bluuebunny/crossref_metadata_2025 huggingface dataset:
The Nature of the Intramembrane Particle
Authors: Verkleij A.J.
Published: June 2020

Freeze-fracturing splits membranes into two helves, thus allowing an
examination of the membrane interior. The 5-10 rm particles visible on both
monolayers are widely assumed to be proteinaceous in nature.

Most membranes do not reveal impressions complementary to particles on
the opposite fracture face, if the membranes are fractured under conditions
without etching. Even if it is considered that shadowing, contamination or
fracturing itself might obscure complementary pits', there is no
satisfactory explanation why under similar physical circimstances matching
halves of other membranes can be visualized. A prominent example of
uncomplementarity is found in the erythrocyte manbrane. It is wall
established that band 3 protein and possibly glycophorin represents these
nonccmplanentary particles. On the other hand a number of membrane types
show pits opposite the particles. Scme well known examples are the ";gap
junction',"; tight junction, the luminal membrane of the bladder epithelial
cells and the outer membrane of Escherichia coli.
Ultrastructure of Granular Cell Tumors of The Human Breast
Authors: Mossier J.A. , Brinkhous A. D. , Ferguson B.J. , Woodard B.H. , Georgiade N. , McCarty K.S. , McCarty K.S.
Published: June 2020

Granular cell tumors are well recognized but poorly understood entities
which occur in a wide variety of visceral and cutaneous sites. These tumors
have been suggested by several investigators to possibly represent neoplasms
or degenerations of muscle, or to be of histiocytic, fibroblastic, or
neurogenic origin.1 Approximately six percent of
granular cell tumors occur in the breast. These tumors are almost invariably
benign but may clinically simulate carcinoma with fixation to muscle and
irregular margins.2 The ultrastructure of three
granular cell tumors of the breast was studied and compared to the
ultrastructure of a lesion observed in an axillary lymph node of a fourth
case. Tissues were fixed in 4% glutaraldehyde, 0.1M cacodylate (pH 7.4) at
20°C, and post-fixed in 2% osmium tetroxide, 0.1M cacodylate (pH 7.0) at
4°C. Tissue was also analyzed for sex steroid receptor by DCCA and SDGA.
Similar fine structure was observed in each case, closely resembling the
findings of granular cell tumors in extramammary
sites.3 In many cells the cytoplasm was filled with
numerous irregular arrays of fine fibrils visible in longitudinal, oblique,
and transverse section in a given cell. Large numbers of cytoplasmic
vesicles of diverse size were present. Some vesicles were membrane limited,
but in others, delimiting membranes were not visible. Many vesicles called
angular bodies had substructure appearing as focal condensations of
cytoplasmic fibrils. Numerous multivesicular bodies with enclosed vacuoles,
solid core particles, and mitochondria in all stages of degeneration were
observed.
Phagocytosis by Hairy Cells as Demonstrated by Serial Sectioning Techniques
Authors: Rosner M. C. , Golomb H. M.
Published: June 2020

Leukemic reticuloendotheliosis or Hairy Cell Leukemia was first described in 1958. The hairy cells have been described as being modified monocytes, B-lymphocytes, B-lymphocytes with phagocytic capacities, or T-lymphocytes. Hairy cells have also been shown to have the ability to ingest foreign particles, a function usually associated with monocytes1. In addition to providing clues to the origin of the disease, phagocytosis has been cited as being useful in providing early identification of potential infectious complications in patients afflicted with the disease. A recent study by Jansen et al2suggested that the particles observed within the cytoplasm of the cell were not ingested but merely entrapped between the cytoplasmic projections of the hairy cell. Our present study was designed to use serial sectioning techniques and electron microscopy evaluations to determine the exact nature of phagocytosis by hairy cells of polystyrene latex and Staphylococcus aureus particles after three hours of incubation.
Rapid Freezing of Freeze-Etch Specimens
Authors: Elgsaeter A. , Espevik T. , Kopstad G.
Published: June 2020

The importance of a high rate of temperature decrease (“rapid freezing”)
when freezing specimens for freeze-etching has long been
recognized1. The two basic methods for achieving
rapid freezing are: 1) dropping the specimen onto a metal surface at low
temperature, 2) bringing the specimen instantaneously into thermal contact
with a liquid at low temperature and subsequently maintaining a high
relative velocity between the liquid and the specimen. Over the last couple
of years the first method has received strong renewed interest,
particularily as the result of a series of important studies by Heuser and
coworkers 2,3. In this paper we will compare these two freezing methods
theoretically and experimentally.
Cephaleuros Zoospores and Reversed Bilateral Symmetry in Green
Algae
Authors: Chapman Russell L. , Henk Margaret C.
Published: June 2020

