scholarly journals De novo transcriptome analysis for examination of the nutrition metabolic system related to the evolutionary process through which stick insects gain the ability of flight (Phasmatodea)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Takuma Sakamoto ◽  
Shunya Sasaki ◽  
Nobuki Yamaguchi ◽  
Miho Nakano ◽  
Hiroki Sato ◽  
...  
Keyword(s):  
De Novo ◽  
Evolutionary Process ◽  
Enrichment Analysis ◽  
Stick Insect ◽  
Metabolic System ◽  
Flight Ability ◽  
Gene Enrichment ◽  
Enolase Superfamily ◽  
Stick Insects ◽  
Insect Group

Abstract Objective Insects are the most evolutionarily successful groups of organisms, and this success is largely due to their flight ability. Interestingly, some stick insects have lost their flight ability despite having wings. To elucidate the shift from wingless to flying forms during insect evolution, we compared the nutritional metabolism system among flight-winged, flightless-winged, and flightless-wingless stick insect groups. Results Here, we report RNA sequencing of midgut transcriptome of Entoria okinawaensis, a prominent Japanese flightless-wingless stick insect, and the comparative analysis of its transcriptome in publicly available midgut transcriptomes obtained from seven stick insect species. A gene enrichment analysis for differentially expressed genes, including those obtained from winged vs wingless and flight vs flightless genes comparisons, revealed that carbohydrate metabolic process-related genes were highly expressed in the winged stick insect group. We also found that the expression of the mitochondrial enolase superfamily member 1 transcript was significantly higher in the winged stick insect group than in the wingless stick insect group. Our findings could indicate that carbohydrate metabolic processes are related to the evolutionary process through which stick insects gain the ability of flight.

scholarly journals Transglutaminases and Obesity in Humans: Association of F13A1 to Adipocyte Hypertrophy and Adipose Tissue Immune Response

2020 ◽  
Vol 21 (21) ◽  
pp. 8289
Author(s):  
Mari T. Kaartinen ◽  
Mansi Arora ◽  
Sini Heinonen ◽  
Aila Rissanen ◽  
Jaakko Kaprio ◽  
...  
Keyword(s):  
Immune Response ◽  
Adipose Tissue ◽  
Family Members ◽  
Enrichment Analysis ◽  
Human Adipose Tissue ◽  
Adipocyte Size ◽  
Gene Enrichment ◽  
Adipocyte Hypertrophy ◽  
Mz Twins

Transglutaminases TG2 and FXIII-A have recently been linked to adipose tissue biology and obesity, however, human studies for TG family members in adipocytes have not been conducted. In this study, we investigated the association of TGM family members to acquired weight gain in a rare set of monozygotic (MZ) twins discordant for body weight, i.e., heavy–lean twin pairs. We report that F13A1 is the only TGM family member showing significantly altered, higher expression in adipose tissue of the heavier twin. Our previous work linked adipocyte F13A1 to increased weight, body fat mass, adipocyte size, and pro-inflammatory pathways. Here, we explored further the link of F13A1 to adipocyte size in the MZ twins via a previously conducted TWA study that was further mined for genes that specifically associate to hypertrophic adipocytes. We report that differential expression of F13A1 (ΔHeavy–Lean) associated with 47 genes which were linked via gene enrichment analysis to immune response, leucocyte and neutrophil activation, as well as cytokine response and signaling. Our work brings further support to the role of F13A1 in the human adipose tissue pathology, suggesting a role in the cascade that links hypertrophic adipocytes with inflammation.

Intersegmental Coordination of Walking Movements in Stick Insects

2005 ◽  
Vol 93 (3) ◽  
pp. 1255-1265 ◽  
Author(s):  
Björn Ch. Ludwar ◽  
Marie L. Göritz ◽  
Joachim Schmidt
Keyword(s):  
Motor Pattern ◽  
Central Pattern Generators ◽  
Stick Insect ◽  
Neural Mechanisms ◽  
Chordotonal Organ ◽  
Adjacent Segment ◽  
Body Segments ◽  
Stick Insects ◽  
Pattern Generators ◽  
Leg Movements

