bluuebunny/crossref_metadata_2025 huggingface dataset:
Baicalin improves the in vitro developmental capacity of pig embryos by inhibiting apoptosis, regulating mitochondrial activity and activating sonic hedgehog signaling
Authors: Guo Qing , Xuan Mei-Fu , Luo Zhao-Bo , Wang Jun-Xia , Han Sheng-Zhong , Ri Myong-Hak , Choe Yong-Gyu , Hwang Kyung-Min , Yin Xi-Jun , Kang Jin-Dan
Published: June 2019

Baicalin, a traditional Chinese medicinal monomer whose chemical structure is known, can be used to treat female infertility. However, the effect of baicalin on embryonic development is unknown. This study investigated the effects of baicalin on in vitro development of parthenogenetically activated (PA) and in vitro fertilized (IVF) pig embryos and the underlying mechanisms involved. Treatment with 0.1 μg/ml baicalin significantly improved (P < 0.05) the in vitro developmental capacity of PA pig embryos by reducing the reactive oxygen species (ROS) levels and apoptosis and increasing the mitochondrial membrane potential (ΔΨm) and ATP level. mRNA and protein expression of sonic hedgehog (SHH) and GLI1, which are related to the SHH signaling pathway, in PA pig embryos at the 2-cell stage, were significantly higher in the baicalin-treated group than in the control group. To confirm that the SHH signaling pathway is involved in the mechanism by which baicalin improves embryonic development, we treated embryos with baicalin in the absence or presence of cyclopamine (Cy), an inhibitor of this pathway. Cy abolished the effects of baicalin on in vitro embryonic development. In conclusion, baicalin improves the in vitro developmental capacity of PA and IVF pig embryos by inhibiting ROS production and apoptosis, regulating mitochondrial activity and activating SHH signaling.
Impact of hypoxia on DNA repair and genome integrity
Authors: Kaplan Alanna R , Glazer Peter M
Published: June 2019

Hypoxia is a hallmark of the tumour microenvironment with profound effects on tumour biology, influencing cancer progression, the development of metastasis and patient outcome. Hypoxia also contributes to genomic instability and mutation frequency by inhibiting DNA repair pathways. This review summarises the diverse mechanisms by which hypoxia affects DNA repair, including suppression of homology-directed repair, mismatch repair and base excision repair. We also discuss the effects of hypoxia mimetics and agents that induce hypoxia on DNA repair, and we highlight areas of potential clinical relevance as well as future directions.
Gcn5-mediated acetylation at MBF-regulated promoters induces the G1/S transcriptional wave
Authors: González-Medina Alberto , Hidalgo Elena , Ayté José
Published: June 2019

In fission yeast, MBF-dependent transcription is inactivated at the end of S phase through a negative feedback loop that involves the co-repressors, Yox1 and Nrm1. Although this repression system is well known, the molecular mechanisms involved in MBF activation remain largely unknown. Compacted chromatin constitutes a barrier to activators accessing promoters. Here, we show that chromatin regulation plays a key role in activating MBF-dependent transcription. Gcn5, a part of the SAGA complex, binds to MBF-regulated promoters through the MBF co-activator Rep2 in a cell cycle-dependent manner and in a reverse correlation to the binding of the MBF co-repressors, Nrm1 or Yox1. We propose that the co-repressors function as physical barriers to SAGA recruitment onto MBF promoters. We also show that Gcn5 acetylates specific lysine residues on histone H3 in a cell cycle-regulated manner. Furthermore, either in a gcn5 mutant or in a strain in which histone H3 is kept in an unacetylated form, MBF-dependent transcription is downregulated. In summary, Gcn5 is required for the full activation and correct timing of MBF-regulated gene transcription.
Gut metabolites: make orphans adopted
Authors: Zhang Weiqiao , Zhu Shu
Published: June 2019

Editor’s note

A commentary on “A forward chemical genetic screen reveals gut microbiota metabolites that modulate host physiology”.
Gelsolin: a new biomarker of disease activity in SLE patients associated with HDL-c
Authors: Parra Sandra , Heras Mercedes , Herrero Pol , Amigó Nuria , Garcés Esperanza , Girona Josefa , Correig Xavier , Canela Nuria , Castro Antoni
Published: June 2019

Objectives

To identify potential biomarkers of disease activity analysing the proteome of high-density lipoprotein (HDL) particles from SLE patients in clinical remission and when they develop a flare compared with a healthy control group.

Methods

Quantitative proteomic analyses of purified HDL were performed using Tandem Mass Tag isobaric tag-labelling and nanoLC-Orbitrap (nLC-MS/MS) from nine SLE patients in clinical remission when they developed a flare and from nine healthy controls (9–9-9). We verified the identified proteins by Western blot and ELISA in a cohort of 104 SLE women patients, 46 healthy women and 14 SLE patients when a flare developed.

Results

We found 17 proteins with a significant fold-change (>1.1) compared with the control group. In lupus patients experiencing a flare compared with those in remission, we identified four proteins with a significant fold-change (C4, Indian Hedgehog protein, S100A8 and gelsolin). Plasma gelsolin (pGSN) levels were decreased in the 104 SLE patients (176.02(74.9) mcg/l) compared with the control group (217.13(86.7) mcg/l); P=0.005 and when they developed a clinical flare (104.84(41.7) mcg/l); P=0.002). pGSN levels were associated with HDL cholesterol levels (r = 0.316, P<0.001). Antimalarial treated patients showed significant higher levels of pGSN (214.56(88.94) mcg/l regarding 170.35(66.36) mcg/l); P = 0.017.

