bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of coffee florigenCaFT1reveals a sustained floral induction window associated with asynchronous flowering in tropical perennials
Authors: Cardon Carlos Henrique , de Oliveira Raphael Ricon , Lesy Victoria , Cherubino Ribeiro Thales Henrique , Fust Catherine , Pereira Luísa Peloso , Colasanti Joseph , Chalfun-Junior Antonio 
Published: November 2021

AbstractThe behavior of florigen(s) and environment-influenced regulatory pathways that control flowering in tropical perennials with complex phenological cycles is poorly understood. Understanding the mechanisms underlying this process is important for food production in the face of climate change. To explore this, homologs ofArabidopsisflorigenFLOWERING LOCUS T(CaFT1) and environment-related regulatorsCONSTANS(CO), PHYTOCHROME INTERACTING FACTOR 4(PIF4) andFLOWERING LOCUS C(FLC) were isolated fromCoffeasp. L. (Rubiaceae). Overexpression ofCaFT1inArabidopsisshowed typical early-flowering and yeast two hybrid studies indicated CaFT1 binding to bZIP floral regulator, FD, demonstrates that CaFT1 is a coffee orthologue of florigen. Expression ofCaFT1and floral regulators were evaluated over one year using three contrasting genotypes: twoC. arabicaand oneC. canephora. All genotypes showed activeCaFT1transcription from February until October, indicating a potential window for floral induction.CaCOexpression, as expected, varied over the day period and monthly with day length, whereas expression of temperature-responsive homologs,CaFLCandCaPIF4, did not correlate with temperature changes. Using coffee as a model, we suggest a continuum of floral induction that allows different starting points for floral activation, which explains developmental asynchronicity and prolonged anthesis events in tropical perennial species.HighlightCoffee florigen CaFT1 and related regulators revealed an extended floral induction window clarifying the asynchronicity and influence of environment for flowering in tropical perennial crops, providing perspectives to its control.
Coronavirus RNA synthesis takes place within membrane-bound sites
Authors: Doyle Nicole , Simpson Jennifer , Hawes Philippa C , Maier Helena J 
Published: November 2021

AbstractInfectious bronchitis virus (IBV), a gammacoronavirus, is an economically important virus to the poultry industry as well as a significant welfare issue for chickens. As for all positive strand RNA viruses, IBV infection causes rearrangements of the host cell intracellular membranes to form replication organelles. Replication organelle formation is a highly conserved and vital step in the viral life cycle. Here, we investigate the localization of viral RNA synthesis and the link with replication organelles in host cells. We have shown that sites of viral RNA synthesis and virus-related dsRNA are associated with one another and, significantly, that they are located within a membrane-bound compartment within the cell. We have also shown that some viral RNA produced early in infection remains within these membranes throughout infection. Importantly, we demonstrate conservation across all four coronavirus genera, including SARS-CoV-2. Under-standing more about the replication of these viruses is imperative in order to effectively find ways to control them.
Conservation of the direct and indirect pathways dichotomy in mouse caudal striatum with uneven distribution of dopamine receptor D1- and D2-expressing neurons
Authors: Ogata Kumiko , Kadono Fuko , Hirai Yasuharu , Inoue Ken-ichi , Takada Masahiko , Karube Fuyuki , Fujiyama Fumino 
Published: November 2021

