bluuebunny/crossref_metadata_2025 huggingface dataset:
Real-Time Quantitative and Ion-Metal Indicator LAMP-Based Assays for Rapid Detection of Sclerotinia sclerotiorum
Authors: Grabicoski Edilaine Mauricia Gelinski , Jaccoud-Filho David de Souza , Lee David , Henneberg Luciane , Pileggi Marcos
Published: February 2020

Sclerotinia sclerotiorum is one of the most devastating and cosmopolitan plant pathogens. Rapid detection of S. sclerotiorum can provide growers an advantage in knowing what control measures should be taken to minimize crop damage and financial losses caused by it. Loop-mediated isothermal amplification (LAMP) is a fast, sensitive, and specific nucleic acid amplification method that does not require a thermal cycler. This study aimed to develop a LAMP-based assay for the specific detection of S. sclerotiorum (Ss-LAMP). A real-time quantitative LAMP reaction (Ss-qLAMP) and a calcein ion indicator-based LAMP reaction (Ss-cLAMP) were designed, optimized, and tested on fungi, plant, and soil samples. The Ss-LAMP reactions were very specific and sensitive. Applying the artificially inoculated soil samples with DNA purified by five protocols in the Ss-qLAMP reaction, it was possible to detect and quantify the pathogen DNA, regardless of the extraction protocol. Naturally infected soybean tissues had the pathogen detected by Ss-cLAMP directly in the reaction tube with no DNA extraction requirement. The assays should be applicable for many types of samples, such as soil, spore traps, and plant tissues from several crops, with no requirement for DNA extraction. The Ss-LAMP reactions took less than 1 h to complete, and they can be made directly in the field with real-time quantitative results (Ss-qLAMP) or qualitative naked-eye visual results (Ss-cLAMP). Results were obtained with 10 pg of DNA or 10 ng of crude mycelium, suggesting a detection limit close to a single DNA copy. Ss-LAMP reactions will allow rapid and accurate diagnosis of S. sclerotiorum and assist in pathogen management and control.
Molecular markers contribute to the clinical diagnosis for pancreatic cystic neoplasms
Authors: Liu Zhen , Zhang Shu
Published: February 2020

A pancreatic cystic neoplasm (PCN) is a rare pancreatic disease. Malignant PCNs are usually identified incidentally while evaluating other lesions. However, PCNs are being identified more frequently owing to the increased use of abdominal imaging. Malignant PCNs have complicated and diverse biological behaviors, including various malignant risk factors, diverse molecular features, natural history, and complex pathological classifications. Although many diagnostic methods, such as cross-sectional imaging and endoscopic evaluation, have been developed, malignant PCNs are still difficult to differentiate from benign tumors. On searching for related articles in the recent decade, we found that some molecular biomarkers such as carcinoembryonic antigen could be useful for discriminating between malignant tumors and benign tumors. However, cytopathologic evaluation is the most useful method for differentiating between benign and malignant lesions. Although cytopathologic evaluation has a specificity of 100% for identifying malignancies, its accuracy is often hampered by the low cellularity of PCN cells in the cystic fluid. Herein, we review the progress in the use of cellular and molecular markers for the accurate identification of PCNs.
Impact of Age and Genotype on Serum Concentrations of Valproic Acid and Its Hepatotoxic Metabolites in Chinese Pediatric Patients With Epilepsy
Authors: Zhao Mingming , Chen Yanan , Wang Minglu , Li Guofei , Zhao Limei
Published: February 2020

Background:

The aim of the study was to investigate how age and genetic polymorphisms of UGT1A6 and UGT2B7 contribute to the concentrations of valproic acid (VPA) and its hepatotoxic metabolites in Chinese pediatric patients with epilepsy.

Methods:

A total of 122 children with epilepsy were genotyped at 19T>G, 541A>G, and 552A>C in UGT1A6 and -161C>T and 802C>T in UGT2B7 using the polymerase chain reaction-restriction fragment length polymorphism method or direct sequencing method. The concentrations of VPA, 4-ene-VPA, and 2,4-diene-VPA were simultaneously determined using ultra-performance liquid chromatography-tandem mass spectrometry.

Results:

Significant association was observed between the UGT2B7 802C>T genotype and dose-adjusted concentrations of VPA, 4-ene-VPA, and 2,4-diene-VPA. The younger children had increased concentrations of the hepatotoxic metabolites and decreased levels of VPA. The allele status of UGT2B7 802C>T had no influence on the metabolite ratios within age groups, but showed a significant difference among the age groups.

Conclusions:

The present study suggests that UGT2B7 802C>T polymorphism and age are factors affecting the concentrations of dose-adjusted VPA and its metabolites. No genotype-related differences were noted in the metabolite ratios of 4-ene-VPA and 2,4-diene-VPA within age-assigned groups. Therefore, careful administration is particularly necessary for younger patients who are UGT2B7 802C>T poor metabolizers.
Combined Mastopexy and Augmentation with Autologous Fat Grafting: First Results with Lipopexy
Authors: De Fazio Domenico , Cingozoglu Carlos Augusto Cutini
Published: February 2020

Background:

The treatment of breast ptosis and gland hypoplasia in a single surgery is a challenging procedure and the result is less predictable. In this surgery, the complications mainly concern the prosthesis, such as implant deflation, capsular contracture, palpability, or malposition. We, therefore, propose a different and new technique that avoids breast prosthesis, combining mastopexy and autologous augmentation with fat grafts.

