bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiology of patients presenting with dyspnea to emergency departments in Europe and the Asia-Pacific region
Authors: Laribi Said , Keijzers Gerben , van Meer Oene , Klim Sharon , Motiejunaite Justina , Kuan Win Sen , Body Richard , Jones Peter , Karamercan Mehmet , Craig Simon , Harjola Veli-Pekka , Holdgate Anna , Golea Adela , Graham Colin , Verschuren Franck , Capsec Jean , Christ Michael , Grammatico-Guillon Leslie , Barletta Cinzia , Garcia-Castrillo Luis , Kelly Anne-Maree
Published: August 2018

Objective

The primary objective of this study was to describe the epidemiology and management of dyspneic patients presenting to emergency departments (EDs) in an international patient population. Our secondary objective was to compare the EURODEM and AANZDEM patient populations.

Patients and methods

An observational prospective cohort study was carried out in Europe and the Asia-Pacific region. The study included consecutive patients presenting to EDs with dyspnea as the main complaint. Data were collected on demographics, comorbidities, chronic treatment, clinical signs and investigations, treatment in the ED, diagnosis, and disposition from ED.

Results

A total of 5569 patients were included in the study. The most common ED diagnoses were lower respiratory tract infection (LRTI) (24.9%), heart failure (HF) (17.3%), chronic obstructive pulmonary disease (COPD) exacerbation (15.8%), and asthma (10.5%) in the overall population. There were more LRTI, HF, and COPD exacerbations in the EURODEM population, whereas asthma was more frequent in the AANZDEM population. ICU admission rates were 5.5%. ED mortality was 0.6%. The overall in-hospital mortality was 5.0%. In-hospital mortality rates were 8.7% for LRTI, 7.6% for HF, and 5.6% for COPD patients.

Conclusion

Dyspnea as a symptom in the ED has high ward and ICU admission rates. A variety of causes of dyspnea were observed in this study, with chronic diseases accounting for a major proportion.
Murine models of autoimmune hemolytic anemia
Authors: Howie Heather L. , Hudson Krystalyn E.
Published: August 2018

Purpose of review

Pathogenic autoantibodies directed against red blood cells (RBCs) may lead to autoimmune hemolytic anemia (AIHA), a severe and sometimes fatal disease. Much of what is known about the etiology and pathogenesis of AIHA has been learned from observations made in human patients and murine models, but many questions remain; importantly, it is still unclear why some people generate RBC-specific autoantibodies. The combination of technological advancements applied to existing models and the development of new AIHA murine models will continue to provide considerable insight into the initiation of AIHA and provide a platform for the design of more effective therapies.

Recent findings

Advancements in well described murine models of AIHA show that reticulocytes are preferentially targeted by anti-RBC autoantibodies and an increase in oxidative stress may trigger autoantibody production. Additionally, a new murine model of erythrocyte autoreactivity demonstrates that T cell tolerance is the stopgap for autoimmunity. Moreover, unlike many self-antigens, data suggest that RBC self-antigens are not presented in the thymus thereby escaping the scrutiny of T cell central tolerance mechanisms and placing emphasis on peripheral tolerance instead. Information gained from this new model provide novel insight into how the immune system responds to RBC autoantigens and provides a tractable platform to discover new therapies for AIHA.

Murine models of AIHA have provided significant understanding into the risk factors for AIHA. The application of new technologies and models of erythrocyte autoreactivity is a pathway with the potential to elucidate how tolerance to RBC autoantigens is established, maintained, and broken down.
Anxiety and Salivary Cortisol Levels in Children Undergoing Esophago‐Gastro‐Duodenoscopy Under Sedation
Authors: Kara Duygu , Bayrak Nevzat Aykut , Volkan Burcu , Uçar Cihat , Cevizci Mehmet Nuri , Yildiz Sedat
Published: August 2018

Objectives:

Esophagogastroduodenoscopy (EGD) can cause fear and anxiety in children. Cortisol, which is the most important glucocorticoid hormone in humans, can increase under physiological stress. The purpose of this study was to measure the salivary cortisol level (SCL) and anxiety level in patients undergoing EGD and evaluate their effects on the procedure.

Methods:

Children undergoing EGD under sedoanalgesia with propofol for various reasons were included. Their basal SCLs were compared with those of healthy age‐ and sex‐matched controls. Moreover, SCL of the patient group at 30 minutes before EGD and 2 hours after the procedure were measured. Their anxiety scores were calculated using the modified Yale Preoperative Anxiety Scale before EGD. Duration of endoscopy, sedation, and recovery and total propofol doses were recorded.

Results:

Demographic properties of the patient group (n = 119; 10.9 ± 3.2 years; 43.7% boys) and control group (n = 85; 11.8 ± 2.8 years; 45.1% boys) were not significantly different. Basal SCLs of both groups were similar (16.9 ± 0.7 vs 19.7 ± 1.8 ng/mL, P = 0.16). SCL before EGD in the patient group was significantly higher than basal and post‐EGD values (P < 0.001 for each). Pre‐EGD SCL was positively correlated with anxiety level, propofol dose, and duration of sedation, procedure, and recovery. Anxiety levels of patients were positively correlated with propofol dose and duration of sedation and recovery, and negatively correlated with age.