AbstractThe striatum is one of the key nuclei for adequate control of voluntary behaviors and reinforcement learning. Two striatal projection neuron types, expressing either dopamine receptor D1 (D1R) or dopamine receptor D2 (D2R) constitute two independent output routes: the direct or indirect pathways, respectively. These pathways co-work in balance to achieve coordinated behavior. Two projection neuron types are equivalently intermingled in most striatal space. However, recent studies revealed two atypical zones in the caudal striatum: the zone in which D1R-neurons are the minor population (D1R-poor zone) and that in which D2R-neurons are the minority (D2R-poor zone). It remains obscure as to whether these imbalanced zones have similar properties on axonal projections and electrophysiology compared to other striatal regions. Based on morphological experiments in mice using immunofluorescence, in situ hybridization, and neural tracing, here, we revealed that the poor zones densely projected to the globus pallidus and substantia nigra pars lateralis, with a few collaterals in substantia nigra pars reticulata and compacta. Similar to that in other striatal regions, D1R-neurons were the direct pathway neurons. We also showed membrane properties of projection neurons in the poor zones were largely similar to those in the conventional striatum using in vitro electrophysiological recording. In addition, the poor zones existed irrespective of the age or sex of mice. We also identified the poor zones in the common marmoset as well as other rodents. These results suggest that the poor zones in the caudal striatum follow the conventional projection patterns irrespective of imbalanced distribution of projection neurons. The poor zones could be an innate structure and common in mammals. The unique striatal zones possessing highly restricted projections could relate to functions different from those of motor-related striatum.
Augmenting Recombinant Antibody Production in HEK293E Cells: Optimising Transfection and Culture Parameters
Authors: Heng Zealyn Shi-Lin , Yeo Joshua Yi , Koh Darius Wen-Shuo , Gan Samuel Ken-En , Ling Wei-Li 
Published: November 2021

ABSTRACTBackgroundOptimising recombinant antibody production is important for cost-effective therapeutics and diagnostics. With impact on commercialisation, higher productivity beyond laboratory scales is highly sought, where efficient production can also accelerate antibody characterisations and investigations.MethodsInvestigating HEK293E cells for mammalian antibody production, various transfection and culture parameters were systematically analysed for antibody light chain production before evaluating them for whole antibody production. Transfection parameters investigated include seeding cell density, the concentration of the transfection reagent and DNA, complexation time, temperature, and volume, as well as culture parameters such as medium replacement, serum deprivation, use of cell maintenance antibiotic, incubation temperature, medium volume, post-transfection harvest day and common nutrient supplements.ResultsUsing 2 mL adherent HEK293E cell culture transfections with 25 kDa linear Polyethylenimine in the most optimised parameters, we demonstrated a ~2-fold production increase for light chain alone and for whole antibody production reaching 536 and 49 μg respectively in a cost-effective manner. With the addition of peptone, κ light chain increased by ~4-fold to 1032 μg while whole antibody increased to a lesser extent by ~2.5-fold to 51 μg, with benefits potentially for antibodies limited by their light chains in production.ConclusionsOur optimised findings show promise for a more efficient and convenient antibody production method through transfection and culture optimisations that can be incorporated to scale up processes and with potential transferability to other mammalian-based recombinant protein production using HEK293E cells.Statement of SignificanceRecombinant antibody production is crucial for antibody research and development. Systematically investigating transfection and culture parameters such as PEI/DNA concentrations, complexation time, volume, and temperature, supplements, etc., we demonstrated a ~4-fold light chain alone production increase to 1032 μg and a 2.5-fold whole antibody production increase to 51 μg from 2 mL transfections.
Comparisons of ribonuclease HI homologs and mutants uncover a multi-state model for substrate recognition
Authors: Martin James A. , Palmer Arthur G. 
Published: November 2021

ABSTRACTRibonuclease HI (RNHI) non-specifically cleaves the RNA strand in RNA:DNA hybrid duplexes in a myriad of biological processes, including retroviral reverse transcription. Several RNHI homologs contain an extended domain, termed the handle region, that is critical to substrate binding. Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations have suggested a kinetic model in which the handle region can exist in open (substrate-binding competent) or closed (substrate-binding incompetent) states in homologs containing arginine or lysine at position 88 (using sequence numbering of E. coli RNHI), while the handle region populates a state intermediate between the open and closed conformers in homologs with asparagine at residue 88 [Stafford, K. A., et al., PLoS Comput. Biol.2013, 9, 1-10]. NMR parameters characterizing handle region dynamics are highly correlated with enzymatic activity for RNHI homologs with two-state (open/closed) handle regions [Martin, J. A., et al., Biochemistry2020, 59, 3201-3205]. The work presented herein shows that homologs with one-state (intermediate) handle regions display distinct structural features compared with their two-state counterparts. Comparisons of RNHI homologs and site-directed mutants with arginine at position 88 support a kinetic model for handle region dynamics that includes 12 unique transitions between eight conformations. Overall, these findings present an example of the structure-function relationships of enzymes and spotlight the use of NMR spectroscopy and MD simulations in uncovering fine details of conformational preferences.
Rapid quantification of tissue perfusion properties with a two-stage look-up table: a simulation study
Authors: Yang Bin 
Published: November 2021