Locomotion requires the coordination of movements across body segments, which in walking animals is expressed as gaits. We studied the underlying neural mechanisms of this coordination in a semi-intact walking preparation of the stick insect Carausius morosus. During walking of a single front leg on a treadmill, leg motoneuron (MN) activity tonically increased and became rhythmically modulated in the ipsilateral deafferented and deefferented mesothoracic (middle leg) ganglion. The pattern of modulation was correlated with the front leg cycle and specific for a given MN pool, although it was not consistent with functional leg movements for all MN pools. In an isolated preparation of a pair of ganglia, where one ganglion was made rhythmically active by application of pilocarpine, we found no evidence for coupling between segmental central pattern generators (CPGs) that could account for the modulation of MN activity observed in the semi-intact walking preparation. However, a third preparation provided evidence that signals from the front leg's femoral chordotonal organ (fCO) influenced activity of ipsilateral MNs in the adjacent mesothoracic ganglion. These intersegmental signals could be partially responsible for the observed MN activity modulation during front leg walking. While afferent signals from a single walking front leg modulate the activity of MNs in the adjacent segment, additional afferent signals, local or from contralateral or posterior legs, might be necessary to produce the functional motor pattern observed in freely walking animals.

scholarly journals EnTAP: Bringing Faster and Smarter Functional Annotation to Non-Model Eukaryotic Transcriptomes

2018 ◽  
Author(s):  
Alexander J. Hart ◽  
Samuel Ginzburg ◽  
Muyang (Sam) Xu ◽  
Cera R. Fisher ◽  
Nasim Rahmatpour ◽  
...  
Keyword(s):  
Similarity Search ◽  
De Novo ◽  
Gene Annotation ◽  
Enrichment Analysis ◽  
Orthologous Gene ◽  
Protein Domain ◽  
Family Assessment ◽  
Ontology Term ◽  
Protein Coding ◽  
Functional Gene Annotation

ABSTRACTEnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates, while focusing primarily on protein-coding transcripts. Following filters applied through assessment of true expression and frame selection, open-source tools are leveraged to functionally annotate the translated proteins. Downstream features include fast similarity search across three repositories, protein domain assignment, orthologous gene family assessment, and Gene Ontology term assignment. The final annotation integrates across multiple databases and selects an optimal assignment from a combination of weighted metrics describing similarity search score, taxonomic relationship, and informativeness. Researchers have the option to include additional filters to identify and remove contaminants, identify associated pathways, and prepare the transcripts for enrichment analysis. This fully featured pipeline is easy to install, configure, and runs significantly faster than comparable annotation packages. EnTAP is optimized to generate extensive functional information for the gene space of organisms with limited or poorly characterized genomic resources.

scholarly journals Arkas: Rapid reproducible RNAseq analysis

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 586 ◽  
Author(s):  
Anthony R. Colombo ◽  
Timothy J. Triche Jr ◽  
Giridharan Ramsingh
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Special Focus ◽  
Gene Set Enrichment ◽  
Cloud Computing Environment ◽  
Gene Set ◽  
Structured Information ◽  
Computing Platforms

The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments.  We offer cloud-scale RNAseq pipelines Arkas-Quantification, which deploys Kallisto for parallel cloud computations, and Arkas-Analysis, which annotates the Kallisto results by extracting structured information directly from source FASTA files with per-contig metadata and calculates the differential expression and gene-set enrichment analysis on both coding genes and transcripts. The biologically informative downstream gene-set analysis maintains special focus on Reactome annotations while supporting ENSEMBL transcriptomes. The Arkas cloud quantification pipeline includes support for custom user-uploaded FASTA files, selection for bias correction and pseudoBAM output. The option to retain pseudoBAM output for structural variant detection and annotation provides a middle ground between de novo transcriptome assembly and routine quantification, while consuming a fraction of the resources used by popular fusion detection pipelines.  Illumina's BaseSpace cloud computing environment, where these two applications are hosted, offers a massively parallel distributive quantification step for users where investigators are better served by cloud-based computing platforms due to inherent efficiencies of scale.

scholarly journals Effect of flapless osteoperforation-assisted tooth movement on atrophic alveolar ridge: Histomorphometric and gene-enrichment analysis

2017 ◽  
Vol 88 (1) ◽  
pp. 82-90 ◽  
Author(s):  
Ji-Won Lee ◽  
Jung-Yul Cha ◽  
Ki-Ho Park ◽  
Yoon-Goo Kang ◽  
Su-Jung Kim
Keyword(s):  
Signaling Pathway ◽  
Tooth Movement ◽  
Osteoclast Differentiation ◽  
Wnt Signaling Pathway ◽  
Enrichment Analysis ◽  
Tissue Response ◽  
Alveolar Ridge ◽  
Mineral Density ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

