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1.  Acidomonas Methanolica-Associated Necrotizing Lymphadenitis in a Patient with Chronic Granulomatous Disease 
Journal of clinical immunology  2012;32(6):1193-1196.
Purpose
Adenitis for which no causative organism can be isolated is a common occurrence in patients with chronic granulomatous disease (CGD). Here we identify Acidomonas methanolica as a pathogen associated with adenitis in a patient with CGD.
Methods
The causative pathogen was obtained after prolonged incubation of an excised lymph node in thioglycolate broth. Identification was carried out by sequencing the 16s rRNA. Immunoblots were prepared utilizing protein extracts from the case patient’s A. methanolica isolate, an ATCC type strain of A. methanolica and G. bethesdensis.
Results
Fastidious gram-negative rods grew after prolonged incubation of an excised lymph node in thioglycolate broth. Sequencing of the 16s rRNA identified the organism as A. methanolica. Immunoblot confirmed the pathogen’s role in the patient’s adenitis by showing the patient’s specific immune response to the organism.
Conclusions
A. methanolica is the second member of the family, Acetobacteaceae to be associated with adenitis in patients with CGD.
doi:10.1007/s10875-012-9728-6
PMCID: PMC4103907  PMID: 22752310
Chronic granulomatous disease; Acidomonas methanolica
2.  PRECLINICAL STROKE RESEARCH: GAINS AND GAPS 
Stroke; a journal of cerebral circulation  2013;44(6 0 1):S114-S115.
doi:10.1161/STROKEAHA.113.002088
PMCID: PMC3723454  PMID: 23709703
3.  Signal transducer and activator of transcription 1 (STAT1) gain-of-function mutations and disseminated coccidioidomycosis and histoplasmosis 
Background
Impaired signaling in the IFN-γ/IL-12 pathway causes susceptibility to severe disseminated infections with mycobacteria and dimorphic yeasts. Dominant gain-of-function mutations in signal transducer and activator of transcription 1 (STAT1) have been associated with chronic mucocutaneous candidiasis.
Objective
We sought to identify the molecular defect in patients with disseminated dimorphic yeast infections.
Methods
PBMCs, EBV-transformed B cells, and transfected U3A cell lines were studied for IFN-γ/IL-12 pathway function. STAT1 was sequenced in probands and available relatives. Interferon-induced STAT1 phosphorylation, transcriptional responses, protein-protein interactions, target gene activation, and function were investigated.
Results
We identified 5 patients with disseminated Coccidioides immitis or Histoplasma capsulatum with heterozygous missense mutations in the STAT1 coiled-coil or DNA-binding domains. These are dominant gain-of-function mutations causing enhanced STAT1 phosphorylation, delayed dephosphorylation, enhanced DNA binding and transactivation, and enhanced interaction with protein inhibitor of activated STAT1. The mutations caused enhanced IFN-γ–induced gene expression, but we found impaired responses to IFN-γ restimulation.
Conclusion
Gain-of-function mutations in STAT1 predispose to invasive, severe, disseminated dimorphic yeast infections, likely through aberrant regulation of IFN-γ–mediated inflammation.
doi:10.1016/j.jaci.2013.01.052
PMCID: PMC3746066  PMID: 23541320
Signal transducer and activator of transcription 1; IFN-γ; progressive multifocal leukoencephalopathy; Histoplasma capsulatum; Coccidioides immitis; thrush
4.  Vascular Endothelial Growth Factors (VEGFs) and Stroke 
Vascular endothelial growth factors (VEGFs) have been shown to participate in atherosclerosis, arteriogenesis, cerebral edema, neuroprotection, neurogenesis, angiogenesis, postischemic brain and vessel repair, and the effects of transplanted stem cells in experimental stroke. Most of these actions involve VEGF-A and the VEGFR-2 receptor, but VEGF-B, placental growth factor, and VEGFR-1 have been implicated in some cases as well. VEGF signaling pathways represent important potential targets for the acute and chronic treatment of stroke.
doi:10.1007/s00018-013-1282-8
PMCID: PMC3634892  PMID: 23475070
vascular endothelial growth factor; stroke; ischemia; neuroprotection; neurogenesis; angiogenesis
5.  Expression Level of Vascular Endothelial Growth Factor in Hippocampus is Associated with Cognitive Impairment in Patients with Alzheimer’s Disease 
Neurobiology of aging  2012;34(5):1412-1415.
