bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence of fosfomycin resistance genes and antimicrobial susceptibility of clinical urinary extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolates
Authors: Jahromy Sahar Honarmand , Rahbar Mohammad , Bialvaei Abed Zahedi , Asadi Arezoo , Jahromy Shaghayegh Honarmand , Eslami Parisa , Mardani Masoud , Kouhsari Ebrahim
Published: November 2019

The antimicrobial susceptibility testing of 284 Enterobacteriaceae isolates responsible for urinary tract infections to ampicillin, ceftazidime, ciprofloxacin, nitrofurantoin, trimethoprin-sulfamethaxole, and fosfomycin was performed by disk diffusion method. Additionally, in fosfomycin-resistant and intermediate susceptible isolates using disk diffusion method, the minimum inhibitory concentration (MIC) of fosfomycin was determined by agar dilution. The presence of fosA and fosA3 genes and ESBL genes was investigated in fosfomycin-resistant isolates and ESBL-producing isolates, respectively. Klebsiella pneumoniae [72.34% (34/47)], and Escherichia coli [58.23% (138/237)] were identified as ESBL-producers by phenotype. These isolates were positive for the presence of blaTEM, blaSHV, blaCTX-M genes in 56.97% (n = 98), 55.23% (n = 95), and 78.48% (n = 135), respectively. Resistance to fosfomycin was detected in 9.4% (13/138) and 5.9% (2/34) of the ESBL-E. coli and ESBL-K. pneumoniae isolates. In fosfomycin-resistant isolates, the presence of the fosA gene was detected in two ESBL-E. coli isolates; the fosA3 gene in one non-ESBL E. coli isolate; and the fosA3 gene co-harboured with blaCTX-M in six ESBL-E. coli (n = 5) and one K. pneumoniae isolates. A high prevalence of ESBL-producing Enterobacteriaceae (72.6%) was detected in urine samples. Fosfomycin showed the highest susceptibility rate (≥87%) of antimicrobials tested in ESBL-producing E. coli and K. pneumoniae isolates.
Catheter-Directed Pharmacologic Thrombolysis for Acute Submassive and Massive Pulmonary Emboli in Children and Adolescents—An Exploratory Report
Authors: Ji Dabin , Gill Anne E. , Durrence Wesley W. , Shah Jay H. , Paden Matthew L. , Patel Kavita N. , Williamson Julie L. , Hawkins C. Matthew
Published: November 2019

Objectives:

The objective of this study is to report a single-center experience of the safety and efficacy of pulmonary artery catheter-directed thrombolysis for both massive and submassive pulmonary emboli in the pediatric and adolescent population.

Design:

A 22-month retrospective review of the electronic medical record and picture archiving and communication system was performed of patients less than 21 years old, presenting with massive or submassive pulmonary emboli treated with pulmonary artery catheter-directed thrombolysis at a single, tertiary care pediatric hospital. Multiple variables were analyzed including indications, technical success, clinical efficacy, and complications.

Setting:

A single, tertiary care pediatric hospital.

Patients:

Nine patients (mean 13.9 yr; range 6–19 yr) with massive and/or submassive pulmonary emboli who underwent pulmonary artery catheter-directed thrombolysis met inclusion criteria.

Interventions:

Catheter-directed thrombolysis.

Measurements and Main Results:

Pulmonary emboli was diagnosed by CT angiography in all cases. Catheter-directed thrombolysis alone was clinically successful (defined as improved cardiopulmonary function following catheter-directed thrombolysis) in seven patients (78%) with two patients not improving following catheter-directed thrombolysis. There were no immediate bleeding complications from catheter-directed thrombolysis therapy. All patients were maintained on anticoagulation treatment following catheter-directed thrombolysis. Catheter-directed thrombolysis was technically successful (defined as successful placement of pulmonary artery infusion catheters with full or partial resolution of thrombus) in all cases. Follow-up pulmonary angiography at the cessation of catheter-directed thrombolysis revealed complete thrombus resolution in four patients (44%) and partial resolution in five patients (55%). Mean pulmonary artery pressures decreased in all patients (mean precatheter-directed thrombolysis pulmonary artery pressure = 37 ± 11 mm Hg; mean postcatheter-directed thrombolysis pulmonary artery pressure = 28 ± 10 mm Hg; p = 0.0164).

Conclusions:

Pulmonary artery catheter-directed thrombolysis is a technically feasible therapeutic option for children and adolescents with submassive and massive pulmonary emboli.
Changes in Provider Perceptions Regarding Early Mobility in the PICU*
Authors: Hanna Eriny S. , Zhao Shilin , Shannon Chevis N. , Betters Kristina A.
Published: November 2019

Objectives:

Early mobility in the PICU is safe and feasible. However, PICUs continue to meet barriers to implementing early mobility. PICU providers were surveyed before and after initiating an early mobility protocol to determine perceived barriers and continued challenges in performing early mobility.

Design:

This single-center prospective study surveyed PICU providers regarding 26 potential barriers to early mobility using a five-point Likert scale. A survey was distributed 1 month prior to and 6 months after beginning an early mobility protocol.

