bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexpression of MdATG8i improves water use efficiency in transgenic apple by modulating photosynthesis, osmotic balance, and autophagic activity under moderate water deficit
Authors: Jia Xin , Mao Ke , Wang Ping , Wang Yu , Jia Xumei , Huo Liuqing , Sun Xun , Che Runmin , Gong Xiaoqing , Ma Fengwang
Published: April 2021

Water deficit is one of the major limiting factors for apple (Malus domestica) production on the Loess Plateau, a major apple cultivation area in China. The identification of genes related to the regulation of water use efficiency (WUE) is a crucial aspect of crop breeding programs. As a conserved degradation and recycling mechanism in eukaryotes, autophagy has been reported to participate in various stress responses. However, the relationship between autophagy and WUE regulation has not been explored. We have shown that a crucial autophagy protein in apple, MdATG8i, plays a role in improving salt tolerance. Here, we explored its biological function in response to long-term moderate drought stress. The results showed that MdATG8i-overexpressing (MdATG8i-OE) apple plants exhibited higher WUE than wild-type (WT) plants under long-term moderate drought conditions. Plant WUE can be increased by improving photosynthetic efficiency. Osmoregulation plays a critical role in plant stress resistance and adaptation. Under long-term drought conditions, the photosynthetic capacity and accumulation of sugar and amino acids were higher in MdATG8i-OE plants than in WT plants. The increased photosynthetic capacity in the OE plants could be attributed to their ability to maintain optimal stomatal aperture, organized chloroplasts, and strong antioxidant activity. MdATG8i overexpression also promoted autophagic activity, which was likely related to the changes described above. In summary, our results demonstrate that MdATG8i-OE apple lines exhibited higher WUE than WT under long-term moderate drought conditions because they maintained robust photosynthesis, effective osmotic adjustment processes, and strong autophagic activity.
Activating mutations in BRAF disrupt the hypothalamo-pituitary axis leading to hypopituitarism in mice and humans
Authors: Gualtieri Angelica , Kyprianou Nikolina , Gregory Louise C. , Vignola Maria Lillina , Nicholson James G. , Tan Rachael , Inoue Shin-ichi , Scagliotti Valeria , Casado Pedro , Blackburn James , Abollo-Jimenez Fernando , Marinelli Eugenia , Besser Rachael E. J. , Högler Wolfgang , Karen Temple I. , Davies Justin H. , Gagunashvili Andrey , Robinson Iain C.A.F. , Camper Sally A. , Davis Shannon W. , Cutillas Pedro R. , Gevers Evelien F. , Aoki Yoko , Dattani Mehul T. , Gaston-Massuet Carles
Published: April 2021

Germline mutations in BRAF and other components of the MAPK pathway are associated with the congenital syndromes collectively known as RASopathies. Here, we report the association of Septo-Optic Dysplasia (SOD) including hypopituitarism and Cardio-Facio-Cutaneous (CFC) syndrome in patients harbouring mutations in BRAF. Phosphoproteomic analyses demonstrate that these genetic variants are gain-of-function mutations leading to activation of the MAPK pathway. Activation of the MAPK pathway by conditional expression of the BrafV600E/+ allele, or the knock-in BrafQ241R/+ allele (corresponding to the most frequent human CFC-causing mutation, BRAF p.Q257R), leads to abnormal cell lineage determination and terminal differentiation of hormone-producing cells, causing hypopituitarism. Expression of the BrafV600E/+ allele in embryonic pituitary progenitors leads to an increased expression of cell cycle inhibitors, cell growth arrest and apoptosis, but not tumour formation. Our findings show a critical role of BRAF in hypothalamo-pituitary-axis development both in mouse and human and implicate mutations found in RASopathies as a cause of endocrine deficiencies in humans.
A Hierarchical Attractor Network Model of perceptual versus intentional decision updates
Authors: Löffler Anne , Sylaidi Anastasia , Fountas Zafeirios , Haggard Patrick
Published: April 2021

Changes of Mind are a striking example of our ability to flexibly reverse decisions and change our own actions. Previous studies largely focused on Changes of Mind in decisions about perceptual information. Here we report reversals of decisions that require integrating multiple classes of information: 1) Perceptual evidence, 2) higher-order, voluntary intentions, and 3) motor costs. In an adapted version of the random-dot motion task, participants moved to a target that matched both the external (exogenous) evidence about dot-motion direction and a preceding internally-generated (endogenous) intention about which colour to paint the dots. Movement trajectories revealed whether and when participants changed their mind about the dot-motion direction, or additionally changed their mind about which colour to choose. Our results show that decision reversals about colour intentions are less frequent in participants with stronger intentions (Exp. 1) and when motor costs of intention pursuit are lower (Exp. 2). We further show that these findings can be explained by a hierarchical, multimodal Attractor Network Model that continuously integrates higher-order voluntary intentions with perceptual evidence and motor costs. Our model thus provides a unifying framework in which voluntary actions emerge from a dynamic combination of internal action tendencies and external environmental factors, each of which can be subject to Change of Mind.
Presence of complete murine viral genome sequences in patient-derived xenografts
Authors: Yuan Zihao , Fan Xuejun , Zhu Jay-Jiguang , Fu Tong-Ming , Wu Jiaqian , Xu Hua , Zhang Ningyan , An Zhiqiang , Zheng W. Jim
Published: April 2021