AbstractTissue perfusion properties reveal crucial information pertinent to clinical diagnosis and treatment. Multispectral spatial frequency domain imaging (SFDI) is an emerging imaging technique that has been widely used to quantify tissue perfusion properties. However, slow processing speed limits its usefulness in real-time imaging applications. In this study, we present a two-stage look-up table (LUT) approach that accurately and rapidly quantifies optical (absorption and reduced scattering maps) and perfusion (total hemoglobin and oxygen saturation maps) properties using stage-1 and stage-2 LUTs, respectively, based on reflectance images at 660nm and 850nm. The two-stage LUT can be implemented on both CPU and GPU computing platforms. Quantifying tissue perfusion properties using the simulated diffuse reflectance images, we achieved a quantification speed of 266, 174, and 74 frames per second for three image sizes 512×512, 1024×1024, and 2048×2048 pixels, respectively. Quantification of tissue perfusion properties was highly accurate with only 3.5% and 2.5% error for total hemoglobin and oxygen saturation quantification, respectively. The two-stage LUT has the potential to be adopted in existing SFDI applications to enable real-time imaging capability of tissue hemodynamics.
CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells
Authors: Ai Yuxi , Liang Dongming , Wilusz Jeremy E. 
Published: November 2021

ABSTRACTCRISPR/Cas13 effectors have garnered increasing attention as easily customizable tools for detecting and depleting RNAs of interest. Near perfect complementarity between a target RNA and the Cas13-associated guide RNA is required for activation of Cas13 ribonuclease activity. Nonetheless, the specificity of Cas13 effectors in eukaryotic cells has been debated as the Cas13 nuclease domains can be exposed on the enzyme surface, providing the potential for promiscuous cleavage of nearby RNAs (so-called collateral damage). Here, using co-transfection assays in Drosophila and human cells, we found that the off-target effects of RxCas13d, a commonly used Cas13 effector, can be as strong as the level of on-target RNA knockdown. The extent of off-target effects is positively correlated with target RNA expression levels, and collateral damage can be observed even after reducing RxCas13d/guide RNA levels. The PspCas13b effector showed improved specificity and, unlike RxCas13d, can be used to deplete a Drosophila circular RNA without affecting the expression of the associated linear RNA. PspCas13b nonetheless still can have off-target effects and we notably found that the extent of off-target effects for Cas13 effectors differs depending on the cell type and target RNA examined. In total, these results highlight the need for caution when designing and interpreting Cas13-based knockdown experiments.
Mutant-SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms
Authors: Carratt Sarah A. , Kong Garth L. , Smith Brittany M. , Schonrock Zachary , Maloney Lauren , Baris Adrian , Druker Brian J. , Braun Theodore P. , Maxson Julia E. 
Published: November 2021

