bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-NGF treatment can reduce chronic neuropathic pain by changing peripheral mediators and brain activity in rats
Authors: da Silva Joyce T. , Evangelista Bianca G. , Venega Rafael A.G. , Seminowicz David A. , Chacur Marucia
Published: September 2018

Neuropathic pain is driven by abnormal peripheral and central processing, and treatments are insufficiently effective. Antibodies against nerve growth factor (anti-NGF) have been investigated as a potent analgesic treatment for numerous conditions. However, the peripheral and brain effects of anti-NGF in neuropathic pain remain unknown. We examined the effectiveness of anti-NGF in reducing chronic pain by local administration in a rat model of sciatic constriction injury (CCI). NGF and substance P in the dorsal root ganglion (DRG) and spinal cord were evaluated. Neuronal activation was measured using c-Fos in the anterior cingulate cortex and ventrolateral periaqueductal gray. At 14 days after CCI, anti-NGF promoted a significant dose-dependent improvement in mechanical threshold, thermal withdrawal latency, and cold sensitivity, lasting for 5 h. NGF upregulation in the DRG and spinal cord after CCI was decreased by anti-NGF, while substance P was increased only in the DRG, and the treatment reduced it. Anti-NGF induced a significant reduction of neuronal activation in the anterior cingulate cortex, but not in the ventrolateral periaqueductal gray. This study provides the first evidence of the anti-NGF effects on brain activity. Thus, our findings suggest that anti-NGF improves chronic neuropathic pain, acting directly on peripheral sensitization and indirectly on central sensitization.
The Boomerang Epicanthoplasty: A Technique That Avoids Hooding
Authors: Kim Joo Ho , Hwang Kun , Park Bumjin
Published: September 2018

Redraping is an increasingly common epicanthoplasty method. However, hooding usually remains at the medial part of the upper eyelid. The authors innovated a modification of redraping epicanthoplasty using excision, resulting in a boomerang-shaped defect that does not lead to hooding of the medial upper eyelid.

Medial line (M-line) was drawn at the most medial point of the palpebral fissure. The canthus point (C-point) was marked approximately 1 to 3 mm laterally from the M-point, depending on the amount of widening needed. From the C-point, upper incision was designed to meet the double eyelid line. A V-shaped lower incision was designed 3 to 4 mm below the ciliary margin. A flap was elevated about 7 mm superiorly, 10 mm medially, and 5 mm inferiorly. The elevated skin flap was redraped and the M’-point, which reflected the M-point on the redraped skin, was marked. A curvilinear incision line reflecting previous incision lines was drawn. The crescent-shaped excess skin was excised and the medial canthus was retracted medially, and then the boomerang-shaped defect was observed. The M-point and M’-point were coapted with a suture. The dog-ear at the lower side was trimmed.

The 525 patients were followed up for ≥3 months postoperatively. The average increase in the palpebral fissure length was 1.2 ± 0.5 mm. The average decrease in the interepicanthal distance was 2.4 ± 0.9 mm. The average satisfaction score was 4.6 ± 0.6.

Boomerang epicanthoplasty can prevent hooding on the medial aspect of the upper eyelid. It is easy to design, requires marking only 1 point, and is tension-free, thereby reducing scar widening.
The IL-33-ST2 Pathway Contributes to Ventilator-Induced Lung Injury in Septic Mice in a Tidal Volume-Dependent Manner
Authors: Ding Xibing , Jin Shuqing , Shao Zhenzhen , Xu Li , Yu Zhuang , Tong Yao , Chen Zhixia , Turnquist Heth , Pitt Bruce R. , Billiar Timothy R. , Zhang Li-Ming , Li Quan
Published: September 2018

Mechanical ventilation (MV) is frequently employed to manage respiratory failure in sepsis patients and is required for the surgical management of intra-abdominal sepsis. The impact of MV varies dramatically depending on tidal volume, with even moderate tidal volume (MTV) ventilation leading to ventilator-induced lung injury, whereas low tidal volume (LTV) ventilation protects against sepsis-induced acute respiratory distress syndrome. Interleukin (IL)-33 is known to contribute to lung injury in sepsis and its release can be induced by mechanical stress. To determine the relationship between the IL-33-suppression of tumorigenicity 2 (ST2) pathway and patterns of lung injury associated with MV in sepsis, mice were subjected to cecal ligation and puncture (CLP) followed 6 h later by either MTV (10 mL/kg) or LTV (6 mL/kg) ventilation for 4 h. MTV and LTV ventilation alone for 4 h had no impact on lung injury. MTV markedly exacerbated lung injury and inflammation, while LTV significantly suppressed these parameters in septic mice. Lung and plasma levels of IL-33 ST2 were significantly elevated by CLP alone at 10 h. MTV caused further and significant increases in IL-33 and sST2 levels, while LTV significantly suppressed levels induced by CLP. Deletion of IL-33 or ST2 prevented the increase in lung injury and inflammation induced by MTV in septic mice, while administration of recombinant IL-33 in the airway reversed the protection seen with LTV. Taken together, these findings implicate the IL-33-ST2 pathway in the pro-inflammatory changes induced by the mechanical ventilation that leads to lung injury in the setting of intra-abdominal sepsis in a tidal volume-dependent manner.
Female Urology and Urogynecology: The Outcome of Patients Participating in Live Surgical Broadcasts
Authors: Itam Sarah , Pakzad Mahreen , Hamid Rizwan , Ockrim Jeremy , Vashisht Arvind , Cutner Alfred , Greenwell Tamsin
Published: September 2018

