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In JoVE (1)
- Preparation of Parasagittal Slices for the Investigation of Dorsal-ventral Organization of the Rodent Medial Entorhinal Cortex
Other Publications (40)
- The Journal of Physiology
- Systematic Parasitology
- Parasitology International
- Folia Parasitologica
- Systematic Parasitology
- The Journal of Parasitology
- Advances in Parasitology
- The Journal of Neuroscience : the Official Journal of the Society for Neuroscience
- The American Journal of Medicine
- American Journal of Surgery
- PLoS Computational Biology
- Frontiers in Cellular Neuroscience
- Systematic Parasitology
- Molecular and Cellular Probes
- Molecular and Cellular Probes
- Nucleic Acids Research
- Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
- PLoS Computational Biology
- Contact Lens & Anterior Eye : the Journal of the British Contact Lens Association
- Trends in Neurosciences
- Molecular and Cellular Probes
- Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
- The Journal of Physiology
- Frontiers in Molecular Neuroscience
- Journal of Bacteriology
- Journal of Bacteriology
- The Journal of Neuroscience : the Official Journal of the Society for Neuroscience
- Advances in Parasitology
- Molecular and Biochemical Parasitology
- Molecular and Cellular Probes
Articles by Matthew Nolan in JoVE
Preparation of Parasagittal Slices for the Investigation of Dorsal-ventral Organization of the Rodent Medial Entorhinal Cortex
Hugh Pastoll1, Melanie White2, Matthew Nolan2
1Neuroinformatics DTC, University of Edinburgh, 2Centre for Integrative Physiology, University of Edinburgh
We describe procedures for preparation and electrophysiological recording from brain slices that maintain the dorsal-ventral axis of the medial entorhinal cortex (MEC). Because neural encoding of location follows a dorsal-ventral organization within the MEC, these procedures facilitate investigation of cellular mechanisms important for navigation and memory.
Other articles by Matthew Nolan on PubMed
Activity-dependent Regulation of HCN Pacemaker Channels by Cyclic AMP: Signaling Through Dynamic Allosteric Coupling
Neuron. Oct, 2002 | Pubmed ID: 12408847
Signal transduction in neurons is a dynamic process, generally thought to be driven by transient changes in the concentration of second messengers. Here we describe a novel regulatory mechanism in which the dynamics of signaling through cyclic AMP are mediated by activity-dependent changes in the affinity of the hyperpolarization-activated, cation nonselective (HCN) channels for cAMP, rather than by changes in cAMP concentration. Due to the allosteric coupling of channel opening and ligand binding, changes in cellular electrical activity that alter the opening of the HCN channels modify the binding of static, basal levels of cAMP. These changes in ligand binding produce long-lasting changes in channel function which can contribute to the regulation of rhythmic firing patterns.
The Journal of Physiology. Jun, 2003 | Pubmed ID: 12702746
The neuropeptides orexin A and B are synthesised by perifornical and lateral hypothalamic (LH) neurones and exert a profound influence on autonomic sympathetic processes. LH neurones project to spinal areas containing sympathetic preganglionic neurones (SPNs) and therefore may directly modulate sympathetic output. In the present study we examined the possibility that orexinergic inputs from the LH influence SPN activity. Orexin-positive neurones in the LH were labelled with pseudorabies virus injected into the liver of parasympathetically denervated animals and orexin fibres were found adjacent to the soma and dendrites of SPNs. Orexin A or B (10-1000 nM) directly and reversibly depolarised SPNs in spinal cord slices. The response to orexin A was significantly reduced in the presence of the orexin receptor 1 (OX1R) antagonist SB334867A at concentrations of 1-10 micro M. Single cell reverse transcriptase-polymerase chain reaction revealed expression of mRNA for both OX1R and OX2R in the majority of orexin-sensitive SPNs. The orexin-induced depolarisation involved activation of pertussis toxin-sensitive G-proteins and closure of a K+ conductance via a protein kinase A (PKA)-dependent pathway that did not require an increase in intracellular Ca2+. Orexins also induced biphasic subthreshold membrane potential oscillations and synchronised activity between pairs of electrically coupled SPNs. Coupling coefficients and estimated junctional conductances between SPNs were not altered indicating synchronisation is due to activation of previously silent coupled neurones rather than modulation of gap junctions. These findings are consistent with a direct excitation and synchronisation of SPNs by orexinergic neurones that in vivo could increase the frequency and coherence of sympathetic nerve discharges and mediate LH effects on sympathetic components of energy homeostasis and cardiovascular control.
The Hyperpolarization-activated HCN1 Channel is Important for Motor Learning and Neuronal Integration by Cerebellar Purkinje Cells
Cell. Nov, 2003 | Pubmed ID: 14651847
In contrast to our increasingly detailed understanding of how synaptic plasticity provides a cellular substrate for learning and memory, it is less clear how a neuron's voltage-gated ion channels interact with plastic changes in synaptic strength to influence behavior. We find, using generalized and regional knockout mice, that deletion of the HCN1 channel causes profound motor learning and memory deficits in swimming and rotarod tasks. In cerebellar Purkinje cells, which are a key component of the cerebellar circuit for learning of correctly timed movements, HCN1 mediates an inward current that stabilizes the integrative properties of Purkinje cells and ensures that their input-output function is independent of the previous history of their activity. We suggest that this nonsynaptic integrative function of HCN1 is required for accurate decoding of input patterns and thereby enables synaptic plasticity to appropriately influence the performance of motor activity.
Ankistromeces Mariae N. G., N. Sp. (Digenea: Sanguinicolidae) from Meuschenia Freycineti (Monacanthidae) off Tasmania
Systematic Parasitology. Feb, 2004 | Pubmed ID: 14755176
Ankistromeces mariae n. g., n. sp. is described from Meuschenia freycineti (Monacanthidae), the six-spined leatherjacket, from off northern Tasmania. The new genus differs from the 21 other sanguinicolid genera in the combination of the anteriorly intercaecal and posteriorly post-caecal single testis, the presence of a cirrus-sac, the absence of an auxiliary external seminal vesicle, separate genital pores, the typically post-ovarian uterus and the H-shaped intestine. A. mariae is the first sanguinicolid to be reported from a monacanthid fish.