Patient-derived xenografts are crucial for drug development but their use is challenged by issues such as murine viral infection. We evaluate the scope of viral infection and its impact on patient-derived xenografts by taking an unbiased data-driven approach to analyze unmapped RNA-Seq reads from 184 experiments. We find and experimentally validate the extensive presence of murine viral sequence reads covering entire viral genomes in patient-derived xenografts. The existence of viral sequences inside tumor cells is further confirmed by single cell sequencing data. Extensive chimeric reads containing both viral and human sequences are also observed. Furthermore, we find significantly changed expression levels of many cancer-, immune-, and drug metabolism-related genes in samples with high virus load. Our analyses indicate a need to carefully evaluate the impact of viral infection on patient-derived xenografts for drug development. They also point to a need for attention to quality control of patient-derived xenograft experiments.
Axial localization and tracking of self-interference nanoparticles by lateral point spread functions
Authors: Liu Yongtao , Zhou Zhiguang , Wang Fan , Kewes Günter , Wen Shihui , Burger Sven , Ebrahimi Wakiani Majid , Xi Peng , Yang Jiong , Yang Xusan , Benson Oliver , Jin Dayong
Published: April 2021

Sub-diffraction limited localization of fluorescent emitters is a key goal of microscopy imaging. Here, we report that single upconversion nanoparticles, containing multiple emission centres with random orientations, can generate a series of unique, bright and position-sensitive patterns in the spatial domain when placed on top of a mirror. Supported by our numerical simulation, we attribute this effect to the sum of each single emitter’s interference with its own mirror image. As a result, this configuration generates a series of sophisticated far-field point spread functions (PSFs), e.g. in Gaussian, doughnut and archery target shapes, strongly dependent on the phase difference between the emitter and its image. In this way, the axial locations of nanoparticles are transferred into far-field patterns. We demonstrate a real-time distance sensing technology with a localization accuracy of 2.8 nm, according to the atomic force microscope (AFM) characterization values, smaller than 1/350 of the excitation wavelength.
Detecting local genetic correlations with scan statistics
Authors: Guo Hanmin , Li James J. , Lu Qiongshi , Hou Lin
Published: April 2021

Genetic correlation analysis has quickly gained popularity in the past few years and provided insights into the genetic etiology of numerous complex diseases. However, existing approaches oversimplify the shared genetic architecture between different phenotypes and cannot effectively identify precise genetic regions contributing to the genetic correlation. In this work, we introduce LOGODetect, a powerful and efficient statistical method to identify small genome segments harboring local genetic correlation signals. LOGODetect automatically identifies genetic regions showing consistent associations with multiple phenotypes through a scan statistic approach. It uses summary association statistics from genome-wide association studies (GWAS) as input and is robust to sample overlap between studies. Applied to seven phenotypically distinct but genetically correlated neuropsychiatric traits, we identify 227 non-overlapping genome regions associated with multiple traits, including multiple hub regions showing concordant effects on five or more traits. Our method addresses critical limitations in existing analytic strategies and may have wide applications in post-GWAS analysis.
A KRAS-responsive long non-coding RNA controls microRNA processing
Authors: Shi Lei , Magee Peter , Fassan Matteo , Sahoo Sudhakar , Leong Hui Sun , Lee Dave , Sellers Robert , Brullé-Soumaré Laura , Cairo Stefano , Monteverde Tiziana , Volinia Stefano , Smith Duncan D. , Di Leva Gianpiero , Galuppini Francesca , Paliouras Athanasios R. , Zeng Kang , O’Keefe Raymond , Garofalo Michela
Published: April 2021

Wild-type KRAS (KRASWT) amplification has been shown to be a secondary means of KRAS activation in cancer and associated with poor survival. Nevertheless, the precise role of KRASWT overexpression in lung cancer progression is largely unexplored. Here, we identify and characterize a KRAS-responsive lncRNA, KIMAT1 (ENSG00000228709) and show that it correlates with KRAS levels both in cell lines and in lung cancer specimens. Mechanistically, KIMAT1 is a MYC target and drives lung tumorigenesis by promoting the processing of oncogenic microRNAs (miRNAs) through DHX9 and NPM1 stabilization while halting the biogenesis of miRNAs with tumor suppressor function via MYC-dependent silencing of p21, a component of the Microprocessor Complex. KIMAT1 knockdown suppresses not only KRAS expression but also KRAS downstream signaling, thereby arresting lung cancer growth in vitro and in vivo. Taken together, this study uncovers a role for KIMAT1 in maintaining a positive feedback loop that sustains KRAS signaling during lung cancer progression and provides a proof of principle that interfering with KIMAT1 could be a strategy to hamper KRAS-induced tumorigenesis.
Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors
Authors: Iketani Sho , Forouhar Farhad , Liu Hengrui , Hong Seo Jung , Lin Fang-Yu , Nair Manoj S. , Zask Arie , Huang Yaoxing , Xing Li , Stockwell Brent R. , Chavez Alejandro , Ho David D.
Published: April 2021

