bluuebunny/crossref_metadata_2025 huggingface dataset:
Fibroblast growth factor-23 promotes rhythm alterations and contractile dysfunction in adult ventricular cardiomyocytes
Authors: Navarro-García José Alberto , Delgado Carmen , Fernández-Velasco María , Val-Blasco Almudena , Rodríguez-Sánchez Elena , Aceves-Ripoll Jennifer , Gómez-Hurtado Nieves , Bada-Bosch Teresa , Mérida-Herrero Evangelina , Hernández Eduardo , Praga Manuel , Salguero Rafael , Solís Jorge , Arribas Fernando , Delgado Juan F , Bueno Héctor , Kuro-O Makoto , Ruilope Luis Miguel , Ruiz-Hurtado Gema
Published: December 2018

Background

Cardiac dysfunction and arrhythmia are common and onerous cardiovascular events in end-stage renal disease (ESRD) patients, especially those on dialysis. Fibroblast growth factor (FGF)-23 is a phosphate-regulating hormone whose levels dramatically increase as renal function declines. Beyond its role in phosphorus homeostasis, FGF-23 may elicit a direct effect on the heart. Whether FGF-23 modulates ventricular cardiac rhythm is unknown, prompting us to study its role on excitation–contraction (EC) coupling.

Methods

We examined FGF-23 in vitro actions on EC coupling in adult rat native ventricular cardiomyocytes using patch clamp and confocal microscopy and in vivo actions on cardiac rhythm using electrocardiogram.

Results

Compared with vehicle treatment, FGF-23 induced a significant decrease in rat cardiomyocyte contraction, L-type Ca2+ current, systolic Ca2+ transients and sarcoplasmic reticulum (SR) load and SR Ca2+-adenosine triphosphatase 2a pump activity. FGF-23 induced pro-arrhythmogenic activity in vitro and in vivo as automatic cardiomyocyte extracontractions and premature ventricular contractions. Diastolic spontaneous Ca2+ leak (sparks and waves) was significantly increased by FGF-23 via the calmodulin kinase type II (CaMKII)-dependent pathway related to hyperphosphorylation of ryanodine receptors at the CaMKII site Ser2814. Both contraction dysfunction and spontaneous pro-arrhythmic Ca2+ events induced by FGF-23 were blocked by soluble Klotho (sKlotho).

Conclusions

Our results show that FGF-23 reduces contractility and enhances arrhythmogenicity through intracellular Ca2+ mishandling. Blocking its actions on the heart by improving sKlotho bioavailability may enhance cardiac function and reduce arrhythmic events frequently observed in ESRD.
Procalcitonin-Guided Antibiotic Therapy Reduces Antibiotic Use for Lower Respiratory Tract Infections in a United States Medical Center: Results of a Clinical Trial
Authors: Townsend Jennifer , Adams Victoria , Galiatsatos Panagis , Pearse David , Pantle Hardin , Masterson Mary , Kisuule Flora , Jacob Elsen , Kiruthi Catherine , Ortiz Paul , Agbanlog Albert , Jurao Robert , Stern Sam , Nayak Seema , Melgar Michael , Sama Jacob , Irwin Jillian , Mazidi Cyrus , Psoter Kevin , McKenzie Robin
Published: December 2018

Background

European trials using procalcitonin (PCT)-guided antibiotic therapy for patients with lower respiratory tract infections (LRTIs) have demonstrated significant reductions in antibiotic use without increasing adverse outcomes. Few studies have examined PCT for LRTIs in the United States.

Methods

In this study, we evaluated whether a PCT algorithm would reduce antibiotic exposure in patients with LRTI in a US hospital. We conducted a controlled pre-post trial comparing an intervention group of PCT-guided antibiotic therapy to a control group of usual care. Consecutive patients admitted to medicine services and receiving antibiotics for LRTI were enrolled in the intervention. Providers were encouraged to discontinue antibiotics according to a PCT algorithm. Control patients were similar patients admitted before the intervention.

Results

The primary endpoint was median antibiotic duration. Overall adverse outcomes at 30 days comprised death, transfer to an intensive care unit, antibiotic side effects, Clostridium difficile infection, disease-specific complications, and post-discharge antibiotic prescription for LRTI. One hundred seventy-four intervention patients and 200 controls were enrolled. Providers complied with the PCT algorithm in 75% of encounters. Procalcitonin-guided therapy reduced median antibiotic duration for pneumonia from 7 days to 6 (P = .045) and acute exacerbation of chronic obstructive pulmonary disease (AECOPD) from 4 days to 3 (P = .01). There was no difference in the rate of adverse outcomes in the PCT and control groups.

Conclusions

A PCT-guided algorithm safely reduced the duration of antibiotics for treating LRTI. Utilization of a PCT algorithm may aid antibiotic stewardship efforts.

This clinical trial was a single-center, controlled, pre-post study of PCT-guided antibiotic therapy for LRTI. The intervention (incorporation of PCT-guided algorithms) started on April 1, 2017: the preintervention (control group) comprised patients admitted from November 1, 2016 to April 16, 2017, and the postintervention group comprised patients admitted from April 17, 2017 to November 29, 2017 (Supplementary Figure 1). The study comprised patients admitted to the internal medicine services to a medical ward, the Medical Intensive Care Unit (MICU), the Cardiac Intensive Care Unit (CICU), or the Progressive Care Unit (PCU) “step down unit”. The registration data for the trails are in the ClinicalTrials.gov database, number NCT0310910.
Utility of Cement Augmentation via Percutaneous Fenestrated Pedicle Screws for Stabilization of Cancer-Related Spinal Instability
Authors: Barzilai Ori , McLaughlin Lily , Lis Eric , Reiner Anne S , Bilsky Mark H , Laufer Ilya
Published: December 2018

BACKGROUND

Cancer patients experience pathological fractures and the typical poor bone quality frequently complicates stabilization. Methods for overcoming screw failure include utilization of fenestrated screws that permit the injection of bone cement into the vertebral body to augment fixation.

