bluuebunny/crossref_metadata_2025 huggingface dataset:
Cdk5rap3 is essential for intestinal Paneth cell development and maintenance
Authors: Quintero Michaela , Liu Siyang , Xia Yanhua , Huang Yonghong , Zou Yi , Li Ge , Hu Ling , Singh Nagendra , Blumberg Richard , Cai Yafei , Xu Hong , Li Honglin
Published: January 2021

Intestinal Paneth cells are professional exocrine cells that play crucial roles in maintenance of homeostatic microbiome, modulation of mucosal immunity, and support for stem cell self-renewal. Dysfunction of these cells may lead to the pathogenesis of human diseases such as inflammatory bowel disease (IBD). Cdk5 activator binding protein Cdk5rap3 (also known as C53 and LZAP) was originally identified as a binding protein of Cdk5 activator p35. Although previous studies have indicated its involvement in a wide range of signaling pathways, the physiological function of Cdk5rap3 remains largely undefined. In this study, we found that Cdk5rap3 deficiency resulted in very early embryonic lethality, indicating its indispensable role in embryogenesis. To further investigate its function in the adult tissues and organs, we generated intestinal epithelial cell (IEC)-specific knockout mouse model to examine its role in intestinal development and tissue homeostasis. IEC-specific deletion of Cdk5rap3 led to nearly complete loss of Paneth cells and increased susceptibility to experimentally induced colitis. Interestingly, Cdk5rap3 deficiency resulted in downregulation of key transcription factors Gfi1 and Sox9, indicating its crucial role in Paneth cell fate specification. Furthermore, Cdk5rap3 is highly expressed in mature Paneth cells. Paneth cell-specific knockout of Cdk5rap3 caused partial loss of Paneth cells, while inducible acute deletion of Cdk5rap3 resulted in disassembly of the rough endoplasmic reticulum (RER) and abnormal zymogen granules in the mature Paneth cells, as well as loss of Paneth cells. Together, our results provide definitive evidence for the essential role of Cdk5rap3 in Paneth cell development and maintenance.
Complete sequences of Schizosaccharomyces pombe subtelomeres reveal multiple patterns of genome variation
Authors: Oizumi Yusuke , Kaji Takuto , Tashiro Sanki , Takeshita Yumiko , Date Yuko , Kanoh Junko
Published: January 2021

Genome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess single SH regions of a standard laboratory strain. In addition, some natural isolates of S. pombe were analyzed using previous sequencing data. Whole sequences of SH regions revealed that each SH region consists of two distinct parts with mosaics of multiple common segments or blocks showing high variation among subtelomeres and strains. Subtelomere regions show relatively high frequency of nucleotide variations among strains compared with the other chromosomal regions. Furthermore, we identified subtelomeric RecQ-type helicase genes, tlh3 and tlh4, which add to the already known tlh1 and tlh2, and found that the tlh1–4 genes show high sequence variation with missense mutations, insertions, and deletions but no severe effects on their RNA expression. Our results indicate that SH sequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.
Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics
Authors: Pillon Monica C. , Frazier Meredith N. , Dillard Lucas B. , Williams Jason G. , Kocaman Seda , Krahn Juno M. , Perera Lalith , Hayne Cassandra K. , Gordon Jacob , Stewart Zachary D. , Sobhany Mack , Deterding Leesa J. , Hsu Allen L. , Dandey Venkata P. , Borgnia Mario J. , Stanley Robin E.
Published: January 2021

Nsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses have shown a common hexameric assembly, yet how the enzyme recognizes and processes RNA remains poorly understood. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15, in both apo and UTP-bound states. The cryo-EM reconstructions, combined with biochemistry, mass spectrometry, and molecular dynamics, expose molecular details of how critical active site residues recognize uridine and facilitate catalysis of the phosphodiester bond. Mass spectrometry revealed the accumulation of cyclic phosphate cleavage products, while analysis of the apo and UTP-bound datasets revealed conformational dynamics not observed by crystal structures that are likely important to facilitate substrate recognition and regulate nuclease activity. Collectively, these findings advance understanding of how Nsp15 processes viral RNA and provide a structural framework for the development of new therapeutics.
TALEN outperforms Cas9 in editing heterochromatin target sites
Authors: Jain Surbhi , Shukla Saurabh , Yang Che , Zhang Meng , Fatma Zia , Lingamaneni Manasi , Abesteh Shireen , Lane Stephan Thomas , Xiong Xiong , Wang Yuchuan , Schroeder Charles M. , Selvin Paul R. , Zhao Huimin
Published: January 2021