Methods:

Combined mastopexy and autologous fat graft augmentation (lipopexy) was performed in women affected by breast ptosis and asymmetric breast or hypomastia. The breast lift technique was determined due to the ptosis level. The process of fat grafting was executed according to the PureGraft and, in some cases, to GID System, to Celution System or Carraway’s techniques.

Results:

Thirty-four patients affected by breast ptosis and hypomastia underwent lipopexy from January 2010 to May 2017. The mean volume of adipose tissue injected for each breast was 225.98 ml. After surgery, the patients were followed for an average of 22.8 months. A mild ptosis relapse with partial fat absorption was observed in 4 cases (11.76%) and the presence of oily cysts was diagnosed in 2 patients (5.88%). One severe complication was recorded (hematoma drainage). All the patients healed uneventfully in 2 weeks.

Conclusions:

This technique allows the surgeon to distribute the desired fat volume along the breasts, avoids implants, and displayed stable results. This treatment has been demonstrated not to interfere with follow-up breast imaging. We, therefore, consider lipopexy a valuable and safe alternative to mastopexy and mild to moderate breast volume augmentation.
Higher Distress in Patients with Breast Cancer Is Associated with Declining Breast Reconstruction
Authors: Corkum Joseph P. , Butler Kate , Zhong Toni
Published: February 2020

Background:

Distress among newly diagnosed patients with breast cancer is common and may have an impact on their surgical decision-making. The revised Edmonton Symptom Assessment System (ESAS-r) is a validated instrument that provides an estimate of patients’ total distress, and no previous study has related preoperative scores to the choice to have breast reconstruction.

Methods:

Women with breast cancer treated at the Princess Margaret Cancer Centre in 2014 were reviewed, and patient and tumor characteristics were collected from local databases. Breast reconstruction status was obtained from patients’ electronic medical records until April 2017. A multivariable logistic regression model assessed for an independent association between preoperative ESAS-r total distress scores and patients’ decision to have breast reconstruction.

Results:

A total of 312 patients were analyzed. ESAS-r values had an overall median score of 10.0 and ranged from 0 to 69 (interquartile range, 17). Of these patients, 82 chose to undergo breast reconstruction surgery (26.8%). Multivariable logistic regression analysis showed that higher ESAS-r scores were associated with patients forgoing breast reconstruction surgery (lumpectomy-alone group: odds ratio estimate, 1.034 [1.004–1.064], P = 0.025; mastectomy-alone group: odds ratio estimate, 1.031 [1.004–1.059], P = 0.023).

Conclusions:

This study of patients with breast cancer found that higher distress scores as measured by the ESAS-r were associated with reduced breast reconstruction. Distress in patients with breast cancer is important to address, as it is often treatable, and its resolution may unmask a desire for breast reconstruction, which has known benefits psychosocially.
A 3-step Mechanical Digestion Method to Harvest Adipose-derived Stromal Vascular Fraction
Authors: Tiryaki Tunc , Condé-Green Alexandra , Cohen Steven R. , Canikyan Serli , Kocak Polen
Published: February 2020

Background:

Adipose stromal vascular fraction (SVF) isolation with enzymatic digestion is the gold standard, but is expensive, having practical and legal concerns. The alternative mechanical SVF isolation methods provide lower cell yields as they employ either centrifugation, emulsification, or digestion steps alone. We combined mechanical processing with buffer incubation and centrifugation steps into an isolation method called “mechanical digestion” and compared the cell yields with that of enzymatic digestion.

Methods:

A total of 40-mL lipoaspirate was harvested from 35 women undergoing liposuction and was submitted to conventional enzymatic digestion for SVF isolation or mechanical digestion using a closed unit harnessing 3 ports with blades, followed by buffer incubation and centrifugation. Culture of the SVFs and flow cytometry were performed.

Results:

The SVF cell yield obtained by enzymatic digestion was significantly higher 3.38 × 106/mL (±3.63; n = 35) than that obtained by mechanical digestion 1.34 × 106/mL (±1.69; n = 35), P = 0.015. The average cell viability was 82.86% ± 10.68 after enzymatic digestion versus 85.86% ± 5.74 after mechanical digestion, which was not significant. Mechanical digested SVF expressed 2-fold higher stem cell surface markers compared with enzymatically digested SVF. Mechanical digestion was less time consuming, cost effective, and did not require a specific laboratory environment.

Conclusions:

Mechanically digested SVF was comparable to enzymatically digested SVF in terms of stromal cell composition and viability. With mechanical digestion, we can isolate 30%–50% SVF cells of that isolated with enzymatic digestion. Further studies are warranted to determine the clinical outcomes.
Absent Internal Mammary Recipient Vein in Autologous Breast Reconstruction
Authors: Muto Mayu , Satake Toshihiko , Masuda Yuma , Kobayashi Saya , Tamura Shihoko , Kobayashi Shinji , Ohtake Tohru , Maegawa Jiro
Published: February 2020

