Noise, transient dynamics, and the generation of realistic interspike interval variation in square-wave burster neurons

First return maps of interspike intervals for biological neurons that generate repetitive bursts of impulses can display stereotyped structures (neuronal signatures). Such structures have been linked to the possibility of multicoding and multifunctionality in neural networks that produce and control rhythmical motor patterns. In some cases, isolating the neurons from their synaptic network revealsirregular, complex signatures that have been regarded as evidence of intrinsic, chaotic behavior. We show that incorporation of dynamical noise into minimal neuron models of square-wave bursting (either conductance-based or abstract) produces signatures akin to those observed in biological examples, without the need for fine-tuning of parameters or ad hoc constructions for inducing chaotic activity. The form of the stochastic term is not strongly constrained, and can approximate several possible sources of noise, e.g. random channel gating or synaptic bombardment. The cornerstone of this signature generation mechanism is the rich, transient, but deterministic dynamics inherent in the square-wave (saddle-node/homoclinic) mode of neuronal bursting. We show that noise causes the dynamics to populate a complex transient scaffolding or skeleton in state space, even for models that (without added noise) generate only periodic activity (whether in bursting or tonic spiking mode).Comment: REVTeX4-1, 18 pages, 9 figure

Squamate Conserved Loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles

The identification of conserved loci across genomes, along with advances in target capture methods and high‐throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches—anchored hybrid enrichment (AHE) and ultraconserved elements (UCE)—and both approaches have proven useful for addressing questions in phylogenomics, phylogeography and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci set, a single integrated probe set that can generate high‐quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness and suggest areas for future improvement.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139986/1/men12681_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139986/2/men12681-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139986/3/men12681.pd

Population Genetic Structure and Species Delimitation of a Widespread, Neotropical Dwarf Gecko

Amazonia harbors the greatest biological diversity on Earth. One trend that spans Amazonian taxa is that most taxonomic groups either exhibit broad geographic ranges or small restricted ranges. This is likely because many traits that determine a species range size, such as dispersal ability or body size, are autocorrelated. As such, it is rare to find groups that exhibit both large and small ranges. Once identified, however, these groups provide a powerful system for isolating specific traits that influence species distributions. One group of terrestrial vertebrates, gecko lizards, tends to exhibit small geographic ranges. Despite one exception, this applies to the Neotropical dwarf geckos of the genus Gonatodes. This exception, Gonatodes humeralis, has a geographic distribution almost 1,000,000 km2 larger than the combined ranges of its 30 congeners. As the smallest member of its genus and a gecko lizard more generally, G. humeralis is an unlikely candidate to be a wide-ranged Amazonian taxon. To test whether or not G. humeralis is one or more species, we generated molecular genetic data using restriction-site associated sequencing (RADseq) and traditional Sanger methods for samples from across its range and conducted a phylogeographic study. We conclude that G. humeralis is, in fact, a single species across its contiguous range in South America. Thus, Gonatodes is a unique clade among Neotropical taxa, containing both wide-ranged and range-restricted taxa, which provides empiricists with a powerful model system to correlate complex species traits and distributions. Additionally, we provide evidence to support species-level divergence of the allopatric population from Trinidad and we resurrect the name Gonatodes ferrugineus from synonymy for this population

A comparison between magnetic resonance angiography at 3 teslas (time-of-flight and contrast-enhanced) and flat-panel digital subtraction angiography in the assessment of embolized brain aneurysms