Setting:

Free-standing academic tertiary care children’s hospital.

Subjects:

PICU providers of various professions.

Interventions:

Implementation of PICU-wide early mobility protocol.

Measurements and Main Results:

Paired pre- and post-early mobility protocol implementation surveys from 97 providers were compared. System-based barriers decreased after implementation of the early mobility protocol, such as lack of guidelines (75–20%; p < 0.01), inadequate training (74–33%; p < 0.01), lack of early mobility orders (72–30%; p < 0.01), and delayed recognition of early mobility candidates (68–35%; p < 0.01). Difficulty coordinating early mobility sessions, although significantly decreased, still remained a concern for 66% of providers in the postsurvey. Lack of resources, specifically staff (85–82%; p = 0.68) and equipment (67–60%; p = 0.36), also remained significant barriers. Presence of an endotracheal tube was a barrier for only 29% of providers’ post-early mobility protocol, compared with 69% prior (p < 0.01). Clinical instability remained a top concern (82–79%; p = 0.63) as well as agitation (74–67%; p = 0.23). Day shift providers, with more early mobility exposure, perceived fewer barriers compared with night shift providers. Ninety percentage of post-early mobility survey participants felt that early mobility positively impacted their patients.

Conclusions:

Implementation of an early mobility protocol significantly changed provider perceptions regarding barriers to early mobility. Certain factors, such as staff availability, coordination difficulty, equipment shortage, and patient clinical factors, continue to be significant challenges to early mobility in the PICU population.
Commentary: Aripiprazole: The Second Wave of the Second-generation Antipsychotics
Authors: KAHN DAVID A.
Published: November 2019

Three cases are presented describing unique clinical responses to aripiprazole in comparison with other second-generation antipsychotics taken by each patient. One case involved an adverse reaction of problem gambling behavior, the second an enhanced antipsychotic response in delusional disorder, and the third a reversal of weight gain that occurred while the patient continued taking olanzapine. Aripiprazole was the first of a subgroup of atypical antipsychotics that are mixed agonists and antagonists of dopamine, likely contributing to unusual responses in some patients.
Best Practices for Aripiprazole Lauroxil Administration: From Formulation Development to Injection Technique
Authors: FARWICK SARAH , HICKEY MAGALI B. , JACOBS GWEN , FALDU SEJAL P. , VANDIVER JENNIFER , WEIDEN PETER J.
Published: November 2019

Long-acting injectable (LAI) antipsychotics are an important treatment option for patients with schizophrenia. Advances and variability in formulation technology have provided several LAI antipsychotic treatment options for schizophrenia, with a wide range of doses and dose intervals. However, clinical reviews of LAIs have not focused on formulation development despite its clinical relevance to injection safety and technique. This article reviews the relationship between formulation technology and clinical practices for LAIs, with a focus on aripiprazole lauroxil, a long-acting atypical antipsychotic indicated for the treatment of schizophrenia. The formulation developed for aripiprazole lauroxil is an aqueous-based suspension suitable for use as a prefilled syringe that, after injection, will release aripiprazole slowly into the plasma. The clinical relationship between the aripiprazole lauroxil formulation and proper injection techniques is explained, including why tapping and shaking the syringe to resuspend the drug particles and rapid injection speed are key steps for best injection practices for this formulation.
Evaluating the Use of a Computerized CBT Program for Outpatients on a Waitlist in a University CBT Unit
Authors: VILLEMAIRE-KRAJDEN ROSANNE , MYHR GAIL
Published: November 2019

Objectives and Design:

The goal of this pilot randomized controlled trial was to determine whether a computerized cognitive-behavioral therapy (cCBT) program for depression and anxiety could reduce symptoms in outpatients on a waitlist for face-to-face CBT for a variety of mental health complaints.

Methods:

Sixty-seven outpatients referred for CBT for disparate problems (eg, anxiety, depression, obsessions or compulsions) were randomized to 1 of 2 conditions: (1) the cCBT program “Good Days Ahead,” which included weekly guidance and support, or (2) a control condition where patients were referred to a freely available online CBT workbook. Measures of psychological distress were administered at the start of study and at the end of the waiting period, when participants were formally diagnosed and assessed for face-to-face therapy.

Results:

For the most part, mixed-design analyses of variances revealed no statistically significant changes in symptom measures over time. Nonsignificant interactions and modest effect sizes between groups across time suggest that the cCBT group did not do better than the control group. The majority of cCBT participants reported that the program was “very” or “extremely useful,” while only a portion of the control group felt the same about the workbook. There were notable differences in the completion rates of the 2 groups in favor of the cCBT program.

Conclusions:

Offering a general cCBT program to waiting list patients may not confer an advantage over referring them to an online workbook, at least in terms of symptom reduction. Results could be partly explained by difficulties translating knowledge into practice, especially if participants’ main problem was not directly addressed by the intervention.
Canalicular Incisional Approach for Recanalization of Punctum: A Modified Surgical Treatment for Acquired Complete Upper and Lower Punctum Occlusions as an Alternative to Bypass Methods
Authors: Demirel Soner , Ozturk Emrah , Dikci Seyhan , Firat Penpe Gül
Published: November 2019

Purpose:

To define the success of surgical technique used in the treatment of epiphora that is caused by bi-canalicular acquired complete punctum occlusion.