Transmission electron microscope studies of the quadriflagellate
zoospores of the parasitic, subaerial green alga Cephaleuros virescens Kunze
have provided a basis for comparison between these motile cells and
biflagellate gametes previously examined.1 As seen in
cross-section (Fig. 1), the four basal bodies form a trapezoid in which the
two upper basal bodies are closer together than the two lower basal bodies.
The basal bodies are parallel, overlapping, and interdigitated. Two flagella
are inserted into either side of the apical papilla and terminate in
diagonally opposed basal bodies. The bilaterally keeled flagella (Fig. 2)
are often closely appressed thereby creating a biflagellate appearance. Each
of the four basal bodies is associated with a microtubular spline which
extends posteriorly beneath the plasmalemma. A densely stained flagellar cap
is present at the end of each basal body and together with the terminal
region of its spline, forms a multilayered structure (MLS). Although the
MLSs associated with the two lower basal bodies (Fig. 3) are virtually
identical to those found in the gametes, those associated with the upper
basal bodies are morphologically different or positioned in such a manner
that “typical” sectional views cannot be obtained. The observations reveal
that although minor differences exist, the zoospores of Cephaleuros are
similar to those of Phycopeltis,2 a related
genus.
Intracytoplasmic Desmosomes in Trypsinized Keratinocytes
Authors: Harven Etienne de , Lee Jisoo , Eisinger Magdalena
Published: June 2020

Human epithelial cells, separated from dermal elements by extended
trypsinization, grow and differentiate in vitro in the absence of dermal
components or medium supplements (Eisinger M et al. , Proc. Natl. Acad. Sci.
USA 76:5340-5344, 1979). These observations prompted us to study the fine
structure of isolated keratinocytes (human and canine) in an attempt to
better understand the potential of these cells for in vitro growth and
differentiation, with special attention to the assembly and fate of
desmosomes.
Electron Microscopic Studies of Microprojections on Aging Cells and
Tissues
Authors: Johnson J. E.
Published: June 2020

Microprojections, and specifically, microvilli, are present on many cell
types. The cells which have them are often involved in either secretion or
absorption In 1975 Bowman and Daniel1 reported that
increased numbers of microvilli were present on WI-38 human fibroblasts in
vitro at higher population doubling levels. A new cell strain, IMR-90 was
recently developed to supplement the depleting supplies of WI-38. We wished
to determine if increased numbers of microvilli were to be found on aging
cells in general and began by examining the IMR-90. Indeed, this cell strain
was also found to show higher indices with increased population doubling
levels2 .
Whole Mount Observation of Cultured Cells
Authors: Hama K.
Published: June 2020

The cellular architecture of cultured cells has been investigated on critical-point dried whole mount preparations with the aid of stereo-high voltage electron microscopy2,4,5. In these preparations, the absence of an embedding material permits an stereoobservation at rather low accelerating voltage1,3. In the present study, whole mount preparations of cultured chick fibroblasts were examined in the electron microscope operated at 100 KV, 200 KV, 500 KV, 750 KV and 1,000 KV to investigate the voltage dependency of the usable specimen thickness and of the image quality at different specimen thickness.
Structural Organization of Detergent-Extracted Cells
Authors: Schliwa Manfred
Published: June 2020

Adequate visualization of the three-dimensional organization has always
been a major problem in studies of cell architecture. Efforts of numerous
investigators weredevoted to the question of how best information can be
collected from specimens prepared with different procedures. In recent
years, the potential of high voltage electron microscopy has been combined
with a technique for sample preparation that circumvents embedding, namely
critical point-drying from CO2, to study the
three-dimensional fine structure of cells in culture. This approach has
revealed new insights into the structural organization of the cytoplasm
(1-4). A system of slender strands or microtrabeculae has been described to
form an elaborate three-dimensional lattice in which other organelles are
embedded. This system has been shown in some cells to undergo rapid
conformational changes (3,5) and in general is believed to be an important
component of the cytoskeleton, being responsible for the gelatious
properties of the cytoplasm.
Observation of Wet Specimens Using a Modified Cambridge Mark II
SEM
Authors: Neal Richard J. , Mills Addison
Published: June 2020

It has become possible in recent years to observe hydrated specimens in
the presence of water in the SEM. Since the advent of the wet cell in 1960
by Thornley1, followed by Lane's work to develop the
environmental cell in 19702, and culminating in the
extensive advances made by Robinson throughout the
1970's3, the development of a method to observe wet
specimens in a SEM while maintaining good image quality and high resolution
capabilities has become a reality. A Cambridge Mark II Stereo-scan SEM has
likewise been modified to study hydrated systems. The modifications made to
the Mark II to allow it to be used as an environmental scanning electron
microscope (ESEM) follow.

A new specimen stage was fabricated and substituted for the Mark II
specimen stage. This new stage has a reservoir for holding 2-3 ml of water,
and is capable of controlled cooling to below O°C Cooling is accomplished by
flowing cold ethanol through this specimen stage.

A separate mechanical rotary pump was used to evacuate the specimen
chamber and the pressure was monitored using a U-tube mercury
manometer.
Applications of Electron Energy Loss Spectroscopy in Materials
Science
Authors: Krivanek Ondrej L.
Published: June 2020

The electron energy loss spectrometer developed at Berkeley differs from
most other ones in four ways: 1) it uses the projector lens crossover as the
spectrometer entrance object plane, 2) its magnet is asymmetric so that the
entrance object is de-magnified about 5x, 3) it counts electrons admitted
through the energy-selecting slit singly at rates up to 20MHz while adding
zero dark count, and 4) it fits neatly at the back of the available leg
space of the electron microscope, and requires no substantial alterations to
the microscope.