Although the enhanced expression of VEGF in the brains of patients with Alzheimer’s disease (AD) has been reported, the functional significance of VEGF level in the progression of AD is still unclear. We examined the VEGF expression in the hippocampus of patients with AD at different stages of progression by Western blot, and found that VEGF (VEGF189) was barely detectable in normal hippocampus, but significantly increased at the early stage of patients with AD. VEGF189 was decreased with advancing stages of AD. Immunostaining shows that VEGF was significantly increased in the cells in the CA1, CA3 and dentate gyrus regions of hippocampus and the layer III and V of entorhinal cortex of patient with AD, compared to normal brain. Confocal images show that VEGF was predominantly expressed in neurons and astrocyte in the hippocampus and entorhinal cortex of patients with AD. Our data suggest that VEGF level is associated with progressive loss of cognitive function in patients with AD.
doi:10.1016/j.neurobiolaging.2012.10.029
PMCID: PMC3570710  PMID: 23182805
VEGF; Alzheimer’s disease; Human; brain; expression
6.  Using Linkage Analysis to Detect Gene-Gene Interaction by Stratifying Family Data on Known Disease, or Disease-Associated, Alleles 
PLoS ONE  2014;9(4):e93398.
Detecting gene-gene interaction in complex diseases is a major challenge for common disease genetics. Most interaction detection approaches use disease-marker associations and such methods have low power and unknown reliability in real data. We developed and tested a powerful linkage-analysis-based gene-gene interaction detection strategy based on conditioning the family data on a known disease-causing allele or disease-associated marker allele. We computer-generated multipoint linkage data for a disease caused by two epistatically interacting loci (A and B). We examined several two-locus epistatic inheritance models: dominant-dominant, dominant-recessive, recessive-dominant, recessive-recessive. At one of the loci (A), there was a known disease-related allele. We stratified the family data on the presence of this allele, eliminating family members who were without it. This elimination step has the effect of raising the “penetrance” at the second locus (B). We then calculated the lod score at the second locus (B) and compared the pre- and post-stratification lod scores at B. A positive difference indicated interaction. We also examined if it was possible to detect interaction with locus B based on a disease-marker association (instead of an identified disease allele) at locus A. We also tested whether the presence of genetic heterogeneity would generate false positive evidence of interaction. The power to detect interaction for a known disease allele was 60–90%. The probability of false positives, based on heterogeneity, was low. Decreasing linkage disequilibrium between the disease and marker at locus A decreased the likelihood of detecting interaction. The allele frequency of the associated marker made little difference to the power.
doi:10.1371/journal.pone.0093398
PMCID: PMC3972093  PMID: 24690899
7.  Draft Genome Sequences of Burkholderia cenocepacia ET12 Lineage Strains K56-2 and BC7 
Genome Announcements  2013;1(5):e00841-13.
The Burkholderia cepacia complex (BCC) is a group of closely related bacteria that are responsible for respiratory infections in immunocompromised humans, most notably those with cystic fibrosis (CF). We report the genome sequences for Burkholderia cenocepacia ET12 lineage CF isolates K56-2 and BC7.
doi:10.1128/genomeA.00841-13
PMCID: PMC3798455  PMID: 24136849
8.  Comparative protein interactomics of neuroglobin and myoglobin 
Journal of neurochemistry  2012;123(1):192-198.
