicpu-f0zvn5, dicpu-f0zxa4, dicpu-f0zyf9, dicpu-f1a3n5, dicpu-f1a5b4, dicpu-f1a269, dicpu-f1a615, dicpu-f0ztw9, dicpu-f0zri3 Abstract BACKGROUND: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. Title: The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J and Dawson SC <14 more author(s)> Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, Salamov A, Lindquist E, Shapiro H, Lucas S, Grigoriev IV, Cande WZ, Fulton C, Rokhsar DS, Dawson SC (- 14) Ref: Cell, 140:631, 2010 : PubMed ESTHER: Fritz-Laylin_2010_Cell_140_631 PubMedSearch: Fritz-Laylin 2010 Cell 140 631 PubMedID: 20211133 Gene_locus related to this paper: naegr-d2ux86, naegr-d2uyl7, naegr-d2uyn1, naegr-d2uzk6, naegr-d2uzp4, naegr-d2v1m1, naegr-d2v3p5, naegr-d2v5p1, naegr-d2v6f6, naegr-d2v6y9, naegr-d2v8x8, naegr-d2v186, naegr-d2v339, naegr-d2v556, naegr-d2vbq7, naegr-d2vdq6, naegr-d2ve51, naegr-d2vga2, naegr-d2vgm9, naegr-d2vh14, naegr-d2vha2, naegr-d2vj80, naegr-d2vjj7, naegr-d2vl41, naegr-d2vmj5, naegr-d2vms7, naegr-d2vqi5, naegr-d2vr44, naegr-d2vrq2, naegr-d2vs01, naegr-d2vs58, naegr-d2vts5, naegr-d2vu69, naegr-d2vvg8, naegr-d2vxp2, naegr-d2vyl1, naegr-d2vzy5, naegr-d2w0l5, naegr-d2w0v9, naegr-d2w3g8, naegr-d2w3v7, naegr-d2w3v8, naegr-d2vct1 Abstract Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules. Title: Acetylcholinesterase biosensor based on gold nanoparticles and cysteamine self assembled monolayer for determination of monocrotophos Du D, Chen W, Cai J, Zhang J, Tu H, Zhang A Ref: J Nanosci Nanotechnol, 9:2368, 2009 : PubMed ESTHER: Du_2009_J.Nanosci.Nanotechnol_9_2368 PubMedSearch: Du 2009 J.Nanosci.Nanotechnol 9 2368 PubMedID: 19437977 Abstract In this paper, a simple method for immobilization of acetylcholinesterase (AChE) on cysteamine assembled glassy carbon electrode coupled with gold nanoparticles (GNPs) was proposed and thus a sensitive, fast and stable amperometric biosensor for quantitative determination of monocrotophos was developed. The fabrication procedure was characterized by cyclic voltammetry, electrochemical impedance spectroscopy and contact angles. The presence of GNPs not only led to an increased effective surface to provide a sufficient amount of sites for binding enzyme, but also promoted electron transfer reactions and catalyzed the electro-oxidation of thiocholine, thus amplifying the detection sensitivity. Due to the notable decrease in voltammetric signal of the immobilized AChE, a simple method for determination of monocrotophos was established. The inhibition of monocrotophos was proportional to its concentration in two ranges, from 0.5 to 10 ng mL(-1) and from 10 to 600 ng mL(-1), with a detection limit lower than 0.3 ng mL(-1). The constructed biosensor processing prominent characteristics and performance such as good precision and reproducibility, acceptable stability and accuracy, fast response and low detection limit has potential application in detection of toxic compounds. Title: A gold nanoparticle labeling strategy for the sensitive kinetic assay of the carbamate-acetylcholinesterase interaction by surface plasmon resonance Huang X, Tu H, Zhu D, Du D, Zhang A Ref: Talanta, 78:1036, 2009 : PubMed ESTHER: Huang_2009_Talanta_78_1036 PubMedSearch: Huang 2009 Talanta 78 1036 PubMedID: 19269469 Abstract The article presents a novel strategy for a sensitive investigation of the interaction between acetylcholinesterase (AChE) and its small molecular carbamate inhibitors. Two carbamate inhibitors with different ether linkages and the terminal lipoate were synthesized and labeled with gold nanoparticles (AuNPs). With the signal amplification of AuNPs, the specific interactions between the AuNPs labeled carbamate inhibitors (ALC1 and ALC2) and the immobilized AChE on sensor chip surface were readily examined. The detection sensitivities of ALC1 and ALC2 were 176 and 121 m degrees /nM, respectively, with the detection limits of 7.0 and 12pM at a signal-to-noise ratio of 3. The association/dissociation constants for the binding interaction between carbamate inhibitors and AChE were reported for the first time. The affinity constants were estimated to be 3.13 x 10(6) and 6.39 x 10(5)M(-1) for ALC1 and ALC2 respectively. This AuNPs labeling strategy is versatile and may be applicable for the direct or competitive SPR kinetic assay of the interaction between small molecule inhibitors and their target proteins with a high sensitivity. Title: Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT and Cullen D <43 more author(s)> Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, Lavin JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kues