Introduction

The aims of this study were to assess the complications and short- and long-term outcomes of patients involved in live surgical broadcasts (LSBs) of female urology and urogynecological surgery and compare the surgical success with operations performed outside this setting by the same surgeons.

Methods

We reviewed our prospectively collected database of all patients who had taken part in LSBs between 2008 and 2015 for the annual female urology and urogynecology course. Data on intraoperative and 30- and 90-day complications and primary outcomes from surgery were collected. Procedure-specific success rates were determined and compared with the center's previously published success rate for these procedures.

Results

Overall, 53 females with a median age of 50 years (range, 23–77 years) underwent 62 procedures during these LSBs. There were no intraoperative complications. There was 1 Clavien-Dindo grade II complication within 30 days of surgery. Within 90 days of surgery, there was 1 Clavien-Dindo grade III complication, which occurred in a patient having removal of anterior pelvic organ prolapse mesh for urethral erosion and simultaneous colposuspension. The majority of operations, 57 (92%) of 62, achieved their intended primary outcome.

Conclusions

With careful planning, LSB can offer a safe way of sharing current operative techniques and decision making with similar 30- and 90-day complication rates to standard practices and comparable functional outcomes to standard practice.
Short “Infraslow” Activity (SISA) With Burst Suppression in Acute Anoxic Encephalopathy: A Rare, Specific Ominous Sign With Acute Posthypoxic Myoclonus or Acute Symptomatic Seizures
Authors: Togo Masaya , Hitomi Takefumi , Murai Tomohiko , Yoshimura Hajime , Matsuhashi Masao , Matsumoto Riki , Kawamoto Michi , Kohara Nobuo , Takahashi Ryosuke , Ikeda Akio
Published: September 2018

Objective:

Slow wave with frequency <0.5 Hz are recorded in various situations such as normal sleep, epileptic seizures. However, its clinical significance has not been fully clarified. Although infra-slow activity was recently defined as activity between 0.01 and 0.1 Hz, we focus on the activity recorded with time constant of 2 seconds for practical usage. We defined short “infraslow” activity (SISA) less than 0.5 Hz recorded with time constant of 2 seconds and investigated the occurrence and clinical significance of SISA in acute anoxic encephalopathy.

Methods:

This study evaluated the findings of electroencephalography in consecutive 98 comatose patients with acute anoxic encephalopathy after cardiac arrest. We first classified electroencephalography findings conventionally, then investigated SISA by time constant of 2 second and a high-cut filter of 120 Hz, to clarify the relationship between SISA and clinical profiles, especially of clinical outcomes and occurrence of acute posthypoxic myoclonus or acute symptomatic seizures.

Results:

Short infra-slow activity was found in six patients (6.2%), superimposed on the burst phase of the burst-suppression pattern. All six patients showed acute posthypoxic myoclonus or acute symptomatic seizures (generalized tonic–clonic seizures) and its prognosis was poor. This 100% occurrence of acute posthypoxic myoclonus or acute symptomatic seizures was significantly higher than that in patients without SISA (39.1%; P < 0.05).

Conclusions:

Short infra-slow activity in acute anoxic encephalopathy could be associated with acute posthypoxic myoclonus and acute symptomatic seizures. Short infra-slow activity could be a practically feasible biomarker for myoclonus or seizures and poor prognosis in acute anoxic encephalopathy, if it occurs with burst suppression.
Sexual conflict in self-fertile hermaphrodites: reproductive differences among species, and between individuals versus cohorts, in the leech genusHelobdella(Lophotrochozoa; Annelida; Clitellata; Hirudinida; Glossiphoniidae)
Authors: Iyer Roshni G. , Rogers D. Valle , Winchell Christopher J. , Weisblat David A.
Published: September 2018