Conclusions:

Childhood EGD is a significant stress factor, which was reflected by the pre‐procedural SCL in this study. Increased anxiety resulted in increased propofol doses and sedoanalgesia‐related procedural durations, which may cause potential complications.
No Useful Field Expansion with Full-field Prisms
Authors: Jung Jae-Hyun , Peli Eli
Published: August 2018

SIGNIFICANCE

Full-field prisms that fill the entire spectacle eye wire have been considered as field expansion devices for homonymous hemianopia (HH) and acquired monocular vision (AMV). Although the full-field prism is used for addressing binocular dysfunction and for prism adaptation training after brain injury as treatment for spatial hemineglect, we show that the full-field prism for field expansion does not effectively expand the visual field in either HH or AMV.

PURPOSE

Full-field prisms may shift a portion of the blind side to the residual seeing side. However, foveal fixation on an object of interest through a full-field prism requires head and/or eye rotation away from the blind side, thus negating the shift of the field toward the blind side.

METHODS

We fit meniscus and flat full-field 7Δ and 12Δ yoked prisms and conducted Goldmann perimetry in HH and AMV. We compared the perimetry results with ray tracing calculations.

RESULTS

The rated prism power was in effect at the primary position of gaze for all prisms, and the meniscus prisms maintained almost constant power at all eccentricities. To fixate on the perimetry target, the subjects needed to turn their head and/or eyes away from the blind side, which negated the field shift into the blind side. In HH, there was no difference in the perimetry results on the blind side with any of the prisms. In AMV, the lower nasal field of view was slightly shifted into the blind side with the flat prisms, but not with the meniscus prisms.

CONCLUSIONS

Full-field prisms are not an effective field expansion device owing to the inevitable fixation shift. There is potential for a small field shift with the flat full-field prism in AMV, but such lenses cannot incorporate refractive correction. Furthermore, in considering the apical scotoma, the shift provides a mere field substitution at best.
An Unusual Murder
Authors: Barranco Rosario , Molinelli Andrea , Ventura Francesco
Published: August 2018

Fatalities due to stabbings are usually caused by large blood vessels or organs injuries resulting in hemorrhagic shock. Vagal inhibition from a stab to the neck is an undeniably exceptional event, infrequently described in the literature. In our case report, we describe one such fatality.

The body of a deceased 38-year-old man was found near a public garden. According to a bystander, the victim had been assaulted by 2 individuals, sustaining a stab wound to the neck with a broken glass bottle. At the autopsy, there was a large, inverted L–shaped cut wound in the left cervical region, measuring approximately 4.5 × 3 cm. The carotid artery and the jugular vein, as well as their main branches, were uninjured. The trachea and bronchi contained no exudate or blood. There was a hematoma near the trunk of the vagus nerve and its branches.

The cause of death was attributed to the deep stab wound to the neck via vasovagal inhibition and parasympathetic nervous system stimulation.
Residual Tumor Index
Authors: Panni Roheena Z. , Gonzalez Ivan , Hartley Christopher P. , Williams Gregory A. , Liu Jingxia , Hawkins William G. , Chatterjee Deyali
Published: August 2018

In the setting of neoadjuvant therapy (NAT) for pancreatic ductual adenocarcinoma (PDAC), accurate measurement of tumor size, and consequently, staging based on AJCC eighth edition, is difficult. Attempts to address the limitations of tumor size in the NAT setting have included correlation of residual tumor percent with survival. However, only cases with complete pathologic response or minimal residual disease have shown better prognosis compared with all other groups. To date, no studies have simultaneously evaluated the prognostic value of tumor size and tumor regression in the setting of PDAC status post NAT (NAT-PDAC). Our aim was to study the prognostic value of residual tumor index (RTI), a metric combining residual tumor percent and tumor bed size as an interaction term (% residual tumor×tumor bed size [cm]). In a cohort of 105 cases of NAT-PDAC, we show that RTI supersedes the prognostic value of AJCC eighth edition T staging via multivariate cox regression. At a binary cutoff of 0.35 for RTI, the hazard ratio for recurrence-free survival is 3.26 (95% confidence interval, 1.51-7.04), P<0.01. We further identified cutoffs of ≤0.2, 0.2 to 2 and >2 that stratified our cases into 3 groups via RTI, which were statistically significant in Kaplan-Meier curve analysis of recurrence-free survival (P<0.01) and overall survival (P<0.01). RTI represents a novel metric for combining the prognostic value of tumor size and residual tumor in NAT-PDAC.
Tumor Grade Is Prognostically Relevant Among Mismatch Repair Deficient Colorectal Carcinomas
Authors: Johncilla Melanie , Chen Zhengming , Sweeney Jacob , Yantiss Rhonda K.
Published: August 2018