Conclusion

Decreased pGSN are associated with clinical disease activity in SLE patients. Antimalarial treatment and HDL cholesterol are associated with higher levels of pGSN.
Mindfulness-Based Stress Reduction-related changes in posterior cingulate resting brain connectivity
Authors: Kral Tammi R A , Imhoff-Smith Ted , Dean Douglas C , Grupe Dan , Adluru Nagesh , Patsenko Elena , Mumford Jeanette A , Goldman Robin , Rosenkranz Melissa A , Davidson Richard J
Published: June 2019

Mindfulness meditation training has been shown to increase resting-state functional connectivity between nodes of the frontoparietal executive control network (dorsolateral prefrontal cortex [DLPFC]) and the default mode network (posterior cingulate cortex [PCC]). We investigated whether these effects generalized to a Mindfulness-Based Stress Reduction (MBSR) course and tested for structural and behaviorally relevant consequences of change in connectivity. Healthy, meditation-naïve adults were randomized to either MBSR (N = 48), an active (N = 47) or waitlist (N = 45) control group. Participants completed behavioral testing, resting-state fMRI scans and diffusion tensor scans at pre-randomization (T1), post-intervention (T2) and ~5.5 months later (T3). We found increased T2–T1 PCC–DLPFC resting connectivity for MBSR relative to control groups. Although these effects did not persist through long-term follow-up (T3–T1), MBSR participants showed a significantly stronger relationship between days of practice (T1 to T3) and increased PCC–DLPFC resting connectivity than participants in the active control group. Increased PCC–DLPFC resting connectivity in MBSR participants was associated with increased microstructural connectivity of a white matter tract connecting these regions and increased self-reported attention. These data show that MBSR increases PCC–DLPFC resting connectivity, which is related to increased practice time, attention and structural connectivity.
The offshore trust industry’s biggest enemy… itself??
Authors: Buckland Edward
Published: June 2019

The offshore trust industry is undoubtedly under sustained and concerted attacks. However, is the industry’s real worst enemy itself? This article considers how many of the wounds suffered have actually been self-inflicted, and calls upon the offshore trust industry to take a long hard look in the mirror before automatically blaming others for its own faults.
Markups, Market Imperfections, and Trade Openness: Evidence from Ghana
Authors: Damoah Kaku Attah
Published: June 2019

This article investigates the impact of Ghana’s World Trade Organization (WTO) accession on firm-level product and labor market imperfections. The article exploits a rich dataset of firm-level information to estimate markups and the degree of monopsony power enjoyed by manufacturing firms. The results indicate that price-cost margins declined while the degree of monopsony power increased in the wake of WTO accession. These diverging dynamics suggest that firms compress real wages to offset loss of market power in the product market due to increased international competition. This gives rise to an increase in the market imperfection gap, which gradually erodes the pro-competitive gains from trade. The article contributes to the literature by identifying channels through which allocative inefficiencies and misallocation can persist even after trade liberalization.
Extreme diversity and parasitism of Late Jurassic squat lobsters (Decapoda: Galatheoidea) and the oldest records of porcellanids and galatheids
Authors: Robins Cristina M , Klompmaker Adiël A
Published: June 2019

Galatheoid decapod crustaceans consist of ~1250 species today, but their evolutionary history and origin are poorly known. We studied the largest known fossil galatheoid assemblage, from the Late Jurassic of Ernstbrunn, Austria. This coral-associated assemblage yielded 2348 specimens, arranged in 53 species, 22 genera and six families. Rarefaction analyses show that nearly all taxa have been collected. In addition to abundant Munidopsidae, this assemblage also contains the oldest members of four of the six galatheoid families, including Galatheidae, Munididae, Paragalatheidae and Porcellanidae. We describe the oldest Porcellanidae and Galatheidae to date, and a catillogalatheid: Vibrissalana jurassica gen. et sp. nov., ?Galathea genesis sp. nov. and Galatheites britmelanarum sp. nov. Our re-examination of the oldest claimed porcellanid, Jurellana tithonia, from Ernstbrunn, indicates that it represents a homolodromioid brachyuran, ascribed to Jurellanidae fam. nov. along with Ovalopus gen. nov. The second-oldest claimed porcellanid, Early Cretaceous Petrolisthes albianicus, is transferred to the catillogalatheid Hispanigalathea. We further document that 10.4% of Ernstbrunn galatheoid specimens were parasitized by epicaridean isopods, as shown by swellings in the gill region. Statistical analyses indicate that infestation is near non-random, varying from 0 to 33% for common species. Thus, Late Jurassic coral-associated habitats were key ecosystems in the evolution of galatheoids and their parasites.
Structure-Function Analysis of Immune Receptor AtRLP23 with Its Ligand nlp20 and Coreceptors AtSOBIR1 and AtBAK1
Authors: Albert Isabell , Zhang Lisha , Bemm Hannah , Nürnberger Thorsten
Published: June 2019