The internal mammary vessels (IMA/Vs) have been used as the first-choice recipient vessels for microsurgical anastomosis and flap inset in autologous breast reconstruction owing to their ease of access and use compared with the thoracodorsal vessels (TDA/Vs). Herein, we report two cases of deep inferior epigastric perforator flap breast reconstructions in which the recipient internal mammary vein (IMV) was lacking. In the first case, a 50-year-old patient underwent delayed two-stage reconstruction, and in the second, a 45-year-old patient underwent delayed reconstruction because of capsular contracture following breast implant reconstruction. Neither patient received preoperative radiation therapy. During IMA/V preparation, we could not find the internal mammary vein (IMV) around the internal mammary artery (IMA) despite careful dissection. No internal mammary lymph node adenopathy and vascular encasement from metastasis were noted. Intraoperative indocyanine green angiography revealed absence of IMV, which was presumed to be congenital. Therefore, microsurgical anastomosis was performed to connect the deep inferior epigastric vessels to the thoracodorsal vessel. The postoperative course was uneventful in both cases. Although many anatomical studies have revealed different locations, diameters, branching patterns, and perforators of the IMA/V, absent IMV has been reported very rarely. In autologous breast reconstruction, plastic surgeons should be prepared for the possibility of the absence of IMV.
Adapting the Ages and Stages Questionnaire to Identify and Quantify Development Among Children With Evidence of Zika Infection
Authors: Attell Jacob E. , Rose Charles , Bertolli Jeanne , Kotzky Kim , Squires Jane , Krishna Nevin K. , Satterfield-Nash Ashley , Peacock Georgina , Ornelas Pereira Isabela , Faria E. Silva Santelli Ana Carolina , Smith Camille
Published: February 2020

This article describes novel methods of applying the Ages and Stages Questionnaire—3rd edition (ASQ-3) to assess and quantify developmental delay among children following the 2015–2016 Zika virus outbreak in Brazil. Many of the children with Zika virus infection were expected to have severe developmental delay. However, administering the ASQ-3 to caregivers of these children according to standard protocol would have screened for the overall presence of delay but not the severity of delay. We adopted an amended protocol for administration of the ASQ-3 to quantify the developmental functioning of children severely affected by Zika virus infection in this investigation. Protocols for administering the ASQ-3 among this population were drafted in consultation with developmental measurement experts and are presented here. Specific developmental estimates are discussed, including developmental age equivalents, developmental quotients, and developmental quotient z scores. The calculations of these estimates are presented with examples in the context of the 2015–2016 Zika virus outbreak and associated microcephaly among prenatally infected children from 2 states in northeastern Brazil. Potential applications of these methods for estimating developmental ability among similar pediatric populations are discussed.
Hyperemesis Gravidarum
Authors: MacGibbon Kimber Wakefield
Published: February 2020

Hyperemesis gravidarum (HG) is a debilitating and potentially life-threatening pregnancy disease marked by weight loss, malnutrition, and dehydration attributed to unrelenting nausea and/or vomiting; HG increases the risk of adverse outcomes for the mother and child(ren). The complexity of HG affects every aspect of a woman's life during and after pregnancy. Without methodical intervention by knowledgeable and proactive clinicians, life-threatening complications may develop. Effectively managing HG requires an understanding of both physical and psychosocial stressors, recognition of potential risks and complications, and proactive assessment and treatment strategies using innovative clinical tools.
Pharmacotherapy in Critically Ill Children: A Retrospective Review of 17,199 Admissions
Authors: Gaetani Melany , Frndova Helena , Seto Winnie , Parshuram Christopher
Published: February 2020

Objectives:

Despite the ubiquitous role of pharmacotherapy in the care of critically ill children, descriptions of the extent of pharmacotherapy in critical illness are limited. Greater understanding of drug therapy can help identify clinically important associations and assist in the prioritization of efforts to address knowledge gaps. The objectives of this study were to describe the diversity, volume, and patterns of pharmacotherapy in critically ill children.

Design:

A retrospective cohort study was performed with patient admissions to the ICU between July 31, 2006, and July 31, 2015.

Setting:

The study took place at a single, free-standing, pediatric, quaternary center.

Patients:

Eligible patient admissions were admitted to the ICU for more than 6 hours and received one or more drug administration. There were a total 17,482 patient-admissions and after exclusion of 283 admissions (2%) with no documented enteral or parenteral drug administration, 17,199 eligible admissions were studied.

Interventions:

None.

Measurements and Main Results:

The 17,199 eligible admissions were admitted to the ICU for 2,208,475 hours and received 515 different drugs. The 1,954,171 administrations were 894,709 (45%) enteral administrations, 998,490 (51%) IV injections and 60,972 (3%) infusions. Infusions were administered for 4,476,538 hours. Twelve-thousand two-hundred seventy-three patients (71%) were administered five or more different drugs on 80,943 of patient days (75%). The 10 most commonly administered drugs comprised of 834,441 administrations (43%).

Conclusions:

Drug administration in the ICU is complex, involves many medications, and the potential for drug interaction and reaction is compounded by the volume and diversity of therapies routinely provided in ICU. Further evaluation of polytherapy could be used to improve outcomes and enhance the safety of pharmacotherapy in critically ill children.
Clinically oriented system-based embryology; a significant course in clinical practice
Authors: Moghadam Samira , Gharebaghi Hamid , Mohamadi Mohamad Javad , Farokhi Ahmad , Ghorbanlou Mehrdad , Arianmanesh Mitra
Published: February 2020

Introduction

Embryology is a branch of medical sciences in developmental biology. Since the knowledge of embryology is of special significance for medical students, this study was conducted with the purpose of elucidating the viewpoint of medical students of Zanjan University of Medical Sciences in Iran on the application of embryology courses in fulfilling clinical purposes.