Intestinal-type colorectal adenocarcinomas are graded based on extent of glandular differentiation, although mucinous, signet-ring cell, and solid cancers are, by convention, classified as high grade. Mismatch repair-deficient tumors frequently show high-grade histologic features, yet the World Health Organization classifies them as low grade to reflect their favorable prognosis compared with mismatch repair-proficient cancers. Although some mismatch repair-deficient colorectal cancers behave aggressively, few authors have identified features that predict their behavior. We performed this study to determine which histologic features, if any, predicted outcome among mismatch repair-deficient colorectal carcinomas. We identified 116 mismatch repair-deficient colorectal carcinomas, including 77 localized (stage I to II) and 39 advanced (stage III to IV) tumors, and evaluated them for extent of gland formation, extracellular mucin, signet-ring cell differentiation, solid growth, nuclear grade, tumor-infiltrating lymphocytes and tumor budding. Relationships between these features, pathologic stage, and disease-free survival were assessed. We found that high-grade mismatch repair-deficient tumors were more often of advanced stage than low-grade tumors (46% vs. 23%, P=0.01). Disease-free survival was inversely associated with the presence of a dominant high-grade component and tumor budding (P=0.01 and 0.04, respectively). Predominantly solid tumors, in particular, were significantly associated with decreased disease-free survival compared with low-grade tumors (P=0.001). Nuclear grade and tumor-infiltrating lymphocytes were not associated with pathologic stage or outcome. We conclude that low-grade mismatch repair-deficient carcinomas present at an earlier stage and pursue a more favorable course than those mostly composed of high-grade elements. These findings suggest that mismatch repair status should not supplant histologic grade in the assessment of colorectal carcinomas.
Acquisition of WNT Pathway Gene Alterations Coincides With the Transition From Precursor Polyps to Traditional Serrated Adenomas
Authors: Hashimoto Taiki , Ogawa Reiko , Yoshida Hiroshi , Taniguchi Hirokazu , Kojima Motohiro , Saito Yutaka , Sekine Shigeki
Published: August 2018

Colorectal traditional serrated adenomas (TSAs) are often associated with precursor polyps, including hyperplastic polyps and sessile serrated adenoma/polyps. To elucidate the molecular mechanisms involved in the progression from precursor polyps to TSAs, the present study analyzed 15 precursor polyp-associated TSAs harboring WNT pathway gene mutations. Laser microdissection-based sequencing analysis showed that BRAF or KRAS mutations were shared between TSA and precursor polyps in all lesions. In contrast, the statuses of WNT pathway gene mutations were different between the 2 components. In 8 lesions, RNF43, APC, or CTNNB1 mutations, were exclusively present in TSA. RNF43 mutations were shared between the TSA and precursor components in 3 lesions; however, they were heterozygous in the precursor polyps whereas homozygous in the TSA. In 4 lesions with PTPRK-RSPO3 fusions, RNA in situ hybridization demonstrated that overexpression of RSPO3, reflecting PTPRK-RSPO3 fusion transcripts, was restricted to TSA components. Consistent with the results of the genetic and in situ hybridization analyses, nuclear β-catenin accumulation and MYC overexpression were restricted to the TSA component in 13 and 12 lesions, respectively. These findings indicate that the WNT pathway gene alterations are acquired during the progression from the precursor polyps to TSAs and that the activation of the WNT pathway plays a critical role in the development of TSA rather than their progression to high-grade lesions.
Recommendations on RBC Transfusion Support in Children With Hematologic and Oncologic Diagnoses From the Pediatric Critical Care Transfusion and Anemia Expertise Initiative
Authors: Steiner Marie E. , Zantek Nicole D. , Stanworth Simon J. , Parker Robert I. , Valentine Stacey L. , Lehmann Leslie E. , Josephson Cassandra D. , Bateman Scot T. , Luban Naomi L. C.
Published: August 2018

Objectives:

To present the recommendations and supporting evidence for RBC transfusions in critically ill children with hematologic and oncologic disease from the Pediatric Critical Care Transfusion and Anemia Expertise Initiative.

Design:

Consensus conference series of international, multidisciplinary experts in RBC transfusion management of critically ill children.

Methods:

The panel of 38 experts developed evidence-based and, when evidence was lacking, expert-based clinical recommendations and research priorities for RBC transfusions in critically ill children. The hematologic/oncologic subgroup included seven experts. Electronic searches were conducted using PubMed, EMBASE, and Cochrane Library databases from 1980 to May 2017. Agreement was obtained using the Research and Development/UCLA Appropriateness Method. Results were summarized using the Grading of Recommendations Assessment, Development, and Evaluation method.

Results:

The hematologic/oncologic subgroup developed 14 recommendations (seven clinical, seven research); all achieved greater than 80% agreement. In patients with sickle cell disease, Transfusion and Anemia Expertise Initiative recommends: 1) RBC transfusion to achieve a target hemoglobin concentration of 10 g/dL rather than hemoglobin of less than 30% prior to surgical procedures requiring general anesthesia and 2) exchange transfusion over simple (nonexchange) transfusion if the child’s condition is deteriorating (based on clinical judgment), otherwise a simple, nonexchange RBC transfusion is recommended. There is insufficient evidence to make recommendations on transfusion thresholds for patients with sickle cell disease prior to minor procedures, with acute stroke or with pulmonary hypertension. For patients with oncologic disease or undergoing hematopoietic stem cell transplant, a hemoglobin concentration of 7–8 g/dL is recommended. Due to lack of evidence, research is needed to clarify the appropriate transfusion thresholds in these patients.

