bluuebunny/crossref_metadata_2025_split huggingface dataset:
Faster, reduced cost calibration method development methods for the analysis of fermentation product using near-infrared spectroscopy (NIRS)
Authors: Agbonkonkon Nosa , Wojciechowski Greg , Abbott Derek A , Gaucher Sara P , Yim Daniel R , Thompson Andrew W , Leavell Michael D 
Published: June 2021

AbstractRecent innovations in synthetic biology, fermentation, and process development have decreased time to market by reducing strain construction cycle time and effort. Faster analytical methods are required to keep pace with these innovations, but current methods of measuring fermentation titers often involve manual intervention and are slow, time-consuming, and difficult to scale. Spectroscopic methods like near-infrared (NIR) spectroscopy address this shortcoming; however, NIR methods require calibration model development that is often costly and time-consuming. Here, we introduce two approaches that speed up calibration model development. First, generalized calibration modeling (GCM) or sibling modeling, which reduces calibration modeling time and cost by up to 50% by reducing the number of samples required. Instead of constructing analyte-specific models, GCM combines a reduced number of spectra from several individual analytes to produce a large pool of spectra for a generalized model predicting all analyte levels. Second, randomized multicomponent multivariate modeling (RMMM) reduces modeling time by mixing multiple analytes into one sample matrix and then taking the spectral measurements. Afterward, individual calibration methods are developed for the various components in the mixture. Time saved from the use of RMMM is proportional to the number of components or analytes in the mixture. When combined, the two methods effectively reduce the associated cost and time for calibration model development by a factor of 10.
Effect of Vegetation on the Abundance of Tick Vectors in the Northeastern United States: A Review of the Literature
Authors: Mathisson Daniel C , Kross Sara M , Palmer Matthew I , Diuk-Wasser Maria A 
Published: June 2021

AbstractTick-borne illnesses have been on the rise in the United States, with reported cases up sharply in the past two decades. In this literature review, we synthesize the available research on the relationship between vegetation and tick abundance for four tick species in the northeastern United States that are of potential medical importance to humans. The blacklegged tick (Ixodes scapularis) (Say; Acari: Ixodidae) is found to be positively associated with closed canopy forests and dense vegetation thickets, and negatively associated with open canopy environments, such as grasslands or old agricultural fields. The American dog tick (Dermacentor variabilis) (Say; Acari: Ixodidae) has little habitat overlap with I. scapularis, with abundance highest in grasses and open-canopy fields. The lone star tick (Amblyomma americanum) (Linnaeus; Acari: Ixodidae) is a habitat generalist without consistent associations with particular types of vegetation. The habitat associations of the recently introduced Asian longhorned tick (Haemaphysalis longicornis) (Neumann; Acari: Ixodidae) in the northeastern United States, and in other regions where it has invaded, are still unknown, although based on studies in its native range, it is likely to be found in grasslands and open-canopy habitats.
Parenting Practices, Bedtime Routines, and Consistency: Associations with Pediatric Sleep Problems
Authors: Shetty Janavi , Newton Adam T , Reid Graham J 
Published: June 2021

Abstract

Objectives
Investigate the direct and moderating effects of daytime parenting practices on the relationship between bedtime routines and pediatric sleep problems.

Methods
A community sample of 407 parents with children 2–10 years old completed measures of parenting practices (i.e., laxness and over-reactivity) and bedtime routines (i.e., consistency and reactivity to changes in routines). Sleep problems (i.e., severity and signaled night waking) were assessed by a parent-report questionnaire and sleep diaries.

Results
Higher parenting laxness (β = .13) and less bedtime routine consistency (β = −.34) significantly predicted sleep problem severity. Laxness moderated the relationship between bedtime reactivity and sleep problem severity: when bedtime reactivity was high, higher parental laxness was associated with more severe sleep problems.

Conclusions
Daytime parenting practices are important to consider when children are reactive to changes in bedtime routines, as permissive or inconsistent daytime parenting practices were found to be associated with more severe sleep problems. Future research should examine the effects of parenting practices and bedtime routines on problematic signaled night waking in a clinical sample of children.
O2-(2,4-dinitrophenyl) diazeniumdiolate derivative induces G2/M arrest via PTEN-mediated inhibition of PI3K/Akt pathway in hepatocellular carcinoma cells
Authors: Liu Ling , Xu Jinglei , Zhai Ziyu , Cao Mengyao , Huang Zile , Xing Yihao , Chen Jingjing 
Published: June 2021

Abstract

Objectives
The study aimed to investigate whether G2/M arrest caused by O2-(2,4-dinitrophenyl) diazeniumdiolate derivative (JS-K) was related to PTEN-mediated inhibition of PI3K/Akt pathway in hepatocellular carcinoma cells.

