bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histone H3K9 acetylation modulates gene expression of key enzymes in the flavonoid and abscisic acid pathways and enhances drought resistance of sea buckthorn
Authors: Li Jiayi , Wei Jihua , Song Yating , Chen Ning , Ni Bingbing , Zhang Jianguo , He Caiyun 
Published: May 2023

AbstractThe effect of histone H3K9 acetylation modification on gene expression and drought resistance in drought‐resistant tree species is not clear. Using the chromatin immunoprecipitation (ChIP) method, this study obtained nine H3K9 acetylated protein‐interacting DNAs from sea buckthorn seedlings, and the ChIP sequencing result predicted about 56,591, 2217 and 5119 enriched region peaks in the control, drought and rehydration comparative groups, respectively. Gene functional analysis of differential peaks from three comparison groups revealed that 105 pathways were involved in the drought resistance process, and 474 genes were enriched in the plant hormone signaling transduction pathways. Combined ChIP‐seq and transcriptome analysis revealed that six genes related to abscisic acid synthesis and signaling pathways, 17 genes involved in flavonoid biosynthesis, and 15 genes involved in carotenoid biosynthesis were positively regulated by H3K9 acetylation modification under drought stress. Under drought stress conditions, the content of abscisic acid and the expression of related genes were significantly up‐regulated, while the content of flavonoids and the expression of key enzymes involved in their synthesis were largely down‐regulated. Meanwhile, after exposure to histone deacetylase inhibitors (trichostatin A), the change of abscisic acid and flavonoids content and their related gene expression were slowed down under drought stress. This study will provide an important theoretical basis for understanding the regulatory mechanisms of histone acetylation modifications in sea buckthorn drought resistance.
A stratagem for primary root elongation under moderate salt stress in the halophyte Schrenkiella parvula
Authors: Şekerci Keriman , Higashitani Nahoko , Ozgur Rengin , Uzilday Baris , Higashitani Atsushi , Turkan Ismail 
Published: May 2023

AbstractSchrenkiella parvula, an Arabidopsis‐related halophyte, grows around Lake Tuz (Salt) in Turkey and can survive up to 600 mM NaCl. Here, we performed physiological studies on the roots of S. parvula and A. thaliana seedlings cultivated under a moderate salt condition (100 mM NaCl). Interestingly, S. parvula germinated and grew at 100 mM NaCl, but germination did not occur at salt concentrations above 200 mM. In addition, primary roots elongated much faster at 100 mM NaCl, while being thinner with fewer roots hair, than under NaCl‐free conditions. Salt‐induced root elongation was due to epidermal cell elongation, but meristem size and meristematic DNA replication were reduced. The expression of genes related to auxin response and biosynthesis was also reduced. Application of exogenous auxin abolished the changes in primary root elongation, suggesting that auxin reduction is the main trigger for root architectural changes in response to moderate salinity in S. parvula. In A. thaliana seeds, germination was maintained up to 200 mM NaCl, but post‐germination root elongation was significantly inhibited. Furthermore, primary roots did not promote elongation even under fairly low salt conditions. Compared to A. thaliana, cell death and ROS content in primary roots of salt‐stressed plants were significantly lower in S. parvula. These changes in the roots of S. parvula seedlings may be an adaptive strategy to reach lower salinity by advancing into deeper soils, while being impaired by moderate salt stress.
Transcription factors TgbHLH42‐1 and TgbHLH42‐2 positively regulate anthocyanin biosynthesis in Tulip (Tulipa gesneriana L.)
Authors: Hu Xianmei , Sun Tianxiao , Liang Zehui , Zhang Hengbin , Fu Qiang , Wang Yanping , Chan Zhulong , Xiang Lin 
Published: May 2023

