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https://www.readbyqxmd.com/read/29222512/improving-gene-regulatory-network-inference-by-incorporating-rates-of-transcriptional-changes
#1
Jigar S Desai, Ryan C Sartor, Lovely Mae Lawas, S V Krishna Jagadish, Colleen J Doherty
Organisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29196322/a-new-high-efficacy-non-invasive-transcranial-electric-stimulation-tuned-to-local-neurodynamics
#2
Carlo Cottone, Andrea Cancelli, Patrizio Pasqualetti, Camillo Porcaro, Carlo Salustri, Franca Tecchio
In this paper, we pose the following working hypothesis: in humans, transcranial electric stimulation (tES) with a time course that mimics the endogenous activity of its target is capable of altering the target's excitability. In our case, the target was the primary motor cortex (M1). We identified the endogenous neurodynamics of hand M1's subgroups of pyramidal neuronal pools in each of our subjects by applying Functional Source Separation (FSS) to their electroencephalographic (EEG) recordings. We then tested whether the cortico-spinal excitability of the hand representation under the above described stimulation, which we named transcranial Individual neuroDynamics Stimulation (tIDS), was higher than in the absence of stimulation (baseline)...
December 1, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29187968/the-xeric-side-of-the-brazilian-atlantic-forest-the-forces-shaping-phylogeographic-structure-of-cacti
#3
Fernando Faria Franco, Cecília Leiko Jojima, Manolo Fernandez Perez, Daniela Cristina Zappi, Nigel Taylor, Evandro Marsola Moraes
In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha)...
November 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29178177/cargo-crowding-at-actin-rich-regions-along-axons-causes-local-traffic-jams
#4
Parul Sood, Kausalya Murthy, T Vinod Kumar, Michael L Nonet, Gautam I Menon, Sandhya P Koushika
Steady axonal cargo flow is central to the functioning of healthy neurons. However, a substantial fraction of cargo in axons remains stationary up to several minutes (Kang, Tian et al. 2008, Tang, Scott et al. 2012, Tang, Scott et al. 2013, Iacobucci, Rahman et al. 2014). We examine the transport of precursors of synaptic vesicles (pre-SVs), endosomes and mitochondria in C. elegans touch receptor neurons (TRNs), showing that stationary cargo are predominantly present at actin-rich regions along the neuronal process...
November 27, 2017: Traffic
https://www.readbyqxmd.com/read/29167679/effects-of-mountain-uplift-and-climatic-oscillations-on-phylogeography-and-species-divergence-in-four-endangered-notopterygium-herbs
#5
Khurram Shahzad, Yun Jia, Fu-Lin Chen, Umar Zeb, Zhong-Hu Li
Mountain uplift and climatic fluctuations are important driving forces that have affected the geographic distribution and population dynamics history of organisms. However, it is unclear how geological and climatic events might have affected the phylogeographic history and species divergence in high-alpine herbal plants. In this study, we analyzed the population demographic history and species differentiation of four endangered Notopterygium herbs on the high-altitude Qinghai-Tibetan Plateau (QTP) and adjacent areas...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163104/transcranial-random-noise-stimulation-does-not-improve-behavioral-and-neurophysiological-measures-in-patients-with-subacute-vegetative-unresponsive-wakefulness-state-vs-uws
#6
Mauro Mancuso, Laura Abbruzzese, Stefania Canova, Giulia Landi, Simone Rossi, Emiliano Santarnecchi
Background: The absence of efficient treatments capable to promote central nervous system recovery in patients in vegetative state (VS) due to a severe acquired brain injury highlights the need of exploring alternative neuromodulatory treatments that can lead to neurobehavioral gains. Some encouraging preliminary observations suggest that transcranial direct current stimulation could be effective in disorders of consciousness (DoC) patients, especially when applied on the dorsolateral prefrontal cortex (DLPFC) in patients with minimally conscious state (MCS) but not in those with VS...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/29158966/mitochondrial-genomes-of-three-tetrigoidea-species-and-phylogeny-of-tetrigoidea
#7
Li-Liang Lin, Xue-Juan Li, Hong-Li Zhang, Zhe-Min Zheng
The mitochondrial genomes (mitogenomes) of Formosatettix qinlingensis, Coptotettix longjiangensis and Thoradonta obtusilobata (Orthoptera: Caelifera: Tetrigoidea) were sequenced in this study, and almost the entire mitogenomes of these species were determined. The mitogenome sequences obtained for the three species were 15,180, 14,495 and 14,538 bp in length, respectively, and each sequence included 13 protein-coding genes (PCGs), partial sequences of rRNA genes (rRNAs), tRNA genes (tRNAs) and a A + T-rich region...
