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1.  BDNF profoundly and specifically increases KCNQ4 expression in neurons derived from embryonic stem cells 
Stem cell research  2012;10(1):29-35.
Neurons resembling the spiral ganglion neurons (SGNs) of the auditory nerve can be generated from embryonic stem cells through induced over-expression of the transcription factor Neurogenin-1 (Neurog1). While recapitulating this developmental pathway produces glutamatergic, bipolar neurons reminiscent of SGNs, these neurons are functionally immature, being characterized by a depolarized resting potential and limited excitability. We explored the effects of two neurotrophins known to be present in the inner ear, brain derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3), on the electrophysiology of neurons following Neurog1-induction. Our data reveal a significant reduction in resting membrane potential (RMP) following neurotrophin exposure, with BDNF producing a more robust effect than NT-3. This effect was accompanied by a profound and specific upregulation of the KCNQ4 subtype, where a 9-fold increase was observed with quantitative PCR. The other neuronally-expressed KCNQ subtypes (2, 3, and 5) exhibited upregulation which was 3-fold or less in magnitude. Quantitative immunohistochemistry confirmed the increase in KCNQ4 expression at the protein level. The present data show a novel link between BDNF and KCNQ4 expression, yielding insight into the restricted expression pattern of a channel known to play a special roles in setting the resting potential of auditory cells and in the etiology of progressive high frequency hearing loss.
doi:10.1016/j.scr.2012.08.005
PMCID: PMC3525722  PMID: 23089626
3.  Substrate Stereo-specificity in Tryptophan dioxygenase and Indoleamine 2,3- dioxygenase 
Proteins  2010;78(14):2961-2972.
The first and rate-limiting step of the kynurenine pathway, in which tryptophan (Trp) is converted to N-formylkynurenine is catalyzed by two heme-containing proteins, Indoleamine 2,3-dioxygenase (IDO) and Tryptophan 2,3-dioxygenase (TDO). In mammals, TDO is found exclusively in liver tissue, IDO is found ubiquitously in all tissues. IDO has become increasingly popular in pharmaceutical research as it was found to be involved in many physiological situations, including immune escape of cancer. More importantly, small-molecule inhibitors of IDO are currently utilized in cancer therapy. One of the main concerns for the design of human IDO (hIDO) inhibitors is that they should be selective enough to avoid inhibition of TDO.
In this work we have used a combination of classical molecular dynamics (MD) and hybrid quantum-classical (QM/MM) methodologies to establish the structural basis that determine the differences in a) the interactions of TDO and IDO with small ligands (CO/O2) and b) the substrate stereo-specificity in hIDO and TDO. Our results indicate that the differences in small ligand bound structures of IDO and TDO arise from slight differences in the structure of the bound substrate complex. The results also show that substrate stereo-specificity of TDO is achieved by the perfect fit of L-Trp, but not D-Trp, which exhibits weaker interactions with the protein matrix-. For hIDO, the presence of multiple stable binding conformations for L/D-Trp reveal the presence of a large and dynamic active site. Taken together, our data allow determination of key interactions useful for the future design of more potent hIDO-selective inhibitors.
doi:10.1002/prot.22819
PMCID: PMC2939288  PMID: 20715188
TDO; IDO; Molecular Dynamics; Structure; Affinity; oxygen; CO; dioxygenase; inhibitors
4.  Subnanomolar Detection Limit Application of Ion-Selective Electrodes with Three-Dimensionally Ordered Macroporous (3DOM) Carbon Solid Contacts 
Solid-contact ion-selective electrodes (SC-ISEs) can exhibit very low detection limits and, in contrast to conventional ISEs, do not require an optimization of the inner filling solution. This work shows that subnanomolar detection limits can also be achieved with SC-ISEs with three-dimensionally ordered macroporous (3DOM) carbon contacts, which have been shown recently to exhibit excellent long-term stabilities and good resistance to the interferences from oxygen and light. The detection limit of 3DOM carbon-contacted electrodes with plasticized poly(vinyl chloride) as membrane matrix can be improved with a high polymer content of the sensing membrane, a large ratio of ionophore and ionic sites, and conditioning with a low concentration of analyte ions. This permits detection limits as low as 1.6×10−7 M for K+ and 4.0×10−11 M for Ag+.