Pattern-triggered immunity is an inherent feature of the plant immune system. Recognition of either microbe-derived surface structures (patterns) or of plant materials released due to the deleterious impact of microbial infection is brought about by plasma membrane pattern recognition receptors (PRRs). PRRs composed of leucine-rich repeat (LRR) ectodomains are thought to mediate sensing of proteinaceous patterns and to initiate signaling cascades culminating in the activation of generic plant defenses. In contrast to LRR receptor kinases, LRR receptor proteins (LRR-RPs) lack a cytoplasmic kinase domain for initiation of downstream signal transduction. LRR-RPs form heteromeric constitutive, ligand-independent complexes with coreceptor SOBIR1. Upon ligand binding to LRR-RPs, recruitment of coreceptor SERK3/BAK1 results in formation of a ternary PRR complex. Structure-function analysis of LRR-RP-type PRRs is missing. AtRLP23 constitutes an LRR-RP PRR that mediates recognition of a peptide motif (nlp20) found in numerous bacterial, fungal, and oomycete necrosis and ethylene-inducing peptide 1-like proteins (NLPs). We here report the use of a series of AtRLP23 variants to decipher subdomains required for ligand binding and interaction with coreceptors AtSOBIR1 and AtBAK1, respectively. Deletion of LRR1 or LRR3 subdomains efficiently abrogated the ability of AtRLP23 receptor variants to confer nlp20 pattern sensitivity, to bind nlp20, and to recruit AtBAK1 into a ternary PRR complex. This suggests that the very N-terminal part of the AtRLP23 ectodomain is crucial for receptor function. Deletion of the intracellular 17-amino-acid tail of AtRLP23 reduced but did not abolish receptor function, suggesting an auxiliary role of this domain in receptor function. We further found that interaction of AtRLP23 and other LRR-RP-type PRRs with AtSOBIR1 does not require the AtRLP23 LRR ectodomain but is brought about by a GxxxG protein dimerization motif in the transmembrane domain and a stretch of negatively charged glutamic acid residues in the outer juxtamembrane domain of the receptor. Further, AtRLP23 levels were found to be unaltered in Atsobir1-1 mutant genotypes, suggesting that AtSOBIR1 does not act as a protein scaffold in stabilizing LRR-RP-type PRRs in Arabidopsis.
A Convergence of Ophthalmic and Life-threatening Emergencies: Acute Angle Closure Glaucoma and Subarachnoid Hemorrhage
Authors: Sobol Ethan K. , Carter Kaylene L. , Ibrahim Kirolos , Alfaro Cesar , Patel Ekta , Pasquale Louis R. , Tung Cynthia
Published: June 2019

Purpose:

To report a unique case of acute angle closure glaucoma in the setting of a subarachnoid hemorrhage due to a ruptured cerebral aneurysm.

Materials and Methods:

Observational case report and review of the literature.

Results:

A 75-year-old woman presented with blurry vision, nausea, vomiting, and left eye pain. She was found to have a complete third nerve palsy, with ptosis, exotropia, hypotropia, and a fixed mydriasis with resultant acute angle closure glaucoma. Pilocarpine was initiated, and neuroimaging revealed a subarachnoid hemorrhage from a ruptured posterior communicating artery aneurysm. The aneurysm was successfully coiled, and outpatient laser iridotomies were subsequently performed. Only 4 prior cases of acute angle closure glaucoma in the setting of a third nerve palsy have been reported in the literature. To our knowledge, this case is the first report of angle closure glaucoma in the setting of a subarachnoid hemorrhage.

Conclusions:

This case of a complete third nerve palsy in the setting of a subarachnoid hemorrhage leading to acute angle closure highlights the importance of ruling out this life-threatening diagnosis when neurological signs of increased intracranial pressure and cranial nerve palsies are present.
Relationship between C-reactive protein-to-albumin ratio and the extent of coronary artery disease in patients with non-ST-elevated myocardial infarction
Authors: Kalyoncuoglu Muhsin , Durmus Gunduz
Published: June 2019

Background

This study aimed to investigate the predictive value of the newly defined C-reactive protein (CRP)-toalbumin ratio (CAR) in determining the extent and severity of coronary artery disease (CAD) in comparison with the other inflammatory markers such as neutrophil-tolymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR), in patients with non-ST-elevated myocardial infarction (NSTEMI).

Patients and methods

This study is retrospectively designed and includes 205 patients with NSTEMI with a mean age of 56.6± 11.4 years. The study cohort was subdivided into two groups according to Synergy Between Percutaneous Coronary Intervention with Taxus and cardiac surgery score (SS) as low (<23) and intermediate-high (≥23). Complete blood counts, serum CRP, and serum albumin were obtained at admission. The CAR, NLR, and PLR values of all patients were calculated. Then, we evaluated the relationship of CAR, NLR, and PLR with the CAD extent and severity.

Results

CAR and NLR were moderately correlated with SS (r = 0.517, P < 0.001; r = 0.222, P = 0.001, respectively), whereas PLR showed weak correlation with SS (r = 0.191, P = 0.006). According to multivariate analysis models, CAR, NLR, and left ventricular ejection fraction were found to be independent predictors of CAD severity (P < 0.05). The area under the curve (AUC) for CAR (AUC: 0.829; 95% confidence interval: 0.770–0.878) was significantly greater than the AUC of NLR (AUC: 0.657; 95% confidence interval: 0.588–0.722), with P value of 0.002. A CAR more than 17 predicted an intermediate-high SS with 86% sensitivity and 76% specificity.