OBJECTIVE

To evaluate the safety and efficacy of cement augmentation via fenestrated screws.

METHODS

A retrospective chart review of patients with neoplastic spinal instability who underwent percutaneous instrumented stabilization with cement augmentation using fenestrated pedicle screws. Patient demographic and treatment data and intraoperative and postoperative complications were evaluated by chart review and radiographic evaluation. Prospectively collected patient reported outcomes (PRO) were evaluated at short (2- <6 mo) and long term (6-12 mo).

RESULTS

Cement augmentation was performed in 216 fenestrated pedicle screws in 53 patients. Three patients required reoperation. One patient had an asymptomatic screw fracture at 6 mo postoperatively that did not require intervention. No cases of lucency around the pedicle screws, rod fractures, or cement extravasation into the spinal canal were observed. Eight cases of asymptomatic, radiographically-detected venous extravasation were found. Systemic complications included a pulmonary cement embolism, a lower extremity deep vein thrombosis, and a postoperative mortality secondary to pulmonary failure from widespread metastatic pulmonary infiltration. Significant improvement in PRO measures was found in short- and long-term analysis.

CONCLUSION

Cement augmentation of pedicle screws is an effective method to enhance the durability of spinal constructs in the cancer population. Risks include cement extravasation into draining blood vessels, but risk of clinically significant extravasation appears to be exceedingly low.
ASSESSMENT OF THE ABSORBED DOSES IN THE ORGANS IN CASE OF RADIATION EMERGENCY WITH THE SEALED GAMMA-SOURCES
Authors: Golikov V
Published: December 2018

The majority of the radiation accidents with early acute clinical effects were associated with the orphan sources used in industrial and medical facilities. These accidents involved members of general public, who were entirely unaware of the exposure to the radiation. In such situations, the exposure commonly occurs when the source is in contact with a body of a victim, primarily located in pockets of clothing or in hands. In this research, the average absorbed doses in internal organs, skin and tissues close to the source were assessed using the phantom modeling of contact human exposure by the sealed 192Ir, 137Cs and 60Co gamma sources. The results allow estimating the RBE-weighted absorbed dose values in organs and tissues to assess the possibility and severity of deterministic medical effects caused by the exposure and to compare them with the reference levels established by IAEA for performing the protective and medical actions.
Anomalous Bodily Maps of Emotions in Schizophrenia
Authors: Torregrossa Lénie J , Snodgress Matthew A , Hong Seok Jin , Nichols Heathman S , Glerean Enrico , Nummenmaa Lauri , Park Sohee
Published: December 2018

Objective

Embodied emotions arise from interoceptive and somatosensory processes, and are essential to the development of a stable sense of self. Emotional embodiment is therefore inherently interwoven with our sense of bodily self-awareness, and allows us to navigate complex social situations. Given that the core feature of schizophrenia (SZ) is characterized by the presence of bodily self-disturbances and social-emotional deficits, we hypothesized that embodiment of emotion would be disrupted in SZ.

Method

Twenty-six medicated individuals with SZ and 26 demographically matched controls used a computerized topographical mapping tool (“EmBODY”) to indicate on a body outline where they felt bodily sensations while experiencing an emotion. There were 13 different emotions plus a neutral state. The resulting bodily maps of emotions were quantitatively compared between groups using linear discriminant analysis and similarity scores.

Results

Bodily maps of emotions were anomalous in SZ as indicated by indistinguishable maps across different emotions. Relative to the control group, patients reported less discrete and less clear bodily sensations across emotions. In particular, bodily maps for low-arousal emotions were atypical in comparison with healthy controls.

Conclusions

Anomalous and undifferentiated mapping of embodied emotions in SZ could lead to deficits in linking bodily sensations to conceptual categories of emotions. Disrupted emotional embodiment could also contribute to poor social functioning. Abnormal bodily sensations of emotions might therefore be a promising target for future psychosocial interventions.
Political Polarization and Long-Term Change in Public Support for Environmental Spending
Authors: Johnson Erik W , Schwadel Philip
Published: December 2018

Public support for environmental protection has evinced declines in recent years that are widely attributed to growing antipathy among self-identified Republicans. Fractures in what was long considered broad and enduring support for the environment in the United States have called attention to the broader socio-political context in which individual opinion on the environment is formed, and especially the role of political parties and their leaders in shaping opinion. Empirical analyses of environmental support, however, remain strongly focused on individual-level correlates of support. We apply recent methodological advances in age-period-cohort models to scrutinize changes in Americans’ willingness to pay more for environmental protection between 1973 and 2014. Analyses distinguish the importance of individual traits, such as political identification, from cohort and especially period-based fluctuations that result from changing economic and political conditions. Individual-level covariate results are reflective of previous research on environmental opinion (e.g., age is negatively and education positively associated with environmental support). We further find that political context across time periods matters as much as, and interacts with, individual political affiliation to influence support for the environment. Americans of all political stripes demonstrate decreases in support for environmental spending during Democratic presidential administrations and during difficult economic times. Declines during Democratic presidencies are especially pronounced among Republicans. Analyses also highlight parallels between the high levels of political polarization in environmental support found at the end of the Obama Presidency and the end of the Carter era.
Characterization of Soybean yellow shoot virus, a New Member of the Family Potyviridae Infecting Soybean Plants in Brazil
Authors: Figueira Antonia dos Reis , Geraldino-Duarte Priscilla S. , Pinzón Nuñez Andrés Mauricio , Lent Jan van , Galvino-Costa Suellen B. F. , Farman M. , Goodin Michael M.
Published: December 2018