Leeches and oligochaetes comprise a monophyletic group of annelids, the Clitellata, whose reproduction is characterized by simultaneous hermaphroditism. While most clitellate species reproduce by cross-fertilization, self-fertilization has been described within the speciose genusHelobdella. Here we document the reproductive life histories and reproductive capacities for three otherHelobdellaspecies. Under laboratory conditions, bothH. robustaandH. octatestisacaexhibit uniparental reproduction, apparently reflecting self-fertility, and suggesting that this trait is ancestral for the genus. However, the third species,H. austinensis, seems incapable of reproduction by self-fertilization, so we inferred its reproductive life history by analyzing reproduction in breeding cohorts. Comparing the reproductive parameters forH. robustareproducing in isolation and in cohorts revealed that reproduction in cohorts is dramatically delayed with respect to that of isolated individuals, and that cohorts of leeches coordinate their cocoon deposition in a manner that is not predicted from the reproductive parameters of individuals reproducing in isolation. Finally, our comparisons of reproductive capacity for individuals versus cohorts forH. robusta, and between different sizes of cohorts forH. austinensis, reveal differences in resource allocation between male and female reproductive roles that are consistent with evolutionary theory.
Function and essentiality of Plasmodium falciparum plasmepsin V
Authors: Boonyalai Nonlawat , Collins Christine R. , Hackett Fiona , Withers-Martinez Chrislaine , Blackman Michael J.
Published: September 2018

The malaria parasite replicates within erythrocytes. The pathogenesis of clinical malaria is in large part due to the capacity of the parasite to remodel its host cell. To do this, intraerythrocytic stages of Plasmodium falciparum export more than 300 proteins that dramatically alter the morphology of the infected erythrocyte as well as its mechanical and adhesive properties. P. falciparum plasmepsin V (PfPMV) is an aspartic protease that processes proteins for export into the host erythrocyte and is thought to play a key role in parasite virulence and survival. However, although standard techniques for gene disruption as well as conditional protein knockdown have been previously attempted with the pfpmv gene, complete gene removal or knockdown was not achieved so direct genetic proof that PMV is an essential protein has not yet been established. Here we have used a conditional gene excision approach combining CRISPR-Cas9 gene editing and DiCre-mediated recombination to functionally inactivate the pfpmv gene. The resulting mutant parasites displayed a severe growth defect. Detailed phenotypic analysis showed that development of the mutant parasites was arrested at the ring-to-trophozoite transition in the erythrocytic cycle following gene excision, likely due to a defect in protein export. Our findings are the first to elucidate the effects of PMV gene disruption, showing that it is essential for parasite viability in asexual blood stages. The mutant parasites can now be used as a platform to further dissect the Plasmodium protein export pathway.
The Ciliopathy GeneFtm/Rpgrip1lControls Mouse Forebrain Patterning via Region-Specific Modulation of Hedgehog/Gli Signaling
Authors: Andreu-Cervera Abraham , Anselme Isabelle , Karam Alice , Catala Martin , Schneider-Maunoury Sylvie
Published: September 2018

Primary cilia are essential for central nervous system development. In the mouse, they play a critical role in patterning the spinal cord and telencephalon via the regulation of Hedgehog/Gli signaling. However, despite the frequent disruption of this signaling pathway in human forebrain malformations, the role of primary cilia in forebrain morphogenesis has been little investigated outside the telencephalon. Here we studied development of the diencephalon, hypothalamus and eyes in mutant mice in which theFtm/Rgprip1lciliopathy gene is disrupted. At the end of gestation,Ftm-/-fetuses displayed anophthalmia, a reduction of the ventral hypothalamus and a disorganization of diencephalic nuclei and axonal tracts. InFtm-/-embryos, we found that the ventral forebrain structures and the rostral thalamus were missing. Optic vesicles formed but lacked the optic cups. We analyzed the molecular causes of these defects. InFtm-/-embryos,Sonic hedgehog(Shh) expression was lost in the ventral forebrain but maintained in the zona limitans intrathalamica (ZLI), the mid-diencephalic organizer. In the diencephalon, Gli activity was dampened in regions adjacent to theShh-expressing ZLI but displayed a higher Hh-independent ground level in the other regions. Our data uncover a complex role of cilia in development of the diencephalon, hypothalamus and eyes via the region-specific control of the ratio of activator and repressor forms of the Gli transcription factors. They call for a closer examination of forebrain defects in severe ciliopathies and for a search for ciliopathy genes as modifiers in other human conditions with forebrain defects.
Extracting information from RNA SHAPE data: Kalman filtering approach
Authors: Vaziri Sana , Koehl Patrice , Aviran Sharon
Published: September 2018

RNA SHAPE experiments have become important and successful sources of information for RNA structure prediction. In such experiments, chemical reagents are used to probe RNA backbone flexibility at the nucleotide level, which in turn provides information on base pairing and therefore secondary structure. Little is known, however, about the statistics of such SHAPE data. In this work, we explore different representations of noise in SHAPE data and propose a statistically sound framework for extracting reliable reactivity information from multiple SHAPE replicates. Our analyses of RNA SHAPE experiments underscore that a normal noise model is not adequate to represent their data. We propose instead a log-normal representation of noise and discuss its relevance. Under this assumption, we observe that processing simulated SHAPE data by directly averaging different replicates leads to bias. Such bias can be reduced by analyzing the data following a log transformation, either by log-averaging or Kalman filtering. Application of Kalman filtering has the additional advantage that a prior on the nucleotide reactivities can be introduced. We show that the performance of Kalman filtering is then directly dependent on the quality of that prior. We conclude the paper with guidelines on signal processing of RNA SHAPE data.
Diet influences early microbiota development in dairy calves without long-term impacts on milk production
Authors: Dill-McFarland Kimberly A. , Weimer Paul J. , Breaker Jacob D. , Suen Garret
Published: September 2018