PURPOSE: To compare the time-of-flight and contrast-enhanced- magnetic resonance angiography techniques in a 3 Tesla magnetic resonance unit with digital subtraction angiography with the latest flat-panel technology and 3D reconstruction in the evaluation of embolized cerebral aneurysms. INTRODUCTION: Many embolized aneurysms are subject to a recurrence of intra-aneurismal filling. Traditionally, imaging surveillance of coiled aneurysms has consisted of repeated digital subtraction angiography. However, this method has a small but significant risk of neurological complications, and many authors have advocated the use of noninvasive imaging methods for the surveillance of embolized aneurysms. METHODS: Forty-three aneurysms in 30 patients were studied consecutively between November 2009 and May 2010. Two interventional neuroradiologists rated the time-of-flight-magnetic resonance angiography, the contrast-enhanced-magnetic resonance angiography, and finally the digital subtraction angiography, first independently and then in consensus. The status of aneurysm occlusion was assessed according to the Raymond scale, which indicates the level of recanalization according to degrees: Class 1: excluded aneurysm; Class 2: persistence of a residual neck; Class 3: persistence of a residual aneurysm. The agreement among the analyses was assessed by applying the Kappa statistic. RESULTS: Inter-observer agreement was excellent for both methods (K = 0.93; 95 % CI: 0.84-1). Inter-technical agreement was almost perfect between time-of-flight-magnetic resonance angiography and digital subtraction angiography (K = 0.98; 95 % CI: 0.93-1) and between time-of-flight-magnetic resonance angiography and contrast-enhanced-magnetic resonance angiography (K = 0.98; 95% CI: 0.93-1). Disagreement occurred in only one case (2.3%), which was classified as Class I by time-of-flight-magnetic resonance angiography and Class II by digital subtraction angiography. The agreement between contrast-enhanced-magnetic resonance angiography and digital subtraction angiography was perfect (K = 1; 95% CI: 1-1). In three patients, in-stent stenosis was identified by magnetic resonance angiography but not confirmed by digital subtraction angiography. CONCLUSION: Digital subtraction angiography and both 3T magnetic resonance angiography techniques have excellent reproducibility for the assessment of aneurysms embolized exclusively with coils. In those cases also treated with stent remodeling, digital subtraction angiography may still be necessary to confirm eventual parent artery stenosis, as identified by magnetic resonance angiography

Cytokines Interleukin-1β and Tumor Necrosis Factor-α Regulate Different Transcriptional and Alternative Splicing Networks in Primary β-Cells

OBJECTIVE: Cytokines contribute to pancreatic beta-cell death in type 1 diabetes. This effect is mediated by complex gene networks that remain to be characterized. We presently utilized array analysis to define the global expression pattern of genes, including spliced variants, modified by the cytokines interleukin (IL)-1beta + interferon (IFN)-gamma and tumor necrosis factor (TNF)-alpha + IFN-gamma in primary rat beta-cells. RESEARCH DESIGN AND METHODS: Fluorescence-activated cell sorter-purified rat beta-cells were exposed to IL-1beta + IFN-gamma or TNF-alpha + IFN-gamma for 6 or 24 h, and global gene expression was analyzed by microarray. Key results were confirmed by RT-PCR, and small-interfering RNAs were used to investigate the mechanistic role of novel and relevant transcription factors identified by pathway analysis. RESULTS Nearly 16,000 transcripts were detected as present in beta-cells, with temporal differences in the number of genes modulated by IL-1beta + IFNgamma or TNF-alpha + IFN-gamma. These cytokine combinations induced differential expression of inflammatory response genes, which is related to differential induction of IFN regulatory factor-7. Both treatments decreased the expression of genes involved in the maintenance of beta-cell phenotype and growth/regeneration. Cytokines induced hypoxia-inducible factor-alpha, which in this context has a proapoptotic role. Cytokines also modified the expression of >20 genes involved in RNA splicing, and exon array analysis showed cytokine-induced changes in alternative splicing of >50% of the cytokine-modified genes. CONCLUSIONS: The present study doubles the number of known genes expressed in primary beta-cells, modified or not by cytokines, and indicates the biological role for several novel cytokine-modified pathways in beta-cells. It also shows that cytokines modify alternative splicing in beta-cells, opening a new avenue of research for the field.Journal ArticleResearch Support, Non-U.S. Gov'tinfo:eu-repo/semantics/publishe

Herpetofauna of protected areas in the Caatinga II: Serra da Capivara National Park, Piauí, Brazil