A new virus species, belonging to the family Potyviridae and capable of infecting most of the soybean cultivars grown in Brazil, was collected in Lavras, Minas Gerais, Brazil, and named Soybean yellow shoot virus (SoyYSV). In this study, the complete 9,052-nucleotide genome of SoyYSV was determined and the structural, biological, and molecular properties of the virus were investigated. The SoyYSV genome encoded a single polyprotein that could be subsequently cleaved, generating 11 proteins. The SoyYSV genome shared 49% nucleotide and 36% amino acid sequence identity with Blackberry virus Y. However, the P1 protein of SoyYSV was much smaller and lacked the ALK1 domain characteristic of the genus Brambyvirus. Electron microscopy revealed flexuous filamentous virus particles, 760 to 780 nm in length, and cytoplasmic inclusions typical of those found in plant cells infected with Potyviridae species. In addition to soybean, SoyYSV infected species in the Amaranthaceae, Caricaceae, Fabaceae, and Solanaceae families. Among the most common potyviruses present in Brazil, only SoyYSV induced local necrotic lesions in Carica papaya L. SoyYSV was transmissible by Myzus persicae and Aphis gossypii but lacked the HC-Pro domain required for aphid transmission in other potyviruses. No seed transmission in soybean was observed.
Naturalizing pollution: a critical social science view on the link between potash mining and salinization in the Llobregat river basin, northeast Spain
Authors: Gorostiza Santiago , Saurí David
Published: December 2018

The scientific literature distinguishes between primary or natural and secondary or human-induced salinization. Assessing this distinction is of vital importance to assign liabilities and responsibilities in pollution cases and for designing the best policy and management actions. In this context, actors interested in downplaying the role of certain drivers of human-induced salinization can attempt to neglect its importance by referring to natural salinization, in a similar fashion to other pollution and health-related cases, from tobacco smoke to climate change. Potash mining, which has experienced continued growth during the last decades and is a significant contributor to salinization, is prone to originate such controversies because natural salinization from the saline geological catch can be mixed with salinization produced by mining waste such as brines and mine tailings, thus obscuring the distinction between causes. By reviewing the long-standing social and environmental conflict caused by potash mining in a region of Mediterranean climate—the Llobregat river basin—in this article, we highlight the importance of the impacts of salinization on human health and provide a critical social science perspective on salinization processes.

This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
Propensity of a picornavirus polymerase to slip on potyvirus-derived transcriptional slippage sites
Authors: Stewart Hazel , Olspert Allan , Butt Benjamin G. , Firth Andrew E.
Published: December 2018

The substitution rates of viral polymerases have been studied extensively. However less is known about the tendency of these enzymes to ‘slip’ during RNA synthesis to produce progeny RNAs with nucleotide insertions or deletions. We recently described the functional utilization of programmed polymerase slippage in the family Potyviridae. This slippage results in either an insertion or a substitution, depending on whether the RNA duplex realigns following the insertion. In this study we investigated whether this phenomenon is a conserved feature of superfamily I viral RdRps, by inserting a range of potyvirus-derived slip-prone sequences into a picornavirus, Theiler’s murine encephalomyelitis virus (TMEV). Deep-sequencing analysis of viral transcripts indicates that the TMEV polymerase ‘slips’ at the sequences U6–7 and A6–7 to insert additional nucleotides. Such sequences are under-represented within picornaviral genomes, suggesting that slip-prone sequences create a fitness cost. Nonetheless, the TMEV insertional and substitutional spectrum differed from that previously determined for the potyvirus polymerase.
A combined in silico, in vitro and clinical approach to characterise novel pathogenic missense variants in PRPF31 in retinitis pigmentosa
Authors: Wheway Gabrielle , Nazlamova Liliya , Meshad Nervine , Hunt Samantha , Jackson Nicola , Churchill Amanda
Published: December 2018

At least six different proteins of the spliceosome, including PRPF3, PRPF4, PRPF6, PRPF8, PRPF31 and SNRNP200, are mutated in autosomal dominant retinitis pigmentosa (adRP). These proteins have recently been shown to localise to the base of the connecting cilium of the retinal photoreceptor cells, elucidating this form of RP as a retinal ciliopathy. In the case of loss-of-function variants in these genes, pathogenicity can easily be ascribed. In the case of missense variants, this is more challenging. Furthermore, the exact molecular mechanism of disease in this form of RP remains poorly understood.

In this paper we take advantage of the recently published cryo EM-resolved structure of the entire human spliceosome, to predict the effect of a novel missense variant in one component of the spliceosome; PRPF31, found in a patient attending the genetics eye clinic at Bristol Eye Hospital. Monoallelic variants in PRPF31 are a common cause of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance. We use in vitro studies to confirm pathogenicity of this novel variant PRPF31 c.341T>A, p.Ile114Asn.