Methods
The cell apoptosis was detected by DAPI staining and Annexin V-FITC/PI dual staining. The cell cycle was analysed by PI staining. The expressions of cell cycle-related proteins, PTEN and PI3K/AKT pathway were measured by Western blot. The rat model of primary hepatic carcinoma was established with diethylnitrosamine to verify the antitumour effects of JS-K.

Key findings
The morphological features of apoptosis were obviously reversed when the cells were pre-treated with bpv(pic), followed by treatment with JS-K. JS-K mediated G2/M arrest and down-regulated expressions of cyclin B1. Meanwhile, it up-regulated the expression of p-Cdk1, p-Chk2 and p-CDC25C while down-regulated that of Cdk1 and CDC25C. Furthermore, JS-K also enhanced the expressions of p21 and p27, PTEN and p53 while decreased the expressions of p-PTEN, PI3K and p-AKT. However, bpv(pic) and Carboxy-PTIO could reverse JS-K-induced G2/M cell arrest and PTEN-mediated inhibition of the PI3K/AKT pathway. The same results were also testified in the rat model of primary hepatic carcinoma.

Conclusions
JS-K caused G2/M arrest through PTEN-mediated inhibition of the PI3K/AKT pathway involving Chk2/CDC25C/Cdk1 checkpoint.
The plant nuclear lamina proteins NMCP1 and NMCP2 form a filamentous network with lateral filament associations
Authors: Masuda Kiyoshi , Hikida Riku , Fujino Kaien 
Published: June 2021

AbstractPlant genomes lack genes encoding intermediate filament proteins, including lamins; however, functional lamin analogues are presumed to exist in plants. Plant-specific coiled-coil proteins, that is, nuclear matrix constituent proteins (NMCPs), are the most likely candidates as the structural elements of the nuclear lamina because they exhibit a lamin-like domain arrangement. They are exclusively localized at the nuclear periphery and have functions that are analogous to those of lamins. However, their assembly into filamentous polymers has not yet been confirmed. In this study, we examined the higher-order structure of NMCP1 and NMCP2 in Apium graveolens cells by using stimulated emission depletion microscopy combined with immunofluorescence cell labelling. Our analyses revealed that NMCP1 and NMCP2 form intricate filamentous networks, which include thick segments consisting of filament bundles, forming a dense filamentous layer extending across the nuclear periphery. Furthermore, the outermost chromatin distribution was found to be in the nucleoplasm-facing region of the nuclear lamina. Recombinant Daucus carota NMCP1 with a His-tag produced in Escherichia coli refolded into dimers and self-assembled into filaments and filament bundles. These results suggest that NMCP1 and NMCP2 organize into the nuclear lamina by forming a filamentous network with filament bundles that localize at the nuclear periphery.
Double-faced role of Bcl-2-associated athanogene 7 in plant–Phytophthora interaction
Authors: Zhou Yang , Yang Kun , Cheng Ming , Cheng Yang , Li Yurong , Ai Gan , Bai Tian , Xu Ruofei , Duan Weiwei , Peng Hao , Li Xiaobo , Xia Ai , Wang Yuanchao , Jing Maofeng , Dou Daolong , Dickman Marty B 
Published: June 2021