Genome editing critically relies on selective recognition of target sites. However, despite recent progress, the underlying search mechanism of genome-editing proteins is not fully understood in the context of cellular chromatin environments. Here, we use single-molecule imaging in live cells to directly study the behavior of CRISPR/Cas9 and TALEN. Our single-molecule imaging of genome-editing proteins reveals that Cas9 is less efficient in heterochromatin than TALEN because Cas9 becomes encumbered by local searches on non-specific sites in these regions. We find up to a fivefold increase in editing efficiency for TALEN compared to Cas9 in heterochromatin regions. Overall, our results show that Cas9 and TALEN use a combination of 3-D and local searches to identify target sites, and the nanoscopic granularity of local search determines the editing outcomes of the genome-editing proteins. Taken together, our results suggest that TALEN is a more efficient gene-editing tool than Cas9 for applications in heterochromatin.
Niche derived netrin-1 regulates hematopoietic stem cell dormancy via its receptor neogenin-1
Authors: Renders Simon , Svendsen Arthur Flohr , Panten Jasper , Rama Nicolas , Maryanovich Maria , Sommerkamp Pia , Ladel Luisa , Redavid Anna Rita , Gibert Benjamin , Lazare Seka , Ducarouge Benjamin , Schönberger Katharina , Narr Andreas , Tourbez Manon , Dethmers-Ausema Bertien , Zwart Erik , Hotz-Wagenblatt Agnes , Zhang Dachuan , Korn Claudia , Zeisberger Petra , Przybylla Adriana , Sohn Markus , Mendez-Ferrer Simon , Heikenwälder Mathias , Brune Maik , Klimmeck Daniel , Bystrykh Leonid , Frenette Paul S. , Mehlen Patrick , de Haan Gerald , Cabezas-Wallscheid Nina , Trumpp Andreas
Published: January 2021

Haematopoietic stem cells (HSCs) are characterized by their self-renewal potential associated to dormancy. Here we identify the cell surface receptor neogenin-1 as specifically expressed in dormant HSCs. Loss of neogenin-1 initially leads to increased HSC expansion but subsequently to loss of self-renewal and premature exhaustion in vivo. Its ligand netrin-1 induces Egr1 expression and maintains quiescence and function of cultured HSCs in a Neo1 dependent manner. Produced by arteriolar endothelial and periarteriolar stromal cells, conditional netrin-1 deletion in the bone marrow niche reduces HSC numbers, quiescence and self-renewal, while overexpression increases quiescence in vivo. Ageing associated bone marrow remodelling leads to the decline of netrin-1 expression in niches and a compensatory but reversible upregulation of neogenin-1 on HSCs. Our study suggests that niche produced netrin-1 preserves HSC quiescence and self-renewal via neogenin-1 function. Decline of netrin-1 production during ageing leads to the gradual decrease of Neo1 mediated HSC self-renewal.
APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling
Authors: Liu Tung-Chang , Lin Chun-Ting , Chang Kai-Cheng , Guo Kai-Wei , Wang Shuying , Chu Jhih-Wei , Hsiao Yu-Yuan
Published: January 2021

The exonuclease activity of Apurinic/apyrimidinic endonuclease 1 (APE1) is responsible for processing matched/mismatched terminus in various DNA repair pathways and for removing nucleoside analogs associated with drug resistance. To fill in the gap of structural basis for exonucleolytic cleavage, we determine the APE1-dsDNA complex structures displaying end-binding. As an exonuclease, APE1 does not show base preference but can distinguish dsDNAs with different structural features. Integration with assaying enzyme activity and binding affinity for a variety of substrates reveals for the first time that both endonucleolytic and exonucleolytic cleavage can be understood by an induced space-filling model. Binding dsDNA induces RM (Arg176 and Met269) bridge that defines a long and narrow product pocket for exquisite machinery of substrate selection. Our study paves the way to comprehend end-processing of dsDNA in the cell and the drug resistance relating to APE1.
LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate
Authors: Jin Run , Klasfeld Samantha , Zhu Yang , Fernandez Garcia Meilin , Xiao Jun , Han Soon-Ki , Konkol Adam , Wagner Doris
Published: January 2021

Master transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet little is known about pioneer transcription factors in this kingdom. Here, we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1. Upon binding, LFY ‘unlocks’ chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between LFY and animal pioneer transcription factor.
Rpd3/CoRest-mediated activity-dependent transcription regulates the flexibility in memory updating in Drosophila
Authors: Takakura Mai , Nakagawa Reiko , Ota Takeshi , Kimura Yoko , NG Man Yung , Alia Abdalla G. , Okuno Hiroyuki , Hirano Yukinori
Published: January 2021

Consolidated memory can be preserved or updated depending on the environmental change. Although such conflicting regulation may happen during memory updating, the flexibility of memory updating may have already been determined in the initial memory consolidation process. Here, we explored the gating mechanism for activity-dependent transcription in memory consolidation, which is unexpectedly linked to the later memory updating in Drosophila. Through proteomic analysis, we discovered that the compositional change in the transcriptional repressor, which contains the histone deacetylase Rpd3 and CoRest, acts as the gating mechanism that opens and closes the time window for activity-dependent transcription. Opening the gate through the compositional change in Rpd3/CoRest is required for memory consolidation, but closing the gate through Rpd3/CoRest is significant to limit future memory updating. Our data indicate that the flexibility of memory updating is determined through the initial activity-dependent transcription, providing a mechanism involved in defining memory state.
Murine liver repair via transient activation of regenerative pathways in hepatocytes using lipid nanoparticle-complexed nucleoside-modified mRNA
Authors: Rizvi Fatima , Everton Elissa , Smith Anna R. , Liu Hua , Osota Elizabeth , Beattie Mitchell , Tam Ying , Pardi Norbert , Weissman Drew , Gouon-Evans Valerie
Published: January 2021