This work demonstrates how in silico modelling of structural effects of missense variants on cryo-EM resolved protein complexes can contribute to predicting pathogenicity of novel variants, in combination with in vitro and clinical studies. It is currently a considerable challenge to assign pathogenic status to missense variants in these proteins.
Group size and collective action in a binary contribution game
Authors: Nöldeke Georg , Peña Jorge
Published: December 2018

We consider how group size affects the private provision of a public good with non-refundable binary contributions. A fixed amount of the good is provided if and only if the number of contributors reaches an exogenous threshold. The threshold, the group size, and the identical, non-refundable cost of contributing to the public good are common knowledge. Our focus is on the case in which the threshold is larger than one, so that teamwork is required to produce the public good. We show that both expected payoffs and the probability that the public good is obtained in the best symmetric equilibrium are decreasing in group size. We also characterize the limit outcome when group size converges to infinity and provide precise conditions under which the expected number of contributors is decreasing or increasing in group size for sufficiently large groups.

JEL classification

C72, D71, H41.
Medroxyprogesterone acetate mediated alteration in the vaginal microbiota and microenvironment in a Kenyan sex worker cohort
Authors: Wessels Jocelyn M. , Lajoie Julie , Hay Cooper Maeve I. J. , Omollo Kenneth , Felker Allison M. , Vitali Danielle , Dupont Haley A. , Nguyen Philip V. , Mueller Kristen , Vahedi Fatemeh , Kimani Joshua , Oyugi Julius , Cheruiyot Juliana , Mungai John N. , Deshiere Alexandre , Tremblay Michel J. , Mazzulli Tony , Stearns Jennifer C. , Ashkar Ali A. , Fowke Keith R. , Surette Michael G. , Kaushic Charu
Published: December 2018

The hormonal contraceptive Medroxyprogesterone Acetate (MPA) is associated with increased risk of Human Immunodeficiency Virus (HIV), via incompletely understood mechanisms. Increased diversity in the vaginal microbiota modulates genital inflammation and is associated with increased HIV-1 acquisition. However, the effect of MPA on diversity of the vaginal microbiota is relatively unknown. In a cohort of female Kenyan sex workers, negative for sexually transmitted infections (STIs), with Nugent Scores <7 (N=58 of 370 screened), MPA correlated with significantly increased diversity of the vaginal microbiota as assessed by 16S rRNA gene sequencing. MPA was also significantly associated with low vaginal glycogen and α-amylase, factors implicated in vaginal colonization by lactobacilli, bacteria believed to protect against STIs. Furthermore, increased diversity of the vaginal microbiota correlated with activation of vaginal HIV-1 target cells. Results were recapitulated in humanized mice where MPA treatment was associated with increased diversity of the vaginal microbiota, low glycogen, and enhanced HIV-1 susceptibility. Together these results suggest MPA-induced hypo-estrogenism may alter key metabolic components necessary for vaginal colonization by certain bacterial species including lactobacilli, and allow for greater bacterial diversity in the vaginal microbiota. Bacterial diversity in the vaginal microbiota correlates with activation of HIV-1 target cells, which might thus contribute to enhanced susceptibility to HIV-1.
ciftify: A framework for surface-based analysis of legacy MR acquisitions
Authors: Dickie Erin W. , Anticevic Alan , Smith Dawn E. , Coalson Timothy S. , Manogaran Mathuvanthi , Calarco Navona , Viviano Joseph D. , Glasser Matthew F. , Van Essen David C. , Voineskos Aristotle N.
Published: December 2018

The preprocessing pipelines of the Human Connectome Project (HCP) were made publicly available for the neuroimaging community to apply the HCP analytic approach to data from non-HCP sources. The HCP analytic approach is surface-based for the cerebral cortex, uses the CIFTI “grayordinate” file format, provides greater statistical sensitivity than traditional volume-based analysis approaches, and allows for a more neuroanatomically-faithful representation of data. However, the HCP pipelines require the acquisition of specific images (namely T2w and field map) that historically have often not been acquired. Massive amounts of this ‘legacy’ data could benefit from the adoption of HCP-style methods. However, there is currently no published framework, to our knowledge, for adapting HCP preprocessing to “legacy” data. Here we present the ciftify project, a parsimonious analytic framework for adapting key modules from the HCP pipeline into existing structural workflows using

FreeSurfer’s recon_all structural and existing functional preprocessing workflows. Within this framework, any functional dataset with an accompanying (i.e. T1w) anatomical data can be analyzed in CIFTI format. To simplify usage for new data, the workflow has been bundled with fMRIPrep following the BIDS-app framework. Finally, we present the package and comment on future neuroinformatics advances that may accelerate the movement to a CIFTI-based grayordinate framework.