We report the identification of three structurally diverse compounds – compound 4, GC376, and MAC-5576 – as inhibitors of the SARS-CoV-2 3CL protease. Structures of each of these compounds in complex with the protease revealed strategies for further development, as well as general principles for designing SARS-CoV-2 3CL protease inhibitors. These compounds may therefore serve as leads for the basis of building effective SARS-CoV-2 3CL protease inhibitors.
Author Correction: Nanoscale-femtosecond dielectric response of Mott insulators captured by two-color near-field ultrafast electron microscopy
Authors: Fu Xuewen , Barantani Francesco , Gargiulo Simone , Madan Ivan , Berruto Gabriele , LaGrange Thomas , Jin Lei , Wu Junqiao , Vanacore Giovanni Maria , Carbone Fabrizio , Zhu Yimei
Published: April 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22477-6
Author Correction: Ultra-bright Raman dots for multiplexed optical imaging
Authors: Zhao Zhilun , Chen Chen , Wei Shixuan , Xiong Hanqing , Hu Fanghao , Miao Yupeng , Jin Tianwei , Min Wei
Published: April 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22585-3.
Author Correction: Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV
Authors: Ou Xiuyuan , Liu Yan , Lei Xiaobo , Li Pei , Mi Dan , Ren Lili , Guo Li , Guo Ruixuan , Chen Ting , Hu Jiaxin , Xiang Zichun , Mu Zhixia , Chen Xing , Chen Jieyong , Hu Keping , Jin Qi , Wang Jianwei , Qian Zhaohui
Published: April 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22614-1.
Activation of NF-κB signaling via cytosolic mitochondrial RNA sensing in kerotocytes with mitochondrial DNA common deletion
Authors: Zhou Xin , Backman Ludvig J. , Danielson Patrik
Published: April 2021

Scar formation as a result of corneal wound healing is a leading cause of blindness. It is a challenge to understand why scar formation is more likely to occur in the central part of the cornea as compared to the peripheral part. The purpose of this study was to unravel the underlying mechanisms. We applied RNA-seq to uncover the differences of expression profile in keratocytes in the central/peripheral part of the cornea. The relative quantity of mitochondrial RNA was measured by multiplex qPCR. The characterization of mitochondrial RNA in the cytoplasm was confirmed by immunofluoresence microscope and biochemical approach. Gene expression was analyzed by western blot and RT qPCR. We demonstrate that the occurrence of mitochondrial DNA common deletion is greater in keratocytes from the central cornea as compared to those of the peripheral part. The keratocytes with CD have elevated oxidative stress levels, which leads to the leakage of mitochondrial double-stranded RNA into the cytoplasm. The cytoplasmic mitochondrial double-stranded RNA is sensed by MDA5, which induces NF-κB activation. The NF-κB activation thereafter induces fibrosis-like extracellular matrix expressions and IL-8 mRNA transcription. These results provide a novel explanation of the different clinical outcome in different regions of the cornea during wound healing.
Outcomes of prostate cancer screening among men using antidiabetic medication
Authors: Vettenranta A. , Murtola T. J. , Talala K. , Taari K. , Stenman U.-H. , Tammela T. L. J. , Auvinen A.
Published: April 2021

Diabetic men have decreased risk for prostate cancer (PCa) overall and lower PSA compared to non-diabetics. This may affect the outcomes of PSA-based screening. We investigated the effect of PSA-based screening at 4-year intervals on PCa incidence and mortality separately among users and non-users of antidiabetic medication with the hypothesis that screening would detect less low-grade cancer and more high-grade cancer in diabetic men. A cohort of 80,458 men from the Finnish Randomized Study of Screening for Prostate Cancer (FinRSPC) were linked to national prescription database to obtain information on antidiabetic medication purchases. PCa risk and mortality were compared between the FinRSPC screening arm (SA) and the control arm (CA) separately among users and non-users of antidiabetic medication. Among antidiabetic medication users median PSA was lower than in non-users (0.93 and 1.09 ng/ml, respectively, P for difference = 0.001). Screening increased overall PCa incidence compared to CA after the first screen both among medication users and non-users (HR 1.31, 95% CI 1.08–1.60 and HR 1.55, 95% CI 1.44–1.66, respectively). On the second and third screen the difference between SA and CA attenuated only among medication users. Detection of Gleason 6 tumors was lower among medication users, whereas no difference was observed in detection of Gleason 8–10 cancers. Concordantly, screening affected PCa mortality similarly regardless of antidiabetic medication use (HR 0.38, 95% CI 0.14–1.07 and HR 0.19, 95% CI 0.11–0.33 among users and non-users after three screens, respectively. P for difference = 0.18). Median PSA is lower in men using antidiabetic drugs than among non-users. Systematic PSA screening detects less low-risk tumors among medication users, whereas detection of high-risk tumors and mortality effects are similar regardless of medication use. This suggests that antidiabetic medication users may form a suitable target group for PCa screening, with less screening-related overdiagnosis of indolent tumors.
An efficient direct screening system for microorganisms that activate plant immune responses based on plant–microbe interactions using cultured plant cells
Authors: Kurokawa Mari , Nakano Masataka , Kitahata Nobutaka , Kuchitsu Kazuyuki , Furuya Toshiki
Published: April 2021

Microorganisms that activate plant immune responses have attracted considerable attention as potential biocontrol agents in agriculture because they could reduce agrochemical use. However, conventional methods to screen for such microorganisms using whole plants and pathogens are generally laborious and time consuming. Here, we describe a general strategy using cultured plant cells to identify microorganisms that activate plant defense responses based on plant–microbe interactions. Microbial cells were incubated with tobacco BY-2 cells, followed by treatment with cryptogein, a proteinaceous elicitor of tobacco immune responses secreted by an oomycete. Cryptogein-induced production of reactive oxygen species (ROS) in BY-2 cells served as a marker to evaluate the potential of microorganisms to activate plant defense responses. Twenty-nine bacterial strains isolated from the interior of Brassica rapa var. perviridis plants were screened, and 8 strains that enhanced cryptogein-induced ROS production in BY-2 cells were selected. Following application of these strains to the root tip of Arabidopsis seedlings, two strains, Delftia sp. BR1R-2 and Arthrobacter sp. BR2S-6, were found to induce whole-plant resistance to bacterial pathogens (Pseudomonas syringae pv. tomato DC3000 and Pectobacterium carotovora subsp. carotovora NBRC 14082). Pathogen-induced expression of plant defense-related genes (PR-1, PR-5, and PDF1.2) was enhanced by the pretreatment with strain BR1R-2. This cell–cell interaction-based platform is readily applicable to large-scale screening for microorganisms that enhance plant defense responses under various environmental conditions.
On the mechanisms governing the critical current reduction in Nb3Sn Rutherford cables under transverse stress
Authors: De Marzi Gianluca , Bordini Bernardo , Baffari Dario
Published: April 2021