Materials and Methods:

The study is a retrospective consecutive case series, who underwent canalicular incisional approach for recanalization (CIAFOR) for acquired bi-canalicular punctum occlusions. The authors have used this technique in the cases not possible to perform a punctum dilatation and not possible to determine the punctum location exactly due to severe fibrosis. Functional and anatomical success was evaluated by the absence of epiphora and with lavage at post-operative 6th months.

Results:

Seven eyes of 5 patients (3 males and 2 females) were included in the study. The ages of the patients were 70, 65, 45, 64, and 70 years, respectively. Current follow-up periods vary between 6 and 23 months. Although functional and anatomical success achieved in all eyes, complication such as accessory punctum observed.

Conclusions:

CIAFOR seems to be a successful and simple surgical technique to treat acquired total punctum occlusion.
Splenectomy associated with increased risk of herpes zoster in a population-based cohort study
Authors: Lai Shih-Wei , Lin Cheng-Li , Liao Kuan-Fu
Published: November 2019

Background/Objective:

No systematic research focuses on the association between splenectomy and herpes zoster. This study aimed to investigate the association between splenectomy and herpes zoster in Taiwan.

Methods:

A population-based cohort study was conducted using the database of Taiwan National Health Insurance Program. There were 640 individuals aged 20–84 years who were newly diagnosed with splenectomy in 2000–2012 as the splenectomy group and 2546 sex-matched and age-matched individuals without splenectomy as the nonsplenectomy group. The incidence of herpes zoster at the end of 2013 was estimated. The multivariable Cox proportional hazards regression model was used to estimate the hazard ratio and 95% confidence interval (CI) for herpes zoster associated with splenectomy.

Results:

The overall incidence of herpes zoster was 1.41-fold higher in the splenectomy group than in the nonsplenectomy group (11.3 vs. 8.05 per 1000 person-years, 95% CI 1.11–1.78). After multivariable adjustments, the adjusted hazard ratio of herpes zoster was 1.57 for individuals with splenectomy (95% CI 1.08–2.29), compared with individuals without splenectomy.

Conclusion:

Individuals with splenectomy are associated with 1.57-fold increased risk for developing herpes zoster in Taiwan. Vaccination against herpes zoster may be considered among these high-risk individuals.
Transient Receptor Potential Ankyrin 1 Mediates Afferent Signals in the Inflammatory Reflex
Authors: Silverman Harold A. , Gunasekaran Manojkumar , Chang Eric H. , Chang Qing , Addorisio Meghan E. , Stiegler Andrew , Kressel Adam M. , Li Jian Hua , Tsaava Tea , Huerta Tomas S. , Pavlov Valentin A. , Andersson Ulf , Chavan Sangeeta S. , Tracey Kevin J.
Published: November 2019

Survival of an organism requires mechanisms to sense damaging factors in the environment. In mammals, bacterial toxins and inflammatory mediators stimulate nociceptive sensory neurons to activate protective reflexes. Whereas the vagus nerve reflex circuit that protects against damaging inflammation, termed the “inflammatory reflex,” was described more than twenty years ago1,2, how the vagus nerve detects inflammation to initiate the inflammatory reflex has remained unknown. Here we show that transient receptor potential ankyrin 1 (TRPA1) in sensory vagus neurons is required to sense interleukin-1β (IL-1β), a central cytokine mediator of inflammation and injury. Selective activation of vagus nerve TRPA1 using optopharmacology stimulated the inflammatory reflex to inhibit innate inflammatory responses to bacterial lipopolysaccharide and IL-1β. Proximity ligation assay and immunohistochemistry revealed that IL-1 receptors are co-expressed with TRPA1 in vagus sensory neurons. Whole-cell patch-clamp recordings reveal that TRPA1 is required to mediate IL-1β-dependent depolarization of vagus sensory neurons. Further, TRPA1-deficient mice lack inflammatory reflex attenuation of inflammation, fail to restrain cytokine release, and have significantly enhanced lethality to bacterial sepsis. Therefore, vagus neurons expressing TRPA1 are necessary and sufficient to activate the sensory arc of the inflammatory reflex to protect against harmful inflammation.
Nix induced mitochondrial fission, mitophagy, and myocyte insulin resistance are abrogated by PKA phosphorylation
Authors: da Silva Rosa Simone Cristina , Martens Matthew D. , Field Jared T. , Nguyen Lucas , Kereliuk Stephanie M. , Hai Yan , Chapman Donald , Diehl-Jones William , Aliani Michel , West Adrian R. , Thliveris James , Ghavami Saeid , Rampitsch Christof , Dolinsky Vernon W. , Gordon Joseph W.
Published: November 2019