Two New Blood Flukes (Digenea: Sanguinicolidae) from Epinephelinae (Perciformes: Serranidae) of the Pacific Ocean
Parasitology International. Dec, 2004 | Pubmed ID: 15464442
Pearsonellum pygmaeus n. sp. is described from Cromileptes altivelis (Serranidae), the Barramundi Cod, from Heron Island (southern Great Barrier Reef) and Lizard Island (northern Great Barrier Reef). This new species differs from Pearsonellum corventum (type and only species) in the combination of smaller overall body size, the relative distance of the brain from the anterior end, the relative lengths of both the oesophagus and the testis, the degree to which the testis extends outside the intercaecal field, the shape of the testis, the shape and size of the ovary and the extent to which the uterus loops around the ovary. There are in addition, 20 base pair differences between the ITS2 rDNA sequence of P. pygmaeus n. sp. and that of P. corventum. Three new host records for P. corventum are reported. Adelomyllos teenae n. g., n. sp. is described from Epinephelus coioides (Serranidae), the Estuary Cod, from Moreton Bay, southeast Queensland. The new genus differs from the 22 other sanguinicolid genera in the combined possession of two testes, a cirrus-sac, separate genital pores, a post-ovarian uterus and an H-shaped intestine. A. teenae n. sp. is the third sanguinicolid described from the Epinephelinae. Sanguinicolids have now been reported from 11 species of Serranidae.
A Behavioral Role for Dendritic Integration: HCN1 Channels Constrain Spatial Memory and Plasticity at Inputs to Distal Dendrites of CA1 Pyramidal Neurons
Cell. Nov, 2004 | Pubmed ID: 15550252
The importance of long-term synaptic plasticity as a cellular substrate for learning and memory is well established. By contrast, little is known about how learning and memory are regulated by voltage-gated ion channels that integrate synaptic information. We investigated this question using mice with general or forebrain-restricted knockout of the HCN1 gene, which we find encodes a major component of the hyperpolarization-activated inward current (Ih) and is an important determinant of dendritic integration in hippocampal CA1 pyramidal cells. Deletion of HCN1 from forebrain neurons enhances hippocampal-dependent learning and memory, augments the power of theta oscillations, and enhances long-term potentiation (LTP) at the direct perforant path input to the distal dendrites of CA1 pyramidal neurons, but has little effect on LTP at the more proximal Schaffer collateral inputs. We suggest that HCN1 channels constrain learning and memory by regulating dendritic integration of distal synaptic inputs to pyramidal cells.
Folia Parasitologica. Dec, 2004 | Pubmed ID: 15729944
The sanguinicolids Paracardicoloides yamagutii Martin, 1974 and Plethorchis acanthus Martin, 1975 were obtained from their definitive hosts, Anguilla reinhardtii Steindachner and Mugil cephalus Linnaeus (respectively) in the tributaries of the Brisbane River, Queensland, Australia. Two putative sanguinicolid cercariae were collected from a hydrobiid gastropod, Posticobia brazieri Smith, in the same waters. The two cercariae differ markedly in size and the form of their sporocysts. Both putative cercariae develop in the digestive gland of Po. brazieri. The ITS2 rDNA region from these sanguinicolids and a Clinostomum species (utilised as an outgroup due to the close morphological similarities between the cercarial stages of the Clinostomidae and the Sanguinicolidae) were sequenced and aligned. Comparison of the ITS2 sequences showed one cercaria to be that of P. yamagutii. This is the first sanguinicolid life history determined by a molecular method. P. yamagutii is the fourth sanguinicolid known to utilise a freshwater hydrobiid gastropod as its intermediate host. ITS2 rDNA is effective in distinguishing sanguinicolids at the species level.
Sanguinicola Maritimus N. Sp. (Digenea: Sanguinicolidae) from Labridae (Teleostei: Perciformes) of Southern Australian Waters
Systematic Parasitology. Jun, 2005 | Pubmed ID: 15980963
A new species of Sanguinicola Plehn, 1905 is described from the marine teleosts Notolabrus parilus (Richardson) and N. tetricus (Richardson) (Perciformes: Labridae) from Western Australian and Tasmanian waters. This host distribution is strikingly anomalous; however, the present material fulfils the morphological criteria of Sanguinicola. S. maritimus n. sp. differs from previously described species in having the combination of a body 1,432--1,701 mum long, the oesophagus 18.3--21.7% of the body length, the testis occupying 42.8--52.3% of the body length, an oviducal seminal receptacle and Mehlis' gland present, ovoid eggs, and vitelline follicles that extend anteriorly past the nerve commissure, laterally past the lateral nerve chords and posteriorly to the anterior margin of the cirrus-sac. S. maritimus also lacks a protrusible anterior proboscis. It also differs in the combination of host and geographical location, being the first Sanguinicola species from a marine teleost and the first from Australian waters.
Chaulioleptos Haywardi N. Gen., N. Sp. (Digenea: Sanguinicolidae) from Filimanus Heptadactyla (Perciformes: Polynemidae) of Moreton Bay, Australia
The Journal of Parasitology. Jun, 2005 | Pubmed ID: 16108558
Here we describe the first species of sanguinicolid blood fluke (Trematoda: Digenea) from a polynemid fish. Chaulioleptos haywardi n. gen., n. sp. is described from Filimanus heptadactyla Cuvier, 1829 (Perciformes: Polynemidae), the sevenfinger threadfin from Sandgate, Moreton Bay (southeast Queensland, Australia). Chaulioleptos haywardi differs from existing sanguinicolid genera in the combined possession of the following 7 characters: 2 testes, an entirely postovarian uterus, a uterine chamber, separate genital pores, an H-shaped intestine with abbreviated anterior caeca, tegumental spines in incomplete ventro-marginal transverse rows that are continuous along the length of the body, and vitelline follicles that are tightly compacted and subsequently appear to form a solid branching mass occupying the area anterior to intestinal bifurcation and extending posteriorly to the level of the posterior margin of the anterior testis. Chaulioleptos haywardi is most closely related to Paracardicola Martin, 1960 and Adelomyllos Nolan and Cribb, 2004.