Conclusion

Novel inflammatory marker CAR can be used as a reliable marker in prediction of CAD severity in patients with NSTEMI.
Financial toxicity is associated with worse physical and emotional long-term outcomes after traumatic injury
Authors: Murphy Patrick B. , Severance Sarah , Savage Stephanie , Obeng-Gyasi Samilia , Timsina Lava R. , Zarzaur Ben L.
Published: June 2019

BACKGROUND

Increasing health care costs and high deductible insurance plans have shifted more responsibility for medical costs to patients. After serious illnesses, financial responsibilities may result in lost wages, forced unemployment, and other financial burdens, collectively described as financial toxicity. Following cancer treatments, financial toxicity is associated with worse long-term health-related quality of life (HRQoL) outcomes. The purpose of this study was to determine the incidence of financial toxicity following injury, factors associated with financial toxicity, and the impact of financial toxicity on long-term HRQoL.

METHODS

Adult patients with an Injury Severity Score of 10 or greater and without head or spinal cord injury were prospectively followed for 1 year. The Short-Form-36 was used to determine overall quality of life at 1 month, 2 months, 4 months, and 12 months. Screens for depression and posttraumatic stress syndrome were administered. The primary outcome was any financial toxicity. A multivariable generalized estimating equation was used to account for variability over time.

RESULTS

Five hundred patients were enrolled, and 88% suffered financial toxicity during the year following injury (64% reduced income, 58% unemployment, 85% experienced stress due to financial burden). Financial toxicity remained stable over follow-up (80–85%). Factors independently associated with financial toxicity were lower age (odds ratio [OR], 0.96 [0.94–0.98]), lack of health insurance (OR, 0.28 [0.14–0.56]), and larger household size (OR, 1.37 [1.06–1.77]). After risk adjustment, patients with financial toxicity had worse HRQoL, and more depression and posttraumatic stress syndrome in a stepwise fashion based on severity of financial toxicity.

CONCLUSION

Financial toxicity following injury is extremely common and is associated with worse psychological and physical outcomes. Age, lack of insurance, and large household size are associated with financial toxicity. Patients at risk for financial toxicity can be identified, and interventions to counteract the negative effects should be developed to improve long-term outcomes.

LEVEL OF EVIDENCE

Prognostic/epidemiologic study, level III.
Predisposed to failure? The challenge of rescue in the medical intensive care unit
Authors: Briggs Alexandra , Handzel Robert M. , Kutcher Matthew E. , Peitzman Andrew B. , Forsythe Raquel M.
Published: June 2019

BACKGROUND

Medical intensive care unit (MICU) patients develop acute surgical processes that require operative intervention. There are limited data addressing outcomes of emergency general surgery (EGS) in this population. The aim of our study was to characterize the breadth of surgical consults from the MICU and assess mortality after abdominal EGS cases.

METHODS

All MICU patients with an EGS consult in an academic medical center between January 2010 and 2016 were identified from an electronic medical record-based registry. Charts were reviewed to determine reason for consult, procedures performed, and to obtain additional clinical data. A multivariate logistic regression was used to determine patient factors associated with patient mortality.

RESULTS

Of 911 MICU patients seen by our service, 411(45%) required operative intervention, with 186 patients undergoing an abdominal operation. The postoperative mortality rate after abdominal operations was 37% (69/186), significantly higher than the mortality of 16% (1833/11192) for all patients admitted to the MICU over the same period (p < 0.05). Damage-control procedures were performed in 64 (34%) patients, with 46% mortality in this group. The most common procedures were bowel resections, with mortality of 42% (28/66) and procedures for severe clostridium difficile, mortality of 38% (9/24). Twenty-seven patients met our definition of surgical rescue, requiring intervention for complications of prior procedures, with mortality of 48%. Need for surgical rescue was associated with increased admission mortality (odds ratio, 13.07; 95% confidence interval, 2.86–59.77). Twenty-six patients had pathology amenable to surgical intervention but did not undergo operation, with 100% mortality. In patients with abdominal pathology at the time of operation, in-hospital delay was associated with increased mortality (odds ratio, 5.13; 95% confidence interval, 1.11–23.77).

CONCLUSION

Twenty percent of EGS consults from the MICU had an abdominal process requiring an operative intervention. While the MICU population as a whole has a high baseline mortality, patients requiring abdominal surgical intervention are an even higher risk.

LEVEL OF EVIDENCE

Prognostic and epidemiological, level III
Read correction for non-uniform coverages
Authors: Marchet Camille , Dufresne Yoann , Limasset Antoine
Published: June 2019

Next generation sequencing produces large volumes of short sequences with broad applications. The noise due to sequencing errors led to the development of several correction methods. The main correction paradigm expects a high (from 30-40X) uniform coverage to correctly infer a reference set of subsequences from the reads, that are used for correction. In practice, most accurate methods use k-mer spectrum techniques to obtain a set of reference k-mers. However, when correcting NGS datasets that present an uneven coverage, such as RNA-seq data, this paradigm tends to mistake rare variants for errors. It may therefore discard or alter them using highly covered sequences, which leads to an information loss and may introduce bias. In this paper we present two new contributions in order to cope with this situation.