Lipotoxicity is a form of cellular stress caused by the accumulation of lipids resulting in mitochondrial dysfunction and insulin resistance in muscle. Previously, we demonstrated that the mitophagy receptor Nix is responsive to lipotoxicity and accumulates in response to diacylglycerols induced by high-fat (HF) feeding. In addition, previous studies have implicated autophagy and mitophagy in muscle insulin sensitivity. To provide a better understanding of these observations, we undertook gene expression array and shot-gun metabolomics studies in soleus muscle from rodents on an HF diet. Interestingly, we observed a modest reduction in several autophagy-related genes including Beclin-1, ATG3, and -5. Moreover, we observed alterations in the fatty acyl composition of cardiolipins and phosphatidic acids. Given the previously reported roles of these phospholipids and Nix in mitochondrial dynamics, we investigated aberrant mitochondrial fission and turn-over as a mechanism of myocyte insulin resistance. In a series of gain-of-function and loss-of-function experiments in rodent and human myotubes, we demonstrate that Nix accumulation triggers mitochondrial depolarization, fragmentation, calcium-dependent activation of DRP1, and mitophagy. In addition, Nix-induced mitochondrial fission leads to myotube insulin resistance through activation of mTOR-p70S6 kinase inhibition of IRS1, which is contingent on phosphatidic acids and Rheb. Finally, we demonstrate that Nix-induced mitophagy and insulin resistance can be reversed by direct phosphorylation of Nix by PKA, leading to the translocation of Nix from the mitochondria and sarcoplasmic reticulum to the cytosol. These findings provide insight into the role of Nix-induced mitophagy and myocyte insulin resistance during an overfed state when overall autophagy-related gene expression is reduced. Furthermore, our data suggests a mechanism by which exercise or pharmacological activation of PKA may overcome myocyte insulin resistance.

Graphical Abstract
Candidate methylation sites associated with endocrine therapy resistance in the TCGA ER+/HER2- breast cancer cohort
Authors: Soleimani Maryam , Borgoni Simone , Sofyalı Emre , Verschure Pernette J. , Wiemann Stefan , Moerland Perry D. , van Kampen Antoine H.C.
Published: November 2019

Background

Estrogen receptor (ER) positive breast cancer is often effectively treated with drugs that inhibit ER signaling, i.e., tamoxifen (TAM) and aromatase inhibitors (AIs). However, about 30% of ER+ breast cancer patients develop resistance to therapy leading to tumour recurrence. Changes in the methylation profile have been implicated as one of the mechanisms through which therapy resistance develops. Therefore, we aimed to identify methylation loci associated with endocrine therapy resistance.

Methods

We used genome-wide DNA methylation profiles of primary ER+ tumors from The Cancer Genome Atlas in combination with curated data on survival and treatment to predict development of endocrine resistance. Association of individual DNA methylation markers with survival was assessed using Cox proportional hazards models in a cohort of ER+/HER2- tumours (N=552) and two sub-cohorts corresponding to the endocrine treatment (AIs or TAM) that patients received (N=210 and N=172, respectively). Models were adjusted for clinical variables tumour stage, age, AI treatment and luminal subtype. We also identified signatures of multiple methylation loci associated with survival using Cox proportional hazards models with elastic net regularization. Individual markers and multivariable signatures were compared with DNA methylation profiles generated in a time course experiment using the T47D ER+ breast cancer cell line treated with tamoxifen or deprived from estrogen.

Results

We identified 132, 9 and 1 CpGs for which DNA methylation is significantly associated with survival in the ER+/HER2-, TAM and AI cohorts respectively. Corresponding multi-locus signatures consisted of 171, 50 and 160 CpGs and showed a large overlap with the corresponding single-locus signatures. Single-locus signatures for the ER+/HER2- and TAM cohorts were conserved among the loci that were differentially methylated in endocrine-resistant T47D cells. Similarly, multi-locus signatures for the ER+/HER2- and AI cohorts were conserved in endocrine-resistant T47D cells.

Conclusions

We identified individual and multivariable DNA methylation markers associated with therapy resistance independently of luminal status. Our results suggest that these markers identified from primary tumours and prior to any endocrine treatment are associated with development of endocrine resistance.
Enzalutamide-induced PTH1R-mediated TGFBR2 decrease in osteoblasts contributes to resistance in prostate cancer bone metastases
Authors: Su Shang , Cao Jingchen , Meng Xiangqi , Liu Ruihua , Ark Alexandra Vander , Woodford Erica , Zhang Reian , Stiver Isabelle , Zhang Xiaotun , Madaj Zachary B. , Bowman Megan J. , Wu Yingying , Xu H. Eric , Chen Bin , Yu Haiquan , Li Xiaohong
Published: November 2019