ABSTRACT Objective: To investigate the effect of flapless osteoperforation on the tissue response of the atrophic alveolar ridge affected by orthodontic tooth movement (OTM). Materials and Methods: An atrophic alveolar ridge model was established in the mandibular quadrants of eight beagle dogs. As a split-mouth design, the quadrants were randomly divided into group C (OTM only) and group OP (OTM with flapless osteoperforation). The rate of OTM for 10 weeks was compared between groups, and micro-CT-based histomorphometric analysis and RNA-sequencing-based gene-enrichment analysis were performed targeting the atrophic ridge. Results: Group OP displayed more rapid tooth movement with lower bone mineral density and higher trabecular fraction in the atrophic ridge than did group C, showing no intergroup difference of total ridge volume. As contributing biological functional pathways in group OP, the genes related to osteoclast differentiation and TNF signaling pathway were up-regulated and those associated with Wnt signaling pathway and AMPK signaling pathway were down-regulated. Conclusions: Flapless osteoperforation facilitated the rate of OTM toward the atrophic ridge, maintaining low bone density, whereas it did not increase the volume of the atrophic ridge.

Pathological and Microbiological Study of Mortality in a Captive Breeding Colony of the Endangered Lord Howe Island Stick Insect (Dryococelus australis)

2018 ◽  
Vol 55 (5) ◽  
pp. 719-730
Author(s):  
Christine Bayley ◽  
Christina Cheng ◽  
Michael Lynch
Keyword(s):  
Captive Breeding ◽  
Positive Culture ◽  
Opportunistic Pathogen ◽  
Stick Insect ◽  
Innate Immune ◽  
Breeding Colony ◽  
Lord Howe Island ◽  
Stick Insects ◽  
Gross Lesions ◽  
Increased Susceptibility

The authors describe pathological and microbiological features of mortalities in a captive breeding colony of Lord Howe Island stick insects ( Dryococelus australis) over a period of 18 months. There were 2 peaks of mortality in this period. In the first, insects presented dead with minimal premonitory signs of illness. In the second, affected insects were ataxic with contracted limbs and inability to climb or right themselves. Gross lesions were uncommon but included pigmented plaques on the gut and cloacal prolapse. Histological lesions in both outbreaks indicated a cellular innate immune response including nodulation characterized by Gram-negative bacterial bacilli entrapped within nodules of pigmented hemocytes, and melanization characterized by melanin within hemocyte nodules and around bacteria. Hemolymph culture findings varied and often yielded a mixed growth. Pure growth of Serratia marcescens was cultured in 44% of animals in Outbreak 1, while pure growth of Pseudomonas aeruginosa was cultured in 30% of animals in Outbreak 2. Cases with S. marcescens-positive culture often showed inflammation at the foregut-midgut junction. The frequency of mixed bacterial culture results did not allow firm conclusions about causality to be made, and may indicate primary bacterial infection or increased susceptibility to hemolymph colonization with an opportunistic pathogen. These findings highlight the utility of histopathology combined with ancillary testing when investigating mortality in captive insect colonies.

scholarly journals Descending octopaminergic neurons modulate sensory-evoked activity of thoracic motor neurons in stick insects

2019 ◽  
Vol 122 (6) ◽  
pp. 2388-2413 ◽  
Author(s):  
Thomas Stolz ◽  
Max Diesner ◽  
Susanne Neupert ◽  
Martin E. Hess ◽  
Estefania Delgado-Betancourt ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Stick Insect ◽  
Neuron Activity ◽  
Sense Organs ◽  
Descending Neurons ◽  
Walking Activity ◽  
Stick Insects ◽  
Evoked Activity ◽  
Sensory Evoked ◽  
Stimulation Of

Neuromodulatory neurons located in the brain can influence activity in locomotor networks residing in the spinal cord or ventral nerve cords of invertebrates. How inputs to and outputs of neuromodulatory descending neurons affect walking activity is largely unknown. With the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and immunohistochemistry, we show that a population of dorsal unpaired median (DUM) neurons descending from the gnathal ganglion to thoracic ganglia of the stick insect Carausius morosus contains the neuromodulatory amine octopamine. These neurons receive excitatory input coupled to the legs’ stance phases during treadmill walking. Inputs did not result from connections with thoracic central pattern-generating networks, but, instead, most are derived from leg load sensors. In excitatory and inhibitory retractor coxae motor neurons, spike activity in the descending DUM (desDUM) neurons increased depolarizing reflexlike responses to stimulation of leg load sensors. In these motor neurons, descending octopaminergic neurons apparently functioned as components of a positive feedback network mainly driven by load-detecting sense organs. Reflexlike responses in excitatory extensor tibiae motor neurons evoked by stimulations of a femur-tibia movement sensor either are increased or decreased or were not affected by the activity of the descending neurons, indicating different functions of desDUM neurons. The increase in motor neuron activity is often accompanied by a reflex reversal, which is characteristic for actively moving animals. Our findings indicate that some descending octopaminergic neurons can facilitate motor activity during walking and support a sensory-motor state necessary for active leg movements. NEW & NOTEWORTHY We investigated the role of descending octopaminergic neurons in the gnathal ganglion of stick insects. The neurons become active during walking, mainly triggered by input from load sensors in the legs rather than pattern-generating networks. This report provides novel evidence that octopamine released by descending neurons on stimulation of leg sense organs contributes to the modulation of leg sensory-evoked activity in a leg motor control system.