Gastrointestinal tract (GIT) microorganisms play important roles in the health of ruminant livestock and impact production of agriculturally relevant products, including milk and meat. Despite this link, interventions to alter the adult microbiota to improve production have proven ineffective as established microbial communities are resilient to change. In contrast, developing communities in young animals may be more easily altered but are less well-studied. Here, we measured the GIT-associated microbiota of 45 Holstein dairy cows from 2 weeks to first lactation using Illumina amplicon sequencing of bacterial (V4 16S), archaeal (V6-8 16S), and fungal (ITS1) communities. Fecal and rumen microbiota were correlated to growth and milk production of animals raised on calf starter grains and/or corn silage to determine if early-life diet has long-term impacts. Significant diet-associated differences in total microbial communities and specific taxa were observed by weaning (8 weeks), but all animals reached an adult-like composition between weaning and 1-year. While some calf diet-driven differences were apparent in the microbiota of adult cows, these dissimilarities did not correlate with animal growth or milk production. This suggests that initial microbial community establishment is impacted by early-life diet, but post-weaning factors have a greater influence on adult communities and production outcomes.

SIGNIFICANCE

The gut microbiota is essential to the survival of many organisms, including ruminants that rely on microorganisms for nutrient acquisition from dietary inputs toward the production of products like milk and meat. While alteration of the adult ruminant microbiota to improve production is possible, changes are often unstable and fail to persist. In contrast, the early-life microbiota may be more amenable to sustained modification; however, few studies have determined the impacts of early-life interventions on downstream production. Here, we investigated the impacts of agriculturally relevant calf diets, including calf starter and corn silage, on gut microbial communities, animal growth, and production through the first lactation cycle. Thus, this work serves to further our understanding of early-life microbiota acquisition as well as informs future practices in livestock management.
VIRULIGN: fast codon-correct alignment and annotation of viral genomes
Authors: Libin Pieter , Deforche Koen , Abecasis Ana B. , Theys Kristof
Published: September 2018

Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit for these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codoncorrect alignments of large datasets, with standardized genome annotation and various alignment export formats.

VIRULIGN is freely available athttps://github.com/rega-cev/virulignas an open source software project.
Profiling grapevine trunk pathogensin planta: A case for community-targeted DNA metabarcoding
Authors: Morales-Cruz Abraham , Figueroa-Balderas Rosa , García Jadran F. , Tran Eric , Rolshausen Philippe E. , Baumgartner Kendra , Cantu Dario
Published: September 2018

DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneousin planta-detectionof multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Their detection is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the Fungal Kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated Ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology. We first performed insilicosimulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namelyPhaeomoniella, Phaeoacremonium, andEutypa, the abundances of which were greatly over- or under-estimated with universal primers. Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.
Deletion of autism risk gene Shank3 disrupts prefrontal connectivity
Authors: Pagani Marco , Bertero Alice , Liska Adam , Galbusera Alberto , Sabbioni Mara , Scattoni Maria Luisa , Pasqualetti Massimo , Gozzi Alessandro
Published: September 2018

Mutations in the synaptic scaffolding protein Shank3 are a major cause of autism, and are associated with prominent intellectual and language deficits. However, the neural mechanisms whereby SHANK3 deficiency affects higher order socio-communicative functions remain unclear. Using high-resolution functional and structural MRI in mice, here we show that loss ofShank3(Shank3B-/-) results in disrupted local and long-range prefrontal functional connectivity, as well as fronto-striatal decoupling. We document that prefrontal hypo-connectivity is associated with reduced short-range cortical projections density, and reduced gray matter volume. Finally, we show that prefrontal disconnectivity is predictive of social communication deficits, as assessed with ultrasound vocalization recordings. Collectively, our results reveal a critical role of SHANK3 in the development of prefrontal anatomy and function, and suggest that SHANK3 deficiency may predispose to intellectual disability and socio-communicative impairments via dysregulation of higher-order cortical connectivity.
Single-cell transcriptional dynamics and origins of neuronal diversity in the developing mouse neocortex
Authors: Telley L. , Agirman G. , Prados J. , Fièvre S. , Oberst P. , Vitali I. , Nguyen L. , Dayer A. , Jabaudon D.
Published: September 2018