U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R, Cullen D (- 43) Ref: Proc Natl Acad Sci U S A, 106:1954, 2009 : PubMed ESTHER: Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954 PubMedSearch: Martinez 2009 Proc.Natl.Acad.Sci.U.S.A 106 1954 PubMedID: 19193860 Gene_locus related to this paper: pospm-b8p1f3, pospm-b8p2q7, pospm-b8p4n0, pospm-b8p4n9, pospm-b8p5g9, pospm-b8p5r9, pospm-b8p6h2, pospm-b8p7b1, pospm-b8p7c4, pospm-b8p8w7, pospm-b8p9j1, pospm-b8p164, pospm-b8p280, pospm-b8p423.1, pospm-b8p423.2, pospm-b8p858, pospm-b8pam2, pospm-b8pam5, pospm-b8pb68, pospm-b8pbm3, pospm-b8pc54, pospm-b8pc56, pospm-b8pce4, pospm-b8pd91, pospm-b8pdk6, pospm-b8ph32, pospm-b8ph43, pospm-b8phc9, pospm-b8php7, pospm-b8phy5, pospm-b8pjg8, pospm-b8pji9, pospm-b8plr5, pospm-b8pmk3, pospm-b8pfg0, pospm-b8pg35, pospm-b8pa20.1, pospm-b8pa20.2, pospm-b8p4g8, pospm-b8phn6 Abstract Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative beta-1-4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H(2)O(2). These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H(2)O(2) react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost. Title: Immobilization of acetylcholinesterase based on the controllable adsorption of carbon nanotubes onto an alkanethiol monolayer for carbaryl sensing Du D, Wang M, Cai J, Tao Y, Tu H, Zhang A Ref: Analyst, 133:1790, 2008 : PubMed ESTHER: Du_2008_Analyst_133_1790 PubMedSearch: Du 2008 Analyst 133 1790 PubMedID: 19082085 Abstract A simple method to immobilize acetylcholinesterase (AChE) on the controllable adsorption of multiwalled carbon nanotubes (MWCNTs) onto an alkanethiol self-assembled monolayer (C(6)H(13)SH SAM) modified Au electrode was proposed. The surface coverage of the MWCNTs was readily controlled by adjusting the immersion time for the adsorption of the MWCNTs. Atomic force microscopy (AFM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used to monitor these controllable fabrication processes. The MWCNTs adsorbed onto the SAM surface substantially restores the heterogeneous electron transfer between the bare Au electrode and the redox system in the solution phase that is almost totally blocked by the SAM of C(6)H(13)SH, and as a result, the prepared MWCNT-SAM-modified electrode possesses good electrode reactivity without a remarkable barrier to heterogeneous electron transfer. Due to the inherent conductive properties of MWCNTs, the immobilized AChE exhibited high affinity to its substrate and produced a detectable and fast response. Thus, a sensitive, efficient and stable amperometric sensor for quantitative determination of carbaryl was developed. The inhibition of carbaryl was proportional to its concentration ranging from 0.001 to 1 microg mL(-1) and 2 to 15 microg mL(-1), with a detection limit of 0.6 ng mL(-1). The determination of carbaryl in garlic samples showed acceptable accuracy, which provided a new promising tool for analysis of enzyme inhibitors. Title: The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA and Boore JL <60 more author(s)> Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin IT, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (- 60) Ref: Science, 319:64, 2008 : PubMed ESTHER: Rensing_2008_Science_319_64 PubMedSearch: Rensing 2008 Science 319 64 PubMedID: 18079367 Gene_locus related to this paper: phypa-a9rbi6, phypa-a9rfh1, phypa-a9rg19, phypa-a9rgt9, phypa-a9rhz9, phypa-a9rkj1, phypa-a9rns2, phypa-a9rp52, phypa-a9rq03, phypa-a9ry17, phypa-a9ry72, phypa-a9s5n8, phypa-a9s6w1, phypa-a9s8c7, phypa-a9s299, phypa-a9san7, phypa-a9sc75, phypa-a9se75, phypa-a9sg07, phypa-a9skf7, phypa-a9skr1, phypa-a9skw1, phypa-a9sl58, phypa-a9slp7, phypa-a9smq5, phypa-a9sp13, phypa-a9ssb0, phypa-a9sse1, phypa-a9ssf6, phypa-a9st85, phypa-a9sx74, phypa-a9sy58, phypa-a9syy4, phypa-a9t0n4, phypa-a9t0p4, phypa-a9t1j2, phypa-a9t5h1, phypa-a9t7g6, phypa-a9t8u8, phypa-a9t9c9, phypa-a9t9d9, phypa-a0a7i4d2t7, phypa-a9t498, phypa-a9tbu4, phypa-a9tc36, phypa-a9tds0, phypa-a9te64, phypa-a9tfw2, phypa-a9tin6, phypa-a9tja4, phypa-a9tmp3, phypa-a9tmr4, phypa-a9tql4, phypa-a9tr83, phypa-a9tsl1, phypa-a9tsv6, phypa-a9tu05, phypa-a9tw81, phypa-a9tyr8, phypa-a9u0c9, phypa-a9u0k3, phypa-a9u0p4, phypa-a9u2u7, phypa-a9u3s0, phypa-a9tfm7, phypa-a9tfp6, phypa-a9syg9, phypa-a9tzk2, phypa-a9tvg4, phypa-a9t1y4, phypa-a9tqt6, phypa-a9st18, phypa-a9tix9, phypa-a0a2k1kfe3, phypa-a9sqk3, phypa-a0a2k1ie71, phypa-a0a2k1kg29, phypa-a0a2k1iji3 Abstract We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics. | |||||||
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