Over 80% of prostate cancer (PCa) patients in the United States die with bone metastases. Second-line hormonal therapies, such as enzalutamide, improve overall survival in about 50% of patients with bone metastases, but almost all responsive patients eventually develop enzalutamide resistance. Our study showed that although enzalutamide significantly inhibited the tumor growth of subcutaneously or orthotopically grafted PCa C4-2B cells, it had no effect on the bone lesion development when C4-2B tumors were grafted in the bone, suggesting a crucial role of the microenvironment in enzalutamide resistance in PCa bone metastasis. We found that enzalutamide significantly decreased the amount of the TGFBR2 (TGF-β type II receptor) in osteoblasts, both in vitro and in patient samples. The osteoblast-specific knockout of Tgfbr2 significantly induced bone metastasis. We showed that the enzalutamide-induced TGFBR2 decrease in osteoblasts was mediated by increased PTH1R (parathyroid hormone/parathyroid hormone-related peptide receptor), which resulted in TGFBR2 degradation, and that blocking PTH1R rescued the TGFBR2 decrease. Furthermore, we found that PTH1R up-regulation by enzalutamide was correlated with increased Pth1r promoter occupancy by transcription factor NR2F1. Our findings highlight a potential enzalutamide-resistance mechanism through TGFBR2 decrease in osteoblasts, thus suggesting future PTH1R-blocking approaches to overcome enzalutamide resistance in PCa bone metastasis.
Ancient balancing selection maintains incompatible versions of a conserved metabolic pathway in yeast
Authors: Boocock James , Sadhu Meru J , Bloom Joshua S , Kruglyak Leonid
Published: November 2019

Differences in nutrient availability have led to the evolution of diverse metabolic strategies across species, but within species these strategies are expected to be similar. Here, we discovered that the galactose metabolic pathway in the yeastSaccharomyces cerevisiaeexists in two functionally distinct, incompatible states maintained by ancient balancing selection. We identified a genetic interaction for growth in galactose among the metabolic genesGAL2, GAL1/10/7, andPGM1. We engineered strains with all allelic combinations at these loci and showed that the reference allele ofPGM1is incompatible with the alternative alleles of the other genes. We observed a strong signature of ancient balancing selection at all three loci and found that the alternative alleles diverged from the reference alleles before the birth of theSaccharomyces sensu strictospecies cluster 10-20 million years ago. Strains with the alternative alleles are found primarily in galactose-rich dairy environments, and they grow faster in galactose, but slower in glucose, revealing a tradeoff on which balancing selection may have acted.
Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading into euchromatic islands
Authors: Méteignier Louis-Valentin , Lecampion Cécile , Velay Florent , Vriet Cécile , Dimnet Laura , Térèse Michel , Rougée Martin , Breuer Christian , Soubigou-Taconnat Ludivine , Sugimoto Keiko , Barneche Fredy , Laloi Christophe
Published: November 2019

The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of theArabidopsis thalianagenome are specifically downregulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some TE loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine (SAM) synthase MAT3, which is required for H3K9me2 deposition. Topoisomerase VI promotes MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a mechanistic insight into the essential role of Topoisomerase VI in the delimitation of chromatin domains.
Epigenomic profiling of neuroblastoma cell lines
Authors: Upton Kristen , Modi Apexa , Patel Khushbu , Conkrite Karina L. , Sussman Robyn T. , Way Gregory P. , Adams Rebecca N. , Sacks Gregory I. , Fortina Paolo , Diskin Sharon J. , Maris John M. , Rokita Jo Lynne
Published: November 2019

Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma.
Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population
Authors: Tsuji Satsuki , Maruyama Atsushi , Miya Masaki , Ushio Masayuki , Sato Hirotoshi , Minamoto Toshifumi , Yamanaka Hiroki
Published: November 2019

Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high-throughput sequencing, denoising was performed using two of the most widely used denoising packages, UNOISE3 and DADA2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (UNOISE3) and 41 (DADA2) haplotypes were detected by eDNA analysis. When DADA2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. This study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large-scale capture-based conventional methods, suggesting that it could become a more efficient survey method for investigating intraspecific genetic diversity in the field.
Automaticity in the reading circuitry
Authors: Joo Sung Jun , Tavabi Kambiz , Caffarra Sendy , Yeatman Jason D.
Published: November 2019

Skilled reading requires years of practice associating visual symbols with speech sounds. Over the course of the learning process, this association becomes effortless and automatic. Here we test whether automatic activation of spoken-language circuits in response to visual words is a hallmark of skilled reading. Magnetoencephalography was used to measure word-selective responses under multiple cognitive tasks (N = 42, 7-12 years of age). Even when attention was drawn away from the words by performing an attention-demanding fixation task, strong word-selective responses were found in a language region (i.e., superior temporal gyrus) starting at ~300 ms after stimulus onset. Critically, this automatic word-selective response was indicative of reading skill: the magnitude of word-selective responses correlated with individual reading skill. Our results suggest that automatic recruitment of spoken-language circuits is a hallmark of skilled reading; with practice, reading becomes effortless as the brain learns to automatically translate letters into sounds and meaning.
Fibrin fragment E potentiates TGF-β-induced myofibroblast activation and recruitment
Authors: Fuchs Peder Fredlund , Heindryckx Femke , Calitz Carlemi , Binet François , Øie Solbak Sara Marie , Danielson Helena U. , Kreuger Johan , Gerwins Pär
Published: November 2019

Background

Fibrin is an essential constituent of the coagulation cascade, and the formation of hemostatic fibrin clots is central to wound healing. Fibrin clots are over time degraded into fibrin degradation products as the injured tissue is replaced by granulation tissue.

Objectives

study the role of the fibrin degradation product fragment E (FnE) in fibroblast activation and migration.