Neuroglobin is a hypoxia-inducible O2-binding protein with neuroprotective effects in cell and animal models of stroke and Alzheimer’s disease. The mechanism underlying neuroglobin’s cytoprotective action is unknown, although several possibilities have been proposed, including antioxidative and antiapoptotic effects. We used affinity purification-mass spectrometry methods to identify neuroglobin-interacting proteins in normoxic and hypoxic murine neuronal (HN33) cell lysates, and to compare these interactions with those of a structurally and functionally related protein, myoglobin. We report that the protein interactomes of neuroglobin and myoglobin overlap substantially and are modified by hypoxia. In addition, neuroglobin-interacting proteins include partners consistent with both antioxidative and antiapoptotic functions, as well as with a relationship to several neurodegenerative diseases.
doi:10.1111/j.1471-4159.2012.07881.x
PMCID: PMC3438380  PMID: 22816983
hypoxia; ischemia; myoglobin; neuroglobin; proteome
9.  Alteration of the microRNA network during the progression of Alzheimer's disease 
EMBO Molecular Medicine  2013;5(10):1613-1634.
An overview of miRNAs altered in Alzheimer's disease (AD) was established by profiling the hippocampus of a cohort of 41 late-onset AD (LOAD) patients and 23 controls, showing deregulation of 35 miRNAs. Profiling of miRNAs in the prefrontal cortex of a second independent cohort of 49 patients grouped by Braak stages revealed 41 deregulated miRNAs. We focused on miR-132-3p which is strongly altered in both brain areas. Downregulation of this miRNA occurs already at Braak stages III and IV, before loss of neuron-specific miRNAs. Next-generation sequencing confirmed a strong decrease of miR-132-3p and of three family-related miRNAs encoded by the same miRNA cluster on chromosome 17. Deregulation of miR-132-3p in AD brain appears to occur mainly in neurons displaying Tau hyper-phosphorylation. We provide evidence that miR-132-3p may contribute to disease progression through aberrant regulation of mRNA targets in the Tau network. The transcription factor (TF) FOXO1a appears to be a key target of miR-132-3p in this pathway.
doi:10.1002/emmm.201201974
PMCID: PMC3799583  PMID: 24014289
Alzheimer's disease; hippocampus; prefrontal cortex; microRNA; miR-132-3p
10.  Serologic Reactivity to the Emerging Pathogen Granulibacter bethesdensis 
The Journal of Infectious Diseases  2012;206(6):943-951.
Background. Granulibacter bethesdensis is a recently described member of the Acetobacteraceae family that has been isolated from patients with chronic granulomatous disease (CGD). Its pathogenesis, environmental reservoir(s), and incidence of infection among CGD patients and the general population are unknown.
Methods. Detected antigens were identified by mass spectroscopy after 2-dimensional electrophoresis and immunoaffinity chromatography. The prevalence of Granulibacter immunoreactivity was assessed through immunoblotting and enzyme-linked immunosorbent assay (ELISA).
Results. Methanol dehydrogenase (MDH) and formaldehyde-activating enzyme were recognized during analysis of sera from infected patients. Unique patterns of immunoreactive bands were identified in Granulibacter extracts, compared with extracts of other Acetobacteraceae species. By use of criteria based on these specific bands, specimens from 79 of 175 CGD patients (45.1%) and 23 of 93 healthy donors (24.7%) reacted to all 11 bands. An ELISA that used native MDH to capture and detect immunoglobulin G was developed and revealed high-titer MDH seroreactivity in culture-confirmed cases and 5 additional CGD patients. Testing of samples collected prior to culture-confirmed infection demonstrated instances of recent seroconversion, as well as sustained seropositivity. Infection of CGD mice with G. bethesdensis confirmed acquisition of high-titer antibody-recognizing MDH.
Conclusions. These serologic tests suggest that Granulibacter immunoreactivity is more common among CGD patients and, perhaps, among healthy donors than was previously suspected. This finding raises the possibility that clinical presentations of Granulibacter infection may be underappreciated.
doi:10.1093/infdis/jis431
PMCID: PMC3501152  PMID: 22782953
11.  How should we be searching for genes for common epilepsy? A critique and a prescription 
Epilepsia  2012;53(0 4):72-80.
