bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of affinity bead–based in vitro metal–ligand binding assay reveals dominant cadmium affinity of thiol-rich small peptides phytochelatins beyond glutathione
Authors: Uraguchi Shimpei , Nagai Kenichiro , Naruse Fumii , Otsuka Yuto , Ohshiro Yuka , Nakamura Ryosuke , Takanezawa Yasukazu , Kiyono Masako 
Published: November 2021

Abstract
For a better understanding of metal–ligand interaction and its function in cells, we developed an easy, sensitive, and high-throughput method to quantify ligand–metal(loid) binding affinity under physiological conditions by combining ligand-attached affinity beads and inductively coupled plasma-optical emission spectrometry (ICP-OES). Glutathione (GSH) and two phytochelatins (PC2 and PC3, small peptides with different numbers of free thiols) were employed as model ligands and attached to hydrophilic beads. The principle of the assay resembles that of affinity purification of proteins in biochemistry: metals binding to the ligand on the beads and the rest in the buffer are separated by a spin column and quantified by ICP-OES. The binding assay using the GSH-attached beads and various metal(loid)s suggested the different affinity of the metal–GSH interactions, in accordance with the order of the Irving–Williams series and the reported stability constants. The binding assay using PC2 or PC3-attached beads suggested positive binding between PCs and Ni(II), Cu(II), Zn(II), Cd(II), and As(III) in accordance with the number of thiols in PC2 and PC3. We then conducted the competition assay using Cd(II), Mn(II), Fe(II), Cu(II), and Zn(II), and the results suggested a better binding affinity of PC2 with Cd(II) than with the essential metals. Another competition assay using PC2 and GSH suggested a robust binding affinity between PCs and Cd(II) compared to GSH and Cd(II). These results suggested the dominance of PC-Cd complex formation in vitro, supporting the physiological importance of PCs for the detoxification of cadmium in vivo. We also discuss the potential application of the assay.
Identifying Crystal Accumulation in Granitoids through Amphibole Composition and In Situ Zircon O Isotopes in North Qilian Orogen
Authors: Chen Shuo , Niu Yaoling , Wang Xiaohong , Xue Qiqi , Sun Wenli 
Published: November 2021

Abstract
Granitoids are the main constituents of the continental crust, and an understanding of their petrogenesis is key to the origin and evolution of continents. Whether crystal fractionation is the dominant way to generate evolved magmas has long been debated, mostly because such processes would produce large volumes of complementary cumulates, which remains elusive. Mafic magmatic enclaves (MMEs) are ubiquitous in granitoids and their presence was initially recognized as cumulates. However, because many MMEs lack obvious evidence of accumulation, such as the classic cumulate textures and modal layering, the cumulate origin of MMEs has been abandoned and the model of magma mixing between mafic and felsic magmas has become popular. In this study, we conduct a combined study of amphibole composition and in situ O isotopes in zircons on three suites of orogenic granitoids with MMEs from the North Qilian Orogenic Belt (NQOB). We find that the MMEs and their host granodiorites show overlapping zircon δ18O values, affirming that they share the same parental magmas. The amphibole compositions indicate that amphiboles from the MMEs are not in equilibrium with a melt whose composition was that of the bulk-rock. These new data, together with the published bulk-rock data, suggest that the MMEs in our study have clear cumulate signatures and are thus of cumulate origin. Our study provides evidence for crystal accumulation in granitoids in the NQOB. This new understanding calls for re-examination on the petrogenesis of some intermediate magmatic rocks (granitoid/andesite) in discussing models of continental crustal growth.
Biochemical characteristics and demography of the marine calanoid copepod Calanus finmarchicus during spring in Icelandic waters
Authors: Th Eysteinsson Stefán , Jónasdóttir Sigrún H , Gislason Astthor , Gudmundsson Kristinn , Olafsdottir Solveig R , Arason Sigurjón , Gudjónsdóttir María 
Published: November 2021

Abstract
The chemical composition of Calanus finmarchicus was analyzed at 21 stations from three regions where 12 transects were sampled from 0 to 50 m depth, including stage composition analysis at the Siglunes and Selvogsbanki transects in relation to the effects of different water masses, during a survey in Icelandic waters during 11–29 May 2018. The stage composition of C. finmarchicus at the northern transect of Siglunes was mostly made up of copepodites CI–CIII, around 76%, whereas older copepods CV–CVI dominated, around 64%, at the southern transect of Selvogsbanki. The dry weight (dw) and lipid content of C. finmarchicus were overall highest in the southwest (160 ± 60 μg dw ind−1 and 60 ± 20 μg lipids ind−1) and lowest in the east (120 ± 20 μg dw ind−1 and 30 ± 10 μg lipids ind−1). Total astaxanthin content ranged from 0.14 to 0.27 μg mg−1 dw. Chitin made up 2–4% of the dw. The diatom marker C20:5n3 was prolific in the copepods southwest of Iceland, while the dinoflagellate markers C18:4n3 and C22:6n3 dominated in the copepods east of Iceland. The results indicate that C. finmarchicus found in the south of Iceland developed faster than those in the north, with the variation in chemical composition and developmental time highly influenced by hydrographic regions.
Modeling the age distribution of retinoblastomas
Authors: Tetearing Alexandr N. 
Published: November 2021