First, we show that starting from non-uniform sequencing coverages, a De Bruijn graph can be cleaned from most errors while preserving biological variability. Second, we demonstrate that reads can be efficiently corrected via local alignment on the cleaned De Bruijn graph paths. We implemented the described method in a tool dubbed BCT and evaluated its results on RNA-seq and metagenomic data. We show that the graph cleaning strategy combined with the mapping strategy leads to save more rare k-mers, resulting in a more conservative correction than previous methods. BCT is also capable to better take advantage of the signal of high depth datasets. We suggest that BCT, being scalable to large metagenomic datasets as well as correcting shallow single cell RNA-seq data, can be a general corrector for non-uniform data. Availability: BCT is open source and available at github.com/Malfoy/BCT under the Affero GPL License.
Genomic Analyses of SLAMF7 CAR-T Cells Manufactured by Sleeping Beauty Transposon Gene Transfer for Immunotherapy of Multiple Myeloma
Authors: Miskey Csaba , Amberger Maximilian , Reiser Michael , Prommersberger Sabrina , Beckmann Julia , Machwirth Markus , Einsele Hermann , Hudecek Michael , Bonig Halvard , Ivics Zoltán ,   on behalf of the CARAMBA consortium
Published: June 2019

Widespread treatment of human diseases with gene therapies necessitates the development of gene transfer vectors that integrate genetic information effectively, safely and economically. Accordingly, significant efforts have been devoted to engineer novel tools that i) achieve high-level stable gene transfer at low toxicity to the host cell; ii) induce low levels of genotoxicity and possess a ‘safe’ integration profile with a high proportion of integrations into safe genomic locations; and iii) are associated with acceptable cost per treatment and scalable/exportable vector production to serve large numbers of patients. The Sleeping Beauty (SB) transposon has been transformed into a vector system that is fulfilling these requirements.

In the CARAMBA project, we use SB transposition to genetically modify T cells with a chimeric antigen receptor (CAR) specific for the SLAMF7 antigen, that is uniformly and highly expressed on malignant plasma cells in multiple myeloma. We have demonstrated that SLAMF7 CAR-T cells confer specific and very potent anti-myeloma reactivity in pre-clinical models, and are therefore preparing a Phase I/IIa clinical trial of adoptive immunotherapy with autologous, patient-derived SLAMF7-CAR T cells in multiple myeloma (EudraCT Nr. 2019-001264-30/CARAMBA-1).

Here we report on the characterization of genomic safety attributes in SLAMF7 CAR-T cells that we prepared in three clinical-grade manufacturing campaigns under good manufacturing practice (GMP), using T cells that we obtained from three healthy donor volunteers. In the SLAMF7 CAR-T cell product, we determined the average transposon copy number, the genomic insertion profile, and presence of residual SB100X transposase. The data show that the SLAMF7 CAR transposon had been inserted into the T cell genome with the close-to-random distribution pattern that is typical for SB, and with an average transposon copy number ranging between 6 and 12 per T cell. No residual SB100X transposase could be detected by Western blotting in the infusion products. With these attributes, the SLAMF7 CAR-T products satisfy criteria set forth by competent regulatory authorities in order to justify administration of SLAMF7 CAR-T cells to humans in the context of a clinical trial. These data set the stage for the CARAMBA clinical trial, that will be the first in the European Union to use virus-free SB transposition for CAR-T engineering.

Disclosures

This project is receiving funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 754658 (CARAMBA).
Dissociable neural systems for unconditioned acute and sustained fear
Authors: Hudson Matthew , Seppälä Kerttu , Putkinen Vesa , Sun Lihua , Glerean Enrico , Karjalainen Tomi , Hirvonen Jussi , Nummenmaa Lauri
Published: June 2019

Fear protects organisms by increasing vigilance and preparedness, and by coordinating survival responses during life-threatening encounters. The fear circuit must thus operate on multiple timescales ranging from preparatory sustained alertness to acute fight-or-flight responses. Here we studied the brain basis of sustained (“looming”) and acute fear using naturalistic functional magnetic resonance imaging (fMRI) enabling analysis of different time-scales of fear responses. Subjects (N = 51) watched feature-length horror movies while their hemodynamic brain activity was measured with fMRI. Time-variable intersubject correlation (ISC) was used to quantify the reliability of brain activity across participants, and seed-based phase synchronization was used for characterizing dynamic connectivity. Subjective ratings of fear were obtained from a separate sample, and were used to assess how synchronization and functional connectivity varied with emotional intensity. These data suggest that acute and sustained fear are supported by distinct neural pathways, with sustained fear amplifying mainly sensory responses, and acute fear increasing activity in brainstem, thalamus, amygdala and cingulate cortices. Sustained fear increased ISC in regions associated with acute fear, and also amplified functional connectivity within this network. The results were replicated in two independent experiments with different subject samples. The functional interplay between cortical networks involved in sustained anticipation of, and acute response to, threat involves a complex and dynamic interaction that depends on the proximity of threat, and the need to employ threat appraisals and vigilance for decision making and response selection.
A resource for analyzing C. elegans’ gene expression data using transcriptional gene modules and module-weighted annotations
Authors: Cary Michael , Podshivalova Katie , Kenyon Cynthia
Published: June 2019