Summary
Despite enormous data collection and analysis efforts, the genetic influences on common epilepsies remain mostly unknown. We propose that reasons for the lack of progress can be traced to three factors: (1) A reluctance to consider fine-grained phenotype definitions based on extensive and carefully collected clinical data; (2) the pursuit of genetic analysis methods that are popular but poorly conceived and are inadequate to the task of resolving the problems inherent in common disease studies; (3) preconceived ideas about the genetic mechanisms that cause epilepsy (which we have discussed elsewhere). We propose a paradigm for finding epilepsy-related loci and alleles that has proven successful in other common diseases.
doi:10.1111/j.1528-1167.2012.03616.x
PMCID: PMC3746521  PMID: 22946724
Exome; Genome-wide association; Linkage analysis; Phenotype; Single nucleotide polymorphisms; Whole genome sequencing
12.  Influence of Pneumococcal Vaccines and Respiratory Syncytial Virus on Alveolar Pneumonia, Israel 
Emerging Infectious Diseases  2013;19(7):1084-1091.
Postlicensure surveillance of pneumonia incidence can be used to estimate whether pneumococcal conjugate vaccines (PCVs) affect incidence. We used Poisson regression models that control for baseline seasonality to determine the impact of PCVs and the possible effects of variations in virus activity in Israel on these surveillance estimates. PCV was associated with significant declines in radiologically confirmed alveolar pneumonia (RCAP) among patients <6 months, 6–17 months, and 18–35 months of age (–31% [95% CI –51% to –15%], –41% [95% CI –52 to –32%], and –34% [95% CI –42% to –25%], respectively). Respiratory syncytial virus (RSV) activity was associated with strong increases in RCAP incidence, with up to 44% of cases attributable to RSV among infants <6 months of age and lower but significant impacts in older children. Seasonal variations, particularly in RSV activity, masked the impact of 7-valent PCVs, especially for young children in the first 2 years after vaccine introduction.
doi:10.3201/eid1907.121625
PMCID: PMC3713978  PMID: 23763864
pneumococcal conjugate vaccines; pneumonia; RSV; influenza; regression model; surveillance; viruses; Israel; respiratory syncytial virus; alveolar pneumonia
13.  Interactions between Vascular Endothelial Growth Factor and Neuroglobin 
Neuroscience Letters  2012;519(1):47-50.
Vascular endothelial growth factor (VEGF) and neuroglobin (Ngb) participate in neuronal responses to hypoxia and ischemia, but the relationship between their effects, if any, is unknown. To address this issue, we measured Ngb levels in VEGF-treated mouse cerebrocortical cultures and VEGF levels in cerebrocortical cultures from Ngb-overexpressing transgenic mice. VEGF stimulated Ngb expression in a VEGFR2/Flk1 receptor-dependent manner, whereas Ngb overexpression suppressed expression of VEGF. These findings provide further insight into hypoxia-stimulated neuronal signaling pathways.
doi:10.1016/j.neulet.2012.05.018
PMCID: PMC3371093  PMID: 22583764
Vascular endothelial growth factor; neuroglobin; hypoxia
14.  Effect of a contralateral lesion on neurological recovery from stroke in rats 
Purpose
Clinical studies suggest a correlation between changes in activity of the contralesional cerebral cortex and spontaneous recovery from stroke, but whether this is a causal relationship is uncertain.
Methods
Young adult Sprague-Dawley male rats underwent unilateral or bilateral permanent distal middle cerebral artery occlusion (dMCAO). Infarct volume was determined by 2,3,5-triphenyltetrazolium chloride (TTC) staining 24 hr after dMCAO, and functional outcome was assessed 1–28 days after dMCAO using the ladder rung walking and limb placing tests.
Results
Infarct volume was unchanged, but functional neurological deficits were reduced 1 day after bilateral compared to unilateral dMCAO.
Conclusions
Activity in the contralesional cerebral cortex may inhibit functional motor recovery acutely after experimental stroke.
doi:10.3233/RNN-2012-120254
PMCID: PMC3652379  PMID: 22868223
Stroke; ischemia; recovery; rat
15.  Draft Genome Sequence Determination for Cystic Fibrosis and Chronic Granulomatous Disease Burkholderia multivorans Isolates 
Journal of Bacteriology  2012;194(22):6356-6357.