Methods

Rat kidney fibroblasts (NRK-49F), human fetal lung fibroblasts (HFL1) and immortalized human foreskin fibroblasts (BJ) were exposed to FnE and TGF-β. Fibroblast activation was measured via quantitative RT-PCR and western blot for α-SMA and Collagen Iα1. A microfluidic chemotaxis assay was used to study directional migration. To investigate if FnE interacts with integrins, direct binding experiments were performed using surface plasmon resonance biosensor technology. Infusion pumps releasing FnE were implanted subcutaneously in mice and profibrotic effects of FnE were analyzed using immunohistochemical staining of the wound area.

Results

We present evidence that FnE is a chemoattractant for fibroblasts and that FnE can potentiate TGF-β-induced myofibroblast formation. FnE forms a stable complex with αVβ3integrin, and the integrin β3subunit is required both for FnE-induced fibroblast migration and for potentiation of TGF-β-induced myofibroblast formation. Finally, subcutaneous infusion of FnE in mice results in a fibrotic response in the hypodermis. These results support a model where FnE released from clots in wounded tissue promote wound healing and fibrosis by both recruitment and activation of fibroblasts. Fibrin fragment E could thus represent a therapeutic target for treatment of pathological fibrosis.

Essentials

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Fibrin is an essential constituent of the coagulation cascade, and fibrin clotting is central to wound healing.

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Fibrin clots are over time degraded into fibrin degradation products, including fibrin fragment E (FnE).

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FnE is a chemoattractant for fibroblasts and can potentiate TGF-β-induced myofibroblast formation.

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FnE released from clots in wounded tissue could promote wound healing and fibrosis.
Human T cells employ conserved AU-rich elements to fine-tune IFN-γ production
Authors: Freen-van Heeren Julian J. , Popović Branka , Guislain Aurélie , Wolkers Monika C.
Published: November 2019

Long-lasting CD8+T cell responses are critical in combatting infections and tumors. The pro-inflammatory cytokine IFN-γ is a key effector molecule herein. We recently showed that in murine T cells, the production of IFN-γ is tightly regulated through AU-rich elements (AREs) that are located in the 3’ Untranslated Region (UTR). Loss of AREs resulted in prolonged cytokine production in activated T cells and boosted anti-tumoral T cell responses. Here, we investigated whether these findings can be translated to primary human T cells. Utilizing CRISPR-Cas9 technology, we deleted the ARE region from theIFNG3’UTR in peripheral blood-derived human T cells. Loss of AREs stabilized theIFNGmRNA in T cells and supported a higher proportion of sustained IFN-γ protein-producing T cells. Importantly, this was also true for tumor antigen-specific T cells. MART-1 TCR engineered T cells that were gene-edited for ARE-deletion showed increased percentages of IFN-γ producing MART-1-specific ARE-Del T cells in response to MART-1 expressing tumor cells. Combined, our study reveals that ARE-mediated post-transcriptional regulation is highly conserved between murine and human T cells. Furthermore, generating antigen-specific ARE-Del T cells is feasible, a feature that could potentially be exploited for therapeutical purposes.
Recapitulating idiopathic pulmonary fibrosis related alveolar epithelial dysfunction in an iPSC-derived air-liquid interface model
Authors: Schruf Eva , Schroeder Victoria , Le Huy Q. , Schönberger Tanja , Raedel Dagmar , Stewart Emily L. , Fundel-Clemens Katrin , Bluhmki Teresa , Weigle Sabine , Schuler Michael , Thomas Matthew J. , Heilker Ralf , Webster Megan J. , Dass Martin , Frick Manfred , Stierstorfer Birgit , Quast Karsten , Garnett James P.
Published: November 2019

An abnormal emergence of airway epithelial-like cells within the alveolar compartments of the lung, herein termed bronchiolization, is a process often observed in patients suffering from idiopathic pulmonary fibrosis (IPF), a fatal disease characterized by progressive fibrotic lung remodeling. However, the origin of this dysfunctional epithelium remains unknown.

In this study, we aimed to investigate the effects of a pro-fibrotic milieu, similar to that found in an IPF lung, on human alveolar epithelial progenitor cell differentiation. We developed an induced pluripotent stem cell (iPSC)-derived air-liquid interface (ALI) model of alveolar type II (ATII)-like cell differentiation and stimulated it with an IPF-relevant cocktail (IPF-RC), composed of cytokines previously reported to be elevated in IPF lungs. iPSC-derived cultures express ATII markers and contain lamellar body-like structures. Stimulation with IPF-RC during the last two weeks of differentiation increases secretion of IPF biomarkers. Transcriptome analysis of IPF-RC treated cultures reveals significant overlap with human IPF data and enrichment of transcripts associated with extracellular matrix organization. IPF-RC stimulation further impairs ATII differentiation by driving a shift towards an airway epithelial-like expression signature.

In conclusion, we show for the first time, the establishment of a human model system that recapitulates aspects of IPF-associated bronchiolizationin vitro. Our findings reveal how aberrant alveolar epithelial progenitor cell differentiation in a pro-fibrotic environment could contribute to alveolar bronchiolization in the distal IPF lung.