AbstractThe floral coloration of tulip flowers is one of the most prominent traits contributing to its high ornamental value. The molecular mechanisms of petal coloration remain elusive in tulip species. In this study, we performed comparative metabolome and transcriptome analyses using four tulip cultivars with distinguished petal colors. Four types of anthocyanins were identified, including cyanidin derivatives and pelargonidin derivatives. Comparative transcriptome analysis identified 22,303 differential expressed genes (DEGs) from the four cultivars, and 2589 DEGs were commonly regulated in three comparison groups (colored vs. white cultivar), including anthocyanins biosynthesis‐related genes and regulatory transcription factors. Two basic helix–loop–helix (bHLH) transcription factors, TgbHLH42‐1 and TgbHLH42‐2, with differential expression levels among cultivars and petal developmental stages, have high homology to TRANSPARENT TESTA 8 (AtTT8) of Arabidopsis. The anthocyanins accumulation in TgbHLH42‐1 overexpressing (OE) seedlings was markedly greater than that in wild‐type seedlings in the presence of methyl jasmonate (MeJA), but not for TgbHLH42‐2 OE seedlings. Both TgbHLH42‐1 and TgbHLH42‐2 restored pigmentation defects in tt8 mutant seeds after complementation assay. TgbHLH42‐1 could interact with MYB protein AtPAP1 to synergistically activate the transcription of AtDFR, whereas TgbHLH42‐2 failed to. Silencing TgbHLH42‐1 or TgbHLH42‐2 individually could not, but simultaneously silencing both TgbHLH42 could reduce the anthocyanin in tulip petals. These results indicate that TgbHLH42‐1 and TgbHLH42‐2 function partially redundantly to positively regulate anthocyanin biosynthesis during tulip petal coloration.
Photo‐oxidative stress leading to oxylipin accumulation may trigger drought‐induced leaf abscission in olive trees
Authors: Villadangos Sabina , González Carmen , Munné‐Bosch Sergi 
Published: May 2023

AbstractOlive trees shed their leaves under severe drought as a defence mechanism. Foliar drought‐induced abscission is a programmed process occurring in a differentiated cell layer at the base of the petiole. Considering the antioxidant properties of vitamin E and its interplay with lipid peroxidation‐derived jasmonates in abiotic stress responses, we hypothesized about their possible role in abscission signaling by forming a jasmonates‐increasing basipetal gradient along the leaf up to the abscission zone. We exposed young olives trees to water withdrawal for 21 days, after which five leaf sections, from the apex to the petiole, were sampled on both attached and detached leaves of irrigated and water‐stressed trees. We found that prolonged drought stress resulted in a sharp reduction in the photosystem II efficiency, chlorophyll and vitamin E contents in leaves, leading to photo‐oxidative stress, reflected by the increase in lipid peroxidation. In addition, the content of chloroplast‐derived oxylipins and phytohormones, such as jasmonoyl‐isoleucine and salicylic acid, increased. At the same time, α‐tocopherol decreased in the petiole of water‐stressed attached leaves, suggesting a conditioning for the abscission process to occur. Although no differences were observed in petioles from attached and detached leaves, the dropped ones showed higher oxidative stress in the leaf blade. It is concluded that redox signaling through oxylipins accumulation may trigger leaf abscission in drought‐stressed olive trees. Mechanical stress is, however, additionally needed to execute leaf abscission once the abscission zone is properly conditioned.
Are commercial genetic injury tests premature?
Authors: Collins Malcolm , September Alison V. 
Published: May 2023

IntroductionSeveral direct‐to‐consumer (DTC) genetic testing companies have emerged that claim to be able to test for susceptibility for musculoskeletal injuries. Although there are several publications on the emergence of this industry, none have critically evaluated the evidence for the use of genetic polymorphisms in commercial tests. The aim of this review was to identify, where possible, the polymorphisms and to evaluate the current scientific evidence for their inclusion.ResultsThe most common polymorphisms included COL1A1 rs1800012, COL5A1 rs12722, and GDF5 rs143383. The current evidence suggests that it is premature or even not viable to include these three polymorphisms as markers of injury risk. A unique set of injury‐specific polymorphisms, which do not include COL1A1, COL5A1, or GDF5, identified from genome‐wide association studies (GWAS) is used by one company in their tests for 13 sports injuries. However, of the 39 reviewed polymorphisms, 22 effective alleles are rare and absent in African, American, and/or Asian populations. Even when informative in all populations, the sensitivity of many of the genetic markers was low and/or has not been independently validated in follow‐up studies.ConclusionsThe current evidence suggests it is premature to include any of the reviewed polymorphisms identified by GWAS or candidate gene approaches in commercial genetic tests. The association of MMP7 rs1937810 with Achilles tendon injuries, and SAP30BP rs820218 and GLCCI1 rs4725069 with rotator cuff injuries does warrant further investigation. Based on current evidence, it remains premature to market any commercial genetic test to determine susceptibility to musculoskeletal injuries.
Why beliefs are not dispositional stereotypes
Authors: Moore Andrew Garford , Botterill George 
Published: May 2023