Methods

This cross-sectional study was conducted in 2018-2019 with a census method on all clinical medical students (trainees and interns). To collect medical students’ opinions, the researcher-designed questionnaire was used. The validity of the questionnaire was confirmed by embryology experts by content validity ratio (CVR) and factor analysis and the reliability of the questionnaire Cronbach’s alpha coefficient (0.9), respectively. Data were analyzed by SPSS (version 24) and Lisrel software. Values with P<0.05 were considered significant.

Results

Descriptive statistics in the field of general and system-based embryology demonstrated that the topics of birth defects and development of body cavities (diaphragm development) have the most influence on clinical practice of medical students.

Conclusions

It seems that more focus on system-based embryology courses leads to a better performance of medical students in clinical courses.
Molecular malaria surveillance using a novel protocol for extraction and analysis of nucleic acids retained on used rapid diagnostic tests
Authors: Guirou Etienne A. , Schindler Tobias , Hosch Salome , Donfack Olivier Tresor , Yoboue Charlene Aya , Krähenbühl Silvan , Deal Anna , Cosi Glenda , Gondwe Linda , Mwangoka Grace , Masuki Heavenlight , Salim Nahya , Mpina Maxmillian , Said Jongo , Abdulla Salim , Hoffman Stephen L. , Nlavo Bonifacio Manguire , Maas Carl , Falla Carlos Cortes , Phiri Wonder P. , Garcia Guillermo A. , Tanner Marcel , Daubenberger Claudia
Published: February 2020

The use of malaria rapid diagnostic tests (RDTs) as a source for nucleic acids that can be analyzed via nucleic acid amplification techniques has several advantages, including minimal amounts of blood, sample collection, simplified storage and shipping conditions at room temperature. We have systematically developed and extensively evaluated a procedure to extract total nucleic acids from used malaria RDTs. The co-extraction of DNA and RNA molecules from small volumes of dried blood retained on the RDTs allows detection and quantification of P. falciparum parasites from asymptomatic patients with parasite densities as low as 1 Pf/µL blood using reverse transcription quantitative PCR. Based on the extraction protocol we have developed the ENAR (Extraction of Nucleic Acids from RDTs) approach; a complete workflow for large-scale molecular malaria surveillance. Using RDTs collected during a malaria indicator survey we demonstrated that ENAR provides a powerful tool to analyze nucleic acids from thousands of RDTs in a standardized and high-throughput manner. We found several, known and new, non-synonymous single nucleotide polymorphisms in the propeller region of the kelch 13 gene among isolates circulating on Bioko Island, Equatorial Guinea.
Tracking and Predicting COVID-19 Epidemic in China Mainland
Authors: Sun Haoxuan , Qiu Yumou , Yan Han , Huang Yaxuan , Zhu Yuru , Chen Song Xi
Published: February 2020

By proposing a varying coefficient Susceptible-Infected-Removal model (vSIR), we track the epidemic of COVID-19 in 30 provinces in China and 15 cities in Hubei province, the epicenter of the outbreak. It is found that the spread of COVID-19 has been significantly slowing down within the two weeks from January 27 to February 10th with 87.0% and 84.3% reductions in the reproduction numberR0among the 30 provinces and 15 Hubei cities, respectively. This suggests the extreme control measures implemented since January 23, which include cutting off Wuhan and many other cities and towns, a great public awareness and high level of self isolation at home, have contributed to a substantial decline in the reproductivity of the COVID-19 in China. We predict that Hubei province will reach its peak between February 20 and 22, 2020, and if the removal rate can be increased to 0.1, the epidemic outside Hubei province will end in May 2020, and inside Hubei in early June.
Clustering of CD3ζ is sufficient to initiate T cell receptor signaling
Authors: Ma Yuanqing , Lim Yean J , Benda Aleš , Goyette Jesse , Gaus Katharina
Published: February 2020

T cell activation is initiated when ligand binding to the T cell receptor (TCR) triggers intracellular phosphorylation of the TCR-CD3 complex. However, it remains unknown how biophysical properties of TCR engagement result in biochemical phosphorylation events. Here, we constructed an optogenetic tool that induces spatial clustering of CD3ζ chains in a light controlled manner. We showed that spatial clustering of the CD3ζ intracellular tail alone was sufficient to initialize T cell triggering including phosphorylation of CD3ζ, Zap70, PLCγ, ERK and initiated Ca2+flux. In reconstituted COS-7 cells, only Lck expression was required to initiate CD3ζ phosphorylation upon CD3ζ clustering, which leads to the recruitment of tandem SH2 domain of Zap70 from cell cytosol to the newly formed CD3ζ clusters at the plasma membrane. Taken together, our data suggest that clustering of the TCR can initialize proximal TCR signaling and thus constitute a biophysical mechanism of TCR triggering.
Spatial maps in piriform cortex during olfactory navigation
Authors: Poo Cindy , Agarwal Gautam , Bonacchi Niccolò , Mainen Zachary
Published: February 2020