The energy resolution attainable routinely at any primary voltage is 3eV
over an energy loss range 0 to 1keV, as illustrated by resolving the π*
transition on the K-edge of amorphous carbon (Fig. 1). The 3 eV limit comes
mainly from 120Hz stray magnetic fields (the 60Hz component has been
compensated out). Fast scanning of the spectrum improves the resolution to
1eV (Fig. 2). This indicates that with proper magnetic shielding of the
electron flight path, especially in the microscope viewing chamber which is
made out of brass, the energy resolution attainable with the spectrometer
will be limited only by the energy spread of the primary beam.
Experimental investigation of beam-steering applied to 2 × 2 MIMO system with single receiving RF chain and time-modulated antenna array
Authors: Bogdan Grzegorz , Godziszewski Konrad , Yashchyshyn Yevhen
Published: June 2020

Multiple antennas and multiple radio frequency (RF) chains in both the transmitter and receiver are required in conventional radio systems employing the multiple-input multiple-output (MIMO) method. This paper presents an experimental investigation of a beam-steering time-modulated MIMO receiver with a single RF chain. Implementation of the receiver is based on a time-modulated antenna array (TMAA) and a software-defined radio. The sidebands generated inherently by the TMAA are utilized as virtual spatial channels with the beam-steering functionality. Performance of the system is investigated experimentally. The bit error rate and condition number of the channel matrix are examined for different radiation patterns in order to determine favorable configurations in a given multipath environment. Obtained results show a considerable impact of the beam-steering on the performance of MIMO transmission.
An Examination of the Spanish Translation of the 50-item International Personality Item Pool Big-five Inventory in a Spanish Speaking Peruvian Sample
Authors: Hughes David J. , de Olazabal Daniel Pizarro , Kratsiotis Ioannis K. , Twumasi Ricardo , Booth Tom
Published: June 2020

The International Personality Item Pool (IPIP) five-factor model inventories are widely used for personality research and have been translated into multiple languages. However, the extent of the psychometric assessment of translated scales is variable, often minimal. The lack of psychometric scrutiny is particularly problematic because translation is an inherently complex process. Here, we present a structural analysis of one Spanish translation of the 50-item IPIP five-factor inventory in a sample of Peruvian, non-university educated, working adults (n = 778). A global confirmatory factor analytic (CFA) model of the a priori five factors failed to fit. So too did single factor models for four of the five factors, the exception being Neuroticism. Fit was improved via use of an exploratory structural equation measurement model, but the resultant solution showed very poor theoretical coherence. So, we explored the data for systematic measurement artefacts and sought to model them to improve the psychometric properties of the scale. Specifically, the pattern of factor loadings suggested that the lack of coherence might be due to the effects of the valence of item wording (i.e., positively or negatively worded items). CFA models including five substantive factors and a series of method factors modelling shared covariance based on item wording, improved fit and coherence. This investigation suggests that unless method factors are explicitly modelled the tested Spanish translation may not be suitable for use in certain Spanish-speaking countries or samples composed of non-university educated participants. More broadly, the study has implications for many translated scales, especially when used without thorough psychometric evaluation.
Identifying Perceptual, Motor, and Cognitive Components Contributing to Slowness of Information Processing in Multiple Sclerosis with and without Depressive Symptoms
Authors: Lubrini Genny , Periáñez José A. , Fernández-Fournier Mireya , Tallón Barranco Antonio , Díez-Tejedor Exuperio , Frank García Ana , Ríos-Lago Marcos
Published: June 2020

Increasing findings suggest that different components of the stimulus-response pathway (perceptual, motor or cognitive) may account for slowed performance in Multiple Sclerosis (MS). It has also been reported that depressive symptoms (DS) exacerbate slowness in MS. However, no prior studies have explored the independent and joint impact of MS and DS on each of these components in a comprehensive manner. The objective of this work was to identify perceptual, motor, and cognitive components contributing to slowness in MS patients with and without DS. The study includes 33 Relapsing-Remitting MS patients with DS, 33 without DS, and 26 healthy controls. Five information processing components were isolated by means of ANCOVA analyses applied to five Reaction Time tasks. Perceptual, motor, and visual search components were slowed down in MS, as revealed by ANCOVA comparisons between patients without DS, and controls. Moreover, the compounding effect of MS and DS exacerbated deficits in the motor component, and slowed down the decisional component, as revealed by ANCOVA comparisons between patients with and without DS. DS seem to exacerbate slowness caused by MS in specific processing components. Identifying the effects of having MS and of having both MS and DS may have relevant implications when targeting cognitive and mood interventions.
VIPIR and 50 MHz Radar Studies of Gravity Wave Signatures in 150‐km Echoes Observed at Jicamarca
Authors: Reyes Pablo M. , Kudeki Erhan , Lehmacher Gerald A. , Chau Jorge L. , Milla Marco A.
Published: June 2020