Within the framework of the HiLumi-LHC project, CERN is currently manufacturing 11 T dipole and quadrupole accelerator magnets using state-of-the-art Nb3Sn Rutherford cables. Even higher magnetic fields are considered by the Hadron Future Circular Collider (FCC-hh) design study, which plans to develop 16 T Nb3Sn bending dipoles. In such high-field magnets, the design pre-stress can reach considerable values (150–200 MPa) and, since Nb3Sn is a brittle compound, this can constitute a technological difficult challenge. Due to the significant impact that a transverse load can have on the performances of a Nb3Sn magnet, CERN has launched a campaign of critical current measurements of reacted and impregnated Nb3Sn cables subjected to transverse pressure up to about 210 MPa. In this paper, results obtained on 18-strand 10-mm-wide cable sample based on a 1-mm-diameter powder-in-tube (PIT) wire are presented. The tests were carried out on a 2-m-long sample by using the FReSCa test station, at T = 4.3 K and background magnetic fields up to 9.6 T. For applied pressures below ≈ 130 MPa, only reversible reductions of the critical current, Ic, are observed. At higher pressures, a permanent Ic reduction occurs; such irreversible behaviour is due to the residual stresses generated by the plastic deformations of the copper stabilizer. This type of current reduction, whether reversible or not, is fully governed by the strain-induced variations of the upper critical field, Bc2. At higher pressures, estimated between 180 and 210 MPa, it is indeed plausible to believe that cracking of filaments occurs, with detrimental consequences for the Nb3Sn cable’s electrical performances. The complete set of critical current data here presented, collected at different pressures and as a function of the applied magnetic field, allows for the first time to investigate the evolution of superconducting parameters such as the upper critical field Bc2 in the irreversibility region, where both the effects of Cu matrix plasticization and/or cracking of filaments may occur. The experimental approach and data interpretation have a general value and can be applied to any typology of Rutherford cable.
Statistical shape modeling of the talocrural joint using a hybrid multi-articulation joint approach
Authors: Lenz Amy L. , Krähenbühl Nicola , Peterson Andrew C. , Lisonbee Rich J. , Hintermann Beat , Saltzman Charles L. , Barg Alexej , Anderson Andrew E.
Published: April 2021

Historically, conventional radiographs have been the primary tool to morphometrically evaluate the talocrural joint, which is comprised of the distal tibia, distal fibula, and proximal talus. More recently, high-resolution volumetric imaging, including computed tomography (CT), has enabled the generation of three-dimensional (3D) reconstructions of the talocrural joint. Weightbearing cone-beam CT (WBCT) technology provides additional benefit to assess 3D spatial relationships and joint congruency while the patient is load bearing. In this study we applied statistical shape modeling, a computational morphometrics technique, to objectively quantify anatomical variation, joint level coverage, joint space distance, and congruency at the talocrural joint. Shape models were developed from segmented WBCT images and included the distal tibia, distal fibula, and full talus. Key anatomical variation across subjects included the fibular notch on the tibia, talar trochlea sagittal plane rate of curvature, tibial plafond curvature with medial malleolus prominence, and changes in the fibular shaft diameter. The shape analysis also revealed a highly congruent talocrural joint with minimal inter-individual morphometric differences at the articular regions. These data are helpful to improve understanding of ankle joint pathologies and to guide refinement of operative treatments.
Adsorption of bacteriophages on polypropylene labware affects the reproducibility of phage research
Authors: Richter Łukasz , Księżarczyk Karolina , Paszkowska Karolina , Janczuk-Richter Marta , Niedziółka-Jönsson Joanna , Gapiński Jacek , Łoś Marcin , Hołyst Robert , Paczesny Jan
Published: April 2021

Hydrophobicity is one of the most critical factors governing the adsorption of molecules and objects, such as virions, on surfaces. Even moderate change of wetting angle of plastic surfaces causes a drastic decrease ranging from 2 to 5 logs of the viruses (e.g., T4 phage) in the suspension due to adsorption on polymer vials' walls. The effect varies immensely in seemingly identical containers but purchased from different vendors. Comparison of glass, polyethylene, polypropylene, and polystyrene containers revealed a threshold in the wetting angle of around 95°: virions adsorb on the surface of more hydrophobic containers, while in more hydrophilic vials, phage suspensions are stable. The polypropylene surface of the Eppendorf-type and Falcon-type can accommodate from around 108 PFU/ml to around 1010 PFU/ml from the suspension. The adsorption onto the container’s wall might result in complete scavenging of virions from the bulk. We developed two methods to overcome this issue. The addition of surfactant Tween20 and/or plasma treatment provides a remedy by modulating surface wettability and inhibiting virions' adsorption. Plastic containers are essential consumables in the daily use of many bio-laboratories. Thus, this is important not only for phage-related research (e.g., the use of phage therapies as an alternative for antibiotics) but also for data comparison and reproducibility in the field of biochemistry and virology.
DNMT3.1 controls trade-offs between growth, reproduction, and life span under starved conditions in Daphnia magna
Authors: Nguyen Nhan Duc , Matsuura Tomoaki , Kato Yasuhiko , Watanabe Hajime
Published: April 2021