Abstract
Due to their sessile nature, plants must respond to various environmental assaults in a coordinated manner. The endoplasmic reticulum is a central hub for plant responses to various stresses. We previously showed that Phytophthora utilizes effector PsAvh262-mediated binding immunoglobulin protein (BiP) accumulation for suppressing endoplasmic reticulum stress-triggered cell death. As a BiP binding partner, Bcl-2-associated athanogene 7 (BAG7) plays a crucial role in the maintenance of the unfolded protein response, but little is known about its role in plant immunity. In this work, we reveal a double-faced role of BAG7 in Arabidopsis–Phytophthora interaction in which it regulates endoplasmic reticulum stress-mediated immunity oppositely in different cellular compartments. In detail, it acts as a susceptibility factor in the endoplasmic reticulum, but plays a resistance role in the nucleus against Phytophthora. Phytophthora infection triggers the endoplasmic reticulum-to-nucleus translocation of BAG7, the same as abiotic heat stress; however, this process can be prevented by PsAvh262-mediated BiP accumulation. Moreover, the immunoglobulin/albumin-binding domain in PsAvh262 is essential for both pathogen virulence and BiP accumulation. Taken together, our study uncovers a double-faced role of BAG7; Phytophthora advances its colonization in planta by utilizing an effector to detain BAG7 in the endoplasmic reticulum.
Natural variations in the P-type ATPase heavy metal transporter gene ZmHMA3 control cadmium accumulation in maize grains
Authors: Tang Bin , Luo Meijie , Zhang Yunxia , Guo Huanle , Li Jingna , Song Wei , Zhang Ruyang , Feng Zhen , Kong Mengsi , Li Han , Cao Zhongyang , Lu Xiaoduo , Li Delin , Zhang Jianhua , Wang Ronghuan , Wang Yuandong , Chen Zhihui , Zhao Yanxin , Zhao Jiuran 
Published: June 2021

Abstract
Cadmium (Cd) accumulation in maize grains is detrimental to human health. Developing maize varieties with low Cd content is important for safe consumption of maize grains. However, the key genes controlling maize grain Cd accumulation have not been cloned. Here, we identified one major locus for maize grain Cd accumulation (qCd1) using a genome-wide association study (GWAS) and bulked segregant RNA-seq analysis with a biparental segregating population of Jing724 (low-Cd line) and Mo17 (high-Cd line). The candidate gene ZmHMA3 was identified by fine mapping and encodes a tonoplast-localized heavy metal P-type ATPase transporter. An ethyl methane sulfonate mutant analysis and an allelism test confirmed that ZmHMA3 influences maize grain Cd accumulation. A transposon in intron 1 of ZmHMA3 is responsible for the abnormal amino acid sequence in Mo17. Based on the natural sequence variations in the ZmHMA3 gene of diverse maize lines, four PCR-based molecular markers were developed, and these were successfully used to distinguish five haplotypes with different grain Cd contents in the GWAS panel and to predict grain Cd contents of widely used maize inbred lines and hybrids. These molecular markers can be used to breed elite maize varieties with low grain Cd contents.
The impact of the CMB on the evolution of high-z blazars
Authors: Ighina L , Caccianiga A , Moretti A , Belladitta S , Della Ceca R , Diana A 
Published: June 2021

ABSTRACT
Different works have recently found an increase of the average X-ray-to-radio luminosity ratio with redshift in the blazar population. We evaluate here whether the inverse Compton interaction between the relativistic electrons within the jet and the photons of the cosmic microwave background (IC/CMB) can explain this trend. Moreover, we test whether the IC/CMB model can also be at the origin of the different space density evolutions found in X-ray and radio-selected blazar samples. By considering the best statistically complete samples of blazars selected in the radio or in the X-ray band and covering a large range of redshift (0.5 ≲ z ≲ 5.5), we evaluate the expected impact of the CMB on the observed X-ray emission on each sample and then we compare these predictions with the observations. We find that this model can satisfactorily explain both the observed trend of the X-ray-to-radio luminosity ratios with redshift and the different cosmological evolutions derived from the radio and X-ray band. Finally, we discuss how currently on-going X-ray missions, like extended ROentgen Survey with an Imaging Telescope Array, could help to further constrain the observed evolution at even higher redshifts (up to z ∼ 6–7).
Trichostatin A mitigates radiation-induced teratogenesis in C57Bl/6 mice
Authors: Haritwal Teena , Goyal Nikita , Gupta Noopur , Parvez Suhel , Agrawala Paban K 
Published: June 2021

Abstract
Radiation exposure in utero is known to lead to serious concerns to both the mother and children, including developmental anomalies in the children. In the recent past, trichostatin A, an HDAC (histone deacetylase) inhibitor and epigenetic modifier, has been shown to mitigate radiation-induced anomalies in the male reproductive system of C57BL/6 mice. Therefore, the current study was undertaken to evaluate the mitigating effects of trichostatin A (TSA) against radiation-induced developmental anomalies in mice. Foetuses of in utero whole-body gamma-irradiated mice during the active organogenesis period were examined for developmental anomalies at 8.5 and 18.5 days of gestation. In utero radiation exposure caused developmental anomalies like microcephaly, microphthalmia, gastroschisis and kinky tail besides prenatal mortality. TSA administration post-irradiation was observed to reduce 50% of prenatal mortality at E18.5 by reducing congenital and developmental anomalies. Observation of such results could be corroborated with the HDAC inhibitory potential of TSA knowing that developmental anomalies may have epigenetic origin. TSA, therefore, can be considered as a potential radiomitigator.
G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol
Authors: Tsukakoshi Kaori , Yamagishi Yasuko , Kanazashi Mana , Nakama Kenta , Oshikawa Daiki , Savory Nasa , Matsugami Akimasa , Hayashi Fumiaki , Lee Jinhee , Saito Taiki , Sode Koji , Khunathai Kanjana , Kuno Hitoshi , Ikebukuro Kazunori 
Published: June 2021