Advances in Parasitology. 2005 | Pubmed ID: 16230103
In just over a decade, the use of molecular approaches for the recognition of parasites has become commonplace. For trematodes, the internal transcribed spacer region of ribosomal DNA (ITS rDNA) has become the default region of choice. Here, we review the findings of 63 studies that report ITS rDNA sequence data for about 155 digenean species from 19 families, and then review the levels of variation that have been reported and how the variation has been interpreted. Overall, complete ITS sequences (or ITS1 or ITS2 regions alone) usually distinguish trematode species clearly, including combinations for which morphology gives ambiguous results. Closely related species may have few base differences and in at least one convincing case the ITS2 sequences of two "good" species are identical. In some cases, the ITS1 region gives greater resolution than the ITS2 because of the presence of variable repeat units that are generally lacking in the ITS2. Intraspecific variation is usually low and frequently apparently absent. Information on geographical variation of digeneans is limited but at least some of the reported variation probably reflects the presence of multiple species. Despite the accepted dogma that concerted evolution makes the individual representative of the entire species, a significant number of studies have reported at least some intraspecific variation. The significance of such variation is difficult to assess a posteriori, but it seems likely that identification and sequencing errors account for some of it and failure to recognise separate species may also be significant. Some reported variation clearly requires further analysis. The use of a "yardstick" to determine when separate species should be recognised is flawed. Instead, we argue that consistent genetic differences that are associated with consistent morphological or biological traits should be considered the marker for separate species. We propose a generalised approach to the use of rDNA to distinguish trematode species.
HCN1 Channels Control Resting and Active Integrative Properties of Stellate Cells from Layer II of the Entorhinal Cortex
The Journal of Neuroscience : the Official Journal of the Society for Neuroscience. Nov, 2007 | Pubmed ID: 18003822
Whereas recent studies have elucidated principles for representation of information within the entorhinal cortex, less is known about the molecular basis for information processing by entorhinal neurons. The HCN1 gene encodes ion channels that mediate hyperpolarization-activated currents (I(h)) that control synaptic integration and influence several forms of learning and memory. We asked whether hyperpolarization-activated, cation nonselective 1 (HCN1) channels control processing of information by stellate cells found within layer II of the entorhinal cortex. Axonal projections from these neurons form a major component of the synaptic input to the dentate gyrus of the hippocampus. To determine whether HCN1 channels control either the resting or the active properties of stellate neurons, we performed whole-cell recordings in horizontal brain slices prepared from adult wild-type and HCN1 knock-out mice. We found that HCN1 channels are required for rapid and full activation of hyperpolarization-activated currents in stellate neurons. HCN1 channels dominate the membrane conductance at rest, are not required for theta frequency (4-12 Hz) membrane potential fluctuations, but suppress low-frequency (<4 Hz) components of spontaneous and evoked membrane potential activity. During sustained activation of stellate cells sufficient for firing of repeated action potentials, HCN1 channels control the pattern of spike output by promoting recovery of the spike afterhyperpolarization. These data suggest that HCN1 channels expressed by stellate neurons in layer II of the entorhinal cortex are key molecular components in the processing of inputs to the hippocampal dentate gyrus, with distinct integrative roles during resting and active states.
The Characteristics and Prognostic Importance of NT-ProBNP Concentrations in Critically Ill Patients
The American Journal of Medicine. Dec, 2007 | Pubmed ID: 18060928
There are limited data for prognostic and diagnostic use of natriuretic peptides in intensive care unit (ICU) patients. We evaluate amino-terminal brain natriuretic peptide (NT-proBNP) in the medical ICU, specifically its correlation with noncardiac admission diagnosis and prognosis of critically ill patients.
Do Sentinel Node Micrometastases Predict Recurrence Risk in Ductal Carcinoma in Situ and Ductal Carcinoma in Situ with Microinvasion?
American Journal of Surgery. Oct, 2008 | Pubmed ID: 18760400
Because the implications of micrometastases found on sentinel node biopsy (SNB) for ductal carcinoma in situ (DCIS) or ductal carcinoma in situ with microinvasion (DCISM) are largely unknown, we wished to determine if SNB pathology predicted recurrence risk in DCIS/DCISM.
Tuning of Synaptic Integration in the Medial Entorhinal Cortex to the Organization of Grid Cell Firing Fields
Neuron. Dec, 2008 | Pubmed ID: 19081381
Neurons important for cognitive function are often classified by their morphology and integrative properties. However, it is unclear if within a single class of neuron these properties tune synaptic responses to the salient features of the information that each neuron represents. We demonstrate that for stellate neurons in layer II of the medial entorhinal cortex, the waveform of postsynaptic potentials, the time window for detection of coincident inputs, and responsiveness to gamma frequency inputs follow a dorsal-ventral gradient similar to the topographical organization of grid-like spatial firing fields of neurons in this area. We provide evidence that these differences are due to a membrane conductance gradient mediated by HCN and leak potassium channels. These findings suggest key roles for synaptic integration in computations carried out within the medial entorhinal cortex and imply that tuning of neural information processing by membrane ion channels is important for normal cognitive function.