The cladoceran crustaceanDaphniahas long been a model of energy allocation studies due to its important position in the trophic cascade of freshwater ecosystems. However, the loci for controlling energy allocation between life history traits still remain unknown. Here, we report CRISPR/Cas-mediated target mutagenesis of DNA methyltransferase 3.1 (DNMT3.1) that is upregulated in response to caloric restriction inDaphnia magna. The resulting biallelic mutant is viable and did not show any change in growth rate, reproduction, and longevity under nutrient rich conditions. In contrast, under starved conditions, the growth rate of this DNMT3.1 mutant was increased but its reproduction was reciprocally reduced compared to the wild type when the growth and reproduction activities competed during a period from instar 4 to 8. The life span of this mutant was significantly shorter than that of the wild type. We also compared transcriptomes between DNMT3.1 mutant and wild type under nutrient-rich and starved conditions. Consistent with the DNMT3.1 mutant phenotypes, the starved condition led to changes in the transcriptomes of the mutant including differential expression of vitellogenin genes. In addition, we found upregulation of theI am not dead yet(INDY) ortholog, which has been known to shorten the life span inDrosophila, explaining the shorter life span of the DNMT3.1 mutant. These results establish DNMT3.1 as a key regulator for life span and energy allocation between growth and reproduction during caloric restriction. Our findings reveal how energy allocation is implemented by selective expression of a DNMT3 ortholog that is widely distributed among animals. We also infer a previously unidentified adaptation ofDaphniathat invests more energy for reproduction than growth under starved conditions.
Modeling the first wave of Covid-19 pandemic in the Republic of Cyprus
Authors: Agapiou Sergios , Anastasiou Andreas , Baxevani Anastassia , Nicolaides Christos , Hadjigeorgiou Georgios , Christofides Tasos , Constantinou Elisavet , Nikolopoulos Georgios , Fokianos Konstantinos
Published: April 2021

We present different data analytic methodologies that have been applied in order to understand the evolution of the first wave of the Coronavirus disease 2019 in the Republic of Cyprus and the effect of different intervention measures that have been taken by the government. Change point detection has been used in order to estimate the number and locations of changes in the behaviour of the collected data. Count time series methods have been employed to provide short term projections and a number of various compartmental models have been fitted to the data providing with long term projections on the pandemic’s evolution and allowing for the estimation of the effective reproduction number.
Identification of novel inhibitors of Keap1/Nrf2 by a promising method combining protein–protein interaction-oriented library and machine learning
Authors: Shimizu Yugo , Yonezawa Tomoki , Sakamoto Junichi , Furuya Toshio , Osawa Masanori , Ikeda Kazuyoshi
Published: April 2021

Protein–protein interactions (PPIs) are prospective but challenging targets for drug discovery, because screening using traditional small-molecule libraries often fails to identify hits. Recently, we developed a PPI-oriented library comprising 12,593 small-to-medium-sized newly synthesized molecules. This study validates a promising combined method using PPI-oriented library and ligand-based virtual screening (LBVS) to discover novel PPI inhibitory compounds for Kelch-like ECH-associated protein 1 (Keap1) and nuclear factor erythroid 2-related factor 2 (Nrf2). We performed LBVS with two random forest models against our PPI library and the following time-resolved fluorescence resonance energy transfer (TR-FRET) assays of 620 compounds identified 15 specific hit compounds. The high hit rates for the entire PPI library (estimated 0.56–1.3%) and the LBVS (maximum 5.4%) compared to a conventional screening library showed the utility of the library and the efficiency of LBVS. All the hit compounds possessed novel structures with Tanimoto similarity ≤ 0.26 to known Keap1/Nrf2 inhibitors and aqueous solubility (AlogP < 5). Reasonable binding modes were predicted using 3D alignment of five hit compounds and a Keap1/Nrf2 peptide crystal structure. Our results represent a new, efficient method combining the PPI library and LBVS to identify novel PPI inhibitory ligands with expanded chemical space.
A highly conserved mechanism for the detoxification and assimilation of the toxic phytoproduct L-azetidine-2-carboxylic acid in Aspergillus nidulans
Authors: Biratsi Ada , Athanasopoulos Alexandros , Kouvelis Vassili N. , Gournas Christos , Sophianopoulou Vicky
Published: April 2021

Plants produce toxic secondary metabolites as defense mechanisms against phytopathogenic microorganisms and predators. L-azetidine-2-carboxylic acid (AZC), a toxic proline analogue produced by members of the Liliaceae and Agavaciae families, is part of such a mechanism. AZC causes a broad range of toxic, inflammatory and degenerative abnormalities in human and animal cells, while it is known that some microorganisms have evolved specialized strategies for AZC resistance. However, the mechanisms underlying these processes are poorly understood. Here, we identify a widespread mechanism for AZC resistance in fungi. We show that the filamentous ascomycete Aspergillus nidulans is able to not only resist AZC toxicity but also utilize it as a nitrogen source via GABA catabolism and the action of the AzhA hydrolase, a member of a large superfamily of detoxifying enzymes, the haloacid dehalogenase-like hydrolase (HAD) superfamily. This detoxification process is further assisted by the NgnA acetyltransferase, orthologue of Mpr1 of Saccharomyces cerevisiae. We additionally show that heterologous expression of AzhA protein can complement the AZC sensitivity of S. cerevisiae. Furthermore, a detailed phylogenetic analysis of AzhA homologues in Fungi, Archaea and Bacteria is provided. Overall, our results unravel a widespread mechanism for AZC resistance among microorganisms, including important human and plant pathogens.
Transcriptional circuitry atlas of genetic diverse unstimulated murine and human macrophages define disparity in population-wide innate immunity
Authors: Mishra Bharat , Athar Mohammad , Mukhtar M. Shahid
Published: April 2021