AbstractIn this work, based on real data on the size of the eyeball (in a fetus, in a child, and in young people under 20), we constructed a model function of the growth of the retinal cell tissue.We used this function to construct a theoretical age distribution of retinoblastomas. We constructed theoretical age distributions for four different models of retinoblastoma: a complex mutational model, a third mutational model, a model with a sequence of key events, and a model of a single oncogenic event with two different latencies (hereditary and non-hereditary retinoblastoma).We compared the theoretical age distribution of retinoblastomas with the real age distribution based on SEER data (Surveillance Epidemiology and End Results; program of the American National Cancer Institute). In total, we examined 843 cases in women and 908 cases in men.For all models (separately for women and men), we obtained estimates of the following cancer parameters: the specific frequency of key events (events that trigger cancer); the duration of the latency period of cancer; the number of key events required for cancer to occur.For the composite age distributions, we calculated the theoretical mean age at diagnosis for hereditary and non-hereditary retinoblastomas.The best approximation accuracy (for male and female forms of retinoblastoma) is shown by a model with a sequence of key events.
Collective polymerase dynamics emerge from DNA supercoiling during transcription
Authors: Sevier Stuart A. , Hormoz Sahand 
Published: November 2021

All biological processes ultimately come from physical interactions. The mechanical properties of DNA play a critical role in transcription. RNA polymerase can over or under twist DNA (referred to as DNA supercoiling) when it moves along a gene resulting in mechanical stresses in DNA that impact its own motion and that of other polymerases. For example, when enough supercoiling accumulates, an isolated polymerase halts and transcription stops. DNA supercoiling can also mediate non-local interactions between polymerases that shape gene expression fluctuations. Here, we construct a comprehensive model of transcription that captures how RNA polymerase motion changes the degree of DNA supercoiling which in turn feeds back into the rate at which polymerases are recruited and move along the DNA. Surprisingly, our model predicts that a group of three or more polymerases move together at a constant velocity and sustain their motion (forming what we call a polymeton) whereas one or two polymerases would have halted. We further show that accounting for the impact of DNA supercoiling on both RNA polymerase recruitment and velocity recapitulates empirical observations of gene expression fluctuations. Finally, we propose a mechanical toggle switch whereby interactions between genes are mediated by DNA twisting as opposed to proteins. Understanding the mechanical regulation of gene expression provides new insights into how endogenous genes can interact and informs the design of new forms of engineered interactions.PACS numbers:
Nanopore ReCappable Sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs
Authors: Ugolini Camilla , Mulroney Logan , Leger Adrien , Castelli Matteo , Criscuolo Elena , Williamson Maia Kavanagh , Davidson Andrew D , Almuqrin Abdulaziz , Giambruno Roberto , Jain Miten , Frige Gianmaria , Olsen Hugh , Tzertzinis George , Schildkraut Ira , Wulf Madalee G. , Corrêa Ivan R. , Ettwiller Laurence , Clementi Nicola , Clementi Massimo , Mancini Nicasio , Birney Ewan , Akeson Mark , Nicassio Francesco , Matthews David A. , Leonardi Tommaso 
Published: November 2021

AbstractThe SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested sub genomic RNAs used to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5′ cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.
CHIQUITA1 maintains temporal transition between proliferation and differentiation in Arabidopsis thaliana
Authors: Bossi Flavia , Jin Benjamin , Lazarus Elena , Cartwright Heather , Dorone Yanniv , Rhee Seung Y. 
Published: November 2021