Stochastically Gating Ion Channels Enable Patterned Spike Firing Through Activity-dependent Modulation of Spike Probability
PLoS Computational Biology. Feb, 2009 | Pubmed ID: 19214199
The transformation of synaptic input into patterns of spike output is a fundamental operation that is determined by the particular complement of ion channels that a neuron expresses. Although it is well established that individual ion channel proteins make stochastic transitions between conducting and non-conducting states, most models of synaptic integration are deterministic, and relatively little is known about the functional consequences of interactions between stochastically gating ion channels. Here, we show that a model of stellate neurons from layer II of the medial entorhinal cortex implemented with either stochastic or deterministically gating ion channels can reproduce the resting membrane properties of stellate neurons, but only the stochastic version of the model can fully account for perithreshold membrane potential fluctuations and clustered patterns of spike output that are recorded from stellate neurons during depolarized states. We demonstrate that the stochastic model implements an example of a general mechanism for patterning of neuronal output through activity-dependent changes in the probability of spike firing. Unlike deterministic mechanisms that generate spike patterns through slow changes in the state of model parameters, this general stochastic mechanism does not require retention of information beyond the duration of a single spike and its associated afterhyperpolarization. Instead, clustered patterns of spikes emerge in the stochastic model of stellate neurons as a result of a transient increase in firing probability driven by activation of HCN channels during recovery from the spike afterhyperpolarization. Using this model, we infer conditions in which stochastic ion channel gating may influence firing patterns in vivo and predict consequences of modifications of HCN channel function for in vivo firing patterns.
Genetic Characterization of Cryptosporidium Parvum from Calves by Mutation Scanning and Targeted Sequencing--zoonotic Implications
Electrophoresis. Aug, 2009 | Pubmed ID: 19637220
This study explored the genetic make-up of Cryptosporidium in fecal samples from 268 individual calves on pasture-based dairy farms in three regions of Victoria, Australia. An integrated approach, using PCR-coupled single-strand conformation polymorphism, targeted sequencing and phylogenetic analysis, was employed to classify the genetic variants (i.e. genotypes and subgenotypes) of Cryptosporidium parvum present in 124 (46.3%) samples and to infer their zoonotic potential. Genotypic and subgenotypic classification was achieved using a portion of the 60 kDa glycoprotein gene (designated pgp60); specific identity was verified using a region within the small subunit of the nuclear ribosomal RNA (pSSU). Twelve sequence types representing ten distinct subgenotypes were defined within genotype IIa, namely IIaA16G3R1 (n=7), IIaA17G2R1 (1), IIaA18G2R1a (2), IIaA18G2R1b (1), IIaA18G4R1 (1), IIaA19G3R1a (80), IIaA19G3R1b (1), IIaA20G2R1 (9), IIaA20G3R1 (1), IIaA20G4R1 (9), IIaA21G3R1 (1) and IIaA23G3R1 (9), of which IIaA18G2R1b, IIaA18G4R1 and IIaA19G3R1b are new records. All of the subgenotypes, except IIaA16G3R1, IIaA18G4R1 and IIaA20G4R1, have been detected previously in humans and are thus considered to be of zoonotic relevance. (Nucleotide sequences reported in this paper are available in the GenBank database under accession numbers FJ825018-FJ825029).
The Impact of Primary Tumor Size, Lymph Node Status, and Other Prognostic Factors on the Risk of Cancer Death
Cancer. Nov, 2009 | Pubmed ID: 19658184
: Although many prognostic factors are associated with differences in cancer lethality, it may not be obvious whether a factor truly makes an independent contribution to lethality or simply is correlated with tumor size. There is currently no method for integrating tumor size, lymph node status, and other prognostic information from a patient into a single risk of death estimate.
Analysis of Nucleotide Variation Within the Triose-phosphate Isomerase Gene of Giardia Duodenalis from Sheep and Its Zoonotic Implications
Electrophoresis. Jan, 2010 | Pubmed ID: 20084628
This study explored the genetic composition of Giardia in fecal samples from 284 individual lambs on pasture-based sheep farms in three regions of Victoria, Australia. An approach, combining targeted sequencing, phylogenetic analysis and PCR-coupled restriction endonuclease fingerprinting, was used to identify and genetically categorize Giardia present in 43 (15.1%) of the 284 samples and to infer their zoonotic potential. The specific identity and genetic classification were based on the phylogenetic analysis of sequence data for a portion of the triose-phosphate isomerase gene. Fourteen different sequence variants (including seven sequences that contained between one and five polymorphic sites) representing two distinct assemblages of Giardia (recognized in the current literature) were defined, of which 13 were new records. One dominant sequence type (with accession no. GQ444447, representing a genotype within assemblage A) has been detected previously in humans and is thus considered to be of zoonotic potential. (Nucleotide sequences reported in this article are available in the GenBank database under accession nos. GQ444447-GQ444451 and GQ444454-GQ444462).
Frontiers in Cellular Neuroscience. 2010 | Pubmed ID: 20126637
Highly Sensitive Non-isotopic Restriction Endonuclease Fingerprinting of Nucleotide Variability in the Gp60 Gene Within Cryptosporidium Species, Genotypes and Subgenotypes Infective to Humans, and Its Implications
Electrophoresis. May, 2010 | Pubmed ID: 20419704
The high-resolution analysis of genetic variation has major implications for the identification of parasites and micro-organisms to species and subspecies as well as for population genetic and epidemiological studies. In this study, we critically assessed the effectiveness of a PCR-based restriction endonuclease fingerprinting (REF) method for the detection of mutations in the 60 kDa glycoprotein gene (gp60) of Cryptosporidium, a genus of parasitic protists of major human and animal health importance globally. This gene displays substantial intraspecific variability in sequence, particularly in a TCA (perfect and imperfect) microsatellite region, is present as a single copy in the nuclear genome and is used widely as a marker in molecular epidemiological studies of Cryptosporidium hominis and C. parvum, the two predominant species that infect humans. The results of this study demonstrated an exquisite capacity of REF to detect nucleotide variability in the gp60 gene within each of the two species. The differentiation of genotypes/subgenotypes based on REF analysis was supported by targeted sequencing, allowing the detection of levels of variation as low as a single-nucleotide transversion for amplicons of approximately 1 kb in size. The high-throughput potential and relatively low-cost of REF make it a particularly useful tool for large-scale genetic analyses of C. hominis and C. parvum. REF could also be utilized for comparative surveys of genetic variability across large nuclear genomic regions. Such analyses of Cryptosporidium in clinical and environmental samples by REF have important implications for identifying sources of infection, modes of transmission and/or possible infectivity to humans, thus assisting in the surveillance and control of cryptosporidiosis. Given its excellent mutation detection capacity, REF should find broad applicability to various single-copy genes as well as a wide range of other protozoan and metazoan parasites.
Two New Species of Flukes (Digenea: Bucephalidae: Prosorhynchinae) from the Western Moray Gymnothorax Woodwardi (Anguilliformes: Muraenidae) from off Western Australia, with Replacement of the Pre-occupied Generic Name Folliculovarium Gu & Shen, 1983
Systematic Parasitology. Jun, 2010 | Pubmed ID: 20437215
Two new species of bucephalid trematodes are described from the rectum and intestine of the western moray eel Gymnothorax woodwardi McCulloch (Anguilliformes: Muraenidae: Muraeninae) off Point Peron in Western Australia. Dollfustrema gibsoni n. sp. is distinguished by body size, a pharynx that is intertesticular and level (latero-dextrally) with the anterior portion of the cirrus-sac, an ovary positioned dextrally to the testes and slightly anterior to (in part) the anterior testis, a uterus that extends anteriorly to the vitelline follicles but not to the level of the rhynchus, and vitelline follicles that form a confluent arc anterior to the gonads. Muraenicola nom. nov. is proposed as a replacement generic name for the pre-occupied Folliculovarium Gu & Shen 1983 nec Singh & Sinha 1981. Muraenicola botti n. sp. is distinguished from its congeners by body size, the size of the cirrus-sac (relative to body size), and in possessing tegumental spines, testes that are oblique (rather than in tandem) and eight ovarian lobes. It differs further in having an intestinal caecum that extends anteriorly to the level of the vitelline follicles and in the position of the pharynx and cirrus-sac relative to each other (lateral in part) as well as to the gonads. M. botti n. sp. also lacks a metraterm. These are the first reports of these genera from fishes off Australia and from the southern hemisphere.
A Theoretical Study to Establish the Relationship Between the Three-dimensional Structure of Triose-phosphate Isomerase of Giardia Duodenalis and Point Mutations in the Respective Gene
Molecular and Cellular Probes. Oct, 2010 | Pubmed ID: 20561582
Predicting how point mutations in genes alter the tertiary and quarternary structure of proteins is central to a number of areas of molecular biology and has implications in relation to the function and evolution of molecules. In the present study, we theoretically assessed the effects of 20 point mutations detected previously in a region of the triose-phosphate isomerase gene (tpi) of the protozoan Giardia duodenalis on the three-dimensional structure of the 'wild-type' protein (TPI). Amino acid substitutions arising from codon variations were mainly located at surface-accessible sites or in hydrophobic pockets of TPI. None of the substitutions was predicted to exert a significant change to the fold or functionality of the enzyme, with the exception of one alteration (Arg100). Almost all substitutions were either conservative or semi-conservative, and retained or even improved the expected stability of the fold. Overall, the findings provide support for the "neutral theory", which contends that evolution at the molecular level is not solely shaped by "Darwinian selection but also by random drift of selectively neutral or nearly neutral mutants".
Genetic Classification of Echinococcus Granulosus Cysts from Humans, Cattle and Camels in Libya Using Mutation Scanning-based Analysis of Mitochondrial Loci
Molecular and Cellular Probes. Dec, 2010 | Pubmed ID: 20659552
We genetically classified Echinococcus granulosus from humans, cattle and camels in Libya utilizing DNA regions (designated pcox1 and pnad1) within the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase 1 (nad1) mitochondrial genes, respectively. Polymerase chain reaction (PCR)-based single-strand conformation polymorphism (SSCP) analysis of pcox1 and pnad1 amplicons derived from genomic DNA samples from individual cysts (n = 176) revealed four distinct electrophoretic profiles for each locus. Direct sequencing of selected amplicons representing each of these profiles defined four different sequence types for each locus, which were present in five different combinations (designated haplotypes A-E) amongst all 176 isolates. Phylogenetic analysis of concatenated sequence data for these five haplotypes, together with a range of well-defined reference sequences, inferred that all cyst isolates from humans (n = 55) and a small number from cattle (13% of 38) belonged to the G1-G3 complex of E. granulosus (or E. granulosus sensu stricto), whereas most (87%) cysts from cattle and all 83 of them from camels were linked to the G6-G10 complex (or Echinococcus canadensis). The present study provides a foundation for future large-scale studies of the epidemiology and ecology of E. granulosus in Libya and other African countries.
A Practical, Bioinformatic Workflow System for Large Data Sets Generated by Next-generation Sequencing
Nucleic Acids Research. Sep, 2010 | Pubmed ID: 20682560
Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism.
Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. Dec, 2010 | Pubmed ID: 20691809
In the United Kingdom, rabbits have been reported to harbour genotypes of Cryptosporidium (now recognized as C. cuniculus) identical to those from human patients exhibiting symptoms of cryptosporidiosis. The high density of rabbits in many regions of Australia, including both rural and urban as well as natural water catchments areas, and the absence of any information on Cryptosporidium from lagomorphs in this country stimulated the present study. We undertook an epidemiological study that genetically characterized Cryptosporidium from rabbits from four locations in Victoria by PCR-coupled sequencing and phylogenetic analysis of sequence data for loci within the small subunit of nuclear ribosomal RNA (SSU; for specific identification) and the 60kDa glycoprotein gene (gp60; for genotypic/subgenotypic identification). Cryptosporidium was detected in 12 (6.8%) of 176 individual faecal samples. For SSU, all 12 sequences were identical to each other and to that of C. cuniculus. For pgp60, all corresponding sequences matched the known genotype Vb, and were classified as subgenotype VbA23R3 (n=11) and VbA26R4 (n=1), which are both new records. Present evidence indicates that genotype Vb is limited to rabbits; however, it would be premature to conclude that this genotype is not zoonotic. Future studies should focus on the zoonotic potential of C. cuniculus from rabbits and a wide range of yet unstudied animals. (Nucleotide sequences reported in this paper are available in the GenBank database under accession nos. HM852431-HM852433).
Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes
PLoS Computational Biology. 2010 | Pubmed ID: 20711353
Neuronal activity is mediated through changes in the probability of stochastic transitions between open and closed states of ion channels. While differences in morphology define neuronal cell types and may underlie neurological disorders, very little is known about influences of stochastic ion channel gating in neurons with complex morphology. We introduce and validate new computational tools that enable efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. Comparison of five morphologically distinct neuronal cell types reveals that when all simulated neurons contain identical densities of stochastic ion channels, the amplitude of stochastic membrane potential fluctuations differs between cell types and depends on sub-cellular location. For typical neurons, the amplitude of membrane potential fluctuations depends on channel kinetics as well as open probability. Using a detailed model of a hippocampal CA1 pyramidal neuron, we show that when intrinsic ion channels gate stochastically, the probability of initiation of dendritic or somatic spikes by dendritic synaptic input varies continuously between zero and one, whereas when ion channels gate deterministically, the probability is either zero or one. At physiological firing rates, stochastic gating of dendritic ion channels almost completely accounts for probabilistic somatic and dendritic spikes generated by the fully stochastic model. These results suggest that the consequences of stochastic ion channel gating differ globally between neuronal cell-types and locally between neuronal compartments. Whereas dendritic neurons are often assumed to behave deterministically, our simulations suggest that a direct consequence of stochastic gating of intrinsic ion channels is that spike output may instead be a probabilistic function of patterns of synaptic input to dendrites.
Contact Lens & Anterior Eye : the Journal of the British Contact Lens Association. Feb, 2011 | Pubmed ID: 20829096
Trends in Neurosciences. Feb, 2011 | Pubmed ID: 21067825
Neuron types are classically defined by anatomical and physiological properties that determine how synaptic inputs are integrated. Here, we provide an overview of the evidence that, among neurons of a single type, integration of synaptic responses is further tuned according to the particular function that individual neurons carry out. Recent data suggest that tuning of synaptic responses is not restricted to sensory pathways, but extends to cognitive and motor circuits. We propose that tuning of synaptic integration results from general cellular mechanisms for optimization of information processing that are distinct from, but complementary to, homeostasis and memory storage. These cellular tuning mechanisms might be crucial for distributed computations underlying sensory, motor and cognitive functions.
Molecular and Cellular Probes. Feb, 2011 | Pubmed ID: 21075201
Polymerase chain reaction (PCR)-based single-strand conformation polymorphism (SSCP) and targeted sequencing were employed to genetically classify Echinococcus granulosus cysts from humans from 12 provinces in Mongolia using two DNA loci, designated pcox-1 and pnad-1, within the mitochondrial cytochrome c oxidase subunit 1 (cox-1) and NADH dehydrogenase subunit 1 (nad-1) genes, respectively. SSCP analysis of pcox-1 and pnad-1 amplicons produced from genomic DNA samples from individual E. granulosus cysts (n = 50) from individual humans displayed four distinct electrophoretic profiles for each pcox-1 and pnad-1. The direct sequencing of selected amplicons representing each of these profiles defined four distinct sequence types for each locus, present in four different combinations (designated as haplotypes M1-M4) for all 50 cyst isolates. Phylogenetic analysis of concatenated sequence data for these four haplotypes, including well-defined reference sequences, inferred that 68% of the cyst isolates belonged to the G1-G3 complex of E. granulosus (or E. granulosus sensu stricto), whereas the remaining (32%) were linked to the G6-G10 complex (or Echinococcus canadensis). Humans infected with E. granulosus cysts of the G1-G3 complex originated mainly from the eastern regions of Mongolia, whereas those harbouring cysts of the G6-G10 complex were from the western part of this country. The present study provides a first glimpse of the genetic composition of E. granulosus from humans in Mongolia, and forms a foundation for future studies of the epidemiology and ecology of the parasite(s) in animals and humans in this and surrounding countries.
A Critical Role for Neurofascin in Regulating Action Potential Initiation Through Maintenance of the Axon Initial Segment
Neuron. Mar, 2011 | Pubmed ID: 21382554
The axon initial segment (AIS) is critical for the initiation and propagation of action potentials. Assembly of the AIS requires interactions between scaffolding molecules and voltage-gated sodium channels, but the molecular mechanisms that stabilize the AIS are poorly understood. The neuronal isoform of Neurofascin, Nfasc186, clusters voltage-gated sodium channels at nodes of Ranvier in myelinated nerves: here, we investigate its role in AIS assembly and stabilization. Inactivation of the Nfasc gene in cerebellar Purkinje cells of adult mice causes rapid loss of Nfasc186 from the AIS but not from nodes of Ranvier. This causes AIS disintegration, impairment of motor learning and the abolition of the spontaneous tonic discharge typical of Purkinje cells. Nevertheless, action potentials with a modified waveform can still be evoked and basic motor abilities remain intact. We propose that Nfasc186 optimizes communication between mature neurons by anchoring the key elements of the adult AIS complex.
Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. Jul, 2011 | Pubmed ID: 21439404
Given the HIV epidemic in Malaysia, genetic information on opportunistic pathogens, such as Cryptosporidium and Giardia, in HIV/AIDS patients is pivotal to enhance our understanding of epidemiology, patient care, management and disease surveillance. In the present study, 122 faecal samples from HIV/AIDS patients were examined for the presence of Cryptosporidium oocysts and Giardia cysts using a conventional coproscopic approach. Such oocysts and cysts were detected in 22.1% and 5.7% of the 122 faecal samples, respectively. Genomic DNAs from selected samples were tested in a nested-PCR, targeting regions of the small subunit (SSU) of nuclear ribosomal RNA and the 60kDa glycoprotein (gp60) genes (for Cryptosporidium), and the triose-phosphate isomerase (tpi) gene (for Giardia), followed by direct sequencing. The sequencing of amplicons derived from SSU revealed that Cryptosporidium parvum was the most frequently detected species (64% of 25 samples tested), followed by C. hominis (24%), C. meleagridis (8%) and C. felis (4%). Sequencing of a region of gp60 identified C. parvum subgenotype IIdA15G2R1 and C. hominis subgenotypes IaA14R1, IbA10G2R2, IdA15R2, IeA11G2T3R1 and IfA11G1R2. Sequencing of amplicons derived from tpi revealed G. duodenalis assemblage A, which is of zoonotic importance. This is the first report of C. hominis, C. meleagridis and C. felis from Malaysian HIV/AIDS patients. Future work should focus on an extensive analysis of Cryptosporidium and Giardia in such patients as well as in domestic and wild animals, in order to improve the understanding of transmission patterns and dynamics in Malaysia. It would also be particularly interesting to establish the relationship among clinical manifestation, CD4 cell counts and genotypes/subgenotypes of Cryptosporidium and Giardia in HIV/AIDS patients. Such insights would assist in a better management of clinical disease in immuno-deficient patients as well as improved preventive and control strategies.
Dorsal-ventral Organization of Theta-like Activity Intrinsic to Entorhinal Stellate Neurons is Mediated by Differences in Stochastic Current Fluctuations
The Journal of Physiology. Jun, 2011 | Pubmed ID: 21502290
The membrane potential dynamics of stellate neurons in layer II of the medial entorhinal cortex are important for neural encoding of location. Previous studies suggest that these neurons generate intrinsic theta-frequency membrane potential oscillations, with a period that depends on neuronal location on the dorsal–ventral axis of themedial entorhinal cortex, and which in behaving animals could support generation of grid-like spatial firing fields. To address the nature and organization of this theta-like activity, we adopt the Lombmethod of least-squares spectral analysis. We demonstrate that peaks in frequency spectra that differ significantly from Gaussian noise do not necessarily imply the existence of a periodic oscillator, but can instead arise from filtered stochastic noise or a stochastic random walk. We show that theta-like membrane potential activity recorded fromstellate neurons in mature brain slices is consistentwith stochastic mechanisms, but not with generation by a periodic oscillator. The dorsal–ventral organization of intrinsic theta-likemembrane potential activity, and themodification of this activity during block of HCN channels, both reflect altered frequency distributions of stochastic spectral peaks, rather than tuning of a periodic oscillator. Our results demonstrate the importance of distinguishing periodic oscillations from stochastic processes.We suggest that dorsal–ventral tuning of theta-like membrane potential activity is due to differences in stochastic current fluctuations resulting from organization of ion channels that also control synaptic integration.
A Molecular Toolbox for Rapid Generation of Viral Vectors to Up- or Down-Regulate Neuronal Gene Expression in Vivo
Frontiers in Molecular Neuroscience. 2011 | Pubmed ID: 21772812
We introduce a molecular toolbox for manipulation of neuronal gene expression in vivo. The toolbox includes promoters, ion channels, optogenetic tools, fluorescent proteins, and intronic artificial microRNAs. The components are easily assembled into adeno-associated virus (AAV) or lentivirus vectors using recombination cloning. We demonstrate assembly of toolbox components into lentivirus and AAV vectors and use these vectors for in vivo expression of inwardly rectifying potassium channels (Kir2.1, Kir3.1, and Kir3.2) and an artificial microRNA targeted against the ion channel HCN1 (HCN1 miRNA). We show that AAV assembled to express HCN1 miRNA produces efficacious and specific in vivo knockdown of HCN1 channels. Comparison of in vivo viral transduction using HCN1 miRNA with mice containing a germ line deletion of HCN1 reveals similar physiological phenotypes in cerebellar Purkinje cells. The easy assembly and re-usability of the toolbox components, together with the ability to up- or down-regulate neuronal gene expression in vivo, may be useful for applications in many areas of neuroscience.
Genome Sequence of Kosmotoga Olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B Oil Platform in the North Sea
Journal of Bacteriology. Oct, 2011 | Pubmed ID: 21914881
Kosmotoga olearia strain TBF 19.5.1 is a member of the Thermotogales that grows best at 65°C and very well even at 37°C. Information about this organism is important for understanding the evolution of mesophiles from thermophiles. Its genome sequence reveals extensive gene gains and a large content of mobile genetic elements. It also contains putative hydrogenase genes that have no homologs in the other member of the Thermotogales.
Genome Sequence of Thermotoga Sp. Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor Near Ribeira Quente, the Azores
Journal of Bacteriology. Oct, 2011 | Pubmed ID: 21952543
Thermotoga sp. strain RQ2 is probably a strain of Thermotoga maritima. Its complete genome sequence allows for an examination of the extent and consequences of gene flow within Thermotoga species and strains. Thermotoga sp. RQ2 differs from T. maritima in its genes involved in myo-inositol metabolism. Its genome also encodes an apparent fructose phosphotransferase system (PTS) sugar transporter. This operon is also found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales. These are the first reported PTS transporters in the Thermotogales.
The Journal of Neuroscience : the Official Journal of the Society for Neuroscience. Nov, 2011 | Pubmed ID: 22072667
Long-term synaptic plasticity requires postsynaptic influx of Ca²⁺ and is accompanied by changes in dendritic spine size. Unless Ca²⁺ influx mechanisms and spine volume scale proportionally, changes in spine size will modify spine Ca²⁺ concentrations during subsequent synaptic activation. We show that the relationship between Ca²⁺ influx and spine volume is a fundamental determinant of synaptic stability. If Ca²⁺ influx is undercompensated for increases in spine size, then strong synapses are stabilized and synaptic strength distributions have a single peak. In contrast, overcompensation of Ca²⁺ influx leads to binary, persistent synaptic strengths with double-peaked distributions. Biophysical simulations predict that CA1 pyramidal neuron spines are undercompensating. This unifies experimental findings that weak synapses are more plastic than strong synapses, that synaptic strengths are unimodally distributed, and that potentiation saturates for a given stimulus strength. We conclude that structural plasticity provides a simple, local, and general mechanism that allows dendritic spines to foster both rapid memory formation and persistent memory storage.