AbstractIn a series of papers, Schwitzgebel has attempted to revive the dispositionalist account of belief by tweaking it a little and claiming a previously unconsidered advantage over representationalism. The tweaks are to include phenomenal and cognitive responses, in addition to overt behaviour, in the manifestations of a given belief; and to soften the account of dispositions by allowing for dispositional stereotypes. The alleged advantage is that dispositionalism can deal with what Schwitzgebel calls cases of in‐between belief, whereas representationalism cannot. In this paper we argue that Schwitzgebel's attempted improvements do not succeed and that, as an account of belief, dispositionalism is seen to be unsatisfactory. The case for this verdict also enables the representationalist position to be enhanced by drawing attention to the diversity of formats in which beliefs are stored.
Natural variations in the Sl‐AKR9 aldo/keto reductase gene impact fruit flavor volatile and sugar contents
Authors: Li Xiang , Tieman Denise , Alseekh Saleh , Fernie Alisdair R. , Klee Harry J. 
Published: May 2023

SUMMARYThe unique flavors of different fruits depend upon complex blends of soluble sugars, organic acids, and volatile organic compounds. 2‐Phenylethanol and phenylacetaldehyde are major contributors to flavor in many foods, including tomato. In the tomato fruit, glucose, and fructose are the chemicals that most positively contribute to human flavor preferences. We identified a gene encoding a tomato aldo/keto reductase, Sl‐AKR9, that is associated with phenylacetaldehyde and 2‐phenylethanol contents in fruits. Two distinct haplotypes were identified; one encodes a chloroplast‐targeted protein while the other encodes a transit peptide‐less protein that accumulates in the cytoplasm. Sl‐AKR9 effectively catalyzes reduction of phenylacetaldehyde to 2‐phenylethanol. The enzyme can also metabolize sugar‐derived reactive carbonyls, including glyceraldehyde and methylglyoxal. CRISPR‐Cas9‐induced loss‐of‐function mutations in Sl‐AKR9 significantly increased phenylacetaldehyde and lowered 2‐phenylethanol content in ripe fruit. Reduced fruit weight and increased soluble solids, glucose, and fructose contents were observed in the loss‐of‐function fruits. These results reveal a previously unidentified mechanism affecting two flavor‐associated phenylalanine‐derived volatile organic compounds, sugar content, and fruit weight. Modern varieties of tomato almost universally contain the haplotype associated with larger fruit, lower sugar content, and lower phenylacetaldehyde and 2‐phenylethanol, likely leading to flavor deterioration in modern varieties.
The TOPLESS corepressor regulates developmental switches in the bryophyte Physcomitrium patens that were critical for plant terrestrialisation
Authors: Causier Barry , McKay Mary , Hopes Tayah , Lloyd James , Wang Dapeng , Harrison C. Jill , Davies Brendan 
Published: May 2023

SUMMARYThe plant‐specific TOPLESS (TPL) family of transcriptional corepressors is integral to multiple angiosperm developmental processes. Despite this, we know little about TPL function in other plants. To address this gap, we investigated the roles TPL plays in the bryophyte Physcomitrium patens, which diverged from angiosperms approximately 0.5 billion years ago. Although complete loss of PpTPL function is lethal, transgenic lines with reduced PpTPL activity revealed that PpTPLs are essential for two fundamental developmental switches in this plant: the transitions from basal photosynthetic filaments (chloronemata) to specialised foraging filaments (caulonemata) and from two‐dimensional (2D) to three‐dimensional (3D) growth. Using a transcriptomics approach, we integrated PpTPL into the regulatory network governing 3D growth and we propose that PpTPLs represent another important class of regulators that are essential for the 2D‐to‐3D developmental switch. Transcriptomics also revealed a previously unknown role for PpTPL in the regulation of flavonoids. Intriguingly, 3D growth and the formation of caulonemata were crucial innovations that facilitated the colonisation of land by plants, a major transformative event in the history of life on Earth. We conclude that TPL, which existed before the land plants, was co‐opted into new developmental pathways, enabling phytoterrestrialisation and the evolution of land plants.
In planta dynamics, transport biases, and endogenous functions of mobile siRNAs in Arabidopsis
Authors: Devers Emanuel A. , Brosnan Christopher A. , Sarazin Alexis , Schott Gregory , Lim Peiqi , Lehesranta Satu , Helariutta Yrjö , Voinnet Olivier 
Published: May 2023