Induction of intrinsic liver regeneration is an unmet need that can be achieved by temporally activating key hepatocyte regenerative pathways. Here, we establish an efficient, safe, non-integrative method to transiently express hepatocyte-growth-factor (HGF) and epidermal-growth-factor (EGF) in hepatocytes via nucleoside-modified, lipid-nanoparticle-encapsulated mRNA (mRNA-LNP) delivery in mice. We confirm specific hepatotropism of mRNA-LNP via intravenous injection of firefly luciferase encoding mRNA-LNP, with protein expression lasting about 3 days. In the liver, virtually all hepatocytes are transfected along with a subpopulation of endothelial and Kupffer cells. In homeostasis, HGF mRNA-LNP efficiently induce hepatocyte proliferation. In a chronic liver injury mouse model recapitulating non-alcoholic fatty liver disease, injections of both HGF and EGF mRNA-LNP sharply reverse steatosis and accelerate restoration of liver function. Likewise, HGF and EGF mRNA-LNP accelerate liver regeneration after acetaminophen-induced acute liver injury with rapid return to baseline ALT levels. This study introduces mRNA-LNP as a potentially translatable safe therapeutic intervention to harness liver regeneration via controlled expression of endogenous mitogens in vivo.
Desynchronized liquid crystalline network actuators with deformation reversal capability
Authors: Xiao Yao-Yu , Jiang Zhi-Chao , Hou Jun-Bo , Zhao Yue
Published: January 2021

Liquid crystalline network (LCN) actuator normally deforms upon thermally or optically induced order-disorder phase transition, switching once between two shapes (shape 1 in LC phase and shape 2 in isotropic state) for each stimulation on/off cycle. Herein, we report an LCN actuator that deforms from shape 1 to shape 2 and then reverses the deformation direction to form shape 3 on heating or under light only, thus completing the shape switch twice for one stimulation on/off cycle. The deformation reversal capability is obtained with a monolithic LCN actuator whose two sides are made to start deforming at different temperatures and exerting different reversible strains, by means of asymmetrical crosslinking and/or asymmetrical stretching. This desynchronized actuation strategy offers possibilities in developing light-fueled LCN soft robots. In particular, the multi-stage bidirectional shape change enables multimodal, light-driven locomotion from the same LCN actuator by simply varying the light on/off times.
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
Authors: Lovell John T. , MacQueen Alice H. , Mamidi Sujan , Bonnette Jason , Jenkins Jerry , Napier Joseph D. , Sreedasyam Avinash , Healey Adam , Session Adam , Shu Shengqiang , Barry Kerrie , Bonos Stacy , Boston LoriBeth , Daum Christopher , Deshpande Shweta , Ewing Aren , Grabowski Paul P. , Haque Taslima , Harrison Melanie , Jiang Jiming , Kudrna Dave , Lipzen Anna , Pendergast Thomas H. , Plott Chris , Qi Peng , Saski Christopher A. , Shakirov Eugene V. , Sims David , Sharma Manoj , Sharma Rita , Stewart Ada , Singan Vasanth R. , Tang Yuhong , Thibivillier Sandra , Webber Jenell , Weng Xiaoyu , Williams Melissa , Wu Guohong Albert , Yoshinaga Yuko , Zane Matthew , Zhang Li , Zhang Jiyi , Behrman Kathrine D. , Boe Arvid R. , Fay Philip A. , Fritschi Felix B. , Jastrow Julie D. , Lloyd-Reilley John , Martínez-Reyna Juan Manuel , Matamala Roser , Mitchell Robert B. , Rouquette Francis M. , Ronald Pamela , Saha Malay , Tobias Christian M. , Udvardi Michael , Wing Rod A. , Wu Yanqi , Bartley Laura E. , Casler Michael , Devos Katrien M. , Lowry David B. , Rokhsar Daniel S. , Grimwood Jane , Juenger Thomas E. , Schmutz Jeremy
Published: January 2021

Long-term climate change and periodic environmental extremes threaten food and fuel security1and global crop productivity2–4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6—knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.
Alarming coastal vulnerability of the deltaic and sandy beaches of North Africa
Authors: Hzami Abderraouf , Heggy Essam , Amrouni Oula , Mahé Gil , Maanan Mohamed , Abdeljaouad Saâdi
Published: January 2021