Burkholderia multivorans is a Gram-negative bacterium and a member of the Burkholderia cepacia complex, which is frequently associated with respiratory infections in people with cystic fibrosis (CF) and chronic granulomatous disease (CGD). We are reporting the genome sequences of 4 B. multivorans strains, 2 from CF patients and 2 from CGD patients.
doi:10.1128/JB.01306-12
PMCID: PMC3486389  PMID: 23105085
16.  Vascular endothelial growth factor-B expression in postischemic rat brain 
Vascular Cell  2013;5:8.
Background
Vascular endothelial growth factor-B (VEGF-B) protects against experimental stroke, but the effect of stroke on VEGF-B expression is uncertain.
Methods
We examined VEGF-B expression by immunohistochemistry in the ischemic border zone 1–7 days after middle cerebral artery occlusion in rats.
Results
VEGF-B immunoreactivity in the border zone was increased after middle cerebral artery occlusion and was associated with neurons and macrophages/microglia, but not astrocytes or endothelial cells.
Conclusions
These findings provide additional evidence for a role of VEGF-B in the endogenous response to cerebral ischemia.
doi:10.1186/2045-824X-5-8
PMCID: PMC3671984  PMID: 23601533
Vascular endothelial growth factor-B (VEGF-B); Stroke; Ischemia
17.  Genome Characterisation of Enteroviruses 117 and 118: A New Group within Human Enterovirus Species C 
PLoS ONE  2013;8(4):e60641.
The more than 120 genotypes of human enteroviruses (HEVs) reflect a wide range of evolutionary divergence, and there are 23 currently classified as human enterovirus C species (HEV-C). Two new HEV-C (EV-C117 and EV-C118) were identified in the Community-Acquired Pneumonia Pediatric Research Initiative (CAP-PRI) study, and the present paper describes the characterisation of the complete genome of one EV-C117 strain (LIT22) and two EV-C118 (ISR38 and ISR10) strains. The EV-C117 and EV-C118 5′UTR sequences were related to those of EV-C104, EV-C105 and EV-C109, and were slightly shorter than those of other HEV A-D species. Similarity plot analyses showed that EV-C117 and EV-C118 have a P1 region that is highly divergent from that of the other HEV-C, and phylogenetic analyses highly supported a monophyletic group consisting of EV-C117, EV-C118, EV-C104, EV-C105 and EV-C109 strains. Phylogenetic, Simplot and Bootscan analyses indicated that recombination was not the main mechanism of EV-C117 and EV-C118 evolution, thus strengthening the hypothesis of the monophyletic origin of the coding regions, as in the case of other HEV-C. Phylogenetic analysis also revealed the emergence of a new group within HEV-C that is divided into two subgroups. Nucleotide and amino acid identity in VP1 sequences have been established as useful criteria for assigning new HEV types, but analysis of the complete P1 region improves resolution.
doi:10.1371/journal.pone.0060641
PMCID: PMC3614900  PMID: 23565264
18.  Unusual Presentations of Pediatric Neurobrucellosis 
Neurobrucellosis is an uncommon complication of pediatric brucellosis. Acute meningitis and encephalitis are the most common clinical manifestations, however symptoms may be protean and diagnosis requires a high index of suspicion in patients from endemic areas. Diagnosis is often based on neurological symptoms, serology, and suggestive brain imaging because cerebrospinal fluid culture yields are low. Two cases of pediatric neurobrucellosis with unusual clinical and radiologic findings are presented.
doi:10.4269/ajtmh.2012.11-0468
PMCID: PMC3269277  PMID: 22302859
19.  Full Genome Sequence of a Novel Human Enterovirus C (EV-C118) Isolated from Two Children with Acute Otitis Media and Community-Acquired Pneumonia in Israel 
Genome Announcements  2013;1(1):e00121-12.