2017: PeerJ
https://www.readbyqxmd.com/read/29155756/transcranial-electrical-brain-stimulation-in-alert-rodents
#8
Brita Fritsch, Anne-Kathrin Gellner, Janine Reis
Transcranial electrical brain stimulation can modulate cortical excitability and plasticity in humans and rodents. The most common form of stimulation in humans is transcranial direct current stimulation (tDCS). Less frequently, transcranial alternating current stimulation (tACS) or transcranial random noise stimulation (tRNS), a specific form of tACS using an electrical current applied randomly within a pre-defined frequency range, is used. The increase of noninvasive electrical brain stimulation research in humans, both for experimental and clinical purposes, has yielded an increased need for basic, mechanistic, safety studies in animals...
November 2, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29142279/modifying-response-times-in-the-simon-task-with-transcranial-random-noise-stimulation
#9
James Robert McIntosh, Carsten Mehring
Perceptual decisions pervade our every-day lives, and can align or conflict with inbuilt biases. We investigated these conflicting biases by applying transcranial random noise stimulation (tRNS) while subjects took part in a visual Simon task - a paradigm where irrelevant spatial cues influence the response times of subjects to relevant colour cues. We found that tRNS reduces the response time of subjects independent of the congruence between spatial and colour cues, but dependent on the baseline response time, both between subjects and across conditions within subjects...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29061290/beyond-time-and-space-the-effect-of-a-lateralized-sustained-attention-task-and-brain-stimulation-on-spatial-and-selective-attention
#10
Nir Shalev, Linde De Wandel, Paul Dockree, Nele Demeyere, Magdalena Chechlacz
The Theory of Visual Attention (TVA) provides a mathematical formalisation of the "biased competition" account of visual attention. Applying this model to individual performance in a free recall task allows the estimation of 5 independent attentional parameters: visual short-term memory (VSTM) capacity, speed of information processing, perceptual threshold of visual detection; attentional weights representing spatial distribution of attention (spatial bias), and the top-down selectivity index. While the TVA focuses on selection in space, complementary accounts of attention describe how attention is maintained over time, and how temporal processes interact with selection...
October 3, 2017: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/29051499/an-integrative-method-to-decode-regulatory-logics-in-gene-transcription
#11
Bin Yan, Daogang Guan, Chao Wang, Junwen Wang, Bing He, Jing Qin, Kenneth R Boheler, Aiping Lu, Ge Zhang, Hailong Zhu
Modeling of transcriptional regulatory networks (TRNs) has been increasingly used to dissect the nature of gene regulation. Inference of regulatory relationships among transcription factors (TFs) and genes, especially among multiple TFs, is still challenging. In this study, we introduced an integrative method, LogicTRN, to decode TF-TF interactions that form TF logics in regulating target genes. By combining cis-regulatory logics and transcriptional kinetics into one single model framework, LogicTRN can naturally integrate dynamic gene expression data and TF-DNA-binding signals in order to identify the TF logics and to reconstruct the underlying TRNs...
October 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/29046685/comparative-analysis-of-the-complete-plastomes-of-apostasia-wallichii-and-neuwiedia-singapureana-apostasioideae-reveals-different-evolutionary-dynamics-of-ir-ssc-boundary-among-photosynthetic-orchids
#12
Zhitao Niu, Jiajia Pan, Shuying Zhu, Ludan Li, Qingyun Xue, Wei Liu, Xiaoyu Ding
Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29038765/the-complete-chloroplast-genome-sequence-of-strawberry-fragaria-%C3%A2-%C3%A3-%C3%A2-ananassa-duch-and-comparison-with-related-species-of-rosaceae
#13
Hui Cheng, Jinfeng Li, Hong Zhang, Binhua Cai, Zhihong Gao, Yushan Qiao, Lin Mi
Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F. × ananassa 'Benihoppe' using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences...
2017: PeerJ
https://www.readbyqxmd.com/read/28986552/phylogeny-historical-biogeography-and-characters-evolution-of-the-drought-resistant-fern-pyrrosia-mirbel-polypodiaceae-inferred-from-plastid-and-nuclear-markers
#14
Xueping Wei, Yaodong Qi, Xianchun Zhang, Li Luo, Hui Shang, Ran Wei, Haitao Liu, Bengang Zhang
Pyrrosia s.l. comprises ca. 60 species with a disjunct Africa/Asia and Australia distribution. The infrageneric classification of Pyrrosia s.l. is controversial based on the phylogenetic analyses of chloroplast markers and morphology. Based on the expanded taxon sampling of Pyrrosia s.l. (51 species), we investigated its phylogeny, biogeography, character evolution and environmental adaptation by employing five chloroplastid markers (rbcL, matK, psbA-trnH, and rps4 + rps4-trnS) and one single (low)-copy nuclear gene, LEAFY...