Cryptic Parasite Revealed Improved Prospects for Treatment and Control of Human Cryptosporidiosis Through Advanced Technologies
Advances in Parasitology. 2011 | Pubmed ID: 22137584
Cryptosporidium is an important genus of parasitic protozoa of humans and other vertebrates and is a major cause of intestinal disease globally. Unlike many common causes of infectious enteritis, there are no widely available, effective vaccine or drug-based intervention strategies for Cryptosporidium, and control is focused mainly on prevention. This approach is particularly deficient for infections of severely immunocompromised and/or suppressed, the elderly or malnourished people. However, cryptosporidiosis also presents a significant burden on immunocompetent individuals, and can, for example have lasting effects on the physical and mental development of children infected at an early age. In the last few decades, our understanding of Cryptosporidium has expanded significantly in numerous areas, including the parasite life-cycle, the processes of excystation, cellular invasion and reproduction, and the interplay between parasite and host. Nonetheless, despite extensive research, many aspects of the biology of Cryptosporidium remain unknown, and treatment and control are challenging. Here, we review the current state of knowledge of Cryptosporidium, with a focus on major advances arising from the recently completed genome sequences of the two species of greatest relevance in humans, namely Cryptosporidium hominis and Cryptosporidium parvum. In addition, we discuss the potential of next-generation sequencing technologies, new advances in in silico analyses and progress in in vitro culturing systems to bridge these gaps and to lead toward effective treatment and control of cryptosporidiosis.
Mutation Scanning-based Analysis of Anisakid Larvae from Sillago Flindersi from Bass Strait, Australia
Electrophoresis. Feb, 2012 | Pubmed ID: 22287178
Anisakidosis is an important fish-borne disease caused by the larvae of anisakid nematodes, which affects humans and a range of other animals. The accurate identification of members of this nematode group is central to investigating the epidemiology of the parasites and in the surveillance and control of anisakidosis. It is now well known that morphological identification alone does not allow specific identification, particularly of larval stages. To better understand the epidemiology of anisakid nematodes in southern Australian fishes and the potential risks posed to human health, a survey of 50 specimens of the commercially important fish, Sillago flindersi, from Bass Strait, Australia was conducted. We characterised anisakid larvae by PCR-coupled mutation scanning, sequencing and phylogenetic analyses of the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA. This study revealed that 92% of the S. flindersi examined were infected with anisakids (n=194), which were represented by seven genotypes. Phylogenetic analyses of the genotypes defined herein, together with reference sequence for Anisakis pegreffii and Hysterothylacium sp. from public databases (i.e. GenBank), revealed the presence of A. pegreffii (n=24), Hysterothylacium larval type IV (n=90) and Hysterothylacium larval type VIII (n=80) in S. flindersi. Thus, the PCR-coupled mutation scanning approach employed herein is an effective tool for the genetic characterisation of anisakid nematodes for diagnostic and analytical purposes (nucleotide sequences reported in this paper are available in the GenBank database under accession nos. JN631796-809).
Molecular and Biochemical Parasitology. Feb, 2012 | Pubmed ID: 22349630
Cystic echinococcosis in humans and livestock animals is caused by infection with the cestode parasite Echinococcus granulosus. A number of genotypes of the parasite (designated G1-G10) are known to exist, with the genotype cluster G1-G3 and genotype G6 being responsible for the majority of humans infections. A recombinant vaccine has been developed for use in livestock to prevent infection with E. granulosus. The vaccine is based on the antigen EG95 which is expressed in the early larval stage (oncosphere) of the parasite. The EG95 antigen was originally cloned from the G1 genotype of E. granulosus and the protein has been found to be encoded by members of a small family of related genes in this genotype. Reliable information has not been available about the likely efficacy of the EG95 vaccine against genotypes other than G1. In this study, genomic DNA cloning techniques were used to characterize seven eg95-related gene fragments from the G6 genotype of E. granulosus. Three proteins appear to be encoded by these genes. Considerable differences were found between the EG95 related proteins from the G6 genotype compared with the EG95 protein from the G1 genotype. These differences suggest that the EG95-related proteins from the G6 genotype may have different antigenic epitopes compared with the current vaccine antigen. Data presented in this study have implications for future vaccine design and provide the information that would enable a G6 genotype-specific vaccine to be developed against E. granulosus, should this be considered a desirable addition to the available tools for control of cystic echinococcosis transmission.
Molecular and Cellular Probes. Feb, 2012 | Pubmed ID: 22056326
Infectious diarrhoeal diseases represent a major socio-economic burden to humans, and are linked to a range of pathogens, including viruses, bacteria and protists. The accurate detection of such pathogens is central to control. However, detection often relies on methods that have limited diagnostic sensitivity and specificity. Here, we assessed an automated, robotic platform for the simultaneous detection of eight major pathogens associated with infectious diarrhoea. Genomic DNA samples (n = 167) from faeces from humans with diarrhoea and diagnosed as cryptosporidiosis, and 100 uninfected control subjects, were tested for adenovirus 40/41, norovirus, Clostridium difficile, Campylobacter, Salmonella, Shigella, Cryptosporidium and Giardia by multiplexed-tandem PCR, and also characterized by single-strand conformation polymorphism analysis (SSCP) and selective sequencing. All 167 samples tested positive for Cryptosporidium, five for adenovirus 40/41, four for Campylobacter, three for C. difficile and seven for Shigella spp., with no false positive results for any assay. The automated PCR exhibited a high sensitivity, with <10 individual pathogens being readily detected. The robotic detection platform assessed here represents a sensitive, high-throughput tool for key pathogens linked to infectious diarrhoea in humans. This platform requires little molecular biological expertise and is well suited to various diagnostic facilities and settings.