Abstract
Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol. Using in vitro selection, one G4-forming aptamer that enhanced chemiluminescence from luminol by myoglobin's peroxidase activity was discovered. Through our strategy—in silico maturation, which is a genetic algorithm-aided sequence manipulation method, the enhancing activity of the aptamer was improved by introducing mutations to the aptamer sequences. The best aptamer conserved the parallel G4 property with over 300-times higher luminol chemiluminescence from peroxidase activity more than myoglobin alone at an optimal pH of 5.0. Furthermore, using hemin and hemin-binding aptamers, we demonstrated that the binding property of the G4 aptamers to heme in myoglobin might be necessary to exert the enhancing effect. Structure determination for one of the aptamers revealed a parallel-type G4 structure with propeller-like loops, which might be useful for a rational design of aptasensors utilizing the G4 aptamer-myoglobin pair.
LEO1 is a partner for Cockayne syndrome protein B (CSB) in response to transcription-blocking DNA damage
Authors: Tiwari Vinod , Kulikowicz Tomasz , Wilson David M , Bohr Vilhelm A 
Published: June 2021

Abstract
Cockayne syndrome (CS) is an autosomal recessive genetic disorder characterized by photosensitivity, developmental defects, neurological abnormalities, and premature aging. Mutations in CSA (ERCC8), CSB (ERCC6), XPB, XPD, XPG, XPF (ERCC4) and ERCC1 can give rise to clinical phenotypes resembling classic CS. Using a yeast two-hybrid (Y2H) screening approach, we identified LEO1 (Phe381-Ser568 region) as an interacting protein partner of full-length and C-terminal (Pro1010-Cys1493) CSB in two independent screens. LEO1 is a member of the RNA polymerase associated factor 1 complex (PAF1C) with roles in transcription elongation and chromatin modification. Supportive of the Y2H results, purified, recombinant LEO1 and CSB directly interact in vitro, and the two proteins exist in a common complex within human cells. In addition, fluorescently tagged LEO1 and CSB are both recruited to localized DNA damage sites in human cells. Cell fractionation experiments revealed a transcription-dependent, coordinated association of LEO1 and CSB to chromatin following either UVC irradiation or cisplatin treatment of HEK293T cells, whereas the response to menadione was distinct, suggesting that this collaboration occurs mainly in the context of bulky transcription-blocking lesions. Consistent with a coordinated interaction in DNA repair, LEO1 knockdown or knockout resulted in reduced CSB recruitment to chromatin, increased sensitivity to UVC light and cisplatin damage, and reduced RNA synthesis recovery and slower excision of cyclobutane pyrimidine dimers following UVC irradiation; the absence of CSB resulted in diminished LEO1 recruitment. Our data indicate a reciprocal communication between CSB and LEO1 in the context of transcription-associated DNA repair and RNA transcription recovery.
In-depth assessment of the PAM compatibility and editing activities of Cas9 variants
Authors: Zhang Weiwei , Yin Jianhang , Zhang-Ding Zhengrong , Xin Changchang , Liu Mengzhu , Wang Yuhong , Ai Chen , Hu Jiazhi 
Published: June 2021