During cortical development, distinct subtypes of glutamatergic neurons are sequentially born and differentiate from dynamic populations of progenitors. The neurogenic competence of these progenitors progresses as corticogenesis proceeds; likewise, newborn neurons transit through sequential states as they differentiate. Here, we trace the developmental transcriptional trajectories of successive generations of apical progenitors (APs) and isochronic cohorts of their daughter neurons using parallel single-cell RNA sequencing between embryonic day (E) 12 and E15 in the mouse cerebral cortex. Our results identify the birthdate- and differentiation stage-related transcriptional dynamics at play during corticogenesis. As corticogenesis proceeds, APs transit through embryonic age-dependent molecular states, which are transmitted to their progeny to generate successive initial daughter cell identities. In neurons, essentially conserved post-mitotic differentiation programs are applied onto these distinct AP-derived ground states, allowing temporally-regulated sequential emergence of specialized neuronal cell types. Molecular temporal patterning of sequentially-born daughter neurons by their respective mother cell thus underlies emergence of neuronal diversity in the neocortex.

One Sentence Summary

During corticogenesis, temporally dynamic molecular birthmarks are transmitted from progenitors to their post-mitotic progeny to generate neuronal diversity.
The neural basis of hand choice: An fMRI investigation of the Posterior Parietal Interhemispheric Competition model
Authors: Fitzpatrick Aoife M. , Dundon Neil M. , Valyear Kenneth F.
Published: September 2018

The current study investigates a new neurobiological model of human hand choice: The Posterior Parietal Interhemispheric Competition (PPIC) model. The model specifies that neural populations in bilateral posterior intraparietal and superior parietal cortex (pIP-SPC) encode actions in hand-specific terms, and compete for selection across and within hemispheres. Actions with both hands are encoded bilaterally, but the contralateral hand is overrepresented. We use a novel fMRI paradigm to test the PPIC model. Participants reach to visible targets while in the scanner, and conditions involving free choice of which hand to use (Choice) are compared with when hand-use is instructed. Consistent with the PPIC model, bilateral pIP-SPC is preferentially responsive for the Choice condition, and for actions made with the contralateral hand. In the right pIP-SPC, these effects include anterior intraparietal and superior parieto-occipital cortex. Left dorsal premotor cortex, and an area in the right lateral occipitotemporal cortex show the same response pattern, while the left inferior parietal lobule is preferentially responsive for the Choice condition and when using the ipsilateral hand. Behaviourally, hand choice is biased by target location – for targets near the left/right edges of the display, the hand in ipsilateral hemispace is favoured. Moreover, consistent with a competitive process, response times are prolonged for choices to more ambiguous targets, where hand choice is relatively unbiased, and fMRI responses in bilateral pIP-SPC parallel this pattern. Our data provide support for the PPIC model, and reveal a selective network of brain areas involved in free hand choice, including bilateral posterior parietal cortex, left-lateralized inferior parietal and dorsal premotor cortices, and the right lateral occipitotemporal cortex.
Landscape of stimulation-responsive chromatin across diverse human immune cells
Authors: Calderon Diego , Nguyen Michelle L. T. , Mezger Anja , Kathiria Arwa , Nguyen Vinh , Lescano Ninnia , Wu Beijing , Trombetta John , Ribado Jessica V. , Knowles David A. , Gao Ziyue , Parent Audrey V. , Burt Trevor D. , Anderson Mark S. , Criswell Lindsey A. , Greenleaf William J. , Marson Alexander , Pritchard Jonathan K.
Published: September 2018

The immune system is controlled by a balanced interplay among specialized cell types transitioning between resting and stimulated states. Despite its importance, the regulatory landscape of this system has not yet been fully characterized. To address this gap, we collected ATAC-seq and RNA-seq data under resting and stimulated conditions for 25 immune cell types from peripheral blood of four healthy individuals, and seven cell types from three fetal thymus samples. We found that stimulation caused widespread chromatin remodeling, including a large class of response elements shared between stimulated B and T cells. Furthermore, several autoimmune traits showed significant heritability in stimulation-responsive elements from distinct cell types, highlighting the critical importance of these cell states in autoimmunity. Use of allele-specific read-mapping identified thousands of variants that alter chromatin accessibility in particular conditions. Notably, variants associated with changes in stimulation-specific chromatin accessibility were not enriched for associations with gene expression regulation in whole blood – a tissue commonly used in eQTL studies. Thus, large-scale maps of variants associated with gene regulation lack a condition important for understanding autoimmunity. As a proof-of-principle we identified variant rs6927172, which links stimulated T cell-specific chromatin dysregulation in theTNFAIP3locus to ulcerative colitis and rheumatoid arthritis. Overall, our results provide a broad resource of chromatin landscape dynamics and highlight the need for large-scale characterization of effects of genetic variation in stimulated cells.
Rapidly Assessing the Quality of Targeted Proteomics Experiments Through Monitoring Stable-isotope Labeled Standards
Authors: Gibbons Bryson C. , Fillmore Thomas L. , Gao Yuqian , Moore Ronald J. , Liu Tao , Nakayasu Ernesto S. , Metz Thomas O. , Payne Samuel H.
Published: September 2018