HIGHLIGHTS

the ciftify package allows for grayordinate-based (CIFTI format) analysis of non-Human Connectome Project (i.e. legacy) MR acquisitions

The workflow and dependencies are distributed as a Docker container, following the BIDS-app interface

Additional ciftify utilities aid in downstream analysis of CIFTI images

We intend for this work to offer bridging solution for legacy data that will allow many researchers to adopt CIFTI format analyses
Tractography Reproducibility Challenge with Empirical Data (TraCED): The 2017 ISMRM Diffusion Study Group Challenge
Authors: Nath Vishwesh , Schilling Kurt , Parvathaneni Prasanna , Hainline Allison E. , Huo Yuankai , Blaber Justin A. , Rowe Matt , Rodrigues Paulo , Prckovska Vesna , Aydogan Baran , Sun Wei , Shi Yonggang , Parker William , Ismail Abdol Aziz Ould , Verma Ragini , Cabeen Ryan P , Toga Arthur W , Newton Allen T , Wasserthal Jakob , Neher Peter , Maier-Hein Klaus H , Savini Giovanni , Palesi Fulvia , Kaden Enrico , Wu Ye , Feng Yuanjing , He Jianzhong , Barakovic Muhamed , Romascano David , Rafael-Pinto Jonathan , Frigo Matteo , Girard Gabriel , Daducci Alessandro , Thiran Jean-Phillipe , Paquette Michael , Rheault Francois M , Sidhu Jasmeen , Lebel Catherine , Leemans Alexander , Descoteaux Maxime , Dyrby Tim , Kang Hakmook , Landman Bennett A
Published: December 2018

Purpose: Fiber tracking with diffusion weighted magnetic resonance imaging has become an essential tool for estimating in vivo brain white matter architecture. Fiber tracking results are sensitive to the choice of processing method and tracking criteria. Phantom studies provide concrete quantitative comparisons of methods relative to absolute ground truths, yet do not capture variabilities because of in vivo physiological factors.
Methods: To date, a large-scale reproducibility analysis has not been performed for the assessment of the newest generation of tractography algorithms with in vivo data. Reproducibility does not assess the validity of a brain connection however it is still of critical importance because it describes the variability for an algorithm in group studies. The ISMRM 2017 TraCED challenge was created to fulfill the gap. The TraCED dataset consists of a single healthy volunteer scanned on two different scanners of the same manufacturer. The multi-shell acquisition included b-values of 1000, 2000 and 3000 s/mm2 with 20, 45 and 64 diffusion gradient directions per shell, respectively.
Results: Nine international groups submitted 46 tractography algorithm entries. The top five submissions had high ICC > 0.88. Reproducibility is high within these top 5 submissions when assessed across sessions or across scanners. However, it can be directly attributed to containment of smaller volume tracts in larger volume tracts. This holds true for the top five submissions where they are contained in a specific order. While most algorithms are contained in an ordering there are some outliers.
Conclusion: The different methods clearly result in fundamentally different tract structures at the more conservative specificity choices (i.e., volumetrically smaller tractograms). The data and challenge infrastructure remain available for continued analysis and provide a platform for comparison.
Extensive field-sampling reveals the uniqueness of a trophy mountain goat population
Authors: Breen Jessica , Britt Meghan , Johnson Justin B. , Martchenko Daria , Shakeri Yasaman , Porter Boyd , White Kevin S. , Shafer Aaron B.A.
Published: December 2018

Collaborations between academic researchers and agencies is crucial for genetic data to have a tangible impact on conservation and wildlife management. Such partnerships are particularly important elusive species where the difficult terrain requires that a significant amount of resources and a combination of methods be used to estimate population parameters needed for conservation. We report and multi-year academic-agency collaboration on the North American mountain goat that used an extensive field sampling of genetic and phenotypic data to determine whether, and to what degree, genetic and phenotypic differences separate an isolated population of mountain goats on the Cleveland Peninsula form those in southeast Alaska. We observed significantly larger horns on the peninsula and the population appears demographically isolated. Isolation-by-distance accompanied by limited migration and low effective population size on the Cleveland Peninsula suggest this population will continue to lose genetic diversity. While the large horns of mountain goats have generated interest in re-opening mountain goat harvest on Cleveland Peninsula, our genetic data suggest this population is vulnerable to demographic and environmental perturbations and is unlikely to support a sustained harvest.
Critical-Period Visual Deprivation Disrupts Binocular Integration but Spares Spatial Acuity in the Geniculocortical Pathway
Authors: Huh Carey Y. L. , Abdelaal Karim , Salinas Kirstie J. , Gu Diyue , Zeitoun Jack , Figueroa Velez Dario X. , Peach John P. , Fowlkes Charless C. , Gandhi Sunil P.
Published: December 2018

Monocular deprivation (MD) during the juvenile critical period leads to long-lasting impairments in binocular function and visual acuity. The site of these changes has been widely considered to be cortical. However, recent evidence indicates that binocular integration may first occur in the dorsolateral geniculate nucleus of the thalamus (dLGN), raising the question of whether MD during the critical period may produce long-lasting deficits in dLGN binocular integration. Using in vivo two-photon Ca2+ imaging of dLGN afferents and excitatory neurons in superficial layers of primary visual cortex (V1), we demonstrate that critical-period MD leads to a persistent and selective loss of binocular dLGN inputs, while leaving spatial acuity in the thalamocortical pathway intact. Despite being few in number, binocular dLGN boutons display remarkably robust visual responses, on average twice stronger than monocular boutons, and their responses are exquisitely well-matched between the eyes. To our surprise, we found that MD leads to a profound binocular mismatch of response amplitude, spatial frequency and orientation tuning detected at the level of single thalamocortical synapses. In comparison, V1 neurons display deficits in both binocular integration and spatial acuity following MD. Our data provide the most compelling evidence to date demonstrating that following critical-period MD, binocular deficits observed at the level of V1 may at least in part originate from dLGN binocular dysfunction, while spatial acuity deficits arise from cortical circuits. These findings highlight a hitherto unknown role of the thalamus as a site for developmental refinement of binocular vision.
PCIF1 catalyzes m6Am mRNA methylation to regulate gene expression
Authors: Sendinc Erdem , Valle-Garcia David , Dhall Abhinav , Chen Hao , Henriques Telmo , Sheng Wanqiang , Adelman Karen , Shi Yang
Published: December 2018