Conclusions:

Transfusion and Anemia Expertise Initiative developed specific pediatric recommendations regarding RBC transfusion management in critically ill children with sickle cell disease, oncologic disease, and hematopoietic stem cell transplant and recommendations to help guide future research priorities.
Retinal Hemorrhages
Authors: Hansen Jennifer B. , Killough Emily F. , Moffatt Mary E. , Knapp Jane F.
Published: August 2018

Abusive head trauma is an important cause of morbidity and mortality in infants and young children. Retinal hemorrhages (RHs) are frequently seen, particularly during dilated eye examination of these children. This review focuses on the evaluation of children with RH, with emphasis on the differential diagnosis, pathophysiology, and distinguishing features of RHs due to abusive head trauma. Many causes exist for RHs in infants and children. Most medical and accidental traumatic causes result in a pattern of RH that is nonspecific and not typical of the pattern and distribution of RHs seen in children with abusive head trauma. In children with intracranial hemorrhage and concerns for abuse, the finding of severe, multilayered RHs extending to the periphery of the retina is very specific for abuse as the cause of the findings, especially if retinoschisis is present. There are few other accidental traumatic mechanisms associated with retinoschisis, and the history of such a traumatic event is readily apparent. The indications for ophthalmologic consult, optimal timing of the eye examination, and significance of the findings are specifically discussed.
Ultrasound Elastography Applications in Pediatrics
Authors: Thumar Vishal , Squires Judy H. , Spicer Paul J. , Robinson Amie L. , Chan Sherwin S.
Published: August 2018

Ultrasound is one of the most important imaging modalities in pediatric imaging because of its accessibility, portability, lack of ionizing radiation, and ability to generally perform examinations without need for sedation. Ultrasound elastography can measure the stiffness of various tissues. This review article aims to discuss how ultrasound elastography has performed in evaluating multiple pathologies in the pediatric population. The best studied pediatric applications are in liver diseases such as fibrosis, biliary atresia, and hepatic vascular congestion. Measuring muscle stiffness in cerebral palsy is the most promising pediatric musculoskeletal application, but many other applications are in the early stages of research. Other applications in pediatric small organ imaging have been explored and still need more study before gaining clinical relevance.
Dupuytren’s Contracture
Authors: Mella Juan Rodolfo , Guo Lifei , Hung Virginia
Published: August 2018

Dupuytren’s contracture, a benign condition characterized by fibrosis of the palmar and digital fascia, may be a debilitating condition that limits daily function. Several techniques exist for managing symptomatic contractures of the hand related to Dupuytren’s. These techniques include the more invasive open fasciotomy or fasciectomy. More recently, less invasive techniques including administration of collagenase Clostridium histolyticum (CCH) or percutaneous needle aponeurotomy (PNA) have become part of the treatment armamentarium. A comprehensive review of the literature is performed and an algorithm for management of Dupuytren’s contracture is proposed.
Chrysalis: A new method for high-throughput histo-cytometry analysis of images and movies
Authors: Kotov Dmitri I. , Pengo Thomas , Mitchell Jason S. , Gastinger Matthew J. , Jenkins Marc K.
Published: August 2018

Advances in imaging have led to the development of powerful multispectral, quantitative imaging techniques, like histo-cytometry. The utility of this approach is limited, however, by the need for time consuming manual image analysis. We therefore developed the software Chrysalis and a group of Imaris Xtensions to automate this process. The resulting automation allowed for high-throughput histo-cytometry analysis of 3D confocal microscopy and two-photon time-lapse images of T cell-dendritic cell interactions in the spleen. It was also applied to epi-fluorescence images to quantify T cell localization within splenic tissue by using a ‘signal absorption’ strategy that avoids computationally intensive distance measurements. In summary, this image processing and analysis software makes histo-cytometry more useful for immunology applications by automating image analysis.
Comparing adult hippocampal neurogenesis across species: translating time to predict the tempo in humans
Authors: Charvet Christine J. , Finlay Barbara L
Published: August 2018

Comparison of neurodevelopmental sequences between species whose initial period of brain organization may vary from one hundred days to one thousand days, and whose progress is intrinsically nonlinear presents large challenges in normalization. Comparing adult timelines when lifespans stretch from one year to seventy-five, when underlying cellular mechanisms under scrutiny do not scale similarly, presents challenges to simple detection and comparison. The question of adult hippocampal neurogenesis has generated numerous controversies regarding its simple presence or absence in humans versus rodents, whether it is best described as the tail of a distribution centered on early neural development, or is several distinct processes. In addition, adult neurogenesis may have substantially changed in evolutionary time in different taxonomic groups. Here we extend and adapt a model of the cross-species transformation of early neurodevelopmental events which presently reaches up to the equivalent of the third human postnatal year for 18 mammalian species (www.translatingtime.net) to address questions relevant to hippocampal neurogenesis, which permit extending the database to adolescence or perhaps to the whole lifespan. We acquired quantitative data delimiting the envelope of hippocampal neurogenesis from cell cycle markers (i.e., Ki67, DCX) and RNA sequencing data for two primates (macaque, humans) and two rodents (rat, mouse). To improve species coverage in primates, we gathered the same data from marmosets (Callithrix jacchus), but additionally gathered data on a number of developmental milestones to find equivalent developmental time points between marmosets and other species. When all species are so modeled, and represented in a common time frame, the envelopes of hippocampal neurogenesis are essentially superimposable. Early developmental events involving the olfactory and limbic system start and conclude possibly slightly early in primates than rodents, and we find a comparable early conclusion of primate hippocampal neurogenesis (as assessed by the relative number of Ki67 cells) suggesting a plateau to low levels at approximately 2 years of age in humans. Marmosets show equivalent patterns within neurodevelopment, but unlike macaque and humans may have wholesale delay in the initiation of neurodevelopment processes previously observed in some precocial mammals such as the guinea pig and multiple large ungulates.
Elevated pyrimidine dimer formation at distinct genomic bases underlie promoter mutation hotspots in UV-exposed cancers
Authors: Elliott Kerryn , Boström Martin , Filges Stefan , Lindberg Markus , den Eynden Jimmy Van , Ståhlberg Anders , Clausen Anders R. , Larsson Erik
Published: August 2018

Sequencing of whole cancer genomes has revealed an abundance of recurrent mutations in gene-regulatory promoter regions, in particular in melanoma where strong mutation hotspots are observed adjacent to ETS-family transcription factor (TF) binding sites. While sometimes interpreted as functional driver events, these mutations have also been suggested to be due to locally inhibited DNA repair or, alternatively, locally increased propensity for UV damage. Here, we provide evidence that base-specific elevations in the efficacy of UV lesion formation underlie these mutations. First, we find that low-dose UV light induces mutations preferably at a known ETS promoter hotspot in cultured cells even in the absence of global or transcription-coupled nucleotide excision repair (NER), ruling out inhibited repair. Further, by genome-wide mapping of cyclobutane pyrimidine dimers (CPDs) shortly after UV exposure and thus before DNA repair, we find that ETS-related mutation hotspots exhibit a strong base-specific increase in CPD formation frequency. Analysis of a large whole genome cohort illustrates the widespread contribution of this effect to recurrent mutations in melanoma. While inhibited NER underlies a general increase in somatic mutation burden in regulatory regions, we conclude that the most recurrently mutated individual DNA bases arise instead due to locally favorable conditions for UV damage formation, thus explaining a key phenomenon in whole-genome cancer analyses.
Validation of the protein kinase PfCLK3 as a multi-stage cross species malarial drug target
Authors: Alam Mahmood M , Sanchez-Azqueta Ana , Janha Omar , Flannery Erika L. , Mahindra Amit , Mapesa Kopano , Brancucci Nicolas , Antonova-Koch Yevgeniya , Crouch Kathryn , Simwela Nelson Victor , Akinwale Jude , Mitcheson Deborah , Solyakov Lev , Dudek Kate , Jones Carolyn , Zapatero Cleofé , Doerig Christian , Nwakanma Davis C. , Jesús Vázquez Maria , Colmenarejo Gonzalo , Jesús Lafuente Maria , Leon Maria Luisa , Waters Andrew P. , Jamieson Andrew G. , Fernandez Alvaro León Elena , Marti Matthias , Winzeler Elizabeth A. , Gamo Francisco Javier , Tobin Andrew B.
Published: August 2018

The requirement for next generation anti-malarials to be both curative and transmission blockers necessitate the identification of molecular pathways essential for viability of both asexual and sexual parasite life stages. Here we identify a selective inhibitor to the Plasmodium falciparum protein kinase PfCLK3 which we use in combination with chemogenetics, whole genome sequencing and transcriptomics to validate PfCLK3 as a druggable target acting at multiple parasite life stages. Consistent with the proposed role of PfCLK3 as a regulator of RNA splicing, inhibition results in the down-regulation of >400 genes essential for parasite survival. Through this mechanism, blocking PfCLK3 activity not only results in rapid killing of asexual blood stage parasites but is also effective on sporozoites and gametocytes as well as showing parasiticidal activity in all Plasmodium species tested. Hence, our data establishes PfCLK3 as a target with the potential to deliver both symptomatic treatment and transmission blocking in malaria.
Single-molecule imaging reveals the interplay between transcription factors, nucleosomes, and transcriptional bursting
Authors: Donovan Benjamin T. , Huynh Anh , Ball David A. , Poirier Michael G. , Larson Daniel R. , Ferguson Matthew L. , Lenstra Tineke L.
Published: August 2018

Transcription factors show rapid and reversible binding to chromatin in living cells, and transcription occurs in sporadic bursts, but how these phenomena are related is unknown. Using a combination of in vitro and in vivo single-molecule imaging approaches, we directly correlated binding of the transcription factor Gal4 with the transcriptional bursting kinetics of the Gal4 target genes GAL3 and GAL10 in living yeast cells. We find that Gal4 dwell times sets the transcriptional burst size. Gal4 dwell time depends on the affinity of the binding site and is reduced by orders of magnitude by nucleosomes. Using a novel imaging platform, we simultaneously tracked transcription factor binding and transcription at one locus, revealing the timing and correlation between Gal4 binding and transcription. Collectively, our data support a model where multiple polymerases initiate during a burst as long as the transcription factor is bound to DNA, and a burst terminates upon transcription factor dissociation.
Troponin-I localizes selected apico-basal cell polarity signals
Authors: Casas-Tintó Sergio , Ferrús Alberto
Published: August 2018