Targeted proteomics experiments based on selected reaction monitoring (SRM) have gained wide adoption in clinical biomarker, cellular modeling and numerous other biological experiments due to their highly accurate and reproducible quantification. The quantitative accuracy in targeted proteomics experiments is reliant on the stable-isotope, heavy-labeled peptide standards which are spiked into a sample and used as a reference when calculating the abundance of endogenous peptides. Therefore, the quality of measurement for these standards is a critical factor in determining whether data acquisition was successful. With improved MS instrumentation that enables the monitoring of hundreds of peptides in hundreds to thousands of samples, quality assessment is increasingly important and cannot be performed manually. We present Q4SRM, a software tool that rapidly checks the signal from all heavy labeled peptides and flags those that fail quality control metrics. Using four metrics, the tool detects problems both with individual SRM transitions and the collective group of transitions that monitor a single peptide. The program’s speed enables its use at the point of data acquisition and can be ideally run immediately upon the completion of an LC-SRM-MS analysis.
Morphological profile determines the frequency of spontaneous calcium events in astrocytic processes
Authors: Wu Yu-Wei , Gordleeva Susan , Tang Xiaofang , Shih Pei-Yu , Dembitskaya Yulia , Semyanov Alexey
Published: September 2018

Astrocytes express a complex repertoire of intracellular Ca2+ transients (events) that represent a major form of signaling within individual cells and in the astrocytic syncytium. These events have different spatiotemporal profiles, which are modulated by neuronal activity. Spontaneous Ca2+ events appear more frequently in distal astrocytic processes and independently from each other. However, little is known about the mechanisms underlying such subcellular distribution of the Ca2+ events. Here we identify the initiation points of the Ca2+ events within the territory of single astrocytes expressing genetically encoded Ca2+ indicator GCaMP2 in culture or in hippocampal slices. We found that most of the Ca2+ events start in thin distal processes. Our mathematical model demonstrated that a high surface-to-volume (SVR) of the thin processes leads to increased amplitude of baseline Ca2+ fluctuations caused by a stochastic opening of Ca2+ channels in the plasma membrane. Suprathreshold fluctuations trigger Ca2+-induced Ca2+ release (CICR) from the Ca2+ stores by activating inositol 1,4,5-trisphosphate (IP3) receptors. In agreement with the model prediction, the spontaneous Ca2+ events frequency depended on the extracellular Ca2+ concentration. Astrocytic depolarization by high extracellular K+ increased the frequency of the Ca2+ events through activation of voltage-gated Ca2+ channels (VGCC) in cultured astrocytes. Our results suggest that the morphological profile of the astrocytic processes is responsible for tuning of the Ca2+ event frequency. Therefore, the structural plasticity of astrocytic processes can be directly translated into changes in astrocytic Ca2+ signaling. This may be important for both physiological and pathological astrocyte remodeling.

Main points

Majority of spontaneous Ca2+ events start in thin astrocytic processes

Higher surface-to-volume ratio of the process is responsible for larger intracellular Ca2+ fluctuations

Larger intracellular Ca2+ fluctuations trigger Ca2+-dependent Ca2+ release
Long-term phenotypic effects following vitrified-thawed embryo transfer in a rabbit model
Authors: Garcia-Dominguez Ximo , Peñaranda David. S. , Estruch Guillem , Blanca José , García-Carpintero Victor , Cañizares Joaquín , Marco-Jiménez Francisco , Vicente José Salvador
Published: September 2018

Since the first human was conceived through in vitro fertilisation in 1978, over 6.5 million babies have been born by assisted reproductive technologies (ARTs). Although most ART babies and children seem healthy, in recent years several studies have evidenced a potential impact of ARTs on long-term development and health. Herein, we have developed an animal model to determine whether vitrified embryo transfer procedure induces phenotypic changes over the growth performance and in the complementary transcriptomic and proteomic analyses at hepatic level. To this end, 2 populations were developed; vitrified embryos transferred to the surrogate mothers (VT) and naturally conceived animals (NC). After delivery, animals were weighed weekly from 1 to 20 weeks of age. In adulthood, animals were euthanized and organs were harvested and weighed. After that, liver tissue was used to identify changes in the transcriptomic and proteomic profile. At adulthood, VT group showed significant lower body, liver and heart weight. After functional analysis of RNA-Seq data, a subset of 96 differentially expressed transcripts in VT animal were related to alteration in zinc homeostasis, lipid metabolism, and hepatic immune pathways. After proteomic analysis, a subset of 76 differentially expressed proteins also revealed some disturbed metabolic pathways related with the lipid and glycan metabolism, and an impaired oxidative metabolism related to ATP synthesis in the mitochondria. Current findings suggest that progeny derived after transfer of vitrified embryos have long-term consequences on growth rate and vital organs weights in adulthood, correlated with molecular signatures at transcriptomic and proteomic level of hepatic tissue.
Regenerative capacity in the lamprey spinal cord is not altered after a repeated transection
Authors: Hanslik Kendra L. , Allen Scott R. , Harkenrider Tessa L. , Fogerson Stephanie M. , Guadarrama Eduardo , Morgan Jennifer R.
Published: September 2018