mRNA modifications play an important role in regulating gene expression. One of the most abundant mRNA modifications is N6,2-O-dimethyladenosine (m6Am). Here, we demonstrate that m6Am is an evolutionarily conserved mRNA modification mediated by the Phosphorylated CTD Interacting Factor 1 (PCIF1), which catalyzes m6A methylation on 2-O-methylated adenine located at the 5’ ends of mRNAs. Furthermore, PCIF1 catalyzes only 5’ m6Am methylation of capped mRNAs, but not internal m6A methylationin vitroandin vivo. Our global mRNA methylation analysis revealed that there is no crosstalk between m6Am and m6A mRNA methylation events, suggesting that m6Am is functionally distinct from m6A. Importantly, our data indicate that m6Am negatively impacts translation of methylated mRNAs by antagonizing cap binding protein eIF4E. Together, we identify the first and only human mRNA m6Am methyltransferase and demonstrate a novel mechanism of gene expression regulation through PCIF1-mediated m6Am mRNA methylation in eukaryotes.

Highlights

PCIF1 is an evolutionarily conserved mRNA m6Am methyltransferase

Loss of PCIF1 leads to a complete loss of m6Am, whereas m6A level and distribution are not affected

PCIF1 mediated m6Am does not affect RNA Pol II transcription or mRNA stability

m6Am-Exo-Seq is a robust methodology that enables global m6Am mapping

m6Am suppresses cap dependent translation
Dynamic landscape and genetic regulation of RNA editing in schizophrenia
Authors: Breen Michael S. , Dobbyn Amanda , Li Qin , Roussos Panos , Hoffman Gabriel E. , Stahl Eli , Chess Andrew , Sklar Pamela , Li Jin Billy , Devlin Bernie , Buxbaum Joseph D. ,   for the CommonMind Consortium (CMC)
Published: December 2018

RNA editing is vital for neurodevelopment and the maintenance of normal neuronal function. We surveyed the global landscape and genetic regulation of RNA editing across several hundred schizophrenia and control postmortem brain samples from the CommonMind Consortium covering two regions, the dorsolateral prefrontal cortex (DLPFC) and anterior cingulate cortex. In schizophrenia, RNA editing sites encoding AMPA glutamate receptors and post-synaptic density genes were less edited, while more editing was detected in sites implicated in translational initiation. These sites replicate between brain regions, map to 3’UTRs, enrich for common sequence motifs and coincide for RNA binding proteins crucial for neurodevelopment. Importantly, these findings cross-validate in hundreds of non-overlapping DLPFC samples. Furthermore, ~30% of RNA editing sites associate with cis-regulatory variants (edQTLs). Fine-mapping edQTLs with schizophrenia GWAS loci revealed colocalization of 11 edQTLs with 6 GWAS loci. This supports a causal role of RNA editing in risk for schizophrenia. Our findings illustrate widespread altered RNA editing in schizophrenia and its genetic regulation, and shed light onto RNA editing-mediated mechanisms in schizophrenia neuropathology.
Speeding up anterior-posterior patterning of insects by differential initialization of the gap gene cascade
Authors: Rudolf Heike , Zellner Christine , El-Sherif Ezzat
Published: December 2018

Recently, it was shown that anterior-posterior patterning genes in the red flour beetleTribolium castaneumare expressed sequentially in waves. However, in the fruit flyDrosophila melanogaster, an insect with a derived mode of embryogenesis compared toTribolium, anterior-posterior patterning genes quickly and simultaneously arise as mature gene expression domains that, afterwards, undergo slight posterior-to-anterior shifts. This raises the question of how a fast and simultaneous mode of patterning, like that ofDrosophila, could have evolved from a rather slow sequential mode of patterning, like that ofTribolium. In this paper, we elucidate a mechanism for this evolutionary transition based on a switch from a uniform to a gradient-mediated initialization of the gap gene cascade by maternal Hb. The model is supported by computational analyses and experiments.
Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model
Authors: Roy Mahua , Finley Stacey D.
Published: December 2018

Mathematical modeling provides the predictive ability to understand the metabolic reprogramming and complex pathways that mediate cancer cells’ proliferation. We present a mathematical model using a multiscale, multicellular approach to simulate avascular tumor growth, applied to pancreatic cancer. The model spans three distinct spatial and temporal scales. At the extracellular level, reaction diffusion equations describe nutrient concentrations over a span of seconds. At the cellular level, a lattice-based energy driven stochastic approach describes cellular phenomena including adhesion, proliferation, viability and cell state transitions, occurring on the timescale of hours. At the sub-cellular level, we incorporate a detailed kinetic model of intracellular metabolite dynamics on the timescale of minutes, which enables the cells to uptake and excrete metabolites and use the metabolites to generate energy and building blocks for cell growth. This is a particularly novel aspect of the model. Certain defined criteria for the concentrations of intracellular metabolites lead to cancer cell growth, proliferation and necrosis. Overall, we model the evolution of the tumor in both time and space. Starting with a cluster of tumor cells, the model produces an avascular tumor that quantitatively and qualitatively mimics experimental measurements of multicellular tumor spheroids. Through our model simulations, we can investigate the response of individual intracellular species under a metabolic perturbation and investigate how that response contributes to the response of the tumor as a whole. The predicted response of intracellular metabolites under various targeted strategies are difficult to resolve with experimental techniques. Thus, the model can give novel predictions as to the response of the tumor as a whole, identifies potential therapies to impede tumor growth, and predicts the effects of those therapeutic strategies. In particular, the model provides quantitative insight into the dynamic reprogramming of tumor cells at the intracellular level in response to specific metabolic perturbations. Overall, the model is a useful framework to study targeted metabolic strategies for inhibiting tumor growth.
Modulation of fear generalization by the zona incerta
Authors: Venkataraman Archana , Brody Natalia , Reddi Preethi , Guo Jidong , Rainnie Donald , Dias Brian George
Published: December 2018