Odors are a fundamental part of the sensory environment used by animals to inform behaviors such as foraging and navigation1, 2. Primary olfactory (piriform) cortex is thought to be dedicated to encoding odor identity3–8. Here, using neural ensemble recordings in freely moving rats performing a novel odor-cued spatial choice task, we show that posterior piriform cortex neurons also carry a robust spatial map of the environment. Piriform spatial maps were stable across behavioral contexts independent of olfactory drive or reward availability, and the accuracy of spatial information carried by individual neurons depended on the strength of their functional coupling to the hippocampal theta rhythm. Ensembles of piriform neurons concurrently represented odor identity as well as spatial locations of animals, forming an “olfactory-place map”. Our results reveal a previously unknown function for piriform cortex in spatial cognition and suggest that it is well-suited to form odor-place associations and guide olfactory cued spatial navigation.
Unexpected variability of allelic imbalance estimates from RNA sequencing
Authors: Mendelevich Asia , Vinogradova Svetlana , Gupta Saumya , Mironov Andrey A. , Sunyaev Shamil , Gimelbrant Alexander A.
Published: February 2020

RNA sequencing and other experimental methods that produce large amounts of data are increasingly dominant in molecular biology. However, the noise properties of these techniques have not been fully understood. We assessed the reproducibility of allele-specific expression measurements by conducting replicate sequencing experiments from the same RNA sample. Surprisingly, variation in the estimates of allelic imbalance (AI) between technical replicates was up to 7-fold higher than expected from commonly applied noise models. We show that AI overdispersion varies substantially between replicates and between experimental series, appears to arise during the construction of sequencing libraries, and can be measured by comparing technical replicates. We demonstrate that compensation for AI overdispersion greatly reduces technical variation and enables reliable differential analysis of allele-specific expression across samples and across experiments. Conversely, not taking AI overdispersion into account can lead to a substantial number of false positives in analysis of allele-specific gene expression
Genome editing enables reverse genetics of multicellular development in the choanoflagellateSalpingoeca rosetta
Authors: Booth David S. , King Nicole
Published: February 2020

In a previous study, we established a forward genetic screen to identify genes required for multicellular development in the choanoflagellate,Salpingoeca rosetta(Levin et al., 2014). Yet, the paucity of reverse genetic tools for choanoflagellates has hampered direct tests of gene function and impeded the establishment of choanoflagellates as a model for reconstructing the origin of their closest living relatives, the animals. Here we establish CRISPR/Cas9-mediated genome editing inS. rosettaby engineering a selectable marker to enrich for edited cells. We then use genome editing to disrupt the coding sequence of aS. rosettaC-type lectin gene,rosetteless, and thereby demonstrate its necessity for multicellular rosette development. This work advancesS. rosettaas a model system in which to investigate how genes identified from genetic screens and genomic surveys function in choanoflagellates and evolved as critical regulators of animal biology.
A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology
Authors: Marken John P. , Xiao Fangzhou , Murray Richard M.
Published: February 2020

Much of the progress in developing our ability to successfully design genetic circuits with predictable dynamics has followed the strategy of molding biological systems to fit into conceptual frameworks used in other disciplines, most notably the engineering sciences. Because biological systems have fundamental differences from systems in these other disciplines, this approach is challenging and the insights obtained from such analyses are often not framed in a biologically-intuitive way. Here, we present a new theoretical framework for analyzing the dynamics of genetic circuits that is tailored towards the unique properties associated with biological systems and experiments. Our framework approximates a complex circuit as a set of simpler circuits, which the system can transition between by saturating its various internal components. These approximations are connected to the intrinsic structure of the system, so this representation allows the analysis of dynamics which emerge solely from the system’s structure. Using our framework, we analyze the presence of structural bistability in a leaky autoactivation motif and the presence of structural oscillations in the Repressilator.
The stability and ABA import activity of NRT1.2 inArabidopsisare regulated by CEPR2 via phosphorylation modification
Authors: Zhang Lei , Yu Zipeng , Xu Yang , Yu Miao , Ren Yue , Zhang Shizhong , Yang Guodong , Huang Jinguang , Yan Kang , Zheng Chengchao , Wu Changai
Published: February 2020

Abscisic acid (ABA) transport plays important role in systematic plant responses to environmental factors. Here, we showed that C-terminally encoded peptide receptor 2 (CEPR2) directly interacted with the ABA transporter NRT1.2. Using transgenic seedlings, we demonstrated that NRT1.2 positively regulated the ABA response, and that CEPR2 acted on NRT1.2 epistatically and negatively. Under normal conditions, CEPR2 phosphorylated NRT1.2 at least at serine 292 to promote the degradation of NRT1.2. However, ABA and serine 292 nonphospharylation strongly inhibited the degradation of NRT1.2, indicating that ABA-inhibited the phosphorylation of NRT1.2. Transport assays in yeast andXenopusoocytes showed that nonphosphorylated NRT1.2 had high levels of ABA-import activity, but phosphorylated NRT1.2 did not import ABA. Analyses of complementnrt1.2mutants by mimicking nonphospharylated and phospharylated NRT1.2 confirmed that nonphospharylated NRT1.2S292Ahad high stability and ABA import activityin planta. Further experiments indicated that NRT1.2 was degraded via the 26S proteasome and vacuolar degradation pathways. UBC32, UBC33, and UBC34 interacted with, and mediated the ubiquitination of NRT1.2. UBC32, UBC33, and UBC34 acted on NRT1.2 epistatically and negativelyin planta. Thus, our results suggested the existence of novel plant mechanisms regulating NRT1.2 stability and ABA import activity in response to environmental conditions.
Commonalities and differences in the Oxidative Phosphorylation of Mitochondria and Neuronal Membranes
Authors: Ravera Silvia , Bartolucci Martina , Calzia Daniela , Morelli Alessandro M. , Panfoli Isabella
Published: February 2020