Beyond its well characterized role in muscle contraction,DrosophilaTroponin I (TnI) is expressed in other cell types where it plays a role in proliferation control. TnI traffics between the nucleus and the cytoplasm through a sumoylation-dependent mechanism. We address here the role of TnI in the cytoplasm. TnI accumulates in the apical region of epidermal cells and neuroblasts. TnI helps to localize and co-immunoprecipitates with Par-3/Bazooka and with disc large (Dlg), two components of the apico-basal polarity system. By contrast, Scribbled is not affected by TnI depletion. In neuroblasts, TnI is required for the polar localization of Miranda while non-polar Dlg is not affected. TnI loss-of-function triggers genome instability, cell apoptosis and extrusion from wing disc epithelia. However, rescue from apoptosis by p35 does not prevent genome instability demonstrating that both features, apoptosis and genome instability, are mechanistically independent. While PI3K is known to contribute to apico-basal polarity of epithelia in vertebrates,DrosophilaPI3K depletion alters neither the apical localization of TnI or Par3/Bazooka, nor the basal localization of Dlg. However, the overexpression of PI3K prevents the polarity defects caused by TnI depletion. Thus, TnI binds certain apico-basal polarity signals in a cell type dependent context, and it unveils a hitherto unsuspected diversity of mechanisms to allocate cell polarity factors.
Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins
Authors: Torrens-Spence Michael P. , Chiang Ying-Chih , Smith Tyler , Vicent Maria A. , Wang Yi , Weng Jing-Ke
Published: August 2018

Radiation of the plant pyridoxal 5’-phosphate (PLP)-dependent aromatic L-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic L-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.

Significance

Plants biosynthesize their own proteinogenic aromatic L-amino acids, namely L-phenylalanine, L-tyrosine and L-tryptophan, not only for building proteins but also for the production of a plethora of aromatic-amino-acid-derived natural products. Pyridoxal 5’-phosphate (PLP)-dependent aromatic L-amino acid decarboxylase (AAAD) family enzymes play important roles in channeling various aromatic L-amino acids into diverse downstream specialized metabolic pathways. Through comparative structural analysis of four functionally divergent plant AAAD proteins together with biochemical characterization and molecular dynamics simulations, we reveal the structural and mechanistic basis for the rich divergent and convergent evolutionary development within the plant AAAD family. Knowledge learned from this study aids our ability to engineer high-value aromatic-L-amino-acid-derived natural product biosynthesis in heterologous chassis organisms.
Genome-scale Capture C promoter interaction analysis implicates novel effector genes at GWAS loci for bone mineral density
Authors: Chesi Alessandra , Wagley Yadav , Johnson Matthew E. , Manduchi Elisabetta , Su Chun , Lu Sumei , Leonard Michelle E. , Hodge Kenyaita M. , Pippin James A. , Hankenson Kurt D. , Wells Andrew D. , Grant Struan F.A.
Published: August 2018

ASBTRACT

Osteoporosis is a devastating disease with an essential genetic component. Genome wide association studies (GWAS) have discovered genetic variants robustly associated with bone mineral density (BMD), however they only report genomic signals and not necessarily the precise localization of culprit effector genes. Therefore, we sought to carry out physical and direct ‘variant to gene mapping’ in a relevant primary human cell type. We developed ‘SPATIaL-seq’ (genome-Scale, Promoter-focused Analysis of chromaTIn Looping), a massively parallel, high resolution Capture-C based method to simultaneously characterize the genome-wide interactions of all human promoters. By intersecting our SPATIaL-seq and ATAC-seq data from human mesenchymal progenitor cell -derived osteoblasts, we observed consistent contacts between candidate causal variants and putative target gene promoters in open chromatin for ~30% of the 110 BMD loci investigated. Knockdown of two novel implicated genes,ING3at ‘CPED1-WNT16’ andEPDR1at ‘STARD3NL’, had pronounced inhibitory effects on osteoblastogenesis. Our approach therefore aids target discovery in osteoporosis and can be applied to other common genetic diseases.
Cerebral Cavernous Malformations Develop through Clonal Expansion of Mutant Endothelial Cells
Authors: Detter Matthew R. , Snellings Daniel A. , Marchuk Douglas A.
Published: August 2018

Rationale

Vascular malformations arise in vessels throughout the entire body. Causative genetic mutations have been identified for many of these diseases; however, little is known about the mutant cell lineage within these malformations.

Objective

We utilize an inducible mouse model of cerebral cavernous malformations (CCMs) coupled with a multi-color fluorescent reporter to visualize the contribution of mutant endothelial cells (ECs) to the malformation.

Methods and Results

We combined a Ccm3 mouse model with the confetti fluorescent reporter to simultaneously delete Ccm3 and label the mutant EC with one of four possible colors. We acquired Z-series confocal images from serial brain sections and created 3D reconstructions of entire CCMs to visualize mutant ECs during CCM development. We observed a pronounced pattern of CCMs lined with mutant ECs labeled with a single confetti color (n=42). The close 3D distribution, as determined by the nearest neighbor analysis, of the clonally dominant ECs within the CCM was statistically different than the background confetti labeling of ECs in non-CCM control brain slices as well as a computer simulation (p<0.001). Many of the small (<100μm diameter) CCMs consisted, almost exclusively, of the clonally dominant mutant ECs labeled with the same confetti color whereas the large (>100μm diameter) CCMs contained both the clonally dominant mutant cells and wildtype ECs. We propose of model of CCM development in which an EC acquires a second somatic mutation, undergoes clonal expansion to initiate CCM formation, and then incorporates neighboring wildtype ECs to increase the size of the malformation.