We provide a list of amphibians, lizards, chelonians, and snakes collected during a 30-day expedition to the Serra da Capivara National Park, Piauí State, Brazil. Thirty-seven pitfall trap arrays composed of 4 buckets each, along with glue traps, funnel traps, and haphazard searches, were used to sample the herpetofaunal diversity. We recorded 17 species of lizards, 1 caecilian, 1 chelonian, 7 frogs, and 11 snakes. Rarefaction curves suggest that local biodiversity is still underestimated. An atypical drought during the period of study may have contributed to lower captures of certain groups, especially amphibians and snakes. The presence of water-dependent and forest-dependent species within local canyons (“Boqueirões”) suggests that these areas harbor faunas associated with relictual rainforest fragments and need to be better studied and managed accordinglyFil: Barbosa de Queiroga Calvacanti, Lucas. Universidade Federal Da Paraiba; BrasilFil: Borges Costa, Tais. Universidade Federal Da Paraiba; BrasilFil: Rinaldi Colli, Guarino. Universidade Do Brasilia; BrasilFil: Corrêa Costa, Gabriel. Universidade Federal Do Rio Grande Do Norte. Centro de Biociencias. Departamento de Boanica, Ecologia E Zoologia; BrasilFil: Rodrigues França, Frederico Gustavo. Universidade Federal Da Paraiba; BrasilFil: Oliveira Mesquita, Daniel. Universidade Federal Da Paraiba; BrasilFil: Silva Palmeira, Cristiane Nikely. Universidade Federal de Alagoas; BrasilFil: Pelegrin, Nicolas. Universidad Nacional de Cordoba. Facultad de Cs.exactas Fisicas y Naturales. Centro de Zoologia Aplicada; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; ArgentinaFil: Soares, Ana Hemínia Bello. Universidade Do Brasilia; BrasilFil: Tucker, Derek B.. University Brigham Young; Estados UnidosFil: Garda, Adrian Antonio. Universidade Federal do Rio Grande do Norte; Brasi

Meta-Analysis of mitochondrial DNA reveals several population bottlenecks during worldwide migrations of cattle

Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role.Facultad de Ciencias VeterinariasInstituto de Genética Veterinari

Analysis of the expression of PIWI-interacting RNAs during cardiac differentiation of human pluripotent stem cells

PIWI-interacting RNAs (piRNAs) are a class of non-coding RNAs initially thought to be restricted exclusively to germline cells. In recent years, accumulating evidence has demonstrated that piRNAs are actually expressed in pluripotent, neural, cardiac and even cancer cells. However, controversy remains around the existence and function of somatic piRNAs. Using small RNA-seq samples from H9 pluripotent cells differentiated to mesoderm progenitors and cardiomyocytes we identified the expression of 447 piRNAs, of which 241 were detected in pluripotency, 218 in mesoderm and 171 in cardiac cells. The majority of them originated from the sense strand of protein coding and lncRNAs genes in all stages of differentiation, though no evidences for secondary piRNAs (ping-pong) were found. Genes hosting piRNAs in cardiac samples were related to critical biological processes in the heart, like contraction and cardiac muscle development. Our results indicate that somatic piRNAs might have a role in fine-tuning the expression of genes involved in differentiation of pluripotent cells to cardiomyocytes.Fil: la Greca, Alejandro Damián. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Scarafia, Maria Agustina. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Hernández Cañás, María Clara. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; ArgentinaFil: Perez, Maria Nelba. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Castañeda, Sheila Lucia. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Colli, Carolina. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Möbbs, Alan Miqueas. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Santín Velazque, Natalia Lucía. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Neiman, Gabriel. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Garate, Ximena. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Aban, Cyntia Estefania. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Waisman, Ariel. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Moro, Lucía Natalia. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Sevlever, Gustavo. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; ArgentinaFil: Luzzani, Carlos Daniel. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Miriuka, Santiago Gabriel. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin