bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glucose dynamics during ozone exposure measured using radiotelemetry: Stress drivers
Authors: Henriquez Andres R. , Snow Samantha J. , Jackson Thomas W. , House John S. , Motsinger-Reif Alison A. , Ward-Caviness Cavin K. , Schladweiler Mette C. , Alewel Devin I. , Miller Colette N. , Farraj Aimen K. , Hazari Mehdi S , Grindstaff Rachel , Diaz-Sanchez David , Ghio Andrew J , Kodavanti Urmila P. 
Published: December 2021

AbstractBackgroundStress-related neurobehavioral and metabolic disorders are associated with altered circulating adrenal-derived hormones and hyperglycemia. Temporal assessment of glucose and these hormones is critical for insights on an individual’s health.ObjectivesHere we used implantable-telemetry in rats to assess real-time changes in circulating glucose during and after exposure to the air pollutant ozone, and link responses to circulating neuroendocrine stress and metabolic hormones. We also compared rodent glucose and corticosterone (cortisol in humans) responses to humans exposed to ozone.MethodsFirst, using a cross-over design, we monitored glucose levels during single or repeated ozone exposures (0.0, 0.2, 0.4 and 0.8-ppm) and non-exposure periods in male Wistar-Kyoto-rats implanted with glucose-telemeters. A second cohort of un-implanted rats was exposed to ozone (0.0, 0.4 or 0.8-ppm) for 30-min, 1-hour, 2-hour, or 4-hour with hormones measured immediately after exposure. Then we assessed glucose metabolism in sham and adrenalectomized rats with or without pharmacological interventions of adrenergic and glucocorticoid receptors. Finally, we assessed glucose and cortisol in serum samples from a clinical study involving exposure of human volunteers to air or 0.3 ppm ozone.ResultsOzone (0.8-ppm) caused hyperglycemia and hypothermia beginning 90-min into exposure, with reversal of effects 4-6 hours post-exposure. Glucose monitoring during four daily 4-hour ozone exposures revealed duration of hyperglycemia, adaptation, and diurnal variations. Ozone-induced hyperglycemia was preceded by increased adrenocorticotropic hormone, corticosterone, and epinephrine, but depletion of thyroid-stimulating, prolactin, and luteinizing hormones. Hyperglycemia was inhibited in rats that were adrenalectomized and/or treated with glucocorticoid inhibitor. The depletion of cortisol was dampened in humans exposed to ozone during intermittent exercise.DiscussionWe demonstrate for the first time the temporality of neuroendocrine-stress-mediated biological sequalae responsible for ozone-induced metabolic dysfunction as exposure occurs. Real-time glucose monitoring with stress hormones assessment may be useful in identifying interactions among pollutants and stress-related illnesses.
The SPEECHLESS-induced stomatal increase is required for the salt tolerance of oil palm
Authors: Song Zhuojun , Wang Le , Lai Chong Cheong , Yang Zituo , Lee May , Yue Gen Hua 
Published: December 2021

AbstractOil palm is the most productive oil producing plant. Salt stress leads to growth damage and decrease in yield of oil palm. However, the physiological responses of oil palm to salt stress and their underlying mechanisms are not clear. RNA-Seq for leaf samples from young palms challenged under three levels of salts (100, 250 and 500 mM NaCl) and control for 14 days was conducted. Diverse signalling pathways were involved in responses to different levels of salt stress. All the three levels of salt stress activated EgSPCH expression and induced stomatal density of oil palm, which was contrasting to that in Arabidopsis. Under strong salt stress group, oil palm removed excessive salt via stomata. Overexpression of EgSPCH in Arabidopsis increased the stomatal production but lowered the salt tolerance. These data suggest that in oil palm, salt activates EgSPCH to generate more stomata in response to salt stress. Our results shed a light on the cellular response to salt stress of oil palm and provide new insights into the mechanisms of different salt-induced stomatal development between halophytes and glycophytes.
Fast in-vitro screening of FLT3-ITD inhibitors using silkworm-baculovirus protein expression system
Authors: Yamamoto Naoki , Kikuchi Jiro , Furukawa Yusuke , Shibayama Naoya 
Published: December 2021