The new enterovirus C strain EV-C118 belongs to the human enterovirus C species of the Picornaviridae family. We report the complete genome sequence of this strain, which was identified in respiratory specimens of two children hospitalized in Israel because of acute otitis media and community-acquired pneumonia who were enrolled in the Community-Acquired Pneumonia Pediatric Research Initiative (CAP-PRI) study.
doi:10.1128/genomeA.00121-12
PMCID: PMC3569292  PMID: 23405305
20.  Changing the responses of cortical neurons from sub- to suprathreshold using single spikes in vivo 
eLife  2013;2:e00012.
Action Potential (APs) patterns of sensory cortex neurons encode a variety of stimulus features, but how can a neuron change the feature to which it responds? Here, we show that in vivo a spike-timing-dependent plasticity (STDP) protocol—consisting of pairing a postsynaptic AP with visually driven presynaptic inputs—modifies a neurons' AP-response in a bidirectional way that depends on the relative AP-timing during pairing. Whereas postsynaptic APs repeatedly following presynaptic activation can convert subthreshold into suprathreshold responses, APs repeatedly preceding presynaptic activation reduce AP responses to visual stimulation. These changes were paralleled by restructuring of the neurons response to surround stimulus locations and membrane-potential time-course. Computational simulations could reproduce the observed subthreshold voltage changes only when presynaptic temporal jitter was included. Together this shows that STDP rules can modify output patterns of sensory neurons and the timing of single-APs plays a crucial role in sensory coding and plasticity.
DOI: http://dx.doi.org/10.7554/eLife.00012.001
eLife digest
Nerve cells, called neurons, are one of the core components of the brain and form complex networks by connecting to other neurons via long, thin ‘wire-like’ processes called axons. Axons can extend across the brain, enabling neurons to form connections—or synapses—with thousands of others. It is through these complex networks that incoming information from sensory organs, such as the eye, is propagated through the brain and encoded.
The basic unit of communication between neurons is the action potential, often called a ‘spike’, which propagates along the network of axons and, through a chemical process at synapses, communicates with the postsynaptic neurons that the axon is connected to. These action potentials excite the neuron that they arrive at, and this excitatory process can generate a new action potential that then propagates along the axon to excite additional target neurons. In the visual areas of the cortex, neurons respond with action potentials when they ‘recognize’ a particular feature in a scene—a process called tuning. How a neuron becomes tuned to certain features in the world and not to others is unclear, as are the rules that enable a neuron to change what it is tuned to. What is clear, however, is that to understand this process is to understand the basis of sensory perception.
Memory storage and formation is thought to occur at synapses. The efficiency of signal transmission between neurons can increase or decrease over time, and this process is often referred to as synaptic plasticity. But for these synaptic changes to be transmitted to target neurons, the changes must alter the number of action potentials. Although it has been shown in vitro that the efficiency of synaptic transmission—that is the strength of the synapse—can be altered by changing the order in which the pre- and postsynaptic cells are activated (referred to as ‘Spike-timing-dependent plasticity’), this has never been shown to have an effect on the number of action potentials generated in a single neuron in vivo. It is therefore unknown whether this process is functionally relevant.
Now Pawlak et al. report that spike-timing-dependent plasticity in the visual cortex of anaesthetized rats can change the spiking of neurons in the visual cortex. They used a visual stimulus (a bar flashed up for half a second) to activate a presynaptic cell, and triggered a single action potential in the postsynaptic cell a very short time later. By repeatedly activating the cells in this way, they increased the strength of the synaptic connection between the two neurons. After a small number of these pairing activations, presenting the visual stimulus alone to the presynaptic cell was enough to trigger an action potential (a suprathreshold response) in the postsynaptic neuron—even though this was not the case prior to the pairing.
This study shows that timing rules known to change the strength of synaptic connections—and proposed to underlie learning and memory—have functional relevance in vivo, and that the timing of single action potentials can change the functional status of a cortical neuron.