AbstractA series of Cas9 variants have been developed to improve the editing fidelity or targeting range of CRISPR–Cas9. Here, we employ a high-throughput sequencing approach primer-extension-mediated sequencing to analyze the editing efficiency, specificity and protospacer adjacent motif (PAM) compatibility of a dozen of SpCas9 variants at multiple target sites in depth, and our findings validate the high fidelity or broad editing range of these SpCas9 variants. With regard to the PAM-flexible SpCas9 variants, we detect significantly increased levels of off-target activity and propose a trade-off between targeting range and editing specificity for them, especially for the near-PAM-less SpRY. Moreover, we use a deep learning model to verify the consistency and predictability of SpRY off-target sites. Furthermore, we combine high-fidelity SpCas9 variants with SpRY to generate three new SpCas9 variants with both high fidelity and broad editing range. Finally, we also find that the existing SpCas9 variants are not effective in suppressing genome instability elicited by CRISPR–Cas9 editing, raising an urgent issue to be addressed.
Assembly of higher-order SMN oligomers is essential for metazoan viability and requires an exposed structural motif present in the YG zipper dimer
Authors: Gupta Kushol , Wen Ying , Ninan Nisha S , Raimer Amanda C , Sharp Robert , Spring Ashlyn M , Sarachan Kathryn L , Johnson Meghan C , Van Duyne Gregory D , Matera A Gregory 
Published: June 2021

Abstract
Protein oligomerization is one mechanism by which homogenous solutions can separate into distinct liquid phases, enabling assembly of membraneless organelles. Survival Motor Neuron (SMN) is the eponymous component of a large macromolecular complex that chaperones biogenesis of eukaryotic ribonucleoproteins and localizes to distinct membraneless organelles in both the nucleus and cytoplasm. SMN forms the oligomeric core of this complex, and missense mutations within its YG box domain are known to cause Spinal Muscular Atrophy (SMA). The SMN YG box utilizes a unique variant of the glycine zipper motif to form dimers, but the mechanism of higher-order oligomerization remains unknown. Here, we use a combination of molecular genetic, phylogenetic, biophysical, biochemical and computational approaches to show that formation of higher-order SMN oligomers depends on a set of YG box residues that are not involved in dimerization. Mutation of key residues within this new structural motif restricts assembly of SMN to dimers and causes locomotor dysfunction and viability defects in animal models.
Cytosine base modifications regulate DNA duplex stability and metabolism
Authors: Rausch Cathia , Zhang Peng , Casas-Delucchi Corella S , Daiß Julia L , Engel Christoph , Coster Gideon , Hastert Florian D , Weber Patrick , Cardoso M Cristina 
Published: June 2021

Abstract
DNA base modifications diversify the genome and are essential players in development. Yet, their influence on DNA physical properties and the ensuing effects on genome metabolism are poorly understood. Here, we focus on the interplay of cytosine modifications and DNA processes. We show by a combination of in vitro reactions with well-defined protein compositions and conditions, and in vivo experiments within the complex networks of the cell that cytosine methylation stabilizes the DNA helix, increasing its melting temperature and reducing DNA helicase and RNA/DNA polymerase speed. Oxidation of methylated cytosine, however, reverts the duplex stabilizing and genome metabolic effects to the level of unmodified cytosine. We detect this effect with DNA replication and transcription proteins originating from different species, ranging from prokaryotic and viral to the eukaryotic yeast and mammalian proteins. Accordingly, lack of cytosine methylation increases replication fork speed by enhancing DNA helicase unwinding speed in cells. We further validate that this cannot simply be explained by altered global DNA decondensation, changes in histone marks or chromatin structure and accessibility. We propose that the variegated deposition of cytosine modifications along the genome regulates DNA helix stability, thereby providing an elementary mechanism for local fine-tuning of DNA metabolism.
Arabidopsis ADF1 is Regulated by MYB73 and is Involved in Response to Salt Stress Affecting Actin Filament Organization
Authors: Wang Lu , Qiu Tianqi , Yue Jianru , Guo Nannan , He Yunjian , Han Xueping , Wang Qiuyang , Jia Pengfei , Wang Hongdan , Li Muzi , Wang Che , Wang Xianling 
Published: June 2021

Abstract
Actin cytoskeleton and transcription factors play key roles in plant response to salt stress; however, little is known about the link between the two regulators in response to salt stress. Actin-depolymerizing factors (ADFs) are conserved actin-binding proteins in eukaryotes. Here, we revealed that the expression level of ADF1 was induced by salt stress. The adf1 mutants showed significantly reduced survival rate, increased percentage of actin cable and reduced density of actin filaments, while ADF1 overexpression seedlings displayed the opposite results when compared with WT under the same condition. Furthermore, biochemical assays revealed that MYB73, a R2R3 MYB transcription factor, binds to the promoter of ADF1 and represses its expression via the MYB-binding site core motif ACCTAC. Taken together, our results indicate that ADF1 participates in salt stress by regulating actin organization and may also serve as a potential downstream target of MYB73, which is a negative regulator of salt stress.