AbstractWe report expression and purification of a FLT3 protein with ITD mutation (FLT3-ITD) with a steady tyrosine kinase activity using a silkworm-baculovirus system, and its application as a fast screening system of tyrosine kinase inhibitors. The FLT3-ITD protein was expressed in Bombyx mori L. pupae infected by gene-modified nucleopolyhedrovirus, and was purified as an active state. We performed an inhibition assay using 17 potential kinase inhibitors, and succeeded in identifying two potent inhibitors for FLT3-ITD. The result has paved the way for screening FLT3-ITD inhibitors in a fast and easy manner, and also for structural studies.
Whole genome resequencing and comparative genome analysis of threePuccinia striiformisf. sp.triticipathotypes prevalent in India
Authors: Yadav Inderjit Singh , Bhardwaj S. C. , Kaur Jaspal , Singla Deepak , Kaur Satinder , Kaur Harmandeep , Rawat Nidhi , Tiwari Vijay Kumar , Saunders Diane , Uauy Cristobal , Chhuneja Parveen 
Published: December 2021

ABSTRACTStripe rust disease of wheat, caused byPuccinia striiformisf. sp.tritici,(Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome sequencing of three prevalent IndianPstpathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively. Pathotypes were found to be highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene family expansion was also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known US, European, African and Asian races. Diagnostic markers developed for the identification of different Pst pathotypes will help tracking of yellow rust at farmers’ field and strategizing resistance gene deployment.
Visual Interpretation of the Meaning of kcat/KM in Enzyme Kinetics
Authors: Park Chiwook 
Published: December 2021

Abstractkcat and kcat/KM are the two fundamental kinetic parameters in enzyme kinetics. kcat is the first-order rate constant that determines the reaction rate when the enzyme is fully occupied at a saturating concentration of the substrate. kcat/KM is the second-order rate constant that determines the reaction rate when the enzyme is mostly free at a very low concentration of the substrate. Both parameters provide critical information on how the enzyme lowers the energy barriers along the reaction pathway for catalysis. However, it is surprising how often kcat/KM is used inappropriately as a composite parameter derived by dividing kcat with KM to assess both catalytic power and affinity to the substrate of the enzyme. The main challenge in explaining the true meaning of kcat/KM is the difficulty to demonstrate how the reaction energetics of enzyme catalysis determines kcat/KM in a simple way. Here, I report a step-by-step demonstration on how to visualize the meaning of kcat/KM on the reaction energy diagram. By using the reciprocal form of the expression of kcat/KM with the elementary rate constants in kinetic models, I show that kcat/KM is a harmonic sum of several kinetic terms that correspond to the heights of the transition states relative to the free enzyme. Then, I demonstrate that the height of the highest transition state has the dominant influence on kcat/KM, i. e. the step with the highest transition state is the limiting step for kcat/KM. The visualization of the meaning of kcat/KM on the reaction energy diagram offers an intuitive way to understand all the known properties of kcat/KM, including the Haldane relationship.
Engineering efficient termination of bacteriophage T7 RNA polymerase transcription
Authors: Calvopina-Chavez Diana G. , Gardner Mikaela A. , Griffitts Joel S. 
Published: December 2021

ABSTRACTThe bacteriophage T7 expression system is one of the most prominent transcription systems used in biotechnology and molecular-level research. However, T7 RNA polymerase is prone to read-through transcription due to its high processivity. As a consequence, enforcing efficient transcriptional termination is difficult. The termination hairpin found natively in the T7 genome is adapted to be inefficient, exhibiting 62% termination efficiency in vivo and even lower efficiency in vitro. In this study, we engineered a series of sequences that outperform the efficiency of the native terminator hairpin. By embedding a previously discovered 8-nucleotide T7 polymerase pause sequence within a synthetic hairpin sequence, we observed in vivo termination efficiency of 91%; by joining two short sequences into a tandem 2-hairpin structure, termination efficiency was increased to 98% in vivo and 91% in vitro. This study also tests the ability of these engineered sequences to terminate transcription of theEscherichia coliRNA polymerase. Two out of three of the most successful T7 polymerase terminators also facilitated termination of the bacterial polymerase with around 99% efficiency.
The contrasting roles of nitric oxide drive microbial community organization as a function of oxygen presence
Authors: Wilbert Steven A. , Newman Dianne K. 
Published: December 2021