SOURCE OF SUPPORT

The research was funded by Boehringer Ingelheim Pharma GmbH & Co. KG.
Palmitate-induced toxicity is associated with impaired mitochondrial respiration and accelerated oxidative stress in cultured cardiomyocytes: the critical role of Coenzyme Q9/10
Authors: Dludla Phiwayinkosi V. , Silvestri Sonia , Orlando Patrick , Mazibuko-Mbeje Sithandiwe E. , Johnson Rabia , Marcheggiani Fabio , Cirilli Ilenia , Muller Christo J.F. , Louw Johan , Chellan Nireshni , Obonye Nnini , Nkambule Bongani B. , Tiano Luca
Published: November 2019

Impaired mitochondrial function concomitant to enhanced oxidative stress-induced damage are well established mechanisms involved in hyperlipidemia-induced cardiotoxicity. Coenzyme Q9/10 (CoQ) is known to be a critical component of the mitochondrial electron transport chain that efficiently supports the process of bioenergetics in addition to its antioxidant activities. However, there is very limited information on the direct effect of myocardial lipid overload on endogenous CoQ levels in association with mitochondrial respiration and oxidative stress status. Here, such effects were explored by exposing H9c2 cardiomyocytes to various doses (0.15 to 1 mM) of palmitate for 24 hours. The results demonstrated that palmitate doses ≥ 0.25 mM are enough to impair mitochondrial respiration and cause oxidative stress. Although endogenous CoQ levels are enhanced by palmitate doses ≤ 5 mM, this is not enough to counteract oxidative stress, but is sufficient to maintain cell viability of cardiomyocytes, suggesting a compensation mechanism. Palmitate doses > 5 mM caused severe mitochondrial toxicity, including reduction of cell viability. Interestingly, enhancement of CoQ levels with the lowest dose of palmitate (0.15 mM) was accompanied by a significantly reduction of CoQ oxidation status, as well as low cytosolic production of reactive oxygen species. From the overall findings, it appears that CoQ response may be crucial to improve mitochondrial function and thus protect against hyperlipidemia-induced insult. These results further suggest that therapeutic agents that can stimulate endogenous levels of CoQ may be beneficial in protecting the myocardium against diabetes associated complications.
Cyclic and Multilevel Causation in Evolutionary Processes
Authors: Warrell Jonathan , Gerstein Mark
Published: November 2019

Many models of evolution are implicitly causal processes. Features such as causal feedback between evolutionary variables and evolutionary processes acting at multiple levels, though, mean that conventional causal models miss important phenomena. We develop here a general theoretical framework for analyzing evolutionary processes drawing on recent approaches to causal modeling developed in the machine-learning literature, which have extended Pearl’s ‘do’-calculus to incorporate cyclic causal interactions and multilevel causation. We also develop information-theoretic notions necessary to analyze causal information dynamics in our framework, introducing a causal generalization of the Partial Information Decomposition framework. We show how our causal framework helps to clarify conceptual issues in the contexts of complex trait analysis and cancer genetics, including assigning variation in an observed trait to genetic, epigenetic and environmental sources in the presence of epigenetic and environmental feedback processes, and variation in fitness to mutation processes in cancer using a multilevel causal model respectively, as well as relating causally-induced to observed variation in these variables via information theoretic bounds. In the process, we introduce a general class of multilevel causal evolutionary processes which connect evolutionary processes at multiple levels via coarse-graining relationships. Further, we show how a range of ‘fitness models’ can be formulated in our framework, as well as a causal analog of Price’s equation (generalizing the probabilistic ‘Rice equation’), clarifying the relationships between realized/probabilistic fitness and direct/indirect selection. Finally, we consider the potential relevance of our framework to foundational issues in biology and evolution, including supervenience, multilevel selection and individuality. Particularly, we argue that our class of multilevel causal evolutionary processes, in conjunction with a minimum description length principle, provides a conceptual framework in which identification of multiple levels of selection may be reduced to a model selection problem.
Evaluation of CD8 T cell killing models with computer simulations of 2-photon imaging experiments
Authors: Rastogi Ananya , Robert Philippe , Halle Stephan , Meyer-Hermann Michael
Published: November 2019

In vivo imaging of cytotoxic T lymphocyte (CTL) killing activity revealed that infected cells have a higher observed probability of dying after multiple contacts with CTLs, suggesting memory effect in CTLs or infected cells. We developed a three-dimensional agent-based model of CTL killing activity to discriminate different hypotheses about how infected cells get killed based on quantitative 2-photon in vivo observations. We compared a constant CTL killing probability with mechanisms of signal integration in CTL or infected cells. The most likely scenario implied increased susceptibility of infected cells with increasing number of CTL contacts where the total number of contacts was a critical factor as opposed to signal integration over many contacts. However, when allowing in silico T cells to interact with apoptotic target cells (zombie contacts), a contact history independent killing mechanism was also in agreement with the experimental datasets. We showed that contacts that take place between CTLs and dying infected cells impact the observed killing dynamics because even in absence of modulation of cell properties, we saw an increase of the observed probability of killing infected cells with more interactions. The duration taken by an infected cell to die and the per capita killing rate (PCKR) of CTLs, parameters hard to measure directly, were determined from the model and turned out predictive to distinguish the different CTL killing models in future experiments. The comparison of observed datasets to simulation results, revealed limitations in interpreting 2-photon data, and provided prediction for additional measurements to distinguish CTL killing models.