The resilience of regeneration in vertebrate tissues is not well understood. Yet understanding how well tissues can regenerate after repeated insults, and identifying any limitations, is an important step towards elucidating the underlying mechanisms of tissue plasticity. This is particularly challenging in tissues such as the nervous system, which contain a large number of terminally differentiated cells (i.e. neurons) and that often exhibits limited regenerative potential in the first place. However, unlike mammals that exhibit very little spinal cord regeneration, many non-mammalian vertebrate species, including lampreys, fishes, amphibians and reptiles, regenerate their spinal cords and functionally recover even after a complete spinal cord transection. It is well established that lampreys undergo full functional recovery of swimming behaviors after a single spinal cord transection, which is accompanied by tissue repair at the lesion as well as axon and synapse regeneration. Here, using the lamprey model, we begin to explore resilience of spinal cord regeneration after a second spinal re-transection. We report that by all functional and anatomical measures tested, the lampreys regenerated after spinal re-transection just as robustly as after single transections. Recovery of swimming behaviors, axon regeneration, synapse and cytoskeletal distributions, and neuronal survival were nearly identical after a single spinal transection or a repeated transection. Thus, regenerative potential in the lamprey spinal cord is largely unaffected by spinal re-transection, indicating a greater persistent regenerative potential than exists in some other highly-regenerative models. These findings establish a new path for uncovering pro-regenerative targets that could be deployed in non-regenerative conditions.
Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae: The impact of a pathogen on the plant root and rhizosphere microbiota
Authors: Lebreton Lionel , Guillerm-Erckelboudt Anne-Yvonne , Gazengel Kévin , Linglin Juliette , Ourry Morgane , Glory Pascal , Sarniguet Alain , Daval Stéphanie , Manzanares-Dauleux Maria J. , Mougel Christophe
Published: September 2018

The temporal dynamics of rhizosphere and root microbiota composition was compared between healthy and infected Chinese cabbage plants by the pathogen Plasmodiophora brassicae. When inoculated with P. brassicae, disease was measured at five sampling dates from early root hair infection to late gall development. The first symptoms of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root from healthy and inoculated plants was characterized through high-throughput DNA sequencing of bacterial (16S) and fungal (18S) molecular markers and compared at each sampling date. In healthy plants, Proteobacteria and Bacteroidetes bacterial phyla dominated the rhizosphere and root microbiota of Chinese cabbage. Rhizosphere bacterial communities contained higher abundances of Actinobacteria and Firmicutes compared to the roots. Moreover, a drastic shift of fungal communities of healthy plants occurred between the two last sampling dates, especially in plant roots, where most of Ascomycota fungi dominated until they were replaced by a fungus assigned to the Chytridiomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly at a late step during the root secondary cortical infection stage of clubroot disease. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytridiomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.
Transcriptomic characterization of signaling pathways associated with osteoblastic differentiation of MC-3T3E1 cells
Authors: Luttrell Louis M. , Dar Moahad S. , Gesty-Palmer Diane , El-Shewy Hesham M. , Robinson Katherine M. , Haycraft Courtney J. , Barth Jeremy L.
Published: September 2018

Bone remodeling involves the coordinated actions of osteoclasts, which resorb the calcified bony matrix, and osteoblasts, which refill erosion pits created by osteoclasts to restore skeletal integrity and adapt to changes in mechanical load. Osteoblasts are derived from pluripotent mesenchymal stem cell precursors, which undergo differentiation under the influence of a host of local and environmental cues. To characterize the autocrine/paracrine signaling networks associated with osteoblast maturation and function, we performed gene network analysis using complementary “agnostic” DNA microarray and “targeted” NanoString™nCounter datasets derived from murine MC3T3-E1 cells induced to undergo synchronized osteoblastic differentiationin vitro. Pairwise datasets representing changes in gene expression associated with growth arrest (day 2 to 5 in culture), differentiation (day 5 to 10 in culture), and osteoblast maturation (day 10 to 28 in culture) were analyzed using Ingenuity Systems™Pathways Analysis to generate predictions about signaling pathway activity based on the temporal sequence of changes in target gene expression. Our data indicate that some pathways known to be involved in osteoblast differentiation, e.g. Wnt/β-catenin signaling, are most active early in the process, while others, e.g. TGFβ/BMP, cytokine/JAK-STAT and TNFα/RANKL signaling, increase in activity as differentiation progresses. Collectively, these pathways contribute to the sequential expression of genes involved in the synthesis and mineralization of extracellular matrix. These results provide insight into the temporal coordination and complex interplay between signaling networks controlling gene expression during osteoblast differentiation. A more complete understanding of these processes may aid the discovery of novel methods to promote osteoblast development for the trea™ent of conditions characterized by low bone mineral density.
Functional analysis of Scratch2 domains: implications in the evolution of Snail transcriptional repressors
Authors: Nakamura Kanno Tatiane Yumi , Fogo Mariana Soares , Goes Carolina Purcell , Vieceli Felipe M. , Irene Yan Chao Yun
Published: September 2018