DOI: http://dx.doi.org/10.7554/eLife.00012.002
doi:10.7554/eLife.00012
PMCID: PMC3552422  PMID: 23359858
synaptic plasticity; STDP; visual cortex; circuits; in vivo; spiking patterns; rat
21.  Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes 
MicroRNAs (miRNAs) are key post transcriptional regulators of their multiple target genes. However, the detailed profile of miRNA expression in Parkinson's disease, the second most common neurodegenerative disease worldwide and the first motor disorder has not been charted yet. Here, we report comprehensive miRNA profiling by next-generation small-RNA sequencing, combined with targets inspection by splice-junction and exon arrays interrogating leukocyte RNA in Parkinson's disease patients before and after deep brain stimulation (DBS) treatment and of matched healthy control volunteers (HC). RNA-Seq analysis identified 254 miRNAs and 79 passenger strand forms as expressed in blood leukocytes, 16 of which were modified in patients pre-treatment as compared to HC. 11 miRNAs were modified following brain stimulation 5 of which were changed inversely to the disease induced changes. Stimulation cessation further induced changes in 11 miRNAs. Transcript isoform abundance analysis yielded 332 changed isoforms in patients compared to HC, which classified brain transcriptomes of 47 PD and control independent microarrays. Functional enrichment analysis highlighted mitochondrion organization. DBS induced 155 splice changes, enriched in ubiquitin homeostasis. Cellular composition analysis revealed immune cell activity pre and post treatment. Overall, 217 disease and 74 treatment alternative isoforms were predictably targeted by modified miRNAs within both 3′ and 5′ untranslated ends and coding sequence sites. The stimulation-induced network sustained 4 miRNAs and 7 transcripts of the disease network. We believe that the presented dynamic networks provide a novel avenue for identifying disease and treatment-related therapeutic targets. Furthermore, the identification of these networks is a major step forward in the road for understanding the molecular basis for neurological and neurodegenerative diseases and assessment of the impact of brain stimulation on human diseases.
doi:10.3389/fnmol.2013.00010
PMCID: PMC3652308  PMID: 23717260
deep brain stimulation; high throughput sequencing; leukocytes; miRNAs; Parkinson's disease; splice junction microarrays; substantia nigra
22.  microRNAs in nociceptive circuits as predictors of future clinical applications 
Neuro-immune alterations in the peripheral and central nervous system play a role in the pathophysiology of chronic pain, and non-coding RNAs – and microRNAs (miRNAs) in particular – regulate both immune and neuronal processes. Specifically, miRNAs control macromolecular complexes in neurons, glia and immune cells and regulate signals used for neuro-immune communication in the pain pathway. Therefore, miRNAs may be hypothesized as critically important master switches modulating chronic pain. In particular, understanding the concerted function of miRNA in the regulation of nociception and endogenous analgesia and defining the importance of miRNAs in the circuitries and cognitive, emotional and behavioral components involved in pain is expected to shed new light on the enigmatic pathophysiology of neuropathic pain, migraine and complex regional pain syndrome. Specific miRNAs may evolve as new druggable molecular targets for pain prevention and relief. Furthermore, predisposing miRNA expression patterns and inter-individual variations and polymorphisms in miRNAs and/or their binding sites may serve as biomarkers for pain and help to predict individual risks for certain types of pain and responsiveness to analgesic drugs. miRNA-based diagnostics are expected to develop into hands-on tools that allow better patient stratification, improved mechanism-based treatment, and targeted prevention strategies for high risk individuals.
doi:10.3389/fnmol.2013.00033
PMCID: PMC3798051  PMID: 24151455
chronic pain; biomarker; polymorphism; miRNA-based diagnostics; miRNA expression patterns; miRNA polymorphisms; antagomir; miRNA-based analgesic
23.  Hypoxia-inducible Factor-1 and Neuroglobin Expression 
Neuroscience letters  2012;514(2):137-140.