Mitochondria are considered the exclusive site of aerobic metabolism. However, in recent years, the functional expression of the oxidative phosphorylation (OxPhos) machinery has been reported in several other membranous structures, including the plasma membrane, endoplasmic reticulum, nucleus, myelin sheath and disks of rod outer segments. Thus, to underline commonalities and differences between extra-mitochondrial and mitochondrial aerobic metabolism, we characterized the aerobic ATP synthesis in isolated myelin sheath (IM) and rod outer segment (OS) disks, using mitochondria-enriched fractions, as a positive control. Oxygen consumption and ATP synthesis were evaluated in the presence of conventional (pyruvate + malate or succinate) and unconventional (NADH) substrates. ATP synthesis was also assayed in the presence of 10-100 µM ATP in the assay medium. Data show that IM and OS disks consumed oxygen and synthesized ATP both in the presence of conventional and unconventional respiratory substrates, while the mitochondria-enriched fraction did not utilize NADH. Only in mitochondria, ATP synthesis was progressively lost in the presence of increasing ATP concentrations. Conversely, only myelin sheath and rod OS disks produced ATP at a later time or after the removal of respiratory substrates, reflecting their ability to accumulate energy and this opens up exciting perspectives in the study of sleep. Thus, these data suggest that the extramitochondrial OxPhos in IM and rod OS displays a different behavior concerning the classic mitochondrial aerobic metabolism, representing a possible basic molecular process involved in the physiology of the nervous system.

Significance Statement

Mitochondria are considered the cell powerhouse, being the site of the oxidative phosphorylation (OxPhos), which produces the major part of cellular chemical energy by oxygen consumption. However, proteomics, microscopy, and biochemical analyses have described the ectopic functional expression of the OxPhos machinery also in other membranous structures, such as isolated myelin (IM) and rod outer segments (OS). The results reported in this work shows that, although the proteins involved in IM and rod OS OxPhos appear the same expressed in mitochondria, the comparison of mitochondrial and extramitochondrial OxPhos display some differences, opening a new scenario about the energy metabolism modulation.

Graphical Abstract
Estimation of the number of synapses in the hippocampus and brain-wide by volume electron microscopy and genetic labeling
Authors: Santuy Andrea , Tomás-Roca Laura , Rodríguez José-Rodrigo , González-Soriano Juncal , Zhu Fei , Qiu Zhen , Grant Seth GN , DeFelipe Javier , Merchan-Perez Angel
Published: February 2020

Determining the number of synapses that are present in different brain regions is crucial to understand brain connectivity as a whole. Membrane-associated guanylate kinases (MAGUKs) are a family of scaffolding proteins that are expressed in excitatory glutamatergic synapses. We used genetic labeling of two of these proteins (PSD95 and SAP102), and Spinning Disc confocal Microscopy (SDM), to estimate the number of fluorescent puncta in the CA1 area of the hippocampus. We also used FIB-SEM, a three-dimensional electron microscopy technique, to calculate the actual numbers of synapses in the same area. We then estimated the ratio between the three-dimensional densities obtained with FIB-SEM (synapses/μm3) and the bi-dimensional densities obtained with SDM (puncta/100 μm2). Given that it is impractical to use FIB-SEM brain-wide, we used previously available SDM data from other brain regions and we applied this ratio as a conversion factor to estimate the minimum density of synapses in those regions. We found the highest densities of synapses in the isocortex, olfactory areas, hippocampal formation and cortical subplate. Low densities were found in the pallidum, hypothalamus, brainstem and cerebellum. Finally, the striatum and thalamus showed a wide range of synapse densities.
Modality-specific dysfunctional neural processing of social-abstract and non-social-concrete information in schizophrenia
Authors: He Yifei , Steines Miriam , Sammer Gebhard , Nagels Arne , Kircher Tilo , Straube Benjamin
Published: February 2020

Schizophrenia is characterized by marked communication dysfunctions encompassing potential impairments in the processing of social-abstract and non-social-concrete information, especially in everyday situations where multiple modalities are present in the form of speech and gesture. To date, the neurobiological basis of these deficits remains elusive. In a functional magnetic resonance imaging (fMRI) study, 17 patients with schizophrenia or schizoaffective disorder, and 18 matched controls watched videos of an actor speaking, gesturing (unimodal), and both speaking and gesturing (bimodal) about social or non-social events in a naturalistic way. Participants were asked to judge whether each video contains person-related (social) or object-related (non-social) information. When processing social-abstract content, patients showed reduced activation in the medial prefrontal cortex (mPFC) only in the gesture but not in the speech condition. For non-social-concrete content, remarkably, reduced neural activation for patients in the left postcentral gyrus and the right insula was observed only in the speech condition. Moreover, in the bimodal conditions, patients displayed improved task performance and comparable activation to controls in both social and non-social content. To conclude, patients with schizophrenia displayed modality-specific aberrant neural processing of social and non-social information, which is not present for the bimodal conditions. This finding provides novel insights into dysfunctional multimodal communication in schizophrenia, and may have potential therapeutic implications.
Non-human primates satisfy utility maximization in compliance with the continuity axiom of Expected Utility Theory
Authors: Ferrari-Toniolo Simone , Bujold Philipe M. , Grabenhorst Fabian , Báez-Mendoza Raymundo , Schultz Wolfram
Published: February 2020