October 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28921774/modulating-vicarious-tactile-perception-with-transcranial-electrical-current-stimulation
#15
Natalie C Bowling, Michael J Banissy
Our capacity to share the experiences of others is a critical part of social behaviour. One process thought to be important for this is vicarious perception. Passively viewing touch activates some of the same network of brain regions as the direct experience of touch. This vicarious experience is usually implicit, but for some people, viewing touch evokes conscious tactile sensations (mirror-touch synaesthesia). Recent work has attempted to induce conscious vicarious touch in those that do not normally experience these sensations, using transcranial direct current stimulation (tDCS)...
October 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/28912671/brownian-optogenetic-noise-photostimulation-on-the-brain-amplifies-somatosensory-evoked-field-potentials
#16
Nayeli Huidobro, Abraham Mendez-Fernandez, Ignacio Mendez-Balbuena, Ranier Gutierrez, Rumyana Kristeva, Elias Manjarrez
Stochastic resonance (SR) is an inherent and counter-intuitive mechanism of signal-to-noise ratio (SNR) facilitation in biological systems associated with the application of an intermediate level of noise. As a first step to investigate in detail this phenomenon in the somatosensory system, here we examined whether the direct application of noisy light on pyramidal neurons from the mouse-barrel cortex expressing a light-gated channel channelrhodopsin-2 (ChR2) can produce facilitation in somatosensory evoked field potentials...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28900180/emotion-perception-improvement-following-high-frequency-transcranial-random-noise-stimulation-of-the-inferior-frontal-cortex
#17
Tegan Penton, Laura Dixon, Lauren Jayne Evans, Michael J Banissy
Facial emotion perception plays a key role in interpersonal communication and is a precursor for a variety of socio-cognitive abilities. One brain region thought to support emotion perception is the inferior frontal cortex (IFC). The current study aimed to examine whether modulating neural activity in the IFC using high frequency transcranial random noise stimulation (tRNS) could enhance emotion perception abilities. In Experiment 1, participants received either tRNS to IFC or sham stimulation prior to completing facial emotion and identity perception tasks...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28889119/sham-transcranial-electrical-stimulation-and-its-effects-on-corticospinal-excitability-a-systematic-review-and-meta-analysis
#18
Thusharika D Dissanayaka, Maryam Zoghi, Michael Farrell, Gary F Egan, Shapour Jaberzadeh
Sham stimulation is used in randomized controlled trials (RCTs) to assess the efficacy of active stimulation and placebo effects. It should mimic the characteristics of active stimulation to achieve blinding integrity. The present study was a systematic review and meta-analysis of the published literature to identify the effects of sham transcranial electrical stimulation (tES) - including anodal and cathodal transcranial direct current stimulation (a-tDCS, c-tDCS), transcranial alternating current stimulation (tACS), transcranial random noise stimulation (tRNS) and transcranial pulsed current stimulation (tPCS) - on corticospinal excitability (CSE), compared to baseline in healthy individuals...
September 11, 2017: Reviews in the Neurosciences
https://www.readbyqxmd.com/read/28874552/global-transcriptional-regulatory-network-for-escherichia-coli-robustly-connects-gene-expression-to-transcription-factor-activities
#19
Xin Fang, Anand Sastry, Nathan Mih, Donghyuk Kim, Justin Tan, James T Yurkovich, Colton J Lloyd, Ye Gao, Laurence Yang, Bernhard O Palsson
Transcriptional regulatory networks (TRNs) have been studied intensely for >25 y. Yet, even for the Escherichia coli TRN-probably the best characterized TRN-several questions remain. Here, we address three questions: (i) How complete is our knowledge of the E. coli TRN; (ii) how well can we predict gene expression using this TRN; and (iii) how robust is our understanding of the TRN? First, we reconstructed a high-confidence TRN (hiTRN) consisting of 147 transcription factors (TFs) regulating 1,538 transcription units (TUs) encoding 1,764 genes...
September 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28804492/population-genetic-differentiation-and-taxonomy-of-three-closely-related-species-of-saxifraga-saxifragaceae-from-southern-tibet-and-the-hengduan-mountains
#20
Qing-Bo Gao, Yan Li, Zhuo-Ma Gengji, Richard J Gornall, Jiu-Li Wang, Hai-Rui Liu, Liu-Kun Jia, Shi-Long Chen
The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM) and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S...
2017: Frontiers in Plant Science
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