Macrophages are ubiquitous custodians of tissues, which play decisive role in maintaining cellular homeostasis through regulatory immune responses. Within tissues, macrophage exhibit extremely heterogeneous population with varying functions orchestrated through regulatory response, which can be further exacerbated in diverse genetic backgrounds. Gene regulatory networks (GRNs) offer comprehensive understanding of cellular regulatory behavior by unfolding the transcription factors (TFs) and regulated target genes. RNA-Seq coupled with ATAC-Seq has revolutionized the regulome landscape influenced by gene expression modeling. Here, we employ an integrative multi-omics systems biology-based analysis and generated GRNs derived from the unstimulated bone marrow-derived macrophages of five inbred genetically defined murine strains, which are reported to be linked with most of the population-wide human genetic variants. Our probabilistic modeling of a basal hemostasis pan regulatory repertoire in diverse macrophages discovered 96 TFs targeting 6279 genes representing 468,291 interactions across five inbred murine strains. Subsequently, we identify core and distinctive GRN sub-networks in unstimulated macrophages to describe the system-wide conservation and dissimilarities, respectively across five murine strains. Our study concludes that discrepancies in unstimulated macrophage-specific regulatory networks not only drives the basal functional plasticity within genetic backgrounds, additionally aid in understanding the complexity of racial disparity among the human population during stress.
Antibody–drug nanoparticle induces synergistic treatment efficacies in HER2 positive breast cancer cells
Authors: Abedin Muhammad Raisul , Powers Kaitlyne , Aiardo Rachel , Barua Dibbya , Barua Sutapa
Published: April 2021

Chemotherapeutic drugs suffer from non-specific binding, undesired toxicity, and poor blood circulation which contribute to poor therapeutic efficacy. In this study, antibody–drug nanoparticles (ADNs) are engineered by synthesizing pure anti-cancer drug nanorods (NRs) in the core of nanoparticles with a therapeutic monoclonal antibody, Trastuzumab on the surface of NRs for specific targeting and synergistic treatments of human epidermal growth factor receptor 2 (HER2) positive breast cancer cells. ADNs were designed by first synthesizing ~ 95 nm diameter × ~ 500 nm long paclitaxel (PTX) NRs using the nanoprecipitation method. The surface of PTXNRs was functionalized at 2′ OH nucleophilic site using carbonyldiimidazole and conjugated to TTZ through the lysine residue interaction forming PTXNR-TTZ conjugates (ADNs). The size, shape, and surface charge of ADNs were characterized using scanning electron microscopy (SEM), SEM, and zeta potential, respectively. Using fluorophore labeling and response surface analysis, the percentage conjugation efficiency was found > 95% with a PTX to TTZ mass ratio of 4 (molar ratio ≈ 682). In vitro therapeutic efficiency of PTXNR-TTZ was evaluated in two HER2 positive breast cancer cell lines: BT-474 and SK-BR-3, and a HER2 negative MDA-MB-231 breast cancer cell using MTT assay. PTXNR-TTZ inhibited > 80% of BT-474 and SK-BR-3 cells at a higher efficiency than individual PTX and TTZ treatments alone after 72 h. A combination index analysis indicated a synergistic combination of PTXNR-TTZ compared with the doses of single-drug treatment. Relatively lower cytotoxicity was observed in MCF-10A human breast epithelial cell control. The molecular mechanisms of PTXNR-TTZ were investigated using cell cycle and Western blot analyses. The cell cycle analysis showed PTXNR-TTZ arrested > 80% of BT-474 breast cancer cells in the G2/M phase, while > 70% of untreated cells were found in the G0/G1 phase indicating that G2/M arrest induced apoptosis. A similar percentage of G2/M arrested cells was found to induce caspase-dependent apoptosis in PTXNR-TTZ treated BT-474 cells as revealed using Western blot analysis. PTXNR-TTZ treated BT-474 cells showed ~ 1.3, 1.4, and 1.6-fold higher expressions of cleaved caspase-9, cytochrome C, and cleaved caspase-3, respectively than untreated cells, indicating up-regulation of caspase-dependent activation of apoptotic pathways. The PTXNR-TTZ ADN represents a novel nanoparticle design that holds promise for targeted and efficient anti-cancer therapy by selective targeting and cancer cell death via apoptosis and mitotic cell cycle arrest.
Incomplete footprint coverage under tension in repair of isolated supraspinatus full-thickness tear
Authors: Yoon Tae-Hwan , Kim Sung-Jae , Choi Yun-Rak , Kim Du-Seong , Chun Yong-Min
Published: April 2021