Range‐time‐intensity (RTI) plots of 50 MHz radar backscatter detected at Jicamarca from the 150‐km region of the equatorial ionosphere exhibit necklace‐shaped multilayered structures first reported by Kudeki and Fawcett (1993, https://doi.org/10.1029/93GL01256). The backscatter layers also exhibit quasi‐periodic intensity fluctuations with periods of about 5–15 min and are separated from adjacent layers by thin and undulating regions of no detectible power returns. A study of the fluctuating backscatter layers and undulating gap regions will be presented using VIPIR ionosonde data taken at the Jicamarca Radio Observatory simultaneously with high‐resolution 50‐MHz radar backscatter data. VIPIR virtual reflection height variations in time are noted to match the RTI gap‐region undulations very closely at selected VIPIR frequencies (or, equivalently, electron densities at reflection heights). This matching enables assigning “true heights” to VIPIR virtual height contour maps, and a joint study of the contour maps with the 50‐MHz radar RTI maps strongly suggests that correlated fluctuations and undulations observed in VIPIR and 50‐MHz radar data are indicative of gravity wave‐induced variations in the 150‐km region ionosphere. Accordingly, a complete explanation of the 150‐km echo phenomenon will need to include gravity wave coupling and forcing effects in the enhancement and suppression processes that can account for the observed fluctuations and gap‐region features of necklace‐shaped 150‐km echo maps.
Influences of Polydisperse Sea Spray Size Distributions on Model Predictions of Air‐Sea Heat Fluxes
Authors: Peng Tianze , Richter David
Published: June 2020

Quantifying the influence of sea spray on air‐sea fluxes under high‐wind conditions is challenging due to a variety of factors. Among existing models, the so‐called bulk air‐sea flux model is commonly used in meteorological applications due to its simplicity, which often involves strong but untested assumptions on spray‐mediated heat fluxes and feedback effects. For example, a common assumption is to treat each droplet size as an independent contribution; that is, it does not interact with other sizes. Thus, the interactions between different size classes of spray are often neglected. In this study, we focus on the polydispersity of the spray size distribution and investigate the appropriateness of assuming an independent contribution from different spray size classes. We implement direct numerical simulations (DNS) with Lagrangian tracking of spray droplets. Based on DNS results, the bulk spray model fails to capture the interactions between different sizes that are observed directly from the droplet and feedback statistics in DNS. Thus, assuming independent contributions from spray droplets results in significant overestimates on the total heat fluxes. We further test different representative sizes of a spray size distribution. We find that the volume‐weighted representative size is capable of predicting the droplet‐modified temperature and humidity fields and generally captures the vertical profiles of spray‐mediated and interfacial heat fluxes. The results indicate that the computation of spray‐mediated fluxes can be simplified in large‐scale parameterizations.
Development of a Data Assimilation Method Using Vibration Equation for Large‐Eddy Simulations of Turbulent Boundary Layer Flows
Authors: Nakayama Hiromasa , Takemi Tetsuya
Published: June 2020

In order to improve the simulation accuracy, it is effective to use a data assimilation technique which is capable of reproducing more realistic simulated states by incorporating observational data into simulation models. One of the simplest ones among data assimilation techniques is a Newtonian relaxation‐type nudging method which has been widely used in mesoscale meteorological models. In this study, we proposed a data assimilation method using a vibration equation which can incorporate turbulence winds toward target mean winds while maintaining small‐scale turbulent fluctuations as a different approach from the conventional nudging method. First, we conducted test simulations in which nudging is applied in a basic turbulent boundary layer (TBL) flow toward a target one. It is shown that the basic TBL flow can be reasonably nudged toward the target one while maintaining the turbulent fluctuations well when prescribing the natural frequency in the vibration equation smaller than the spectral peak frequency in the TBL flow. Then, we applied the proposed nudging method by incorporating data obtained from meteorological observations located in the actual city of Kyoto. The mean wind velocity profiles were reasonably nudged toward the target observed profile and the turbulence statistics were also favorably maintained. It is concluded that the data assimilation method using the vibration equation successfully nudges toward the target mean winds while maintaining small‐scale turbulent fluctuations well.
Focusing of Fast Magnetosonic Waves in the Dayside Magnetosphere
Authors: Leonovich A. S. , Kozlov D. A.
Published: June 2020

The spatial structure of ultra‐low‐frequency (ULF) fast magnetosonic (FMS) waves is calculated in the dayside magnetosphere. A balanced model is developed of a dipole magnetosphere with a plasma rotating in the azimuthal direction. The magnetopause is in the form of a smooth transition layer. It is shown that the largest‐scale FMS eigen harmonics are either weakly unstable or neutrally stable. The calculations show that the eigen oscillation amplitudes increase greatly from the magnetopause into the magnetosphere. Presumably, the dayside magnetosphere plays the role of a sort of focusing lens for ULF FMS waves. Hence, one can expect a significant increase in the magnetosonic oscillation amplitudes in the inner part of the magnetosphere when the FMS oscillations (determining the magnetopause eigen oscillation amplitudes) are amplified in the magnetosheath.
Immunoglobulin gene analysis in chronic lymphocytic leukemia in the era of next generation sequencing
Authors: Davi Frédéric , Langerak Anton W. , de Septenville Anne Langlois , Kolijn P. Martijn , Hengeveld Paul J. , Chatzidimitriou Anastasia , Bonfiglio Silvia , Sutton Lesley-Ann , Rosenquist Richard , Ghia Paolo , Stamatopoulos Kostas ,   on behalf of ERIC, the European Research Initiative on CLL, and the EuroClonality-NGS Working Group
Published: June 2020

Twenty years after landmark publications, there is a consensus that the somatic hypermutation (SHM) status of the clonotypic immunoglobulin heavy variable (IGHV) gene is an important cornerstone for accurate risk stratification and therapeutic decision-making in patients with chronic lymphocytic leukemia (CLL). The IGHV SHM status has traditionally been determined by conventional Sanger sequencing. However, NGS has heralded a new era in medical diagnostics and immunogenetic analysis is following this trend. There is indeed a growing demand for shifting practice and using NGS for IGHV gene SHM assessment, although it is debatable whether it is always justifiable, at least taking into account financial considerations for laboratories with limited resources. Nevertheless, as this analysis impacts on treatment decisions, standardization of both technical aspects, and data interpretation becomes essential. Also, the need for establishing new recommendations and providing dedicated education and training on NGS-based immunogenetics is greater than ever before. Here we address potential and challenges of NGS-based immunogenetics in CLL. We are convinced that this perspective helps the hematological community to better understand the pros and cons of this new technological development for CLL patient management.
Wnt/β-catenin activation cooperates with loss of p53 to cause adrenocortical carcinoma in mice
Authors: Borges Kleiton Silva , Pignatti Emanuele , Leng Sining , Kariyawasam Dulanjalee , Ruiz-Babot Gerard , Ramalho Fernando Silva , Taketo Makoto Mark , Carlone Diana L. , Breault David T.
Published: June 2020

Adrenocortical carcinoma (ACC) is a rare and aggressive malignancy with limited therapeutic options. The lack of mouse models that recapitulate the genetics of ACC has hampered progress in the field. We analyzed The Cancer Genome Atlas (TCGA) dataset for ACC and found that patients harboring alterations in both p53/Rb and Wnt/β-catenin signaling pathways show a worse prognosis compared with patients that harbored alterations in only one. To model this, we utilized theCyp11b2(AS)Cremouse line to generate mice with adrenocortical-specific Wnt/β-catenin activation,Trp53deletion, or the combination of both. Mice with targeted Wnt/β-catenin activation orTrp53deletion showed no changes associated with tumor formation. In contrast, alterations in both pathways led to ACC with pulmonary metastases. Similar to ACCs in humans, these tumors produced increased levels of corticosterone and aldosterone and showed a high proliferation index. Gene expression analysis revealed that mouse tumors exhibited downregulation ofStarandCyp11b1and upregulation ofEzh2, similar to ACC patients with a poor prognosis. Altogether, these data show that altering both Wnt/β-catenin and p53/Rb signaling is sufficient to drive ACC in mouse. This autochthonous model of ACC represents a new tool to investigate the biology of ACC and to identify new treatment strategies.
Isoprenylcysteine carboxylmethyltransferase is required for the impact of mutant KRAS on TAZ protein level and cancer cell self-renewal
Authors: Chai Tin Fan , Manu Kanjoormana Aryan , Casey Patrick J. , Wang Mei
Published: June 2020

Cancer stem cells possess the capacity for self-renewal and resistance to chemotherapy. It is therefore crucial to understand the molecular regulators of stemness in the quest to develop effective cancer therapies. TAZ is a transcription activator that promotes stem cell functions in post-development mammalian cells; suppression of TAZ activity reduces or eliminates cancer stemness in select cancers. Isoprenylcysteine carboxylmethyltransferase (ICMT) is the unique enzyme of the last step of posttranslational prenylation processing pathway that modifies several oncogenic proteins, including RAS. We found that suppression of ICMT results in reduced self-renewal/stemness in KRAS-driven pancreatic and breast cancer cells. Silencing of ICMT led to significant reduction of TAZ protein levels and loss of self-renewal ability, which could be reversed by overexpressing mutant KRAS, demonstrating the functional impact of ICMT modification on the ability of KRAS to control TAZ stability and function. Contrary to expectation, YAP protein levels appear to be much less susceptible than TAZ to the regulation by ICMT and KRAS, and YAP is less consequential in regulating stemness characteristics in these cells. Further, we found that the ICMT-dependent KRAS regulation of TAZ was mediated through RAF, but not PI3K, signaling. Functionally, we demonstrate that a signaling cascade from ICMT modification of KRAS to TAZ protein stability supports cancer cell self-renewal abilities in both in vitro and in vivo settings. In addition, studies using the proof-of-concept small molecule inhibitors of ICMT confirmed its role in regulating TAZ and self-renewal, demonstrating the potential utility of targeting ICMT to control aggressive KRAS-driven cancers.
Correction to: CDK4/6 inhibition blocks cancer metastasis through a USP51-ZEB1-dependent deubiquitination mechanism
Authors: Zhang Zhen , Li Jianjun , Ou Yang , Yang Guang , Deng Kaiyuan , Wang Qiong , Wang Zhaoyang , Wang Wenhao , Zhang Quansheng , Wang Hang , Sun Wei , Sun Peiqing , Yang Shuang
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Noncoding RNAs: the shot callers in tumor immune escape
Authors: Liu Lei , Wang Qin , Qiu Zhilin , Kang Yujuan , Liu Jiena , Ning Shipeng , Yin Yanling , Pang Da , Xu Shouping
Published: June 2020