Identification of gene co-expression patterns (gene modules) is widely used for grouping functionally-related genes during transcriptomic data analysis. An organism-wide atlas of high quality fundamental gene modules would provide a powerful tool for unbiased detection of biological signals from gene expression data. Here, using a method of independent component analysis we call DEXICA, we have defined and optimized 209 modules that broadly represent transcriptional wiring of the key experimental organism C. elegans. Interrogation of these modules reveals processes that are activated in long-lived mutants in cases where traditional analyses of differentially-expressed genes fail to do so. Using this resource, users can easily identify active modules in their gene expression data and access detailed descriptions of each module. Additionally, we show that modules can inform the strength of the association between a gene and an annotation (e.g. GO term). Analysis of “module-weighted annotations” improves on several aspects of traditional annotation-enrichment tests and can aid in functional interpretation of poorly annotated genes. Interactive access to the resource is provided at http://genemodules.org/.
Reach and Grasp Altered in Pantomime String-Pulling: A Test of the Action/Perception Theory in a Bilateral Reaching Task
Authors: Singh Surjeet , Mandziak Alexei , Barr Kalob , Blackwell Ashley A , Mohajerani Majid H , Wallace Douglas G , Whishaw Ian Q
Published: June 2019

The action/perception theory of cortical organization is supported by the finding that pantomime hand movements of reaching and grasping are different from real movements. Frame-by-frame video analysis and MATLAB®based tracking examined real/pantomime differences in a bilaterally movement, string-pulling, pulling down a rope with hand-over-hand movements. Sensory control of string-pulling varied from visually-direct when cued, visually-indirect when non cued and somatosensory controlled in the absence of vision. Cued grasping points were visual tracked and the pupils dilated in anticipation of the grasp, but when noncued, visual tracking and pupil responses were absent. In real string-pulling, grasping and releasing the string featured an arpeggio movement in which the fingers close and open in the sequence 5 through 1 (pinki first, thumb last); in pantomime, finger order was reversed, 1 through 5. In real string-pulling, the hand is fully opened and closed to grasp and release; in pantomime, hand opening was attenuated and featured a gradual opening centered on the grasp. The temporal structure of arm movements in real string-pulling featured up-arm movements that were faster than down-arm movement. In pantomime, up/down movements had similar speed. In real string-pulling, up/down arm movements were direct and symmetric; in pantomime, they were more circular and asymmetric. That pantomime string-pulling featured less motoric and temporal complexity than real string-pulling is discussed in relation to the action/perception theory and in relation to the idea that pantomimed string-pulling may feature the substitution of gestures for real movement.

Significant Statement

Most laboratory studies investigating hand movements made by humans feature single hand movements, the current study presents a novel string-pulling task to study bimanual coordination of left and right hands in real and pantomime conditions. The results show that pantomime string-pulling featured less motoric and temporal complexity than real string-pulling. These findings are relevant to the contemporary theory of action and perception that the dorsal stream (parietal cortex) is related to actions and the ventral stream (temporal cortex) is related to perception.
Rescue of Tomato spotted wilt tospovirus entirely from cDNA clones, establishment of the first reverse genetics system for a segmented (-)RNA plant virus
Authors: Feng Mingfeng , Cheng Ruixiang , Chen Minglong , Guo Rong , Li Luyao , Feng Zhike , Wu Jianyan , Xie Li , Hong Jian , Zhang Zhongkai , Kormelink Richard , Tao Xiaorong
Published: June 2019

The group of negative strand RNA viruses (NSVs) includes not only dangerous pathogens of medical importance but also serious plant pathogens of agronomical importance. Tomato spotted wilt tospovirus (TSWV) is one of those plant NSVs that cause severe diseases on agronomic crops and pose major threats to global food security. Its negative-strand segmented RNA genome has, however, always posed a major obstacle to molecular genetic manipulation. In this study, we report the complete recovery of infectious TSWV entirely from cDNA clones, the first reverse genetics (RG) system for a segmented plant NSV. First, a replication and transcription competent mini-genome replication system was established based on 35S-driven constructs of the S(-)-genomic (g) or S(+)-antigenomic (ag) RNA template, flanked by a 5’ Hammerhead and 3’ Ribozyme sequence of Hepatitis Delta virus, a nucleocapsid (N) protein gene and codon-optimized viral RNA dependent RNA polymerase (RdRp) gene. Next, a movement competent mini-genome replication system was developed based on M(-)-gRNA, which was able to complement cell-to-cell and systemic movement of reconstituted ribonucleoprotein complexes (RNPs) of S RNA replicon. After further optimization, infectious TSWV and derivatives carrying eGFP reporters were successfully rescuedin plantavia simultaneous expression of full-length cDNA constructs coding for S(+)-agRNA, M(-)-gRNA and L(+)-agRNA. Viral rescue occurred in the additional presence of various viral suppressors of RNAi, but TSWV NSs interfered with the rescue of genomic RNA. The establishment of a RG system for TSWV now allows detailed molecular genetic analysis of all aspects of tospovirus life cycle and their pathogenicity.