Although it is well known that repairing large or massive tears under tension may have an adverse effect on healing of the repaired tendons, only few studies have addressed this issue in medium-sized isolated supraspinatus full-thickness tear. The purpose of this study was to compare the clinical outcomes and structural integrity of arthroscopic rotator cuff repair with tension versus without it. This study retrospectively investigated 90 patients who underwent arthroscopic repair in a single-row for medium-sized isolated supraspinatus full-thickness tear. The patients were assigned to either repaired under tension (Group A, n = 38) or repaired without tension (Group B, n = 52) groups. Functional outcomes were assessed using the patient reported subjective values and the active range of motion (ROM). Postoperative radiographic evaluation was performed 6 months after the surgery to assess the structural integrity of the repaired tendons. Changes in the subjective shoulder scores from initial to 2 years after surgery showed no statistical significance between the two groups. The ROMs measured at initial and 2 years after surgery also showed no statistical difference between the two groups. Postoperative radiological evaluations found a significantly higher re-tear rate in Group A (28.9%, 11/38) than in Group B (9.6%, 5/52). The torn cuff tendons that were repaired under tension as retraction with limited mobility had significantly higher re-tear rate despite having immobilized for 6 weeks after surgery, but their clinical outcomes showed no significant difference from the outcomes of repaired tendons without tension.
Structure–function engineering of novel fish gelatin-derived multifunctional peptides using high-resolution peptidomics and bioinformatics
Authors: Mirzapour-Kouhdasht Armin , Moosavi-Nasab Marzieh , Lee Chul Won , Yun Hyosuk , Eun Jong-Bang
Published: April 2021

The multifunctional properties of fish gelatin hydrolysates have not been completely elucidated. Here, the biological characterization of these peptides was performed to engineer multifunctional peptides. Bioactive peptides were produced from mackerel byproducts via successive enzymatic hydrolysis reactions using subtilisin A and actinidin as microbial and herbal proteases. The antibacterial activity against both gram-negative and -positive food-borne pathogens, includingEscherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, andKlebsiella pneumoniae, as well as the inhibitory potential of angiotensin-converting enzyme (ACE) and dipeptidyl peptidase IV (DPP-IV), was accessed in vitro. The synthesized peptides demonstrated multifunctional properties, which were further confirmed by in silico protocols. The ACE and DPP-IV inhibitory (IC50) values of P1, P2, and P3 were 0.92 and 0.87, 0.51 and 0.93, 0.78 and 1.16 mg mL−1, respectively. Moreover, the binding energy was sufficient for all three peptides to inhibit both ACE and DPP-IV enzymes with excellent three-dimensional conformation (RMSD = 0.000) for all six docking mechanisms.
Recent increase in the occurrences of Christmas typhoons in the Western North Pacific
Authors: Basconcillo Joseph , Moon Il-Ju
Published: April 2021

To imply the gravity of their impact on Christmas celebration, the term Christmas typhoon recently became more popular to refer to tropical cyclones (TC) in the Western North Pacific (WNP) during its less active season. The past 9 years from 2012 to 2020 saw more than 70% (210%) increases in Christmas typhoon occurrences in the WNP (Philippines). Furthermore, Mindanao Island, which is located in southern Philippines, has experienced an unprecedented 480% increase in TC passage in the same period. Here we show that the detected recent increase in Christmas typhoons are mainly associated with the shift of the Pacific Decadal Oscillation to its positive phase in early 2010s, which led to favorable changes in the large-scale environment for TC development such as higher relative vorticity, anomalous low-level westerlies, warmer sea surface temperatures in the central Pacific, and extended WNP subtropical high. We also found that the poleward shift of the Intertropical Convergence Zone and possibly, the recent recovery of the Siberian High contributed to such increased occurrences. As opposed to the more active TC season, there is a wide research gap during the less active season. We aim to fill in this knowledge gap to gain better insights on TC risk reduction.
Neurocysticercosis in patients with active epilepsy in the tea garden community of Assam, Northeast India
Authors: Devi K. Rekha , Borbora Debasish , Upadhyay Narayan , Goswami Dibyajyoti , Rajguru S. K. , Narain Kanwar
Published: April 2021

Neurocysticercosis is a significant cause of epilepsy in the tropics. The present cross-sectional survey was conducted in the socioeconomically backward tea garden community of Assam to gauge the prevalence of neurocysticercosis in patients with active epilepsy and to determine the associated risk factors. In a door to door survey, a total of 1028 individuals from every fifth household of the study Teagarden were enrolled to identify self-reported seizure cases, followed by a neurological examination to confirm the diagnosis of active epilepsy. Patients with active epilepsy underwent clinical, epidemiological, neuroimaging (contrast-enhanced computerized tomography) and immunological evaluations to establish the diagnosis of neurocysticercosis. Clinically confirmed 53 (5.16%) active epilepsy were identified; 45 agreed to further assessment for neurocysticercosis and 19 (42.2%) cases fulfilled either definitive or probable diagnostic criteria for neurocysticercosis. Patients with epilepsy due to neurocysticercosis were more likely to suffer from taeniasis (20.0% vs 0.0%), rear pigs (57.9% vs 15.4%) or have pigs in their neighbourhood (78.9% vs 53.8%) relative to epileptic patients without neurocysticercosis. Rearing pigs (aOR 14.35, 95% CI: 3.98–51.75) or having pigs in the neighbourhood (aOR 12.34, 95% CI: 2.53–60.31) were independent risk factors of neurocysticercosis. In this community, the prevalence of taeniasis (adult worm infection) was 6.6% based on microscopy. The study reports a high prevalence of active epilepsy in the tea garden community of Assam and neurocysticercosis as its primary cause. The high prevalence of taeniasis is also a significant concern.
An opioid-sparing protocol with intravenous parecoxib can effectively reduce morphine consumption after simultaneous bilateral total knee arthroplasty
Authors: Ma Hsuan-Hsiao , Chou Te-Feng Arthur , Wang Hsin-Yi , Tsai Shang-Wen , Chen Cheng-Fong , Wu Po-Kuei , Chen Wei-Ming
Published: April 2021