AbstractBody size varies widely among species, populations, and individuals depending on the environment. Transitioning between proliferation and differentiation is a crucial determinant of final organ size, but how the timing of this transition is established and maintained remains unknown. Using cell proliferation markers and genetic analysis, we show that CHIQUITA1 (CHIQ1) is required to maintain the timing of the transition from proliferation to differentiation in Arabidopsis thaliana. Combining kinematic and cell lineage tracking studies, we found that the number of actively dividing cells in chiquita1-1 plants decreases prematurely compared to wild type plants, suggesting CHIQ1 maintains the proliferative capacity in dividing cells and ensures that cells divide a certain number of times. CHIQ1 belongs to a plant-specific gene family of unknown molecular function and physically and genetically interacts with three close members of its family to control the timing of proliferation exit. Our work reveals the interdependency between cellular and organ-level processes underlying final organ size determination.SignificanceTiming of the transition between proliferation and differentiation is fundamental for determining the final size of organs and organisms. In agriculture, controlling organ and organism size can influence key agronomic traits such as yield and biomass. Dwarfism prevents lodging and was the trait responsible for the Green Revolution. Today, more sophisticated traits are needed for generating crops that are both resilient and sustainable. Revealing the molecular mechanisms that control the temporal transition between proliferation and differentiation will help unlock the potential of next-generation crops. Here, we report that CHIQUITA 1 in Arabidopsis thaliana is needed to maintain the proper timing of the transition between proliferation and differentiation in leaves and roots.
Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition
Authors: Reis Andre Martins , Hammond Jillian , Stevanovski Igor , Arnold Jonathon C , McGregor Iain S. , Deveson Ira , Gururajan Anand 
Published: November 2021

AbstractOur understanding of the molecular pathology of posttraumatic stress disorder (PTSD) is rapidly evolving and is being driven by advances in sequencing techniques. Conventional short-read RNA sequencing (RNA-seq) is a central tool in transcriptomics research that enables unbiased gene expression profiling. With the recent emergence of Oxford Nanopore direct RNA-seq (dRNA-seq), it is now also possible to interrogate diverse RNA modifications, collectively known as the ‘epitranscriptome’. Here, we present our analyses of the male and female mouse amygdala transcriptome and epitranscriptome, obtained using parallel Illumina RNA-seq and Oxford Nanopore dRNA-seq, associated with the acquisition of PTSD-like fear induced by Pavlovian cued-fear conditioning. We report significant sex-specific differences in the amygdala transcriptional response during fear acquisition, and a range of shared and dimorphic epitranscriptomic signatures. Differential RNA modifications are enriched among mRNA transcripts associated with neurotransmitter regulation and mitochondrial function, many of which have been previously implicated in PTSD. Very few differentially modified transcripts are also differentially expressed, suggesting an influential, expression-independent role for epitranscriptional regulation in PTSD-like fear-acquisition. Overall, our application of conventional and newly developed methods provides a platform for future work that will lead to new insights into and therapeutics for PTSD.
Stable and functionally diverse versatile peroxidases by computational design directly from sequence
Authors: Barber-Zucker Shiran , Mindel Vladimir , Garcia-Ruiz Eva , Weinstein Jonathan J. , Alcalde Miguel , Fleishman Sarel J. 
Published: November 2021

ABSTRACTWhite-rot fungi secrete a repertoire of high-redox potential oxidoreductases to efficiently decompose lignin. Of these enzymes, versatile peroxidases (VPs) are the most promiscuous biocatalysts. VPs are attractive enzymes for research and industrial use, but their recombinant production is extremely challenging. To date, only a single VP has been structurally characterized and optimized for recombinant functional expression, stability and activity. Computational enzyme optimization methods can be applied to many enzymes in parallel, but they require accurate structures. Here, we demonstrate that model structures computed by deep-learning based ab initio structure prediction methods are reliable starting points for one-shot PROSS stability-design calculations. Four designed VPs encoding as many as 43 mutations relative to the wild type enzymes are functionally expressed in yeast whereas their wild type parents are not. Three of these designs exhibit substantial and useful diversity in reactivity profile and tolerance to environmental conditions. The reliability of the new generation of structure predictors and design methods increases the scale and scope of computational enzyme optimization, enabling efficient discovery and exploitation of the functional diversity in natural enzyme families.
Lysophosphatidylcholine acyltransferase 2 (LPCAT2) Regulates The Expression of Macrophage Phenotype Markers in RAW264.7 Cells
Authors: Poloamina Victory Ibigo , Alrammah Hanaa , Abate Wondwossen , Avent Neil , Fejer Gyorgy , Jackson Simon K. 
Published: November 2021

1AbstractMacrophages are key antigen presenting cells that also secrete cytokines during inflammation. They can be polarised to M1 or M2 phenotypes. Molecules such as CD206 and inducible Nitric Oxide Synthase are considered macrophage phenotype markers because they are highly expressed in either M1 or M2 macrophages. LPCAT2 is a phospholipid modifying enzyme that influences inflammatory responses in macrophages. However, how LPCAT2 influences inflammation is not fully understood.In this study, we have used genetic technology to study the influence of LPCAT2 on macrophage phenotype markers.Our results show for the first time that overexpression of LPCAT2 promotes the expression of M1 macrophage phenotype markers, and attenuates the expression of M2 macrophage markers.
Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination
Authors: Arvindekar Shreyas , Jackman Matthew J. , Low Jason K.K. , Landsberg Michael J. , Mackay Joel P. , Viswanath Shruthi 
Published: November 2021