scholarly journals Transcriptome Sequencing of Two Kentucky Bluegrass (Poa pratensis L.) Genotypes in Response to Heat Stress

2018 ◽  
Vol 47 (2) ◽  
pp. 328-338
Author(s):  
Qiong LI ◽  
Yali HE ◽  
Mingyue TU ◽  
Junhui YAN ◽  
Liangliang YU ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
De Novo ◽  
Average Length ◽  
Poa Pratensis ◽  
Brachypodium Distachyon ◽  
Enrichment Analysis ◽  
Basic Mechanism ◽  
Kentucky Bluegrass ◽  
Summer Stress

Kentucky bluegrass (Poa pratensis L.) (KBG) is a major cool-season turfgrass. However, as its complex genetic background and production modes, limited genomic and transcriptomic information of KBG was known so far. In this study, a transcriptome study between wild type material Ninglan (summer stress sensitive) and cultivar material KBG03 (summer stress tolerant) was conducted, under optimal (25 °C) and high (40 °C) temperatures. A total of 81.42 Gb clean reads were generated and de novo assembled into 110,784 unigenes with an average length of 1,105 bp. About 50% KBG unigenes were similar to the non-redundant (NR) database. Among the NR BLASTx top hits, 27.47% unigenes were matched to Brachypodium distachyon. After heat stress, a massive amount of unigenes showed significantly differential expression in both genotypes. After 2h heat stress, more specially up-regulated differentially expressed unigenes (DEGs) and less down-regulated DEGs were detected in Ninglan than in KBG03. At 24h, the expression of 1710 and 730 unigenes were increased and decreased uniquely in Ninglan, and 1361 up-regulated DEGs and 757 down-regulated DEGs were just found in KBG03. More heat shock proteins (HSPs) and heat shock transcription factors (HSFs) DEGs were also identified at 2h than 24h in both genotypes. In addition, by Gene Ontology (GO) enrichment analysis, three core terms (“protein folding”, “response to heat”, and “response to hydrogen peroxide”) of biological process (BP) ontology were found in both genotypes under different heat stress time. The DEGs shared in both genotypes might be related to the basic mechanism of thermal response in KBG.

Load Signals Assist the Generation of Movement-Dependent Reflex Reversal in the Femur–Tibia Joint of Stick Insects

2006 ◽  
Vol 96 (6) ◽  
pp. 3532-3537 ◽  
Author(s):  
Turgay Akay ◽  
Ansgar Büschges
Keyword(s):  
Time Course ◽  
Stick Insect ◽  
Motor Output ◽  
Chordotonal Organ ◽  
Frequency Of Occurrence ◽  
Stick Insects ◽  
Extensor Motoneuron ◽  
Motoneuron Activity ◽  
First Time ◽  
Stimulation Of

Reinforcement of movement is an important mechanism by which sensory feedback contributes to motor control for walking. We investigate how sensory signals from movement and load sensors interact in controlling the motor output of the stick insect femur–tibia (FT) joint. In stick insects, flexion signals from the femoral chordotonal organ (fCO) at the FT joint and load signals from the femoral campaniform sensilla (fCS) are known to individually reinforce stance-phase motor output of the FT joint by promoting flexor and inhibiting extensor motoneuron activity. We quantitatively compared the time course of inactivation in extensor tibiae motoneurons in response to selective stimulation of fCS and fCO. Stimulation of either sensor generates extensor activity in a qualitatively similar manner but with a significantly different time course and frequency of occurrence. Inactivation of extensor motoneurons arising from fCS stimulation was more reliable but more than threefold slower compared with the extensor inactivation in response to flexion signals from the fCO. In contrast, simultaneous stimulation of both sense organs produced inactivation in motoneurons with a time course typical for fCO stimulation alone, but with a frequency of occurrence characteristic for fCS stimulation. This increase in probability of occurrence was also accompanied by a delayed reactivation of the extensor motoneurons. Our results indicate for the first time that load signals from the leg affect the processing of movement-related feedback in controlling motor output.

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