doi:10.1007/s10008-008-0579-2
PMCID: PMC2795580  PMID: 20046876
Solid-contact ion-selective electrode; Three-dimensionally ordered macroporous (3DOM) carbon; Detection limit; Subnanomolar; Silver; Potassium
5.  Developmental expression of BK channels in chick cochlear hair cells 
Background
Cochlear hair cells are high-frequency sensory receptors. At the onset of hearing, hair cells acquire fast, calcium-activated potassium (BK) currents, turning immature spiking cells into functional receptors. In non-mammalian vertebrates, the number and kinetics of BK channels are varied systematically along the frequency-axis of the cochlea giving rise to an intrinsic electrical tuning mechanism. The processes that control the appearance and heterogeneity of hair cell BK currents remain unclear.
Results
Quantitative PCR results showed a non-monotonic increase in BK α subunit expression throughout embryonic development of the chick auditory organ (i.e. basilar papilla). Expression peaked near embryonic day (E) 19 with six times the transcript level of E11 sensory epithelia. The steady increase in gene expression from E11 to E19 could not explain the sudden acquisition of currents at E18-19, implicating post-transcriptional mechanisms. Protein expression also preceded function but progressed in a sequence from diffuse cytoplasmic staining at early ages to punctate membrane-bound clusters at E18. Electrophysiology data confirmed a continued refinement of BK trafficking from E18 to E20, indicating a translocation of BK clusters from supranuclear to subnuclear domains over this critical developmental age.
Conclusions
Gene products encoding BK α subunits are detected up to 8 days before the acquisition of anti-BK clusters and functional BK currents. Therefore, post-transcriptional mechanisms seem to play a key role in the delayed emergence of calcium-sensitive currents. We suggest that regulation of translation and trafficking of functional α subunits, near voltage-gated calcium channels, leads to functional BK currents at the onset of hearing.
doi:10.1186/1471-213X-9-67
PMCID: PMC2803478  PMID: 20003519
6.  The genome of the simian and human malaria parasite Plasmodium knowlesi 
Nature  2008;455(7214):799-803.
Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the ‘kra’ monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia1,2. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated3, and it has a close phylogenetic relationship to Plasmodium vivax​4, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or ‘hypnozoite’ in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone5) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome4 and other sequenced Plasmodium genomes6-8. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs9, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.
doi:10.1038/nature07306
PMCID: PMC2656934  PMID: 18843368
8.  Relative high frequency of the c.255delA parkin gene mutation in Spanish patients with autosomal recessive parkinsonism 
Objectives: To search for the presence of parkin gene mutations in Spanish patients with Parkinson's disease (PD) and characterise the phenotype associated with these mutations.
Methods: Thirty seven PD patients with either early onset or autosomal recessive pattern of inheritance were selected for genetic study.
Results: Mutations were identified in seven index patients (19%). Homozygous mutations were detected in six patients and a heterozygous mutation in one. The age at onset was lower in patients with mutations than in patients without mutations. Dystonia at onset was present in two patients with parkin gene mutations. The disease began in two patients with postural tremor in the upper limbs mimicking essential tremor. Four patients exhibited a long term response to dopamine agonists. The c.255delA mutation was identified in four unrelated families. This is a frameshift mutation leading to protein truncation.
Conclusions: Parkin gene mutations are present in Spanish patients with early onset and/or an autosomal recessive parkinsonism. The c.255delA is the most frequent mutation found, suggesting a relative high prevalence in the Spanish population.
doi:10.1136/jnnp.73.5.582
PMCID: PMC1738117  PMID: 12397156
9.  Phenotypic and Transcriptional Characterization of the Meningococcal PhoPQ System, a Magnesium-Sensing Two-Component Regulatory System That Controls Genes Involved in Remodeling the Meningococcal Cell Surface†  
Journal of Bacteriology  2005;187(14):4967-4975.