The arid coasts of North Africa, extending over 4633 km from the Gulf of Tunis to the Nile Delta, are undergoing pronounced shoreline retreats and coastal floodings that are reported as a consequence of the ongoing sea level rise resulting from global warming. Of particular interest are the abnormal shoreline dynamics for deltaic and sandy beaches, which are severely impacted by abrupt decadal variabilities in both climatic and anthropogenic drivers resulting in their increased vulnerability to disturbances from coastal hazards. Unfortunately, the evolution, distribution and impacts of these drivers remain largely unquantified, let alone understood, for these extensive arid coasts that harbor the major portion of North Africa’s population as well as unique and fragile marine ecosystems. To address this deficiency, we use GIS-based multi-criteria approaches combined with analytic hierarchy process to map the Coastal Vulnerability Index and the Socioeconomic Vulnerability Index along these coasts to investigate the amplitude and extent of shoreline deterioration resulting from sudden fluctuations in sediment transport to the coastline. We use the western bay of the Gulf of Tunis, the coasts of Tripoli and the Nile Delta as three validation sites for our vulnerability assessment. The statistical Integrated Coastal Vulnerability Index map reveals that 47% of arid North African coasts are characterized by high to very high vulnerability. In particular, we observe that the densely populated deltaic coasts in both Tunisia and Egypt are 70% more vulnerable than any others coast in the eastern Mediterranean Basin. These abnormally high-vulnerability extensive areas are also correlated with significant deterioration of coastal aquifers and hence in crop production, compromising local food security and resulting in increasing outflow migration trends. Both Tunisia and Egypt observed dramatic increases in the net population outflow migration by respectively 62% and 248% between 2000 and 2016, mostly from coastal areas. Our source analysis of the amplitude and extent of these high coastal vulnerabilities suggests that they result from the anthropogenic drivers of damming and rapid urban growth over the last few decades rather than the effects of global warming.
Cyclophosphamide arrhythmogenicitytesting using human-induced pluripotent stem cell-derived cardiomyocytes
Authors: Podgurskaya A. D. , Slotvitsky M. M. , Tsvelaya V. A. , Frolova S. R. , Romanova S. G. , Balashov V. A. , Agladze K. I.
Published: January 2021

Cyclophosphamide (CP) is an anticancer drug, an alkylating agent. Cardiotoxicity of CP is associated with one of its metabolites, acrolein, and clinical cardiotoxicity manifestations are described for cases of taking CP in high doses. Nevertheless, modern arrhythmogenicity prediction assays in vitro include evaluation of beat rhythm and rate as well as suppression of cardiac late markers after acute exposure to CP, but not its metabolites. The mechanism of CP side effects when taken at low doses (i.e., < 100 mg/kg), especially at the cellular level, remains unclear. In this study conduction properties and cytoskeleton structure of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) obtained from a healthy donor under CP were evaluated. Arrhythmogenicity testing including characterization of 3 values: conduction velocity, maximum capture rate (MCR) measurements and number of occasions of re-entry on a standard linear obstacle was conducted and revealed MCR decrease of 25% ± 7% under CP. Also, conductivity area reduced by 34 ± 15%. No effect of CP on voltage-gated ion channels was found. Conduction changes (MCR and conductivity area decrease) are caused by exposure time-dependent alpha-actinin disruption detected both in hiPSC-CMs and neonatal ventricular cardiomyocytes in vitro. Deviation from the external stimulus frequency and appearance of non-conductive areas in cardiac tissue under CP is potentially arrhythmogenic and could develop arrhythmic effects in vivo.
The novel Dbl homology/BAR domain protein, MsgA, of Talaromyces marneffei regulates yeast morphogenesis during growth inside host cells
Authors: Weerasinghe Harshini , Bugeja Hayley E. , Andrianopoulos Alex
Published: January 2021

Microbial pathogens have evolved many strategies to evade recognition by the host immune system, including the use of phagocytic cells as a niche within which to proliferate. Dimorphic pathogenic fungi employ an induced morphogenetic transition, switching from multicellular hyphae to unicellular yeast that are more compatible with intracellular growth. A switch to mammalian host body temperature (37 °C) is a key trigger for the dimorphic switch. This study describes a novel gene, msgA, from the dimorphic fungal pathogen Talaromyces marneffei that controls cell morphology in response to host cues rather than temperature. The msgA gene is upregulated during murine macrophage infection, and deletion results in aberrant yeast morphology solely during growth inside macrophages. MsgA contains a Dbl homology domain, and a Bin, Amphiphysin, Rvs (BAR) domain instead of a Plekstrin homology domain typically associated with guanine nucleotide exchange factors (GEFs). The BAR domain is crucial in maintaining yeast morphology and cellular localisation during infection. The data suggests that MsgA does not act as a canonical GEF during macrophage infection and identifies a temperature independent pathway in T. marneffei that controls intracellular yeast morphogenesis.
Dendrons containing boric acid and 1,3,5-tris(2-hydroxyethyl)isocyanurate covalently attached to silica-coated magnetite for the expeditious synthesis of Hantzsch esters
Authors: Sam Mahsa , Dekamin Mohammad G. , Alirezvani Zahra
Published: January 2021