AbstractColony stimulating factor 3 receptor (CSF3R) mutations lead to JAK pathway activation and are the molecular hallmark of chronic neutrophilic leukemia (CNL). Approximately half of CNL patients also have mutations in SET binding protein 1 (SETBP1). In this study, we developed models of SETBP1-mutant leukemia to understand the role that SETBP1 plays in CNL. SETBP1 mutations promote self-renewal of CSF3R-mutant hematopoietic progenitors in vitro and prevent cells from undergoing terminal differentiation. In vivo, SETBP1 mutations accelerate leukemia progression, leading to the rapid development of hepatosplenomegaly and granulocytosis. Through transcriptomic and epigenomic profiling, we found that SETBP1 enhances progenitor-associated programs—most strongly upregulating Myc and Myc target genes. This upregulation of Myc can be reversed by epigenetic modulatory drugs. In summary, we find that SETBP1 mutations promote aggressive hematopoietic cell expansion when expressed with mutant CSF3R through the upregulation of Myc-associated gene expression programs.Statement of SignificanceSETBP1 is frequently mutated in chronic neutrophilic leukemia, but its role in the biology of this disease is unclear. We find that mutant SETBP1 enhances transcription of Myc and Myc target genes to promote aggressive disease biology, and that these oncogenic transcriptional programs can be reversed by epigenetic modulatory drugs.
Raman microspectroscopy imaging analysis of extracellular vesicles (EVs) biogenesis by filamentous fungusPenicilium chrysogenum
Authors: Samuel Ashok Zachariah , Horii Shumpei , Nakashima Takuji , Shibata Naoko , Ando Masahiro , Takeyama Haruko 
Published: November 2021

AbstractMechanism of production of extracellular vesicles (EVs) and their molecular contents are of great interest owing to their diverse roles in biological systems and are far from being completely understood. Even though, cellular cargo release mediated by EVs have been demonstrated in several cases, their role in secondary metabolite production and release remains elusive. In this study we investigate this aspect in detail using Raman micro-spectroscopic imaging. We provide considerable evidence to suggest that the release of antibiotic penicillin by filamentous fungusPenicillium chrysogenuminvolves EVs. Morphological modifications of the fungal body during biogenesis, changes in cell composition at the locus of biogenesis, and major molecular contents of the released EVs are also revealed in this study.ImportanceExtracellular vesicles (EVs) play a key role in cellular communications. EVs role in functioning of fungi are relatively less explored. Here we show selective enrichment of chemical contents at certain locations of mycelium ofP. chrysogenumforming protruding regions. Secondary metabolite penicillin is excessively localized in them. We provide evidence to show that EVs are released from these protrusions. Raman imaging has been applied for molecular profiling of the mycelium and for characterizing chemical contents of the EVs. Our study suggests a possible general role of EVs in the release of antibiotics from the producing organisms.
Shank promotes action potential repolarization by recruiting BK channels to calcium nanodomains
Authors: Gao Luna , Zhao Jian , Ardiel Evan , Hall Qi , Nurrish Stephen , Kaplan Joshua M. 
Published: November 2021

SummaryMutations altering the scaffolding protein Shank are linked to several psychiatric disorders, and to synaptic and behavioral defects in mice. Among its many binding partners, Shank directly binds CaV1 voltage activated calcium channels. Here we show that the C. elegans SHN-1/Shank promotes CaV1 coupling to calcium activated potassium channels. Mutations inactivating SHN-1, and those preventing SHN-1 binding to EGL-19/CaV1 all increase action potential durations in body muscles. Action potential repolarization is mediated by two classes of potassium channels: SHK-1/KCNA and SLO-1 and SLO-2 BK channels. BK channels are calcium-dependent, and their activation requires tight coupling to EGL-19/CaV1 channels. SHN-1’s effects on AP duration are mediated by changes in BK channels. In shn-1 mutants, SLO-2 currents and channel clustering are significantly decreased in both body muscles and neurons. Finally, increased and decreased shn-1 gene copy number produce similar changes in AP width and SLO-2 current. Collectively, these results suggest that an important function of Shank is to promote nanodomain coupling of BK with CaV1.
A homochiral coordination polymer of cobalt(II) and L-serine
Authors: Dzesse T. Christelle N. , Majoumo-Mbe Felicite , Nfor Emmanuel N. , Bourne Susan A. 
Published: November 2021