Highlights

Killing of infected cells by cytotoxic T cells typically involves more than a single contact.

Cytotoxic T cells or infected cells integrate signals from multiple interactions.

T cell contacts with dying infected cells have a major impact on in vivo data interpretation.

Significance Statement

Despite having a clear understanding of cytotoxic T lymphocyte (CTL) mediated cytotoxicity mechanisms, the quantitative dynamics remain unexplored at a cellular level. We developed an agent-based model to compare different hypotheses for mechanisms of CTL mediated cytotoxicity that could lead to an increase in observed probability of killing infected cells at higher interactions with CTLs as seen in vivo. We showed that this behaviour can be explained by modulation of properties by infected cells or CTLs with increasing number of contacts. For the modulation, we compared two modes of signal integration and showed that time is not a relevant parameter in signal integration. We also studied the impact of contacts between CTLs and apoptotic infected cells on observed killing properties.
Alpha 6 integrins promote cytokinesis by regulating the expression of RSK2 and MKLP1
Authors: Singh Neetu , Xu Hao , Thiemann Renee , DeSantis Kara A. , Larsen Melinda , LaFlamme Susan E.
Published: November 2019

The integrin-mediated interaction of cells with components of the extracellular matrix (ECM) regulates many cellular processes including cell division. Cytokinesis is the last step of cell division and is critical for normal development and tissue homeostasis as it ensures the proper segregation of genetic and cytoplasmic material between daughter cells. Cytokinesis failure leads to defects in development and tissue differentiation, as well as tumorigenesis. Abscission of intercellular bridge that connects presumptive daughter cells is the last step of cell division. The mitotic kinesin-like protein 1 (MKLP1) plays a central role in positioning the abscission machinery. Here, we show that α6 integrins promote successful cytokinesis in salivary gland epithelial cells by regulating the expression of MKLP1. RNAi-mediated depletion of α6 integrins inhibits cytokinesis and the expression of MKLP1 and p90 ribosomal-S6-kinase 2 (RSK2). Depletion of RSK2 results in similar defects in cytokinesis and also inhibits the expression of MKLP1, suggesting that the expression of RSK2 is required downstream of integrins to promote MKLP1 expression and successful cytokinesis. RNAi-mediated depletion of RSK2 in embryonic salivary glands in organ culture also results in the inhibition of cytokinesis and MKLP1 expression, indicating the physiological significance of this pathway.
Pathogen transmission from vaccinated hosts can cause dose-dependent reduction in virulence
Authors: Bailey Richard I. , Cheng Hans H. , Chase-Topping Margo , Mays Jody K. , Anacleto Osvaldo , Dunn John R. , Doeschl-Wilson Andrea
Published: November 2019

Many livestock and human vaccines are leaky as they block symptoms but do not prevent infection or onward transmission. This leakiness is concerning as it increases vaccination coverage required to prevent disease spread, and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek’s disease virus in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine can have unforeseen positive consequences in controlling the spread and symptoms of disease.
GmPTF1 Modifies Root Architecture Responses to Phosphate Starvation in Soybean
Authors: Yang Zhaojun , He Ying , Liu Yanxing , Lai Yelin , Zheng Jiakun , Li Xinxin , Liao Hong
Published: November 2019

Though root architecture modifications may be critically important for improving phosphorus (P) efficiency in crops, the regulatory mechanisms triggering these changes remain unclear. In this study, we demonstrate that genotypic variation in GmEXPB2 expression is strongly correlated with root elongation and P acquisition efficiency, and enhancing its transcription significantly improves soybean yield in the field. Promoter deletion analysis was performed using six 5’ truncation fragments (P1-P6) of GmEXPB2 fused with the GUS reporter gene in transgenic hairy roots, which revealed that the P1 segment containing 3 E-box elements significantly enhances induction of gene expression in response to phosphate (Pi) starvation. Further experimentation demonstrated that GmPTF1, a bHLH transcription factor, is the regulatory factor responsible for the induction of GmEXPB2 expression in response to Pi starvation. In short, Pi starvation induced expression of GmPTF1, with the GmPTF1 product not only directly binding the E-box motif in the P1 region of the GmEXPB2 promoter, but also activating GUS expression in a dosage dependent manner. Further work with soybean transgenic composite plants showed that, altering GmPTF1 expression significantly impacted GmEXPB2 transcription, and thereby affected root growth, biomass and P uptake. Taken together, this work identifies a novel regulatory factor, GmPTF1, involved in changing soybean root architecture through regulation the expression of GmEXPB2. These findings contribute to understanding the molecular basis of root architecture modifications in response to P deficiency, and, in the process, suggest candidate genes and a promoter region to target for improving soybean yield through molecular breeding of P efficiency.

One Sentence Summary

The bHLH transcription factor GmPTF1 regulates the expression of β-expansin gene GmEXPB2 to modify root architecture, and thus promote phosphate acquisition, and biomass in soybean.