Immunotherapy, designed to exploit the functions of the host immune system against tumors, has shown considerable potential against several malignancies. However, the utility of immunotherapy is heavily limited due to the low response rate and various side effects in the clinical setting. Immune escape of tumor cells may be a critical reason for such low response rates. Noncoding RNAs (ncRNAs) have been identified as key regulatory factors in tumors and the immune system. Consequently, ncRNAs show promise as targets to improve the efficacy of immunotherapy in tumors. However, the relationship between ncRNAs and tumor immune escape (TIE) has not yet been comprehensively summarized. In this review, we provide a detailed account of the current knowledge on ncRNAs associated with TIE and their potential roles in tumor growth and survival mechanisms. This review bridges the gap between ncRNAs and TIE and broadens our understanding of their relationship, providing new insights and strategies to improve immunotherapy response rates by specifically targeting the ncRNAs involved in TIE.
Therapeutic siRNA: state of the art
Authors: Hu Bo , Zhong Liping , Weng Yuhua , Peng Ling , Huang Yuanyu , Zhao Yongxiang , Liang Xing-Jie
Published: June 2020

RNA interference (RNAi) is an ancient biological mechanism used to defend against external invasion. It theoretically can silence any disease-related genes in a sequence-specific manner, making small interfering RNA (siRNA) a promising therapeutic modality. After a two-decade journey from its discovery, two approvals of siRNA therapeutics, ONPATTRO® (patisiran) and GIVLAARI™ (givosiran), have been achieved by Alnylam Pharmaceuticals. Reviewing the long-term pharmaceutical history of human beings, siRNA therapy currently has set up an extraordinary milestone, as it has already changed and will continue to change the treatment and management of human diseases. It can be administered quarterly, even twice-yearly, to achieve therapeutic effects, which is not the case for small molecules and antibodies. The drug development process was extremely hard, aiming to surmount complex obstacles, such as how to efficiently and safely deliver siRNAs to desired tissues and cells and how to enhance the performance of siRNAs with respect to their activity, stability, specificity and potential off-target effects. In this review, the evolution of siRNA chemical modifications and their biomedical performance are comprehensively reviewed. All clinically explored and commercialized siRNA delivery platforms, including the GalNAc (N-acetylgalactosamine)–siRNA conjugate, and their fundamental design principles are thoroughly discussed. The latest progress in siRNA therapeutic development is also summarized. This review provides a comprehensive view and roadmap for general readers working in the field.
Ischemic damage may play an important role in spinal cord injury during dancing
Authors: Tong An-Ni , Zhang Jun-Wei , Zhou Hong-Jun , Tang He-Hu , Bai Jin-Zhu , Wang Fang-Yong , Lv Zhen , Chen Shi-Zheng , Liu Shu-Jia , Liu Jie-Sheng , Hong Yi
Published: June 2020

Study design

Retrospective analysis.

Setting

China Rehabilitation Research Center, Beijing, China.

Objective

To explore possible mechanisms underlying spinal cord injury (SCI) in children caused by hyperextension of the spine while dancing.

Methods

The clinical records of 88 children with SCI (mean age, 5.97 years; age range, 4–10 years) admitted to our hospital from January 1989 to October 2019 were retrospectively reviewed. Computed tomography and magnetic resonance imaging were performed on the day of injury. The time from injury to development of paralysis, as well as post-injury activities were surveyed, while abnormal patterns on images, the range of the involved vertebrae, and the extents of edema and atrophy were assessed.

Results

Among the 88 patients, 6 (6.8%) were unable to move immediately after SCI, while paralysis occurred in 42, 23, and 17 patients at <30, 30–60, and >60 min after SCI, respectively. The neurological level of injury of 84 patients was between T4 and T12. On sagittal T2-weighted images (T2WIs), the longitudinal range of spinal cord edema was more than one vertebral body in 65 patients, while spinal cord atrophy below T8 was found in 40 patients. On axial T2WIs, although three patients had none, long T2 signals were found in the central gray matter of seven patients. Meanwhile, necrosis of the central area combined with the peripheral white matter was observed in 57 patients, while three patients had total involvement on a cross section.

Conclusion

Ischemia-related damage, rather than direct trauma to the spinal cord, may play an important role in SCI due to spinal hyperextension during dancing.
Linking depressive symptom dimensions to cerebellar subregion volumes in later life
Authors: Bogoian Hannah R. , King Tricia Z. , Turner Jessica A. , Semmel Eric S. , Dotson Vonetta M.
Published: June 2020

The present study examined the relationship between subthreshold depressive symptoms and gray matter volume in subregions of the posterior cerebellum. Structural magnetic resonance imaging data from 38 adults aged 51 to 80 years were analyzed along with participants’ responses to the Center for Epidemiologic Studies Depression Scale. Subscale scores for depressed mood, somatic symptoms, and lack of positive affect were calculated, and multiple regression analyses were used to examine the relationship between symptom dimensions and cerebellar volumes. Greater total depressive symptoms and greater somatic symptoms of depression were significantly related to larger volumes of vermis VI, a region within the salience network, which is altered in depression. Exploratory analyses revealed that higher scores on the lack of positive affect subscale were related to larger vermis VIII volumes. These results support that depressive symptom profiles have unique relationships within the cerebellum that may be important as the field move towards targeted treatment approaches for depression.
Epigenome-wide association study of attention-deficit/hyperactivity disorder in adults
Authors: Rovira Paula , Sánchez-Mora Cristina , Pagerols Mireia , Richarte Vanesa , Corrales Montserrat , Fadeuilhe Christian , Vilar-Ribó Laura , Arribas Lorena , Shireby Gemma , Hannon Eilis , Mill Jonathan , Casas Miquel , Ramos-Quiroga Josep Antoni , Soler Artigas María , Ribasés Marta
Published: June 2020