Fear expressed towards threat-associated stimuli is an adaptive behavioral response. In contrast, the generalization of fear responses toward non-threatening cues is maladaptive and a debilitating dimension of trauma- and anxiety-related disorders. Expressing fear to appropriate stimuli and suppressing fear generalization requires integration of relevant sensory information and motor output. While thalamic and sub-thalamic brain regions play important roles in sensorimotor integration, very little is known about the contribution of these regions to the phenomenon of fear generalization. In this study, we sought to determine whether fear generalization could be modulated by the zona incerta (ZI), a sub-thalamic brain region that influences sensory discrimination, defensive responses, and retrieval of fear memories. To do so, we combined differential intensity-based auditory fear conditioning protocols in mice with C-FOS immunohistochemistry and DREADD-based manipulation of neuronal activity in the ZI. C-FOS immunohistochemistry revealed an inverse relationship between ZI activation and fear generalization with the ZI being less active in animals that generalized fear. In agreement with this relationship, chemogenetic inhibition of the ZI resulted in fear generalization, while chemogenetic activation of the ZI suppressed fear generalization. Furthermore, targeted stimulation of GABAergic cells in the ZI reduced fear generalization. To conclude, our data suggest that stimulation of the ZI could be used to treat fear generalization in the context of trauma- and anxiety-related disorders.
Main constraints for RNAi induced by expressed long dsRNA in mouse cells
Authors: Demeter Tomas , Vaskovicova Michaela , Malik Radek , Horvat Filip , Pasulka Josef , Svobodova Eliska , Flemr Matyas , Svoboda Petr
Published: December 2018

RNA interference (RNAi) is sequence-specific mRNA degradation guided by small RNAs (siRNAs) produced from long double-stranded RNA (dsRNA) by RNase Dicer. Proteins executing RNAi are present in mammalian cells but sustain a gene-regulating microRNA pathway while dsRNA-induced innate immunity relies on a sequence-independent interferon response. While striving to benchmark mammalian RNAi analysis, we report that the main RNAi constraint is siRNA production, which integrates Dicer activity, dsRNA structure, and siRNA targeting efficiency. Unexpectedly, increased expression of dsRNA-binding Dicer co-factors TARBP2 or PACT reduces RNAi but not microRNA function. Elimination of Protein Kinase R, a key dsRNA sensor for interferon response, had minimal positive effects in fibroblasts. Without increasing Dicer activity, RNAi can occur when the first Dicer cleavage of an abundant dsRNA produces an efficient siRNA. In mammals, efficient RNAi may effectively employ substrates, which have some features of microRNA precursors, hence bringing the two pathways mechanistically even closer. At the same time, Dicer substrate optimization, which viruses would avoid, represents an opportunity for evolving RNAi, yet unlikely as an antiviral system.
Visual mismatch negativity to disappearing parts of objects and textures
Authors: Gaál Zsófia Anna , Czigler István , Sulykos István , File Domonkos , Kojouharova Petia
Published: December 2018

Visual mismatch negativity (vMMN), an event-related signature of automatic detection of events violating sequential regularities is traditionally investigated to the onset of frequent (standard) and rare (deviant) events. In a previous study [4] we obtained vMMN to vanishing parts of continuously presented objects (diamonds with diagonals), and we concluded that the offset-related vMMN is a model of sensitivity to irregular partial occlusion of objects. In the present study we replicated the previous results, but to test the object-related interpretation we applied a new condition with a set of separate visual stimuli: a texture of bars with two orientations. In the texture condition (offset of bars with irregular vs. regular orientation) we obtained vMMN, showing that the continuous presence of objects is unnecessary for offset-related vMMN. However, unlike in the object-related condition, reappearance of the previously vanishing lines also elicited vMMN. In a formal way reappearance of the stimuli is an event with probability 1.0, and according to the results, object condition reappearance is an expected event. However, offset and onset of texture elements seems to be treated separately by the system underlying vMMN. As an advantage of the present method, the whole stimulus set during the inter-stimulus interval saturates the visual structures sensitive to stimulus input. Accordingly, the offset-related vMMN is less sensitive to low-level adaptation difference between the deviant and standard stimuli.
Climate and vegetation collectively drive soil respiration in montane forest-grassland landscapes of the southern Western Ghats, India
Authors: Joshi Atul Arvind , Ratnam Jayashree , Paramjyothi Harinandanan , Sankaran Mahesh
Published: December 2018