A new multifunctional dendritic nanocatalyst containing boric acid and 1,3,5-tris(2-hydroxyethyl)isocyanurate covalently attached to core–shell silica-coated magnetite (Fe3O4@SiO2@PTS-THEIC-(CH2)3OB(OH)2) was designed and properly characterized by different spectroscopic or microscopic methods as well as analytical techniques used for mesoporous materials. It was found that the combination of both aromatic π–π stacking and boron–oxygen ligand interactions affords supramolecular arrays of dendrons. Furthermore, the use of boric acid makes this dendritic catalyst a good choice, from corrosion, recyclability and cost points of view. The catalytic activity of Fe3O4@SiO2@PTS-THEIC-(CH2)3OB(OH)2, as an efficient magnetically recoverable catalyst, was investigated for the synthesis of polyhydroacridines (PHAs) as well as polyhydroquinolines (PHQs) via one-pot multicomponent reactions of dimedone and/or ethyl acetoacetate, different aldehydes and ammonium acetate in EtOH under reflux conditions. Very low loading of the catalyst, high to quantitative yields of the desired PHAs or PHQs products, short reaction times, wide scope of the substrates, eliminating any toxic heavy metals or corrosive reagents for the modification of the catalyst, and simple work-up procedure are remarkable advantages of this green protocol. An additional advantage of this magnetic nanoparticles catalyst is its ability to be separated and recycled easily from the reaction mixture with minimal efforts in six subsequent runs without significant loss of its catalytic activity. This magnetic and dendritic catalyst can be extended to new two- and three-dimensional covalent organic frameworks with different applications.
Long-term tillage effect on with-in season variations in soil conditions and respiration from dryland winter wheat and soybean cropping systems
Authors: Zapata Diana , Rajan Nithya , Mowrer Jake , Casey Kenneth , Schnell Ronnie , Hons Frank
Published: January 2021

Soil respiration from agricultural soils is a major anthropogenic source of CO2to the atmosphere. With-in season emission of soil CO2from croplands are affected by changes in weather, tillage, plant row spacing, and plant growth stage. Tillage involves physical turning of soils which accelerate residue decomposition and CO2emission. No-tillage lacks soil disturbance and residues undergo slower decomposition at the surface. In this study, we compared with-in season soil conditions (temperature and moisture) and soil respiration from two major crops (soybean and winter wheat) by making high temporal frequency measurements using automated chambers at half-hourly intervals. The experiment lasted for 179 days. Total number of measurements made from conventional and no-tillage soybean and winter wheat plots were 6480 and 4456, respectively. Average flux after the winter-dormancy period of wheat was 37% higher in tilled soil compared to no-till soil. However, average flux during the soybean growing season was 8% lower in conventional till compared to no-till soil. This differential response of soil respiration in wheat and soybean was primarily due to tillage-induced changes in surface characteristics (residue cover) and soil environmental conditions (soil temperature and soil moisture). Results from this study can help elucidate relationships for modeling and assessment of field-scale soil CO2emissions from dryland wheat and soybean crops grown in sub-tropics.
Classification of colorectal tissue images from high throughput tissue microarrays by ensemble deep learning methods
Authors: Nguyen Huu-Giao , Blank Annika , Dawson Heather E. , Lugli Alessandro , Zlobec Inti
Published: January 2021

Tissue microarray (TMA) core images are a treasure trove for artificial intelligence applications. However, a common problem of TMAs is multiple sectioning, which can change the content of the intended tissue core and requires re-labelling. Here, we investigate different ensemble methods for colorectal tissue classification using high-throughput TMAs. Hematoxylin and Eosin (H&E) core images of 0.6 mm or 1.0 mm diameter from three international cohorts were extracted from 54 digital slides (n = 15,150 cores). After TMA core extraction and color enhancement, five different flows of independent and ensemble deep learning were applied. Training and testing data with 2144 and 13,006 cores included three classes: tumor, normal or “other” tissue. Ground-truth data were collected from 30 ngTMA slides (n = 8689 cores). A test augmentation is applied to reduce the uncertain prediction. Predictive accuracy of the best method, namely Soft Voting Ensemble of one VGG and one CapsNet models was 0.982, 0.947 and 0.939 for normal, “other” and tumor, which outperformed to independent or ensemble learning with one base-estimator. Our high-accuracy algorithm for colorectal tissue classification in high-throughput TMAs is amenable to images from different institutions, core sizes and stain intensity. It helps to reduce error in TMA core evaluations with previously given labels.
Birth elicits a conserved neuroendocrine response with implications for perinatal osmoregulation and neuronal cell death
Authors: Hoffiz Yarely C. , Castillo-Ruiz Alexandra , Hall Megan A. L. , Hite Taylor A. , Gray Jennifer M. , Cisternas Carla D. , Cortes Laura R. , Jacobs Andrew J. , Forger Nancy G.
Published: January 2021

Long-standing clinical findings report a dramatic surge of vasopressin in umbilical cord blood of the human neonate, but the neural underpinnings and function(s) of this phenomenon remain obscure. We studied neural activation in perinatal mice and rats, and found that birth triggers activation of the suprachiasmatic, supraoptic, and paraventricular nuclei of the hypothalamus. This was seen whether mice were born vaginally or via Cesarean section (C-section), and when birth timing was experimentally manipulated. Neuronal phenotyping showed that the activated neurons were predominantly vasopressinergic, and vasopressin mRNA increased fivefold in the hypothalamus during the 2–3 days before birth. Copeptin, a surrogate marker of vasopressin, was elevated 30-to 50-fold in plasma of perinatal mice, with higher levels after a vaginal than a C-section birth. We also found an acute decrease in plasma osmolality after a vaginal, but not C-section birth, suggesting that the difference in vasopressin release between birth modes is functionally meaningful. When vasopressin was administered centrally to newborns, we found an ~ 50% reduction in neuronal cell death in specific brain areas. Collectively, our results identify a conserved neuroendocrine response to birth that is sensitive to birth mode, and influences peripheral physiology and neurodevelopment.
The inflammatory response induced by Pseudomonas aeruginosa in macrophages enhances apoptotic cell removal
Authors: Jäger Adriana Valeria , Arias Paula , Tribulatti Maria Virginia , Brocco Marcela Adriana , Pepe Maria Victoria , Kierbel Arlinet
Published: January 2021