Expected Utility Theory (EUT), the first axiomatic theory of risky choice, describes choices as a utility maximization process: decision makers assign a subjective value (utility) to each choice option and choose the one with the highest utility. The continuity axiom, central to EUT and its modifications, is a necessary and sufficient condition for the definition of numerical utilities. The axiom requires decision makers to be indifferent between a gamble and a specific probabilistic combination of a more preferred and a less preferred gamble. While previous studies demonstrated that monkeys choose according to combinations of objective reward magnitude and probability, a concept-driven experimental approach for assessing the axiomatically defined conditions for maximizing subjective utility by animals is missing. We experimentally tested the continuity axiom for a broad class of gamble types in four male rhesus macaque monkeys, showing that their choice behavior complied with the existence of a numerical utility measure as defined by the economic theory. We used the numerical quantity specified in the continuity axiom to characterize subjective preferences in a magnitude-probability space. This mapping highlighted a trade-off relation between reward magnitudes and probabilities, compatible with the existence of a utility function underlying subjective value computation. These results support the existence of a numerical utility function able to describe choices, allowing for the investigation of the neuronal substrates responsible for coding such rigorously defined quantity.

SIGNIFICANCE STATEMENT

A common assumption of several economic choice theories is that decisions result from the comparison of subjectively assigned values (utilities). This study demonstrated the compliance of monkey behavior with the continuity axiom of Expected Utility Theory, implying a subjective magnitude-probability trade-off relation which supports the existence of numerical subjective utility directly linked to the theoretical economic framework. We determined a numerical utility measure able to describe choices, which can serve as a correlate for the neuronal activity in the quest for brain structures and mechanisms guiding decisions.
An unbiased drug screen for seizure suppressors in Dup15q syndrome reveals 5HT1Aand dopamine pathway activation as potential therapies
Authors: Roy Bidisha , Han Jungsoo , Hope Kevin A. , Peters Tracy L. , Palmer Glen , Reiter Lawrence T.
Published: February 2020

Duplication 15q syndrome (Dup15q) is a rare neurogenetic disorder characterized by autistic features and difficult to control (pharmacoresistant) epileptic seizures. Most individuals with isodicentric (idic15) have been on multiple medications to control their seizures and some are still seizing after years of treatment. We recently developed a model of Dup15q in Drosophila by elevating levels of fly Dube3a in glial cells, not neurons. Unlike other Dup15q models, these flies develop seizures that worsen as flies age. Here we used this new model to screen for previously approved compounds from the Prestwick Chemical Library which are able to suppress seizures in flies over-expressing Dube3a in glia using the pan glial driverrepo-GAL4. We identified 17 out of 1280 compounds in the library that could suppress a bang sensitive (seizure) phenotype. Eight of these compounds were able to suppress seizures significantly in both males and females by at least 50%. Half of these strong seizure suppressors regulated either serotoninergic or dopaminergic signaling and subsequent experiments confirmed that seizure suppression occurs through stimulation of serotonin receptor 5-HT1Abut can be further suppressed with the addition of L-Dopa (Levodopa). We provide further support for a seizure model where Dube3a regulation of the Na+/K+ exchanger ATPα in glia can also be modulated by serotonin/dopamine signaling. Finally, based on these pharmacological and genetic studies, we present an argument for the use of 5-HT1Aagonists in the treatment of Dup15q epilepsy.
SEEKING CANDIDATE MOLECULES AS PROGNOSTIC HEALING MARKERS IN CHRONIC VENOUS ULCERS
Authors: Cavassan Nayara Rodrigues Vieira , Mariani Noemia Aparecida Partelli , Camargo Caio Cavassan , Wolf Ivan Rodrigo , Barraviera Benedito , Ferreira Rui Seabra , Valente Guilherme Targino , Silva Erick José Ramos , Miot Hélio Amante , Abbade Luciana Patrícia Fernandes , dos Santos Lucilene Delazari
Published: February 2020

Seeking and identifying biomarker molecules in inflammatory exudate of chronic venous ulcers (CVUs) can aid health professionals in the healing prognosis. The therapeutic failure or cure is related to the quantitative expression of determinate proteins. This work aimed to identify the proteins expressed in inflammatory exudates from CVUs and correlate them with reduction or increase in the wound size. For 90 days, 28 participants that received standard treatment for 37 CVUs were monitored. The inflammatory exudates were collected before treatment initiation (T=0) and analyzed via the Label-free Shotgun. After 90 days the wound area was reduced in 25 (67.6%) of them. Mass spectrometry analysis of all the inflammatory exudates showed four proteins differentially expressed and related to favorable or unfavorable evolution of the healing process. Complement C3 and ceruloplasmin were identified in all the lesions analyzed and were expressed differentially in lesions that presented diminished area in the studied period. Apoliprotein A1 and neutrophil defensin-1 presented differential expression in ulcers that either did not diminish or augmented their wound area through 90 days. These results suggest that Complement C3, Ceruloplasmin, Apoliprotein A1 and Neutrophil-defensin-1 proteins are potential candidate molecules for prognostic healing markers in chronic venous ulcers.
CRISPR-based Live Imaging of Epigenetic Modification-Mediated Genome Reorganization
Authors: Feng Ying , Wang Yao , Yang Chen , Naseri Ardalan , Pederson Thoru , Zheng Jing , Xiao Xiao , Zhang Shaojie , Xie Wei , Ma Hanhui
Published: February 2020