A one-dimensional chiral cobalt(II) coordination polymer, namely, catena-poly[[[(S)-2-amino-3-hydroxypropanoato-κ2
N,O
1]cobalt(II)]-μ-(S)-2-amino-3-hydroxypropanoato-κ4
O
1,O
3:N,O
1′], [Co(C3H6NO3)2]
n
or Δ-[Co(L-Ser-κ2
N,O)2]
n
(L-Ser = L-serine) (1), has been synthesized and characterized using elemental and thermal analyses, IR spectroscopy and single-crystal and powder X-ray diffraction techniques. The asymmetric unit of 1 consists of two serine anions which are coordinated to a Co2+ ion to give three chelate rings. These extend the structure into a helical chain with pendant chelate rings which participate in interchain hydrogen bonding. The ability of 1 to undergo transmetallation was evaluated. Among a range of divalent metal ions, only copper(II) partially replaced cobalt(II).
Assessing word-of-mouth reputation of influencers on B2C live streaming platforms: the role of the characteristics of information source
Authors: Wang Lin , Wang Zhihua , Wang Xiaoying , Zhao Yang 
Published: November 2021

PurposeThe purpose of this paper is to assess the influence mechanism of the word-of-mouth reputation of influencers.Design/methodology/approachThis study explored word-of-mouth reputation from four characteristics of information source of influencers: credibility, professionalism, interactivity and attractiveness. The grounded theory was used to extract the characteristic indicators of influencers and used questionnaire surveys to obtain 218 valid samples. The fuzzy-set qualitative comparative analysis (fsQCA) was used for the configuration analysis.FindingsThe results revealed the following: (1) a causal asymmetric correlation exists between the driving mechanism of high word-of-mouth reputation and non-high word-of-mouth reputation; (2) influencers matching high word-of-mouth reputation comprises potential, developmental and almighty types, whereas live streaming influencer matching non-high word-of-mouth reputation comprises elementary and groping types; and (3) all factors must be combined to play a role, and neutral permutations of two solutions were found among the three overall solutions to attain high word-of-mouth reputation; (4) the combination of high user activity and high exposure is the core configuration that results in high word-of-mouth reputation.Practical implicationsThis study provides recommendation for consumers, live streamers, brand and e-commerce platform on how to promote the sustainable and healthy development of influencer marketing.Originality/valueThis study focused on elucidating how the characteristics of information source affect the word-of-mouth reputation of influencers and have a reference value for the research on word-of-mouth reputation in the context of live commerce.
The role of organization intermediaries in science-/techno-push versus user-centric approaches in health care innovation
Authors: Merindol Valerie , Le Chaffotec Alexandra , Versailles David W. 
Published: November 2021

PurposeHealth care ecosystems instantiate different innovation trajectories, driven either by science-/techno-push or user-centric rationales. This article focuses on organization intermediaries (OIs), respectively, active in health care ecosystems driven by science- and techno-push versus user-centric innovation processes; it aims at characterizing their operation and intervention modes. The analysis elaborates on network and content brokerage. Innovation also needs to consider various challenges associated with physical vicinity. The authors check whether territorial anchoring plays a role in brokerage, depending on the innovation model.Design/methodology/approachThe article offers an investigation of eight French organizations matching the definition of OIs and active in different areas of health care-related innovation. It follows a qualitative and abductive research protocol adhering to the precepts of grounded theory.FindingsFirst, the authors show that content and network brokerage specialize in specific activities in each innovation model. On network brokerage, the authors show that OIs foster the development of communities of practice in the science-/techno-push model, while they nurture communities of innovation in the user-centric model. Services materializing content brokerage are typical consequences of activities performed in each model. The second contribution deals with physical vicinity. In the science-/techno-push model, OIs install a physical space (the “internal” dimension) to support the development of communities of practice, while the “external” dimension copes with agglomeration effects. In the user-centric model, OIs deliver services thanks to the “internal” space; communities of innovation create a leverage effect on the physical space to operate their activities that are supported by “external” network effects.Originality/valueThe originality of the article lies in the description of the alternative roles plaid by organization intermediaries in the science-/techno-push versus user-centric approaches of innovation. In these two approaches, (contents and network) brokerage and physical vicinity play different roles.