Pathogens phagocytosis and the uptake of apoptotic cells (efferocytosis) are essential macrophages tasks, classically considered as mutually exclusive. Macrophages have been observed to polarize into either pro-inflammatory/microbicidal or anti-inflammatory/efferocytic phenotypes. However, macrophage functions have shown to be more complex. Furthermore, little is known about the regulation of efferocytosis under inflammatory conditions. In this study, we elucidate the modulation of the macrophage efferocytic function during an inflammatory stimulus. We find that bone marrow-derived macrophages (BMDM) are very efficient in engulfing both the bacterial pathogen Pseudomonas aeruginosa and apoptotic cells. BMDM showed a high bactericidal capacity unaffected by the concomitant presence of apoptotic material. Plasticity in macrophage programming, in response to changing environmental cues, may modulate efferocytic capability. In this work, we further show that, after phagocyting and processing Pseudomonas aeruginosa, macrophages highly increase their efferocytic capacity without affecting their phagocytic function. Moreover, we demonstrate that Pseudomonas aeruginosa enhances efferocytosis of these phagocytes through the IL-6 signaling pathway. Our results show that the inflammatory response generated by the bacterial processing enhances these macrophages’ capacity to control inflammation through an increased efferocytosis.
Epithelial and stromal remodelling following femtosecond laser–assisted stromal lenticule addition keratoplasty (SLAK) for keratoconus
Authors: Nubile Mario , Salgari Niccolò , Mehta Jodhbir S. , Calienno Roberta , Erroi Emanuele , Bondì Jessica , Lanzini Manuela , Liu Yu-Chi , Mastropasqua Leonardo
Published: January 2021

The purpose of this study was to evaluate corneal epithelium and stromal remodelling with anterior segment optical coherence tomography in patients who have undergone stromal lenticule addition keratoplasty (SLAK) for advanced keratoconus. This was a prospective non-comparative observational study. Fifteen eyes of 15 patients with advanced keratoconus underwent implantation with a cadaveric, donor negative meniscus-shaped intrastromal lenticule, produced with a femtosecond laser, into a stromal pocket dissected in the recipient cornea at a depth of 120 μm. Simulated keratometry, central corneal thickness (CTT), corneal thinnest point (CTP), central epithelial thickness (CET), central and peripheral lenticule thickness, anterior and posterior stromal thickness were measured. Regional central corneal epithelial thickness (CET) and variations in the inner annular area (IAT) and outer annular area (OAT) were also analysed. All parameters were measured preoperatively and 1, 3, and 6 months postoperatively. The average anterior Sim-k decreased from 59.63 ± 7.58 preoperatively to 57.19 ± 6.33 D 6 months postoperatively. CCT, CTP, CET, and OAT increased and IAT decreased significantly after 1 month. All parameters appeared unchanged at 6-months except that of OAT that further increased. Lenticule thickness was stable. In conclusion we observed that SLAK reshapes the cornea by central flattening with stromal thickening and epithelial thickness restoration.
Effect of alcohol consumption on kidney function: population-based cohort study
Authors: Lee Yu-Ji , Cho Seong , Kim Sung Rok
Published: January 2021

The association between alcohol consumption and kidney function is intriguing, but study results are mixed and controversial. We examined the association of alcohol consumption with the overall change in kidney function over 12 years. We analyzed data from a population-based cohort that was part of the Korean Genome and Epidemiology Study. Primary exposure was total alcohol intake (non-drinkers, 0 to < 10 g/day, 10 to < 30 g/day, and ≥ 30 g/day). Main outcome was decline in kidney function over 12 years. Our study included 5729 participants (mean [SD] age, 51 [8] years; 46% males). Compared to non-drinkers, higher alcohol intake groups had lesser reduction in estimated glomerular filtration rate (eGFR) over 12 years; fully adjusted beta coefficients and 95% confidence intervals were 0.45 (− 0.27, 1.18), 1.87 (0.88, 2.87), and 3.08 (1.93, 4.24) for participants with alcohol intake of < 10, 10 to < 30, and ≥ 30 g/day, respectively. However, this association was attenuated among women, smoker, and age ≥ 60 year. Compared with not drinking, more frequent alcohol consumption and binge drinking were associated with lesser reduction in eGFR. Our findings suggest that alcohol consumption may have a favorable effect on kidney function among the general population.
Lab-on-chip analyser for the in situ determination of dissolved manganese in seawater
Authors: Geißler Felix , Achterberg Eric P. , Beaton Alexander D. , Hopwood Mark J. , Esposito Mario , Mowlem Matt C. , Connelly Douglas P. , Wallace Douglas
Published: January 2021