Land-use conversion to non-native species plantations not only affects biodiversity but also alters important ecosystem functions including above- and below-ground carbon sequestration, and CO2 release rates from soils via soil respiration. Though the role of soil temperature and moisture on soil respiration is well recognized, little is known about how their effects vary across different land-use types. This study looked at the effects of land-cover change on temporal patterns of soil respiration in a montane forest-grassland-plantation matrix, a highly diverse but climatically sensitive ecosystem in the tropical Western Ghats of India. Among native vegetation types, soil respiration rates were higher in grassland compared to forest patches. Invasion of grassland by an exotic tree species - wattle (Acacia mearnsii) reduced soil respiration rates to levels similar to that of forests. However, conversion of native grasslands to non-native pine (Pinus patula) plantations led to the largest declines in soil respiration rates. In addition, the sensitivity of soil respiration to changes in temperature and moisture differed between different vegetation types. Across all vegetation types, respiration was largely insensitive to changes in soil temperature when moisture levels were low. However, when soil moisture levels were high, respiration increased with temperature in grassland and wattle patches, decreased in the case of pine plantations, and remained largely unchanged in shola forests. Our results suggest that changes in aboveground vegetation type can significantly affect soil C cycling even in the absence of any underlying differences in soil type.
Immunoprecipitation and SDS-PAGE for Cross-Linking Immunoprecipitation (CLIP)
Authors: Darnell Jennifer C. , Mele Aldo , Hung Ka Ying Sharon , Darnell Robert B.
Published: December 2018

This first part of this protocol is designed to optimize purification of the RNABP by immunoprecipitation for cross-linking immunoprecipitation (CLIP) experiments. The key variables to assess are the quality and quantity of antibody needed to immunoprecipitate most but not quite all of the RNABP (the titration will decrease nonspecific binding), and the tolerance of the antibody:antigen interaction to stringent wash conditions. The results of these experiments can be checked first by western blot, and subsequently using the pilot CLIP protocol described in the second half of this protocol. RNase-treated cross-linked RNABP:RNA complexes from mixed lysates or cell pellets are immunoprecipitated using conditions optimized in the first half of the protocol. 3′ Linkers are added, the RNA is radiolabeled, and the complexes are purified on SDS-PAGE. The pilot experiment will identify the optimal RNase concentration for the particular sample and will assess the quality and purity of the RNABP–RNA complexes following labeling of the RNA tags with 32P. This can be done without ligation of the 3′ linker as described in the main protocol below. The pilot experiment assesses whether sufficient RNA–protein complexes can be detected by autoradiography and whether contaminating RNA ligands are present in immunoprecipitations compared with control samples. Once it is confirmed that the signal-to-noise ratio for detection of RNA–protein complexes after immunoprecipitation is sufficient, the optimal immunoprecipitation conditions should be incorporated into the general CLIP protocol including the steps of cross-linking, RNase digestion, linker ligation, and labeling of RNA “tags,” and the results analyzed by autoradiography.
Isolation of the RNA Cross-Linking Immunoprecipitation (CLIP) Tags, 5′-Linker Ligation, Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Amplification, and Sequencing
Authors: Darnell Jennifer C. , Mele Aldo , Hung Ka Ying Sharon , Darnell Robert B.
Published: December 2018

This protocol describes purification of RNA cross-linking immunoprecipitation (CLIP) tags by proteinase K digestion of the cross-linked protein, addition of a 5′ linker to the RNA tags, and amplification of the product by transcription-polymerase chain reaction (RT-PCR). Use of this protocol adds another important purification step: sizing of the PCR products to enrich for those derived from RNA originally cross-linked to the desired RNABP. Finally, sequencing of the PCR products is described. There are two strategies for sequencing the PCR products of “CLIPed” RNA. Low-throughput sequencing involves cloning of PCR products, conventional minipreps, and sequencing. This can be performed on the PCR products generated here using standard protocols for A-tailing the PCR product and TA-cloning. This may be a worthwhile strategy when analyzing a small number of clones. In general, particularly in light of falling costs, high-throughput sequencing is the preferred method for sequencing the products of CLIPed RNA. This protocol describes a method for reamplifying PCR products with primers suitable for use on Illumina’s Solexa platform. Although this protocol is specific to the Illumina deep-sequencing platform, similar schemes for reamplification of the initial PCR products can be used to add platform-specific sequences to the termini of the PCR-amplified DNA.
Optical Transfection
Authors: Kumar Priti , Nagarajan Arvindhan , Uchil Pradeep D.
Published: December 2018

Strategies for the delivery of genes into eukaryotic cells fall into three categories: transfection by biochemical methods, transfection by physical methods, and virus-mediated transduction. “Optical transfection”—a physical transfection method—exploits the ability of light to create small transient pores in the plasma membrane of mammalian cells.
Mapping of In Vivo RNA-Binding Sites by Ultraviolet (UV)-Cross-Linking Immunoprecipitation (CLIP)
Authors: Darnell Jennifer C. , Mele Aldo , Hung Ka Ying Sharon , Darnell Robert B.
Published: December 2018

RNA “CLIP” (cross-linking immunoprecipitation), the method by which RNA–protein complexes are covalently cross-linked and purified and the RNA sequenced, has attracted attention as a powerful means of developing genome-wide maps of direct, functional RNA–protein interaction sites. These maps have been used to identify points of regulation, and they hold promise for understanding the dynamics of RNA regulation in normal cell function and its dysregulation in disease.