We previously identified and characterized a two-component regulatory system in the meningococcus with homology to the phoP-phoQ system in salmonella and showed that allele replacement of the NMB0595 regulator gene led to loss of virulence, sensitivity to antimicrobial peptides, perturbed protein expression, and magnesium-sensitive growth. On the basis of these findings we proposed that the system should be designated the meningococcal PhoPQ system. Here we further characterized the NMB0595 mutant and demonstrated that it had increased membrane permeability and was unable to form colonies on solid media with low magnesium concentrations, features that are consistent with disruption of PhoPQ-mediated modifications to the lipooligosaccharide structure. We examined the transcriptional profiles of wild-type and NMB0595 mutant strains and found that magnesium-regulated changes in gene expression are completely abrogated in the mutant, indicating that, similar to the salmonella PhoPQ system, the meningococcal PhoPQ system is regulated by magnesium. Transcriptional profiling of the mutant indicated that, also similar to the salmonella PhoPQ system, the meningococcal system is involved in control of virulence and remodeling of the bacterial cell surface in response to the host environment. The results are consistent with the hypothesis that the PhoP homologue plays a role in the meningococcus similar to the role played by PhoP in salmonella. Elucidating the role that the PhoPQ system and PhoPQ-regulated genes play in the response of the meningococcus to the host environment may provide new insights into the pathogenic process.
doi:10.1128/JB.187.14.4967-4975.2005
PMCID: PMC1169531  PMID: 15995212
11.  Obsessive-compulsive symptoms in Parkinson's disease 
To systematically investigate obsessive-compulsive traits in Parkinson's disease, patients were administered the Maudsley obsessional-compulsive inventory (MOCI) and a modification of the Leyton obsessional inventory (LOI) to a sample of non-demented and non-depressed patients with Parkinson's disease. Patients with severe Parkinson's disease showed more obsessive traits than normal controls in MOCI and LOI total scores, and in the "checking", "doubting", and "cleaning" subscales of the MOCI. By contrast, patients with mild disease did not differ from controls. A significant correlation was found between severity and duration of illness and MOCI total score. These results support the involvement of basal ganglia in obsessive-compulsive symptomatology. As patients with mild Parkinson's disease did not differ from controls, obsessive-compulsive disorder does not seem to be directly related to the initial nigrostriatal dopaminergic deficiency which causes clinical Parkinson's disease symptomatology. The appearance of obsessive symptoms could be related to the subset of neurochemical changes taking place at the level of the basal ganglia circuitry as disease progresses.


doi:10.1136/jnnp.70.3.394
PMCID: PMC1737280  PMID: 11181867
12.  Intra-arterial chemotherapy in locally advanced or recurrent carcinomas of the penis and anal canal: an active treatment modality with curative potential 
British Journal of Cancer  2000;83(12):1637-1642.
The prognosis of locally advanced or recurrent carcinomas of the penis (PE) and of the anal canal (AC) after conventional treatment is dismal. We report 16 patients (eight with AC carcinomas and eight with PE cancers) treated by intra-arterial (IA) chemotherapy. Fifteen of them were treated for locally advanced or recurrent disease and one in an adjuvant setting. The chemotherapy was administered via a femoral IA catheter with its tip located above the aortic bifurcation, under the inferior mesenteric artery. It consisted of eight push injections, given over a 48-h period, of the following drug combination: cisplatin 8.5 mg m–2, 5-FU 275 mg m–2, methotrexate 27.5 mg m–2, mitomycin C 1.2 mg m–2, and bleomycin 4 mg m–2. Leucovorin was given po, 4 × 15 mg day–1, during the chemotherapy and for 3 days thereafter. A total of 52 cycles of treatment were administered. Of the 15 patients evaluable for response, six obtained a CR (three PE, three AC) and eight a PR. Among the complete responders, four are alive and disease-free 2–15 years after treatment. The other patients enjoyed an objective response lasting 3–25 months (median 7 months). Four patients developed grade III/IV haematological toxicity with three episodes of febrile neutropenia, one of them with a fatal outcome due to patient's failure to obtain medical attention at the onset of his fever, one a grade III mucositis of the glans, and four a grade III/IV cutaneous toxicity, the latter caused by the IA administration of bleomycin. In conclusion, IA chemotherapy is effective and potentially curative in locoregionally advanced or recurrent carcinomas of the penis and of the anus. Its contribution in the primary management of advanced penile or anal carcinoma should be prospectively investigated. © 2000 Cancer Research Campaign http://www.bjcancer.com
doi:10.1054/bjoc.2000.1525
PMCID: PMC2363463  PMID: 11104558
penile cancer; anal canal cancer; intra-arterial chemotherapy; intra-arterial bleomycin

Results 1-12 (12)