Attention-deficit/hyperactivity disorder (ADHD) is a highly heritable neurodevelopmental disorder that often persists into adulthood. There is growing evidence that epigenetic dysregulation participates in ADHD. Given that only a limited number of epigenome-wide association studies (EWASs) of ADHD have been conducted so far and they have mainly focused on pediatric and population-based samples, we performed an EWAS in a clinical sample of adults with ADHD. We report one CpG site and four regions differentially methylated between patients and controls, which are located in or near genes previously involved in autoimmune diseases, cancer or neuroticism. Our sensitivity analyses indicate that smoking status is not responsible for these results and that polygenic risk burden for ADHD does not greatly impact the signatures identified. Additionally, we show an overlap of our EWAS findings with genetic signatures previously described for ADHD and with epigenetic signatures for smoking behavior and maternal smoking. These findings support a role of DNA methylation in ADHD and emphasize the need for additional efforts in larger samples to clarify the role of epigenetic mechanisms on ADHD across the lifespan.
YBX1 mediates autophagy by targeting p110β and decreasing the sensitivity to cisplatin in NSCLC
Authors: Cui Yanwei , Li Fengzhou , Xie Qiang , Zhao Shilei , Guo Tao , Guo Ping , Hu Sheng , Hao Jiaojiao , Tian Chunfang , Yu Wendan , Li Zhuoshi , Fang Lei , Zhao Lei , Chen Manyu , Wu Taihua , Gu Chundong
Published: June 2020

Y-box binding protein 1 (YBX1) is involved in the development of multiple types of tumors. However, the relationship between YBX1 and autophagy in non-small cell lung cancer (NSCLC) remains unclear. In this study, we analyzed the expression and clinical significance of YBX1 and markers of autophagy (LC3I/II) in NSCLC and examined their roles in regulating sensitivity to cisplatin in NSCLC. The retrospective analysis of patients with NSCLC indicated that YBX1 was positively correlated with autophagy. Increased levels of YBX1 or autophagy also observed in NSCLC cells compared with those in 16HBE cells. Compared to the controls, the knockdown of YBX1 expression suppressed autophagy, increased drug sensitivity and promoted apoptosis in response to cisplatin in NSCLC cells by targeting the p110β promoter and inhibiting p110β/Vps34/beclin1 signaling pathways. We also demonstrated in an in vivo study that the overexpressed YBX1 effectively increased NSCLC growth and progression and decreased the sensitivity to cisplatin by inducing autophagy in a xenograft tumor model, and these effects were concomitant with the increasing of p110β and beclin1 expression. Collectively, these results show that YBX1 plays an essential role in autophagy in NSCLC.
Delivering genome sequencing for rapid genetic diagnosis in critically ill children: parent and professional views, experiences and challenges
Authors: Hill Melissa , Hammond Jennifer , Lewis Celine , Mellis Rhiannon , Clement Emma , Chitty Lyn S.
Published: June 2020

Rapid genomic sequencing (RGS) is increasingly being used in the care of critically ill children. Here we describe a qualitative study exploring parent and professional perspectives around the usefulness of this test, the potential for unintended harms and the challenges for delivering a wider clinical service. The Rapid Paediatric Sequencing (RaPS) study offered trio RGS for diagnosis of critically ill children with a likely monogenic disorder. Main and actionable secondary findings were reported. Semi-structured interviews were conducted with parents of children offered RGS (n = 11) and professionals (genetic clinicians, non-genetic clinicians, scientists and consenters) (n = 19) by telephone (parents n = 10/professionals n = 1) or face-to-face (parents n = 1/professionals n = 18). We found that participants held largely positive views about RGS, describing clinical and emotional benefits from the opportunity to obtain a rapid diagnosis. Parental stress surrounding their child’s illness complicates decision making. Parental concerns are heightened when offered RGS and while waiting for results. The importance of multidisciplinary team working to enable efficient delivery of a rapid service was emphasised. Our findings give insight into the perceived value of RGS for critically ill children. Careful pre-test counselling is needed to support informed parental decision making. Many parents would benefit from additional support while waiting for results. Education of mainstream clinicians is required to facilitate clinical implementation.
Non-cooperative 4E-BP2 folding with exchange between eIF4E-binding and binding-incompatible states tunes cap-dependent translation inhibition
Authors: Dawson Jennifer E. , Bah Alaji , Zhang Zhenfu , Vernon Robert M. , Lin Hong , Chong P. Andrew , Vanama Manasvi , Sonenberg Nahum , Gradinaru Claudiu C. , Forman-Kay Julie D.
Published: June 2020