Significance

For many different animal-infecting segmented negative-strand viruses (NSVs), a reverse genetics system has been established that allows the generation of mutant viruses to study disease pathology and the role ofcis- andtrans-acting elements in the virus life cycle. In contrast to the relative ease to establish RG systems for animal-infecting NSVs, establishment of such system for the plant-infecting NSVs with a segmented RNA genome so far has not been successful. Here we report the first reverse genetics system for a segmented plant NSV, the Tomato spotted wilt tospovirus, a virus with a tripartite RNA genome. The establishment of this RG system now provides us with a new and powerful platform to study their disease pathology during a natural infection.
CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes
Authors: Efremova Mirjana , Vento-Tormo Miquel , Teichmann Sarah A. , Vento-Tormo Roser
Published: June 2019

Cell-cell communication mediated by receptor-ligand complexes is crucial for coordinating diverse biological processes, such as development, differentiation and responses to infection. In order to understand how the context-dependent crosstalk of different cell types enables physiological processes to proceed, we developed CellPhoneDB, a novel repository of ligands, receptors and their interactions1. Our repository takes into account the subunit architecture of both ligands and receptors, representing heteromeric complexes accurately. We integrated our resource with a statistical framework that predicts enriched cellular interactions between two cell types from single-cell transcriptomics data. Here, we outline the structure and content of our repository, the procedures for inferring cell-cell communication networks from scRNA-seq data and present a practical step-by-step guide to help implement the protocol. CellPhoneDB v2.0 is a novel version of our resource that incorporates additional functionalities to allow users to introduce new interacting molecules and reduce the time and resources needed to interrogate large datasets. CellPhoneDB v2.0 is publicly available at https://github.com/Teichlab/cellphonedb and as a user-friendly web interface at http://www.cellphonedb.org/. In our protocol, we demonstrate how to reveal meaningful biological discoveries from CellPhoneDB v2.0 using published data sets.
APOC2 accelerates colorectal cancer progression via modulating lipid metabolism and transcriptional activity of PHF8
Authors: Chen Jian , Xiao Chao , Wang Yupeng , Song Guohe , Wang Xiaoliang , Liu Xueni , Chen Jiayi , Lu Huijun , Kuai Jing , Qin Xuebin , Guo Weiping , Tang Huamei , Peng Zhihai
Published: June 2019

The apolipoproteins (APOs) are the major proteins in blood lipid transportation. Emerging evidence has demonstrated that APOs might exert important function in tumor cells, but the underlying mechanism remains inclusive. In this study, we aim to explore the relationship between APOC2 dysfunction and colorectal cancer (CRC) malignancy. By analyzing the expression of APOC2 in 507 patients with CRC, we demonstrated that the APOC2 was overexpressed and associated with poor prognosis in CRC. We then found that high levels of APOC2 resulted in proliferation, invasion and metastasis of CRC cells in vitro and in vivo. Mechanistically, we revealed that APOC2 directly interacted with FASN which resulted in decreased levels of omega-3 fatty acids and increased levels of alpha-ketoglutarate (α-KG). Both RNA-seq and ChIP-seq analysis revealed that APOC2 overexpression resulted accumulation of α-KG leads to activation on the transcriptional program of PHF8 and thereby contributed to activation on genes involved in cell proliferation, invasion and metastasis. Together, our study unveiled the oncogenic role of APOC2 in tumor cells, which sheds new light on the potential of APOC2 as a biomarker in the prognosis of CRC.
A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes
Authors: Paritosh Kumar , Yadava Satish Kumar , Singh Priyansha , Bhayana Latika , Mukhopadhyay Arundhati , Gupta Vibha , Bisht Naveen Chandra , Zhang Jianwei , Kudrna David , Copetti Dario , Wing Rod A , Lachagari Vijay Bhaskar Reddy , Pradhan Akshay Kumar , Pental Deepak
Published: June 2019

Brassica juncea (AABB; genome size ∼920 Mb), commonly referred to as mustard, is a natural allopolyploid of two diploid species – B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ∼100x PacBio single-molecule real-time (SMRT) reads providing contigs with an N50 value of >5Mb. Assembled contigs were corrected and scaffolded with BioNano optical mapping. Three different linkage maps containing a large number of GBS markers were developed and used to anchor scaffolds/contigs to the 18 linkage groups of B. juncea. The resulting chromosome-scale assembly is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content, and gene block associations. Both A and B genomes contain highly fragmented gene block arrangements. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The genome assembly reported here will provide a fillip to the breeding work on oleiferous types of mustard that are grown extensively in the dry land areas of South Asia and elsewhere.
Robust emergence of sharply tuned place cell responses in hippocampal neurons with structural and biophysical heterogeneities
Authors: Basak Reshma , Narayanan Rishikesh
Published: June 2019