A spectrophotometric approach for quantification of dissolved manganese (DMn) with 1-(2-pyridylazo)-2-naphthol (PAN) has been adapted for in situ application in coastal and estuarine waters. The analyser uses a submersible microfluidic lab-on-chip device, with low power (~ 1.5 W) and reagent consumption (63 µL per sample). Laboratory characterization showed an absorption coefficient of 40,838 ± 1127 L⋅mol−1⋅cm−1 and a detection limit of 27 nM, determined for a 34.6 mm long optical detection cell. Laboratory tests showed that long-term stability of the PAN reagent was achieved by addition of 4% v/v of a non-ionic surfactant (Triton-X100). To suppress iron (Fe) interferences with the PAN reagent, the Fe(III) masking agents deferoxamine mesylate (DFO-B) or disodium 4,5-dihydroxy-1,3-benzenedisulfonate (Tiron) were added and their Fe masking efficiencies were investigated. The analyser was tested during a deployment over several weeks in Kiel Fjord (Germany), with successful acquisition of 215 in situ data points. The time series was in good agreement with DMn concentrations determined from discretely collected samples analysed via inductively coupled plasma mass spectrometry (ICP-MS), exhibiting a mean accuracy of 87% over the full deployment duration (with an accuracy of > 99% for certain periods) and clear correlations to key hydrographic parameters.
Heterotrimeric G-protein α subunit (RGA1) regulates tiller development, yield, cell wall, nitrogen response and biotic stress in rice
Authors: Pathak Ravi Ramesh , Mandal Vikas Kumar , Jangam Annie Prasanna , Sharma Narendra , Madan Bhumika , Jaiswal Dinesh Kumar , Raghuram Nandula
Published: January 2021

G-proteins are implicated in plant productivity, but their genome-wide roles in regulating agronomically important traits remain uncharacterized. Transcriptomic analyses of rice G-protein alpha subunit mutant (rga1) revealed 2270 differentially expressed genes (DEGs) including those involved in C/N and lipid metabolism, cell wall, hormones and stress. Many DEGs were associated with root, leaf, culm, inflorescence, panicle, grain yield and heading date. The mutant performed better in total weight of filled grains, ratio of filled to unfilled grains and tillers per plant. Protein–protein interaction (PPI) network analysis using experimentally validated interactors revealed many RGA1-responsive genes involved in tiller development. qPCR validated the differential expression of genes involved in strigolactone-mediated tiller formation and grain development. Further, the mutant growth and biomass were unaffected by submergence indicating its role in submergence response. Transcription factor network analysis revealed the importance of RGA1 in nitrogen signaling with DEGs such as Nin-like, WRKY, NAC, bHLH families, nitrite reductase, glutamine synthetase, OsCIPK23 and urea transporter. Sub-clustering of DEGs-associated PPI network revealed that RGA1 regulates metabolism, stress and gene regulation among others. Predicted rice G-protein networks mapped DEGs and revealed potential effectors. Thus, this study expands the roles of RGA1 to agronomically important traits and reveals their underlying processes.
Health impact assessment to predict the impact of tobacco price increases on COPD burden in Italy, England and Sweden
Authors: Fuertes Elaine , Marcon Alessandro , Potts Laura , Pesce Giancarlo , Lhachimi Stefan K. , Jani Virjal , Calciano Lucia , Adamson Alex , Quint Jennifer K. , Jarvis Debbie , Janson Christer , Accordini Simone , Minelli Cosetta
Published: January 2021

Raising tobacco prices effectively reduces smoking, the main risk factor for chronic obstructive pulmonary disease (COPD). Using the Health Impact Assessment tool “DYNAMO-HIA”, this study quantified the reduction in COPD burden that would occur in Italy, England and Sweden over 40 years if tobacco prices were increased by 5%, 10% and 20% over current local prices, with larger increases considered in secondary analyses. A dynamic Markov-based multi-state simulation modelling approach estimated the effect of changes in smoking prevalence states and probabilities of transitioning between smoking states on future smoking prevalence, COPD burden and life expectancy in each country. Data inputs included demographics, smoking prevalences and behaviour and COPD burden from national data resources, large observational cohorts and datasets within DYNAMO-HIA. In the 20% price increase scenario, the cumulative number of COPD incident cases saved over 40 years was 479,059 and 479,302 in Italy and England (populous countries with higher smoking prevalences) and 83,694 in Sweden (smaller country with lower smoking prevalence). Gains in overall life expectancy ranged from 0.25 to 0.45 years for a 20 year-old. Increasing tobacco prices would reduce COPD burden and increase life expectancy through smoking behavior changes, with modest but important public health benefits observed in all three countries.
Evaluation of factors inducing variability of faecal nutrients in captive red deer under variable demands
Authors: Čupić Stipan , García Andrés J. , Holá Michaela , Ceacero Francisco
Published: January 2021