The Snail superfamily of transcription factors have a modular organization and their similarities and divergences are the basis for subdividing the superfamily into the Snail1/2 and Scratch families. As it is generally accepted that the Snail and Scratch families originated through gene duplication, understanding the functional contribution of each module could provide us with further insight about the molecular and functional evolution of the Snail superfamily. Thus, in this work, we investigated the function of the SNAG and SCRATCH domains in chicken Scratch2. Through evolutionary comparison analysis we identified a novel HINGE domain that lies between the SNAG and SCRATCH domain. Similar to members of the Snail1/2 families, Scratch2- mediated transcriptional repression requires SNAG and nuclear localization requires the zinc-finger domain. We also identified a novel HINGE domain that lies between the SNAG and SCRATCH domain. HINGE is highly conserved in amniotes. Single mutations of the conserved Tyrosine and Serine residues of HINGE downregulated Scratch2-mediated transcriptional repression. This effect depended on the presence of the SCRATCH domain.
How do firms utilize the deferred patent examination system? Evidence from Korea
Authors: Cao Siwei , Lei Zhen , Oh Junbyoung
Published: September 2018

Purpose

The purpose of this paper is to investigate firm behaviors on patent examination request under the deferred patent examination system in Korea. The authors examine firm decisions on whether and when to request patent examinations when they face both uncertainty about invention’s value and market competition.

Design/methodology/approach

The authors provide a simple theoretical model and test a couple of hypothesis using Korea patent data. The authors employ KIPO (Korean intellectual patent office) patent applications data during 2006–2009 and incorporate it with firm financial data retrieved from1 Korea investor service-financial analysis system (KIS-FAS) database in Korea. The authors use the variation in the probability of lapsed patent applications filed in the same year and in the same technology field (at the four-digit IPC class level) of a patent application i as a proxy for the value of uncertainty, and further use one minus a firm’s market share (at the three-digit SIC industry level) as an indicator of the market competition faced by the firm/applicant.

Findings

The authors find that the examination requests of firms in Korea have interesting bipolar distribution, and both uncertainty about an invention’s value and market competition have significant impacts on firm’s decision for examination request. Applicants tend to utilize option value of waiting when uncertainty is high, but market competition attenuates the option value: the higher the competition, the less likely applicants are to delay or forego examination.

Originality/value

The authors’ study makes interesting contributions to the literature on the optimal design of the patent system in general and the deferred patent examination request system in particular. By considering the roles of both uncertainty and market competition in firm decisions, it provides a more comprehensive perspective on the deferred patent examination system. The study also provides empirical evidences on the broader research topic regarding firm decision for irreversible investment when faced with both uncertainty and competition, for which a strand of theoretical literature exists but empirical literature is largely limited. This study, which explicitly takes into account uncertainty and market competition, extends this line of empirical literature and fills the gap in the literature.
Employees’ preferences for services and facilities offered in serviced offices
Authors: Appel-Meulenbroek Rianne , van de Kar Mike , van den Berg Pauline , Arentze Theo
Published: September 2018

Purpose

Serviced offices are popular, offering many services and facilities to attract tenants. As research showed that most business centres occupy similar buildings, services are important to differentiate. All kinds of people use them (from freelancers to employees of large corporates) and their characteristics are likely to influence how they value different services. This study aims to identify which services/facilities are perceived as most important and whether end-user characteristics explain differences between users regarding these preferences. Serviced office owners and operators can use the insights obtained from this study to differentiate their product offer from competitors and aim for specific tenant market segments.

Design/methodology/approach

Data were collected through a questionnaire among 137 end-users in 13 serviced offices in The Netherlands. With principal component analysis, 31 services and facilities could be reduced to six independent factors and four additional services. Multiple regression analysis was used to determine effects of user characteristics (employee demographics, job characteristics and reasons for using serviced offices) on perceived importance of each service/facility (factor).

Findings

Results showed that organisational characteristics had little effect on perceived importance of services and facilities. Especially the time spent at the office and the reasons for using it showed effects on importance of different services and facilities. Amenities like a gym and childcare were not deemed important by most of the respondents.

Originality/value

So far, research on office users focused largely on single-tenant offices and large corporates. Serviced offices have only been studied from the supply side until now.