Conclusions

This is the first study to visualize, with single-cell resolution, the clonal expansion of mutant ECs within CCMs. The incorporation of wildtype ECs into the growing malformation presents another series of cellular events whose elucidation would enhance our understanding of CCMs and may provide novel therapeutic opportunities.
Hydroxymethylated-P16 Allele Is Transcription-Inactive
Authors: Gan Ying , Li Paiyun , Han Xiao , Qin Sisi , Cui Chenghua , Liu Zhaojun , Zhou Jing , Gu Liankun , Lu Zhe-ming , Zhang Baozhen , Deng Dajun
Published: August 2018

Background

5-Methylcytosine can be oxidized into 5-hydroxymethylcytosine (5hmC) in the genome. Methylated-P16 (P16M) can be oxidized into completely hydroxymethylated-P16 (P16H) in human cancer and precancer cells. The aim of this study is to investigate the biological function of P16H.

Methods

True P16M and P16H were analyzed using bisulfite/TAB-based assays. A ZFP-based P16-specific dioxygenase (P16-TET) was constructed and used to induce P16H. Cell proliferation and migration were determined with a series of biological analyses.

Results

(A) The 5hmCs were enriched in the antisense-strand of the P16 exon-1 in HCT116 and AGS cells containing methylated-P16 alleles (P16M). (B) P16-TET induced both P16H and P16 demethylation in H1299 and AGS cells and reactivated P16 expression. Notably, P16H was only detectable in the sorted P16-TET H1299 and AGS cells that did not show P16 expression. (C) P16-TET significantly inhibited the xenograft growth derived from H1299 cells in NOD-SCID mice, but did not inhibit the growth of P16-deleted A549 control cells. P16-siRNA knockdown could rescue P16-TET-inhibited cell migration.

Conclusion

Hydroxymethylated P16 alleles are transcriptionally inactive.

AUTHOR SUMMARY

It is well known that 5-methylcytosine (5mC) in genomic DNA of mammalian cells can be oxidized into 5-hydroxymethylcytosine (5hmC) and other derivates by DNA dioxygenase TETs. While conversion of 5mC to 5hmC plays an important role in active DNA demethylation through further oxidations, a certain proportion of 5hmCs remain in the genome. Although it is supposed that occurrence of 5hmCs may contribute to the flexibility of chromatin and the protection of the bivalent promoters from hypermethylation, the direct effect of 5hmCs on gene transcription is unknown. In the present study, we engineered a zinc-finger protein-based P16-specific DNA dioxygenase and used it to induce P16 hydroxymethylation and demethylation in cancer cells. Our results demonstrate, for the first time, that the hydroxymethylated P16 alleles retain transcriptionally inactive. This is supported by our recent findings that mRNAs are always transcribed only from the unmethylated P16 strands, but not from the hydroxymethylated/methylated strands in HCT116 cells, and that the risks for malignant transformation are similar for patients with the P16 methylation-positive oral epithelial dysplasia with and without P16 hydroxymethylation in a prospective study.
Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability
Authors: Emden Thomas van , Forn Marta , Forné Ignasi , Sarkadi Zsuzsa , Capella Matías , Caballero Lucía Martín , Fischer-Burkart Sabine , Brönner Cornelia , Simonetta Marco , Toczyski David , Halic Mario , Imhof Axel , Braun Sigurd
Published: August 2018

Telomeres and the shelterin complex cap and protect the ends of chromosomes. Telomeres are flanked by the subtelomeric sequences that have also been implicated in telomere regulation, although their role is not well defined. Here we show that, in Schizosaccharomyces pombe, the telo-mere-associated sequences (TAS) present on most subtelomeres are hyper-recombinogenic, have metastable nucleosomes, and unusual low levels of H3K9 methylation. Ccq1, a subunit of shelter-in, protects TAS from nucleosome loss by recruiting the heterochromatic repressor complexes CLRC and SHREC, thereby linking nucleosome stability to gene silencing. Nucleosome instability at TAS is independent of telomeric repeats and can be transmitted to an intrachromosomal locus containing an ectopic TAS fragment, indicating that this is an intrinsic property of the underlying DNA sequence. When telomerase recruitment is compromised in cells lacking Ccq1, DNA se-quences present in the TAS promote recombination between chromosomal ends, independent of nucleosome abundance, implying an active function of these sequences in telomere maintenance. We propose that Ccq1 and fragile subtelomeres co-evolved to regulate telomere plasticity by con-trolling nucleosome occupancy and genome stability.
Quantifying Molecular Forces with Serially Connected Force Sensors
Authors: Murad Y. , Li I. T.S.
Published: August 2018