SUMMARYIn RNA interference (RNAi), small interfering RNAs (siRNAs) produced from double‐stranded RNA guide ARGONAUTE (AGO) proteins to silence sequence‐complementary RNA/DNA. RNAi can propagate locally and systemically in plants, but despite recent advances in our understanding of the underlying mechanisms, basic questions remain unaddressed. For instance, RNAi is inferred to diffuse through plasmodesmata (PDs), yet how its dynamics in planta compares with that of established symplastic diffusion markers remains unknown. Also is why select siRNA species, or size classes thereof, are apparently recovered in RNAi recipient tissues, yet only under some experimental settings. Shootward movement of endogenous RNAi in micro‐grafted Arabidopsis is also yet to be achieved, while potential endogenous functions of mobile RNAi remain scarcely documented. Here, we show (i) that temporal, localized PD occlusion in source leaves' companion cells (CCs) suffices to abrogate all systemic manifestations of CC‐activated mobile transgene silencing, including in sink leaves; (ii) that the presence or absence of specific AGOs in incipient/traversed/recipient tissues likely explains the apparent siRNA length selectivity observed upon vascular movement; (iii) that stress enhancement allows endo‐siRNAs of a single inverted repeat (IR) locus to translocate against the shoot‐to‐root phloem flow; and (iv) that mobile endo‐siRNAs generated from this locus have the potential to regulate hundreds of transcripts. Our results close important knowledge gaps, rationalize previously noted inconsistencies between mobile RNAi settings, and provide a framework for mobile endo‐siRNA research.
ELONGATED HYPOCOTYL5 (HY5) and HY5 HOMOLOGUE (HYH) maintain shade avoidance suppression in UV‐B
Authors: Sharma Ashutosh , Pridgeon Ashley J. , Liu Wei , Segers Francisca , Sharma Bhavana , Jenkins Gareth I. , Franklin Keara A. 
Published: May 2023

SUMMARYReductions in red to far‐red ratio (R:FR) provide plants with an unambiguous signal of vegetational shade and are monitored by phytochrome photoreceptors. Plants integrate this information with other environmental cues to determine the proximity and density of encroaching vegetation. Shade‐sensitive species respond to reductions in R:FR by initiating a suite of developmental adaptations termed shade avoidance. These include the elongation of stems to facilitate light foraging. Hypocotyl elongation is driven by increased auxin biosynthesis promoted by PHYTOCHROME INTERACTING FACTORs (PIF) 4, 5 and 7. UV‐B perceived by the UV RESISTANCE LOCUS 8 (UVR8) photoreceptor rapidly inhibits shade avoidance, in part by suppressing PIF4/5 transcript accumulation and destabilising PIF4/5 protein. Here, we show that longer‐term inhibition of shade avoidance is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOGUE (HYH), which regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification. HY5 and HYH are elevated in UV‐B and suppress the expression of XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) genes involved in cell wall loosening. They additionally increase expression GA2‐OXIDASE1 (GA2ox1) and GA2ox2, encoding gibberellin catabolism enzymes that act redundantly to stabilise the PIF‐inhibiting DELLA proteins. UVR8 therefore regulates temporally distinct signalling pathways to first rapidly inhibit and subsequently maintain suppression of shade avoidance following UV‐B exposure.
Retrospective phylogenetic analysis of rabies virus G and N genes from Serbia
Authors: Milićević Vesna , Glišić Dimitrije , Veljović Ljubiša , Maletić Jelena , Kureljušić Branislav 
Published: May 2023

AbstractRabies is a viral disease of the central nervous system of all warm‐blooded animals and one of the oldest and most important zoonoses. In the Republic of Serbia, rabies is controlled by compulsory vaccination of dogs and cats and oral vaccination of wild carnivores, which has been implemented since 2010. In the period 2009–2018, 367 rabies cases were recorded. The last rabies case in Serbia was recorded in 2018 in a red fox (Vulpes vulpes), while the last case in dogs was diagnosed in 2011. This study aimed to perform a retrospective phylogenetic analysis of G and N genes of the rabies virus from Serbia from 2009 to 2018 to understand sources and pathways of infection better and to enable molecular virus tracing in the future based on the association of rabies virus genetic lineages with the geographic distribution. For the phylogenetic analysis of the rabies virus, 14 historically positive brain samples of red foxes from 2009 to 2018, collected in central Serbia, were used. All field strains from Serbia were identified as classic rabies virus and grouped within the Cosmopolitan lineage. Phylogenetic analysis of N gene sequences revealed that 13 rabies virus strains (92.9%) from Serbia belonged to the EE sub‐lineage of isolates, while one virus (7.1%) ON988027 from 2011 clustered together with isolates from the WE sub‐lineage.
Designing Hybrid Neural Network Using Physical Neurons—A Case Study of Drill Bit-Rock Interaction Modeling
Authors: Zhang Zihang , Song Xingyong 
Published: May 2023