SummaryMicrobial assemblages are omnipresent in the biosphere, forming communities on the surfaces of roots, rocks, and within living tissues. These communities can exhibit strikingly beautiful compositional structures, with certain members reproducibly occupying particular spatiotemporal microniches. Despite this reproducibility, we lack the ability to explain these spatial patterns. We hypothesize that certain spatial patterns in microbial communities may be explained by the exchange of redox-active metabolites whose biological function is sensitive to microenvironmental gradients. To test this, we developed a simple community consisting of synthetic Pseudomonas aeruginosa strains with a partitioned denitrification pathway: a strict consumer and strict producer of nitric oxide (NO), a key pathway intermediate. Because NO can be both toxic or beneficial depending on the amount of oxygen present, this system provided an opportunity to investigate whether dynamic oxygen gradients can tune metabolic cross-feeding and fitness outcomes in a predictable fashion. Using a combination of genetic analysis, controlled growth environments and imaging, we show that oxygen availability dictates whether NO cross-feeding is deleterious or mutually beneficial, and that this organizing principal maps to the microscale. More generally, this work underscores the importance of considering the contrasting and microenvironmentally tuned roles redox-active metabolites can play in shaping microbial communities.
Rec8 cohesin-mediated axis-loop chromatin architecture is required for meiotic recombination
Authors: Sakuno Takeshi , Tashiro Sanki , Tanizawa Hideki , Iwasaki Osamu , Ding Da-Qiao , Haraguchi Tokuko , Noma Ken-ichi , Hiraoka Yasushi 
Published: December 2021

ABSTRACTDuring meiotic prophase, cohesin-dependent axial structures are formed in the synaptonemal complex (SC). However, the functional correlation between these structures and cohesion remains elusive. Here, we examined the formation of cohesin-dependent axial structures in the fission yeastSchizosaccharomyces pombe. This organism forms atypical SCs composed of linear elements (LinEs) resembling the lateral elements of SC but lacking the transverse filaments. Hi-C analysis using a highly synchronous population of meioticS. pombecells revealed that the axis-loop chromatin structure formed in meiotic prophase was dependent on the Rec8 cohesin complex. In contrast, the Rec8-mediated formation of the axis-loop structure occurred in cells lacking components of LinEs. To dissect the functions of Rec8, we identified arec8-F204Smutant that lost the ability to assemble the axis-loop structure without losing cohesion of sister chromatids. This mutant showed defects in the formation of the axis-loop structure and LinE assembly and thus exhibited reduced meiotic recombination. Collectively, our results demonstrate that the Rec8-dependent axis-loop structure provides a structural platform essential for LinE assembly, facilitating meiotic recombination of homologous chromosomes, independently of its role in sister chromatid cohesion.
Expressional Diversity and Cancer-prone Phenotypes in Cigarette-smoking Lungs at Single Cell Resolution
Authors: Nakayama Jun , Yamamoto Yusuke 
Published: December 2021

AbstractSingle-cell RNA-seq (scRNA-seq) technologies have been broadly utilized to reveal molecular mechanisms of respiratory pathology and physiology at single-cell resolution. Here, we established single-cell meta-analysis (scMeta-analysis) by integrating data from 8 public datasets, including 104 lung scRNA-seq samples with clinicopathological information and designated a cigarette smoking lung atlas. The atlas revealed early carcinogenesis events and defined the alterations of single-cell transcriptomics, cell population, and fundamental properties of biological pathways induced by smoking. In addition, we developed two novel scMeta-analysis methods: VARIED (Visualized Algorithms of Relationships In Expressional Diversity) and AGED (Aging-related Gene Expressional Differences). VARIED analysis revealed expressional diversity associated with smoking carcinogenesis. AGED analysis revealed differences in gene expression related to both aging and smoking states. The scMeta-analysis pave the way to utilize publicly -available scRNA-seq data and provide new insights into the effects of smoking and into cellular diversity in human lungs, at single-cell resolution.
Probing the segregation of evoked and spontaneous neurotransmission via photobleaching and recovery of a fluorescent glutamate sensor
Authors: Wang Camille S. , Chanaday Natali L. , Monteggia Lisa M. , Kavalali Ege T. 
Published: December 2021

AbstractSynapses maintain both action potential-evoked and spontaneous neurotransmitter release, however, organization of these two forms of release within an individual synapse remains unclear. Here, we used photobleaching properties of iGluSnFR, a fluorescent probe that detects glutamate, to investigate the subsynaptic organization of evoked and spontaneous release. In non-neuronal cells and neuronal dendrites, iGluSnFR fluorescence is intensely photobleached and recovers via diffusion of non-photobleached probes within 10-seconds. After photobleaching, while evoked iGluSnFR events could be rapidly suppressed, their recovery required several hours. In contrast, iGluSnFR responses to spontaneous release were comparatively resilient to photobleaching, unless the complete pool of iGluSnFR was activated by glutamate perfusion. This differential effect of photobleaching on different modes of neurotransmission is consistent with a subsynaptic organization where sites of evoked glutamate release are clustered and corresponding iGluSnFR probes are diffusion restricted, while spontaneous release sites are broadly spread across a synapse with readily diffusible iGluSnFR probes.
Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana
Authors: Morales A. , de Boer H. J. , Douma J. C. , Elsen S. , Engels S. , Glimmerveen T. , Sajeev N. , Huber M. , Luimes M. , Luitjens E. , Raatjes K. , Hsieh C. , Teapal J. , Wildenbeest T. , Jiang Z. , Pareek A. , Singla-Pareek S. L. , Yin X. , Evers J.B. , Anten N.P.R. , van Zanten M. , Sasidharan R. 
Published: December 2021