To understand the mechanical forces involved in cell adhesion, molecular force sensors have been developed to study tension through adhesion proteins. Recently, a class of molecular force sensors called tension gauge tether (TGT) have been developed that rely on irreversible force-dependent dissociation of DNA duplex to study cell adhesion forces. While the TGT offer high signal-to-noise ratio and is ideal for studying fast / single molecular adhesion processes, quantitative interpretation of experimental results has been challenging. Here we used computational approach to investigate how TGT fluorescence readout can be quantitatively interpreted. In particular we studied force sensors made of a single TGT, multiplexed single TGTs, and two TGTs connected in series. Our results showed that fluorescence readout using a single TGT can result from drastically different combinations of force history and adhesion event density that span orders of magnitude. In addition, the apparent behaviour of the TGT is influenced by the tethered receptor-ligand, making it necessary to calibrate the TGT with every new receptor-ligand. To solve this problem, we proposed a system of two serially connected TGTs. Our result shows that not only is the ratiometric readout of serial TGT independent of the choice of receptor-ligand, it is able to reconstruct force history with sub-pN force resolution. This is also not possible by simply multiplexing different types of TGTs together. Lastly, we systematically investigated how sequence composition of the two serially connected TGTs can be tuned to achieve different dynamic range. This computational study demonstrated how serially connected irreversible molecular dissociation processes can accurately quantify molecular force, and laid the foundation for subsequent experimental studies.
Impending Regeneration Failure of the Iucn Vulnerable Borneo Ironwood (Eusideroxylon Zwageri)
Authors: Qie Lan , Elsy Alexander D. , Stumvoll Ashley , Kwasnicka Magdalena , Peel Anna L. , Sullivan Joseph A. , Ettinger Maisie S. , Robertson Alasdair J. , Brisbane Jeanelle K. , Sawyer Amber L. , Lui Yan N. , Ow Siew Ngim , Sebastianelli Matteo , Majcher Bartosz , Duan Muying , Vigus Hannah , Pounsin Grace , Nilus Reuben , Ewers Robert
Published: August 2018

The regeneration of many climax species in tropical forest critically depends on adequate seed dispersal and seedling establishment. Here we report the decreased abundance and increased spatial aggregation of younger trees of the Borneo ironwood (Eusideroxylon zwageri) in a protected forest in Sabah Malaysia. We observed a high level of seedling herbivory with strong density dependence, likely exacerbated by local aggregation and contributing to the progressively shrinking size-distribution. We also note the largely undocumented selective herbivory by sambar deer on E.zwageriseedlings. This study highlights the combined impact of altered megafauna community on a tree population through interlinked ecological processes and the need for targeted conservation intervention for this iconic tropical tree species.
Sensory neurons control heritable adaptation to stress through germline reprogramming
Authors: Zuco Giusy , Kache Vikas , Robles Pedro , Chaudhuri Jyotiska , Hill Beth , Bateson Christine , Pires-daSilva Andre
Published: August 2018

Maternal neuronal signaling has been reported to program adaptive changes in offspring physiology in diverse organisms [1, 2]. However, the mechanisms for the inheritance of adaptive maternal effects through the germline are largely unknown. In the nematode Auanema freiburgensis, stress-resistance and sex of the offspring depend on environmental cues experienced by the mother. Maternal sensing of high population densities results in the production of stress-resistant larvae (dauers) that develop into hermaphrodites. Ablation of the maternal ASH chemosensory neurons results only in non-dauer offspring that develop into males or females. High population densities correlate with changes in the methylation status of H3K4 and H3K9 in the maternal germline. Inhibition of JMJD histone demethylases prevents mothers from producing dauers and hermaphrodite offspring in high-density conditions. Our results demonstrate a case of soma-to-germline transmission of environmental information that influences the phenotype of the following generation through changes in histone modifications of the maternal germline.

Highlights

High population density leads to the production of hermaphrodite offspring.

The ASH neuron in the hermaphrodite mother senses population density.

Histone modifications in the maternal germline correlate with the sex of offspring.

Inhibition of histone demethylases results in female offspring in all conditions.
Divergence in the face of gene flow in twoCharadriusplovers along the Chinese coast
Authors: Wang Xuejing , Que Pinjia , Heckel Gerald , Hu Junhua , Zhang Xuecong , Chiang Chung-Yu , Huang Qin , Liu Simin , Martinez Jonathan , Zhang Nan , Pagani-Núñez Emilio , Dingle Caroline , Yan Leung Yu , Székely Tamás , Zhang Zhengwang , Liu Yang
Published: August 2018

Speciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary contacts, e.g. caused by past glaciation cycles or the manifestation of speciation with gene flow, which hampers our understanding of how different forces drive diversification. Here we studied genetic, phenotypic and ecological aspects of divergence in a pair of incipient species, the Kentish (Charadrius alexandrinus) and the white-faced Plovers (C. dealbatus), shorebirds with parapatric breeding ranges along the Chinese coast. We assessed divergence based on molecular markers with different modes of inheritance and quantified phenotypic and ecological divergence in aspects of morphometric, dietary and climatic niches. These analyses revealed small to moderate levels of genetic and phenotypic distinctiveness with symmetric gene flow across the contact area at the Chinese coast. The two species diverged approximately half a million years ago in dynamical isolation and secondary contact due to cycling sea level changes between the Eastern and Southern China Sea in the mid-late Pleistocene. We found evidence of character displacement and ecological niche differentiation between the two species, invoking the role of selection in facilitating divergence despite gene flow. These findings imply that the ecology can indeed counter gene flow through divergent selection and thus contribute to incipient speciation in these plovers. Furthermore, our study highlights the importance of using integrative datasets to reveal the evolutionary history and underlying mechanisms of speciation.