Abstract
Neural networks have been widely applied in system dynamics modeling. One particular type of networks, hybrid neural networks, combines a neural network model with a physical model, which can increase rate of convergence in training. However, most existing hybrid neural network methods require an explicit physical model constructed, which sometimes might not be feasible in practice or could weaken the capability of capturing complex and hidden physical phenomena. In this paper, we propose a novel approach to construct a hybrid neural network. The new method incorporates the physical information to the structure of network construction, but does not need an explicit physical model constructed. The method is then applied to modeling of bit-rock interaction in the down-hole drilling system as a case study, to demonstrate its effectiveness in modeling complex process and efficiency of convergence in training.
A Method for Robust Partial Quadratic Eigenvalue Assignment With Repeated Eigenvalues
Authors: Xie Huiqing 
Published: May 2023

Abstract
A new method is proposed for robust partial quadratic eigenvalue assignment problem (RPQEAP) with repeated prescribed eigenvalues. We first derive a result on the solution of partial quadratic eigenvalue assignment problem, which leads to the partial Schur form of the closed-loop system. Then by minimizing the normality departure of the partial Schur form of the closed-loop system, we assign the prescribed eigenvalues step by step such that the closed-loop system is as robust as possible. Our method allows the prescribed eigenvalues are repeated. Moreover, the proposed method does not use the unchanged eigenpairs of the open-loop system and avoids transforming the second-order control system to the first-order system. Numerical experiments show that the proposed method is efficient for solving the RPQEAP with repeated eigenvalues.
Influence of Impinging Jet Nozzle Movement on Heat Transfer Characteristics of a Flat Plate
Authors: Abo El–Wafa A. , Attalla M. , Maghrabie Hussein M. , Shmroukh Ahmed N. 
Published: May 2023

Abstract
The purpose of the current experimental study is to assess the influence of impinging air jet movement on the heat transfer of a fixed flat plate. The experiments are conducted with varying the nozzle velocity (Vn) from 400 to 1000 mm/min, and the Reynolds number (Re) from 8000 to 20,000 at a nozzle-to-plate distance (H/D) of 2 and 6. A comparison between a movable nozzle and a fixed nozzle based on the temperature contours and local Nusselt number is presented. Additionally, the local Nusselt number, heat transfer uniformity index, and uniformity of heat transfer are evaluated. The results demonstrate that the local Nusselt number of 24.8 has a maximum value at a Vn of 400 mm/min, a Re of 20,000, and a H/D of 2. The uniformity of heat transfer is enhanced by increasing the Vn, and its maximum value of 89.5% is maintained at a Vn of 1000 mm/min, Re of 20,000, and H/D of 6. Additionally, the heat transfer uniformity index decreases with increasing the Vn where its maximum value is 0.34 at a Vn of 400 mm/min, a Re of 8000, and a H/D of 2.
Comparative Maps of Safety Features for Fission and Fusion Reactors
Authors: Nguyen Tu , Patterson Eann A. , Taylor Richard J. , Tseng Y. S. , Waldon Chris 
Published: May 2023

Abstract
The differences between nuclear fission and fusion have been discussed widely in the literature. However, little has been done to investigate the key differences in safety designs and regulatory requirements between the nuclear reactor types. In this study, an innovative methodology was successfully developed to map nuclear safety features to the fundamental safety principles set out by the nuclear regulators. Three safety cases were assessed in the mapping study, a research fusion reactor (Joint European Torus), a research fission reactor (Tsing Hua Open-pool Reactor) and a commercial fission reactor (Hinkley Point C). The graphical representation allowed a comparative analysis of the safety features and fundamental principles which revealed differences between the hazard profiles of fission and fusion reactors and provided important insights for the creation of a similar map for a future commercial fusion device.