Neuroglobin (Ngb) is a hypoxia-inducible protein with cytoprotective effects in animal models of stroke, Alzheimer's disease, and related disorders, but the molecular mechanisms involved in its induction are unknown. We tested the hypothesis that hypoxia-inducible factor-1 (HIF-1) regulates Ngb levels, using shRNA-mediated knockdown and lentiviral vector-mediated overexpression of the HIF-1α subunit, in cultured neural (HN33) cells. HIF-1α knockdown decreased and HIF-1α overexpression increased Ngb levels, consistent with a connection between HIF-1 and Ngb induction. These findings may have implications for understanding the hypoxia-response repertoire of neural cells and devising therapeutic strategies for neurologic disorders.
doi:10.1016/j.neulet.2012.01.080
PMCID: PMC3526664  PMID: 22342914
neuroglobin; hypoxia; hypoxia-inducible factor-1; stroke
24.  Computer Simulation Is an Undervalued Tool for Genetic Analysis: A Historical View and Presentation of SHIMSHON – A Web-Based Genetic Simulation Package 
Human Heredity  2011;72(4):247-257.
Computer simulation methods are under-used tools in genetic analysis because simulation approaches have been portrayed as inferior to analytic methods. Even when simulation is used, its advantages are not fully exploited. Here, I present SHIMSHON, our package of genetic simulation programs that have been developed, tested, used for research, and used to generated data for Genetic Analysis Workshops (GAW). These simulation programs, now web-accessible, can be used by anyone to answer questions about designing and analyzing genetic disease studies for locus identification. This work has three foci: (1) the historical context of SHIMSHON's development, suggesting why simulation has not been more widely used so far. (2) Advantages of simulation: computer simulation helps us to understand how genetic analysis methods work. It has advantages for understanding disease inheritance and methods for gene searches. Furthermore, simulation methods can be used to answer fundamental questions that either cannot be answered by analytical approaches or cannot even be defined until the problems are identified and studied, using simulation. (3) I argue that, because simulation was not accepted, there was a failure to grasp the meaning of some simulation-based studies of linkage. This may have contributed to perceived weaknesses in linkage analysis; weaknesses that did not, in fact, exist.
doi:10.1159/000330633
PMCID: PMC3726233  PMID: 22189467
Linkage analysis; Association analysis; Mode of inheritance; GWAS; Type 1 error; Affected sib pairs; LOD scores
25.  THE BROMODOMAIN-CONTAINING GENE BRD2 IS REGULATED AT TRANSCRIPTION, SPLICING, AND TRANSLATION LEVELS 
Journal of cellular biochemistry  2011;112(10):2784-2793.
The human BRD2 gene has been linked and associated with a form of common epilepsy and electroencephalographic abnormalities. Disruption of Brd2 in the mouse revealed that it is essential for embryonic neural development and that viable Brd2+/- heterozygotes show both decreased GABAergic neuron counts and increased susceptibility to seizures. To understand the molecular mechanisms by which mis-expression of BRD2 might contribute to epilepsy, we examined its regulation at multiple levels. We discovered that BRD2 expresses distinct tissue-specific transcripts that originate from different promoters and have strikingly different lengths of 5’ untranslated regions (5’UTR). We also experimentally confirmed the presence of a highly conserved, alternatively spliced exon, inclusion of which would result in a premature termination of translation. Downstream of this alternative exon is a polymorphic microsatellite (GT-repeats). Manipulation of the number of the GT-repeats revealed that the length of the GT-repeats affects the ratio of the two alternative splicing products. In vitro translation and expression in cultured cells revealed that among the four different mRNAs (long and short 5’UTR combined with regular and alternative splicing), only the regularly spliced mRNA with the short 5’UTR yields full-length protein. In situ hybridization and immunohistochemical studies showed that although Brd2 mRNA is expressed in both the hippocampus and cerebellum, Brd2 protein only can be detected in the cerebellar Purkinje cells and not in hippocampal cells. These multiple levels of regulation would likely affect the production of functional BRD2 protein during neural development and hence, its role in the etiology of seizure susceptibility.
doi:10.1002/jcb.23192
PMCID: PMC3178676  PMID: 21608014
BRD2; Bromodomain; Alternative splicing; translation; expression regulation

Results 1-25 (127)