Hippocampal pyramidal neurons sustain propagation of fast electrical signals and are electrotonically non-compact structures exhibiting cell-to-cell variability in their complex dendritic arborization. In this study, we demonstrate that sharp place-field tuning and several somato-dendritic functional maps concomitantly emerge despite the presence of geometrical heterogeneities in these neurons. We establish this employing an unbiased stochastic search strategy involving thousands of models that spanned several morphologies and distinct profiles of dispersed synaptic localization and channel expression. Mechanistically, employing virtual knockout models, we explored the impact of bidirectional modulation in dendritic spike prevalence on place-field tuning sharpness. Consistent with prior literature, we found that across all morphologies, virtual knockout of either dendritic fast sodium channels orN-methyl-D-aspartate receptors led to a reduction in dendritic spike prevalence, whereasA-type potassium channel knockouts resulted in a nonspecific increase in dendritic spike prevalence. However, place-field tuning sharpness was critically impaired in all three sets of virtual knockout models, demonstrating that sharpness in feature tuning is maintained by an intricate balance between mechanisms that promote and those that prevent dendritic spike initiation. From the functional standpoint of the emergence of sharp feature tuning and intrinsic functional maps, within this framework, geometric variability was compensated by a combination of synaptic democracy, the ability of randomly dispersed synapses to yield sharp tuning through dendritic spike initiation, and ion-channel degeneracy. Our results suggest electrotonically non-compact neurons to be endowed with several degrees of freedom, encompassing channel expression, synaptic localization and morphological micro-structure, in achieving sharp feature encoding and excitability homeostasis.
An integrated personal and population-based Egyptian genome reference
Authors: Wohlers Inken , Künstner Axel , Munz Matthias , Olbrich Michael , Fähnrich Anke , Calonga-Solís Verónica , Ma Caixia , Hirose Misa , El-Mosallamy Shaaban , Salama Mohamed , Busch Hauke , Ibrahim Saleh
Published: June 2019

The human genome is composed of chromosomal DNA sequences consisting of bases A, C, G and T – the blueprint to implement the molecular functions that are the basis of every individual’s life. Deciphering the first human genome was a consortium effort that took more than a decade and considerable cost. With the latest technological advances, determining an individual’s entire personal genome with manageable cost and effort has come within reach. Although the benefits of the all-encompassing genetic information that entire genomes provide are manifold, only a small number of de novo assembled human genomes have been reported to date 1–3, and few have been complemented with population-based genetic variation 4, which is particularly important for North Africans who are not represented in current genome-wide data sets 5–7. Here, we combine long- and short-read whole-genome next-generation sequencing data with recent assembly approaches into the first de novo assembly of the genome of an Egyptian individual. The resulting assembly demonstrates well-balanced quality metrics and is complemented with high-quality variant phasing via linked reads into haploblocks, which we can associate with gene expression changes in blood. To construct an Egyptian genome reference, we further assayed genome-wide genetic variation occurring in the Egyptian population within a representative cohort of 110 Egyptian individuals. We show that differences in allele frequencies and linkage disequilibrium between Egyptians and Europeans may compromise the transferability of European ancestry-based genetic disease risk and polygenic scores, substantiating the need for multi-ethnic genetic studies and corresponding genome references. The Egyptian genome reference represents a comprehensive population data set based on a high-quality personal genome. It is a proof of concept to be considered by the many national and international genome initiatives underway. More importantly, we anticipate that the Egyptian genome reference will be a valuable resource for precision medicine targeting the Egyptian population and beyond.
The role of cultural norms in shaping attitudes towards amphibians in Cape Town, South Africa
Authors: Brom Peta , Anderson Pippin , Channing Alan , Underhill Leslie G.
Published: June 2019

Urban ecosystems are increasingly viewed as an important component within strategies for wildlife conservation but are shaped as much by natural systems as they are by social and political processes. At the garden scale, attitudes and preferences govern design and maintenance choices including the decision to encourage or discourage specific faunal presence. At the global scale, charismatic taxa that are well-liked attract more conservation funding and volunteer stewardship. Amphibians are a class of animals that are both loved and loathed making them a suitable subject for comparing and unpacking the drivers of preference and attitudes towards animals. We conducted a mixed methods survey of 192 participants in three adjacent neighbourhoods in Cape Town, South Africa. The survey included both quantitative and qualitative questions which were analysed thematically and used to explain the quantitative results. The results revealed that attitudes formed during childhood tended to be retained into adulthood, were shaped by cultural norms, childhood experiences and the attitudes of primary care-givers. The findings are significant for environmental education programmes aimed at building connectedness to nature and biophilic values.
Damage-related changes in the cerebellum of juvenileOncorhynchus masou: reactivation of neurogenic niches and astrocytic response
Authors: Pushchina Eugenyia V. , Stukaneva Maryia E. , Varaksin Anatoly A.
Published: June 2019

In the cerebellum of juvenileOncorhynchus masou, proliferating BrdU+ and HuCD+ cells and constitutive neurogenic niches were detected in different zones; the largest number of labeled cells were found in the dorsal part of the molecular layer and the dorsal matrix zone (DMZ). Cells labeled with glutamine synthetase (GS) and radial glia were also present in the intactO. masoucerebellum. The most intensive proliferation was detected in the rostral part of cerebellum. This part is assumed to contain active zones of constitutive neurogenesis. After an injury inflicted to the cerebellum, the number of BrdU+ and HuCD+ cells increased significantly. The number of BrdU+ cells after this type of injury was much greater than after a telencephalon trauma. A quantitative analysis revealed that after the cerebellum injury the proliferative activity in the caudal part of CCb is increased compared to that in the control. A reactivation of neurogenic and neuroepithelial niches and their transformation into reactive neurogenic domains, with an increased distribution density of intensely labeled HuCD+ cells of different types, were observed. The increase in the number of HuCD+ differentiated cells in the basal area suggests that the processes of neuronal differentiation are intensified in the cerebellum of juvenileO. masouafter injury. The number of GS positive cells (GS+) and fibers increased in all the zones of cerebellum. The most intensive astrocytic response was noted in the dorsal part of cerebellum. The data of the enzyme immunoassay confirm the multiple variations in the level of GS after a traumatic injury to cerebellum inO. masou.