ABSTRACTPlant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sub-lethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analyzed the phenotypic responses of 1782 individuals across these stresses and different developmental stages.Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analyzed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses.Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sub-lethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.
DeepPlnc: Bi-modal Deep Learning for Highly Accurate Plant lncRNA Discovery
Authors: Ritu  , Gupta Sagar , Sharma Nitesh Kumar , Shankar Ravi 
Published: December 2021

AbstractWe present here a bi-modal CNN based deep-learning system, DeepPlnc, to identify plant lncRNAs with high accuracy while using sequence and structural properties. Unlike most of the existing software, it works accurately even in conditions with ambiguity of boundaries and incomplete sequences. It scored consistently high for performance metrics while breaching accuracy of >98% when tested across a large number of validated instances. During benchmarking it consistently outperformed all the compared tools and maintained a highly significant lead in the range of 4.6%-10.3% from the second best performing tool (p-value << 0.01). DeepPlnc was used to annotate a de novo assembled transcriptome of a himalayan species where again it suggested its much better suitability for genome and transcriptome annotation purposes than the existing tools. DeepPlnc has been made freely available as a web-server and stand-alone program at https://scbb.ihbt.res.in/DeepPlnc/.
Adjoint-based methods to compute higher-order topological derivatives with an application to elasticity
Authors: Baumann Phillip , Sturm Kevin 
Published: December 2021

PurposeThe goal of this paper is to give a comprehensive and short review on how to compute the first- and second-order topological derivatives and potentially higher-order topological derivatives for partial differential equation (PDE) constrained shape functionals.Design/methodology/approachThe authors employ the adjoint and averaged adjoint variable within the Lagrangian framework and compare three different adjoint-based methods to compute higher-order topological derivatives. To illustrate the methodology proposed in this paper, the authors then apply the methods to a linear elasticity model.FindingsThe authors compute the first- and second-order topological derivatives of the linear elasticity model for various shape functionals in dimension two and three using Amstutz' method, the averaged adjoint method and Delfour's method.Originality/valueIn contrast to other contributions regarding this subject, the authors not only compute the first- and second-order topological derivatives, but additionally give some insight on various methods and compare their applicability and efficiency with respect to the underlying problem formulation.
Fractional order plasma modeling based on linear polarization of LASER light: an Atangana–Baleanu Caputo approach
Authors: Zubair Tamour , Usman Muhammad , Lu Tiao 
Published: December 2021

PurposeThe purpose of this offered research is to articulate a multifaceted kind of highly unstable initial perturbation and further analyze the performance of the plasma particles for time-fractional order evaluation.Design/methodology/approachFor this purpose, the authors designed specific geometry and further interpreted it into the mathematical model using the concepts of the Vlasov Maxwell system. The suggested algorithm is based on the finite-difference and spectral estimation philosophy. The management of time and memory in generic code for computational purposes is also discussed.FindingsThe main purpose is to analyze the fractional behavior of plasma particles and also the capability of the suggested numerical algorithm. Due to initial perturbations, there are a lot of sudden variations that occurred in the formulated system. Graphical behavior shows that SR parameter produces devastation as compared to others. The variation of fractional parameter between the defend domain demonstrates the hidden pictures of plasma particles. The design scheme is efficient, convergent and has the capability to cover the better physics of the problem.Practical implicationsPlasma material is commonly used in different areas of science. Therefore, in this paper, the authors increase the capability of the mathematical plasma model with specific geometry, and further suitable numerical algorithm is suggested with detailed physical analysis of the outcomes. The authors gave a new direction to study the performance of plasma particles under the influence of LASER light.Originality/valueIn the recent era, science has produced a lot of advancements to study and analyze the physical natural process, which exist everywhere in the real word. On behalf of this current developments, it is now insufficient to study the first-order time evaluation of the plasma particles. One needs to be more precise and should move toward the bottomless state of it, that is, macroscopic and microscopic time-evaluation scales, and it is not wrong to say that there exits a huge gap, to study the time evaluation in this discussed manner. The presented study is entirely an advanced and efficient way to investigate the problem into the new directions. The capability of the proposed algorithm and model with fractional concepts can fascinate the reader to extend to the other dimensions.