Based on the assumption that dietary and faecal nitrogen correlate, the number of studies using faecal samples collected in the wild to understand diet selection by wild herbivores and other ecological patterns has been growing during the last years, especially due to the recent development of cheap tools for analysis of nutrients like Near-Infrared Reflectance Spectroscopy (NIRS). Within the annual reproductive cycle, cervids (members of the family Cervidae) face strong seasonal variations in nutritional demands, different for hinds (gestation and lactation) and stags (antler growth) and reflected in differential patterns of seasonal diet selection. In this study we aimed to quantify how pasture availability, season and individual factors like sex, age, reproductive status, body mass and body condition affect faecal nutrients in captive red deer with the goal of understanding how these factors may influence the interpretation of results from samples obtained in the wild with little or no information about the animals who dropped those faeces. We used NIRS for analysing nitrogen, neutral and acid detergent fibres in faeces. The relative influence of some individual factors like pregnancy was low (around 4%), while age and weight may induce a variability up to 18%. The presence or absence of pasture contributed to a variability around 13%, while the season contributed to an average variability around 17% (and up to 21% in certain situations). This high variability in faecal nutrients was observed in a controlled setting with captive animals and controlled diets. Thus, in natural situations we suspect that there would be even greater variation. According to the results, we recommend that preliminary research with captive animals of the species of interest should be conducted before collecting samples in the wild, which should help in the interpretation of results.
An integrated approach to understanding RF vacuum arcs
Authors: Norem J. , Insepov Z. , Hassanein A.
Published: January 2021

Although used in the design and costing of large projects such as linear colliders and fusion tokamaks, the theory of vacuum arcs and gradient limits is not well understood. Almost 120 years after the isolation of vacuum arcs, the exact mechanisms of the arcs and the damage they produce are still being debated. We describe our simple and general model of the vacuum arc that can incorporate all active mechanisms and aims to explain all relevant data. Our four stage model, is based on experiments done at 805 MHz with a variety of cavity geometries, magnetic fields, and experimental techniques as well as data from Atom Probe Tomography and failure analysis of microelectronics. The model considers the trigger, plasma formation, plasma evolution and surface damage phases of the RF arc. This paper also examines how known mechanisms can explain the observed sharp field dependence, fast breakdown times and observed surface damage. We update the model and discuss new features while also pointing out where new data would be useful in extending the model to a wider range of frequencies.
Predicting individual emotion from perception-based non-contact sensor big data
Authors: Komuro Nobuyoshi , Hashiguchi Tomoki , Hirai Keita , Ichikawa Makoto
Published: January 2021

This study proposes a system for estimating individual emotions based on collected indoor environment data for human participants. At the first step, we develop wireless sensor nodes, which collect indoor environment data regarding human perception, for monitoring working environments. The developed system collects indoor environment data obtained from the developed sensor nodes and the emotions data obtained from pulse and skin temperatures as big data. Then, the proposed system estimates individual emotions from collected indoor environment data. This study also investigates whether sensory data are effective for estimating individual emotions. Indoor environmental data obtained by developed sensors and emotions data obtained from vital data were logged over a period of 60 days. Emotions were estimated from indoor environmental data by machine learning method. The experimental results show that the proposed system achieves about 80% or more estimation correspondence by using multiple types of sensors, thereby demonstrating the effectiveness of the proposed system. Our obtained result that emotions can be determined with high accuracy from environmental data is a useful finding for future research approaches.
Inflammation and regulatory T cell genes are differentially expressed in peripheral blood mononuclear cells of Parkinson’s disease patients
Authors: Karaaslan Zerrin , Kahraman Özlem Timirci , Şanlı Elif , Ergen Hayriye Arzu , Ulusoy Canan , Bilgiç Başar , Yılmaz Vuslat , Tüzün Erdem , Hanağası Haşmet Ayhan , Küçükali Cem İsmail
Published: January 2021

Our aim was to identify the differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMC) of Parkinson’s disease (PD) patients and healthy controls by microarray technology and analysis of related molecular pathways by functional annotation. Thirty PD patients and 30 controls were enrolled. Agilent Human 8X60 K Oligo Microarray was used for gene level expression identification. Gene ontology and pathway enrichment analyses were used for functional annotation of DEGs. Protein–protein interaction analyses were performed with STRING. Expression levels of randomly selected DEGs were quantified by real time quantitative polymerase chain reaction (RT-PCR) for validation. Flow cytometry was done to determine frequency of regulatory T cells (Tregs) in PBMC. A total of 361 DEGs (143 upregulated and 218 downregulated) were identified after GeneSpring analysis. DEGs were involved in 28 biological processes, 12 cellular components and 26 molecular functions. Pathway analyses demonstrated that upregulated genes mainly enriched in p53 (CASP3, TSC2, ATR, MDM4, CCNG1) and PI3K/Akt (IL2RA, IL4R, TSC2, VEGFA, PKN2, PIK3CA, ITGA4, BCL2L11) signaling pathways. TP53 and PIK3CA were identified as most significant hub proteins. Expression profiles obtained by RT-PCR were consistent with microarray findings. PD patients showed increased proportions of CD49d+ Tregs, which correlated with disability scores. Survival pathway genes were upregulated putatively to compensate neuronal degeneration. Bioinformatics analysis showed an association between survival and inflammation genes. Increased CD49d+ Treg ratios might signify the effort of the immune system to suppress ongoing neuroinflammation.