Epigenetic modifications play an essential role in chromatin architecture and dynamics. The role of epigenetic modification in chromatin organization has been studied by Hi-C from population cells, but imaging techniques to study their correlation and regulation in single living cells are lacking. Here we develop a CRISPR-based EpiGo (Epigenetic perturbation induced Genome organization) system to track epigenetic modification-mediated relocation, interaction or reorganization of genomic regions in living cells. EpiGo-KRAB is sufficient to induce the relocation of genomic loci to HP1α condensates and trigger genomic interactions. EpiGo-KRAB also triggers the induction of H3K9me3 at large genomic regions, which decorate on the surface of HP1α condensates possibly driven by phase separation.
Response to Tavares et al., “Covariation analysis with improved parameters reveals conservation in lncRNA structures”
Authors: Rivas Elena , Eddy Sean R.
Published: February 2020

Tavares’ conclusions depend on an assumption that the statistic they use (RAFS) is an appropriate measure of RNA base pair covariation, but RAFS was not designed to measure covariation alone. RAFS detects positive signals in common patterns of primary sequence conservation in absence of any covariation. To illustrate the severity of the problem, we show that Tavares’ analysis reports “significantly covarying base pairs” in 100% identical sequence alignments with no variation or covariation. We use Tavares’ sequence alignment of HOTAIR domain 1 as an example to show that the base pairs they identify as significantly covarying actually arise from primary sequence conservation patterns. Their analysis still reports similar numbers of “significant covarying” base pairs in a negative control in which we permute residues in independent alignment columns to destroy covariation. There remains no significant covariation support for evolutionarily conserved RNA structure in the HOTAIR lncRNA or other lncRNA structures and alignments we have analyzed.
Generative modeling of brain maps with spatial autocorrelation
Authors: Burt Joshua B. , Helmer Markus , Shinn Maxwell , Anticevic Alan , Murray John D.
Published: February 2020

Studies of large-scale brain organization have revealed interesting relationships between spatial gradients in brain maps across multiple modalities. Evaluating the significance of these findings requires establishing statistical expectations under a null hypothesis of interest. Through generative modeling of synthetic data that instantiate a specific null hypothesis, quantitative benchmarks can be derived for arbitrarily complex statistical measures. Here, we present a generative null model, provided as an open-access software platform, that generates surrogate maps with spatial autocorrelation (SA) matched to SA of a target brain map. SA is a prominent and ubiquitous property of brain maps that violates assumptions of independence in conventional statistical tests. Our method can simulate surrogate brain maps, constrained by empirical data, that preserve the SA of cortical, subcortical, parcellated, and dense brain maps. We characterize how SA impactsp-values in pairwise brain map comparisons. Furthermore, we demonstrate how SA-preserving surrogate maps can be used in gene ontology enrichment analyses to test hypotheses of interest related to brain map topography. Our findings demonstrate the utility of SA-preserving surrogate maps for hypothesis testing in complex statistical analyses, and underscore the need to disambiguate meaningful relationships from chance associations in studies of large-scale brain organization.
Structure and immune recognition of the porcine epidemic diarrhea virus spike protein
Authors: Kirchdoerfer Robert N. , Bhandari Mahesh , Martini Olnita , Sewall Leigh M. , Bangaru Sandhya , Yoon Kyoung-Jin , Ward Andrew B.
Published: February 2020

Porcine epidemic diarrhea virus is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides new insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.
μ-Lat: A Mouse Model to Evaluate Human Immunodeficiency Virus Eradication Strategies
Authors: Sperber Hannah S. , Togarrati Padma Priya , Raymond Kyle A. , Bouzidi Mohamed S. , Gilfanova Renata , Gutierrez Alan G. , Muench Marcus O. , Pillai Satish K.
Published: February 2020

A critical barrier to the development of a human immunodeficiency virus (HIV) cure is the lack of a scalable animal model that enables robust evaluation of eradication approaches prior to testing in humans. We established a humanized mouse model of latent HIV infection by transplanting “J-Lat” cells, Jurkat cells harboring a latent HIV provirus encoding an enhanced green fluorescent protein (GFP) reporter, into irradiated adult NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice. J-Lat cells exhibited successful engraftment in several tissues including spleen, bone barrow, peripheral blood, and lung, in line with the diverse natural tissue tropism of HIV. Administration of tumor necrosis factor (TNF)-α, an established HIV latency reversal agent, significantly induced GFP expression in engrafted cells across tissues, reflecting viral reactivation. These data suggest that our murine latency (“μ-Lat”) model enables efficient determination of how effectively viral eradication agents, including latency reversal agents, penetrate and function in diverse anatomical sites harboring HIVin vivo.