Phosphorylation of intrinsically disordered eIF4E binding proteins (4E-BPs) regulates cap-dependent translation by weakening their ability to compete with eIF4G for eIF4E binding within the translation initiation complex. We previously showed that phosphorylation of T37 and T46 in 4E-BP2 induces folding of a four-stranded beta-fold domain, partially sequestering the canonical eIF4E-binding helix. The C-terminal intrinsically disordered region (C-IDR), remaining disordered after phosphorylation, contains the secondary eIF4E-binding site and three other phospho-sites, whose mechanisms in inhibiting binding are not understood. Here we report that the domain is non-cooperatively folded, with exchange between beta strands and helical conformations. C-IDR phosphorylation shifts the conformational equilibrium, controlling access to eIF4E binding sites. The hairpin turns formed by pT37/pT46 are remarkably stable and function as transplantable units for phospho-regulation of stability. These results demonstrate how non-cooperative folding and conformational exchange leads to graded inhibition of 4E-BP2:eIF4E binding, shifting 4E-BP2 into an eIF4E binding-incompatible conformation and regulating translation initiation.
The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
Authors: Schulze Stefan , Adams Zachary , Cerletti Micaela , De Castro Rosana , Ferreira-Cerca Sébastien , Fufezan Christian , Giménez María Inés , Hippler Michael , Jevtic Zivojin , Knüppel Robert , Legerme Georgio , Lenz Christof , Marchfelder Anita , Maupin-Furlow Julie , Paggi Roberto A. , Pfeiffer Friedhelm , Poetsch Ansgar , Urlaub Henning , Pohlschroder Mechthild
Published: June 2020

While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.
A dietary fatty acid counteracts neuronal mechanical sensitization
Authors: Romero Luis O. , Caires Rebeca , Nickolls Alec R. , Chesler Alexander T. , Cordero-Morales Julio F. , Vásquez Valeria
Published: June 2020

PIEZO2 is the essential transduction channel for touch discrimination, vibration, and proprioception. Mice and humans lacking Piezo2 experience severe mechanosensory and proprioceptive deficits and fail to develop tactile allodynia. Bradykinin, a proalgesic agent released during inflammation, potentiates PIEZO2 activity. Molecules that decrease PIEZO2 function could reduce heightened touch responses during inflammation. Here, we find that the dietary fatty acid margaric acid (MA) decreases PIEZO2 function in a dose-dependent manner. Chimera analyses demonstrate that the PIEZO2 beam is a key region tuning MA-mediated channel inhibition. MA reduces neuronal action potential firing elicited by mechanical stimuli in mice and rat neurons and counteracts PIEZO2 sensitization by bradykinin. Finally, we demonstrate that this saturated fatty acid decreases PIEZO2 currents in touch neurons derived from human induced pluripotent stem cells. Our findings report on a natural product that inhibits PIEZO2 function and counteracts neuronal mechanical sensitization and reveal a key region for channel inhibition.
Leucine regulates autophagy via acetylation of the mTORC1 component raptor
Authors: Son Sung Min , Park So Jung , Stamatakou Eleanna , Vicinanza Mariella , Menzies Fiona M. , Rubinsztein David C.
Published: June 2020

Macroautophagy (“autophagy”) is the main lysosomal catabolic process that becomes activated under nutrient-depleted conditions, like amino acid (AA) starvation. The mechanistic target of rapamycin complex 1 (mTORC1) is a well-conserved negative regulator of autophagy. While leucine (Leu) is a critical mTORC1 regulator under AA-starved conditions, how Leu regulates autophagy is poorly understood. Here, we describe that in most cell types, including neurons, Leu negatively regulates autophagosome biogenesis via its metabolite, acetyl-coenzyme A (AcCoA). AcCoA inhibits autophagy by enhancing EP300-dependent acetylation of the mTORC1 component raptor, with consequent activation of mTORC1. Interestingly, in Leu deprivation conditions, the dominant effects on autophagy are mediated by decreased raptor acetylation causing mTORC1 inhibition, rather than by altered acetylation of other autophagy regulators. Thus, in most cell types we examined, Leu regulates autophagy via the impact of its metabolite AcCoA on mTORC1, suggesting that AcCoA and EP300 play pivotal roles in cell anabolism and catabolism.
Mutually stabilizing interactions between proto-peptides and RNA
Authors: Frenkel-Pinter Moran , Haynes Jay W. , Mohyeldin Ahmad M. , C Martin , Sargon Alyssa B. , Petrov Anton S. , Krishnamurthy Ramanarayanan , Hud Nicholas V. , Williams Loren Dean , Leman Luke J.
Published: June 2020

The close synergy between peptides and nucleic acids in current biology is suggestive of a functional co-evolution between the two polymers. Here we show that cationic proto-peptides (depsipeptides and polyesters), either produced as mixtures from plausibly prebiotic dry-down reactions or synthetically prepared in pure form, can engage in direct interactions with RNA resulting in mutual stabilization. Cationic proto-peptides significantly increase the thermal stability of folded RNA structures. In turn, RNA increases the lifetime of a depsipeptide by >30-fold. Proto-peptides containing the proteinaceous amino acids Lys, Arg, or His adjacent to backbone ester bonds generally promote RNA duplex thermal stability to a greater magnitude than do analogous sequences containing non-proteinaceous residues. Our findings support a model in which tightly-intertwined biological dependencies of RNA and protein reflect a long co-evolutionary history that began with rudimentary, mutually-stabilizing interactions at early stages of polypeptide and nucleic acid co-existence.