Multimodal pain management protocol effectively relieves pain following simultaneous bilateral total knee arthroplasty (SBTKA) but is associated with administration of large amounts of opioids in the perioperative period. In this prospective, randomized, assessor-blinded, single-surgeon clinical trial, the goal was to validate the efficacy of an opioid-sparing protocol for SBTKA with a reduced opioid dose, while achieving similar pain relief with few adverse events. Fifty-six patients who had undergone SBTKA were randomly allocated to receive either an opioid-sparing or opioid-based protocol. The primary outcome parameters were visual analogue scale (VAS) scores at rest, with movement, and cumulative morphine dose, through time. Secondary outcome parameters included drug-related adverse events and range of motion with continuous passive motion device, through time. In the opioid-sparing group, a lower VAS score with movement at postoperative 24 and 72 h was observed compared with the opioid-based group, but the difference did not reach the minimal clinically importance difference. A reduced cumulative morphine dose was noted in the opioid-sparing group at postoperative 24, 48 and 72 h. In conclusion, the opioid-sparing protocol may be used as an alternative modality for pain management following SBTKA. Similar pain relief effects may be achieved utilizing a reduced cumulative opioid dose, with few opioid related adverse events.
Tumor innervation and clinical outcome in pancreatic cancer
Authors: Ferdoushi Aysha , Griffin Nathan , Marsland Mark , Xu Xiaoyue , Faulkner Sam , Gao Fangfang , Liu Hui , King Simon J. , Denham James W. , van Helden Dirk F. , Jobling Phillip , Jiang Chen Chen , Hondermarck Hubert
Published: April 2021

Pancreatic cancer is a highly aggressive malignancy characterized by poor survival, recurrence after surgery and resistance to therapy. Nerves infiltrate the microenvironment of pancreatic cancers and contribute to tumor progression, however the clinicopathological significance of tumor innervation is unclear. In this study, the presence of nerves and their cross-sectional size were quantified by immunohistochemistry for the neuronal markers S-100, PGP9.5 and GAP-43 in a series of 99 pancreatic cancer cases versus 71 normal adjacent pancreatic tissues. A trend was observed between the presence of nerves in the tumor microenvironment of pancreatic cancer and worse overall patient survival (HR = 1.8, 95% CI 0.77–4.28, p = 0.08). The size of nerves, as measured by cross-sectional area, were significantly higher in pancreatic cancer than in the normal adjacent tissue (p = 0.002) and larger nerves were directly associated with worse patient survival (HR = 0.41, 95% CI 0.19–0.87, p = 0.04). In conclusion, this study suggests that the presence and size of nerves within the pancreatic cancer microenvironment are associated with tumor aggressiveness.
A cell-specific regulatory region of the human ABO blood group gene regulates the neighborhood gene encoding odorant binding protein 2B
Authors: Sano Rie , Takahashi Yoichiro , Fukuda Haruki , Harada Megumi , Hayakawa Akira , Okawa Takafumi , Kubo Rieko , Takeshita Haruo , Tsukada Junichi , Kominato Yoshihiko
Published: April 2021

The human ABO blood group system is of great importance in blood transfusion and organ transplantation.ABOtranscription is known to be regulated by a constitutive promoter in a CpG island and regions for regulation of cell-specific expression such as the downstream + 22.6-kb site for epithelial cells and a site in intron 1 for erythroid cells. Here we investigated whether the + 22.6-kb site might play a role in transcriptional regulation of the gene encoding odorant binding protein 2B (OBP2B), which is located on the centromere side 43.4 kb from the + 22.6-kb site. In the gastric cancer cell line KATOIII, quantitative PCR analysis demonstrated significantly reduced amounts ofOBP2BandABOtranscripts in mutant cells with biallelic deletions of the site created using the CRISPR/Cas9 system, relative to those in the wild-type cells, and Western blotting demonstrated a corresponding reduction of OBP2B protein in the mutant cells. Moreover, single-molecule fluorescence in situ hybridization assays indicated that the amounts of both transcripts were correlated in individual cells. These findings suggest thatOBP2Bcould be co-regulated by the + 22.6-kb site ofABO.
Intracranial failure after hippocampal-avoidance prophylactic cranial irradiation in limited-stage small-cell lung cancer patients
Authors: Cho Yeona , Lee Joongyo , Lee Ik Jae , Kim Jun Won , Baek Jong Geol , Jung Dong Min , Cho Byoung Chul , Hong Min Hee , Kim Hye Ryun , Lee Chang Geol , Yoon Hong In
Published: April 2021

We evaluated intracranial failure after hippocampus-avoidance-prophylactic cranial irradiation (HA-PCI) for limited-stage small-cell lung cancer (SCLC). Data of 106 patients who received PCI with 25 Gy were retrospectively reviewed. The patients were divided into two groups based on whether they underwent HA-PCI: the HA-PCI group (n = 48) and the conventional PCI (C-PCI) group (n = 58). Twenty-one patients experienced intracranial failure: 11 and 10 patients in the C-PCI and HA-PCI groups, respectively. Using the log-rank test, the intracranial failure rate was not significantly different between the groups (p = 0.215). No clinical factor was significantly associated with intracranial failure in multivariate Cox regression analysis, but HA-PCI tended to be associated with increased incidence of intracranial failure (HR 2.87, 95% CI 0.86–9.58, p = 0.087). Among patients who received HA-PCI, two developed peri-hippocampal recurrence. A higher thoracic radiotherapy dose (≥ 60 Gy) was significantly associated with DFS (HR 0.52, p = 0.048) and OS (HR 0.35, p = 0.003). However, HA-PCI was associated with neither DFS nor OS. Although HA-PCI may be associated with an increased risk of intracranial failure, HA-PCI did not impair disease control or survival. Future prospective randomized trials are needed to reach a definite conclusion.