AbstractThe Nucleosome Remodeling and Deacetylase (NuRD) complex is a chromatin-modifying assembly that regulates gene expression and DNA damage repair. Despite its importance, limited structural information describing the complete NuRD complex is available and a detailed understanding of its mechanism is therefore lacking. Drawing on information from SEC-MALLS, DIA-MS, XLMS, negative-stain EM, X-ray crystallography, NMR spectroscopy, secondary structure predictions and homology models, we applied Bayesian integrative structure determination to investigate the molecular architecture of three NuRD sub-complexes: MTA1-HDAC1-RBBP4 (MHR), MTA1N-HDAC1-MBD3GATAD2CC (MHM), and MTA1-HDAC1-RBBP4-MBD3-GATAD2A (NuDe). The integrative structures were corroborated by examining independent crosslinks, cryo-EM maps, biochemical assays, known cancer-associated mutations, and structure predictions from AlphaFold. The robustness of the models was assessed by jack-knifing. Localization of the full-length MBD3, which connects the deacetylase and chromatin remodeling modules in NuRD, has not previously been possible; our models indicate two different locations for MBD3, suggesting a mechanism by which MBD3 in the presence of GATAD2A asymmetrically bridges the two modules in NuRD. Further, our models uncovered three previously unrecognized subunit interfaces in NuDe: HDAC1C-MTA1BAH, MTA1BAH-MBD3MBD, and HDAC160-100-MBD3MBD. Our approach also allowed us to localize regions of unknown structure, such as HDAC1C and MBD3IDR, thereby resulting in the most complete and robustly cross-validated structural characterization of these NuRD sub-complexes so far.
Supplementary motor area contributions to rhythm perception
Authors: Leow Li-Ann , Rinchon Cricia , Emerick Marina , Grahn Jessica A. 
Published: November 2021

AbstractTiming is everything, but our understanding of the neural mechanisms of timing remains limited, particularly for timing of sequences. Temporal sequences can be represented relative to a recurrent beat (beat-based or relative timing), or as a series of absolute durations (non-beat-based or absolute timing). Neuroimaging work suggests involvement of the basal ganglia, supplementary motor area (SMA), the premotor cortices, and the cerebellum in both beat- and non-beat-based timing. Here we examined how beat-based timing and non-beat-based sequence timing were affected by modulating excitability of the supplementary motor area, the right cerebellum, and the bilateral dorsal premotor cortices, using transcranial direct current stimulation (tDCS). Participants were subjected to a sham stimulation session, followed an active stimulation session where anodal or cathodal 2mA tDCS was applied to the SMA, right premotor cortex, left premotor cortex, or the cerebellum. During both sessions, participants discriminated changes in rhythms which differentially engage beat-based or non-beat-based timing. Rhythm discrimination performance was improved by increasing SMA excitability, and impaired by decreasing SMA excitability. This polarity-dependent effect on rhythm discrimination was absent for cerebellar or premotor cortex stimulation, suggesting a crucial role of the SMA and/or its functionally connected networks in rhythmic timing mechanisms.
Design of adaptive sliding mode controller applied to ultrasonic motor
Authors: Yan Gangfeng 
Published: November 2021

Purpose
The purpose of this paper is to achieve high-precision sliding mode control without chattering; the control parameters are easy to adjust, and the entire controller is easy to use in engineering practice.

Design/methodology/approach
Using double sliding mode surfaces, the gain of the control signal can be adjusted adaptively according to the error signal. A kind of sliding mode controller without chattering is designed and applied to the control of ultrasonic motors.

Findings
The results show that for a position signal with a tracking amplitude of 35 mm, the traditional sliding mode control method has a maximum tracking error of 0.3326 mm under the premise of small chattering; the boundary layer sliding mode control method has a maximum tracking error of 0.3927 mm without chattering, and the maximum tracking error of continuous switching adaptive sliding mode control is 0.1589 mm, and there is no chattering. Under the same control parameters, after adding a load of 0.5 kg, the maximum tracking errors of the traditional sliding mode control method, the boundary layer sliding mode control method and the continuous switching adaptive sliding mode control are 0.4292 mm, 0.5111 mm and 0.1848 mm, respectively.

Originality/value
The proposed method not only switches continuously, but also the amplitude of the switching signal is adaptive, while maintaining the robustness of the conventional sliding mode control method, which has strong engineering application value.