bluuebunny/crossref_metadata_2025 huggingface dataset:
Promoter editing for the genetic improvement of crops
Authors: Shi Lu , Su Jing , Cho Myeong-Je , Song Hao , Dong Xiaoou , Liang Ying , Zhang Zhiyong
Published: May 2023

Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.
Phytochrome-interacting factor PIF3 integrates phytochrome B and UV-B signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls
Authors: Zhao Jianyu , Bo Kailiang , Pan Yupeng , Li Yuhong , Yu Daoliang , Li Chuang , Chang Jiang , Wu Shuang , Wang Zhongyi , Zhang Xiaolan , Gu Xingfang , Weng Yiqun
Published: May 2023

In Arabidopsis, the photoreceptors phytochrome B (PhyB) and UV-B resistance 8 (UVR8) mediate light responses that play a major role in regulating photomorphogenic hypocotyl growth, but how they crosstalk to coordinate this process is not well understood. Here we report map-based cloning and functional characterization of an ultraviolet (UV)-B-insensitive, long-hypocotyl mutant, lh1, and a wild-type-like mutant, lh2, in cucumber (Cucumis sativus), which show defective CsPhyB and GA oxidase2 (CsGA20ox-2), a key gibberellic acid (GA) biosynthesis enzyme, respectively. The lh2 mutation was epistatic to lh1 and partly suppressed the long-hypocotyl phenotype in the lh1lh2 double mutant. We identified phytochrome interacting factor (PIF) CsPIF3 as playing a critical role in integrating the red/far-red and UV-B light responses for hypocotyl growth. We show that two modules, CsPhyB–CsPIF3–CsGA20ox-2–DELLA and CsPIF3–auxin response factor 18 (CsARF18), mediate CsPhyB-regulated hypocotyl elongation through GA and auxin pathways, respectively, in which CsPIF3 binds to the G/E-box motifs in the promoters of CsGA20ox-2 and CsARF18 to regulate their expression. We also identified a new physical interaction between CsPIF3 and CsUVR8 mediating CsPhyB-dependent, UV-B-induced hypocotyl growth inhibition. Our work suggests that hypocotyl growth in cucumber involves a complex interplay of multiple photoreceptor- and phytohormone-mediated signaling pathways that show both conservation with and divergence from those in Arabidopsis.
Spatiotemporal patterns of wheat response toPyrenophora tritici-repentisin asymptomatic regions revealed by transcriptomic and X-ray fluorescence microscopy analyses
Authors: Moolhuijzen Paula , Sanglard Lilian M V P , Paterson David J , Gray Sean , Khambatta Karina , Hackett Mark J , Zerihun Ayalsew , Gibberd Mark R , Naim Fatima
Published: May 2023

Pathogen attacks elicit dynamic and widespread molecular responses in plants. While our understanding of plant responses has advanced considerably, little is known of the molecular responses in the asymptomatic ‘green’ regions adjoining lesions. Here, we explore gene expression data and high-resolution elemental imaging to report the spatiotemporal changes in the asymptomatic green region of susceptible and moderately resistant wheat cultivars infected with a necrotrophic fungal pathogen, Pyrenophora tritici-repentis. We show, with improved spatiotemporal resolution, that calcium oscillations are modified in the susceptible cultivar, resulting in ‘frozen’ host defence signals at the mature disease stage, and silencing of the host’s recognition and defence mechanisms that would otherwise protect it from further attacks. In contrast, calcium accumulation and a heightened defence response were observed in the moderately resistant cultivar in the later stage of disease development. Furthermore, in the susceptible interaction, the asymptomatic green region was unable to recover after disease disruption. Our targeted sampling technique also enabled detection of eight previously predicted proteinaceous effectors in addition to the known ToxA effector. Collectively, our results highlight the benefits of spatially resolved molecular analysis and nutrient mapping to provide high-resolution spatiotemporal snapshots of host–pathogen interactions, paving the way for disentangling complex disease interactions in plants.
A 1.55 R⊕ habitable-zone planet hosted by TOI-715, an M4 star near the ecliptic South Pole
Authors: Dransfield Georgina , Timmermans Mathilde , Triaud Amaury H M J , Dévora-Pajares Martín , Aganze Christian , Barkaoui Khalid , Burgasser Adam J , Collins Karen A , Cointepas Marion , Ducrot Elsa , Günther Maximilian N , Howell Steve B , Murray Catriona A , Niraula Prajwal , Rackham Benjamin V , Sebastian Daniel , Stassun Keivan G , Zúñiga-Fernández Sebastián , Almenara José Manuel , Bonfils Xavier , Bouchy François , Burke Christopher J , Charbonneau David , Christiansen Jessie L , Delrez Laetitia , Gan Tianjun , García Lionel J , Gillon Michaël , Gómez Maqueo Chew Yilen , Hesse Katharine M , Hooton Matthew J , Isopi Giovanni , Jehin Emmanuël , Jenkins Jon M , Latham David W , Mallia Franco , Murgas Felipe , Pedersen Peter P , Pozuelos Francisco J , Queloz Didier , Rodriguez David R , Schanche Nicole , Seager Sara , Srdoc Gregor , Stockdale Chris , Twicken Joseph D , Vanderspek Roland , Wells Robert , Winn Joshua N , de Wit Julien , Zapparata Aldo
Published: May 2023

A new generation of observatories is enabling detailed study of exoplanetary atmospheres and the diversity of alien climates, allowing us to seek evidence for extraterrestrial biological and geological processes. Now is therefore the time to identify the most unique planets to be characterized with these instruments. In this context, we report on the discovery and validation of TOI-715 b, a $R_{\rm b}=1.55\pm 0.06\rm R_{\oplus }$ planet orbiting its nearby (42 pc) M4 host (TOI-715/TIC 271971130) with a period $P_{\rm b} = 19.288004_{-0.000024}^{+0.000027}$ d. TOI-715 b was first identified by TESS and validated using ground-based photometry, high-resolution imaging and statistical validation. The planet’s orbital period combined with the stellar effective temperature $T_{\rm eff}=3075\pm 75~\rm K$ give this planet an installation $S_{\rm b} = 0.67_{-0.20}^{+0.15}~\rm S_\oplus$, placing it within the most conservative definitions of the habitable zone for rocky planets. TOI-715 b’s radius falls exactly between two measured locations of the M-dwarf radius valley; characterizing its mass and composition will help understand the true nature of the radius valley for low-mass stars. We demonstrate TOI-715 b is amenable for characterization using precise radial velocities and transmission spectroscopy. Additionally, we reveal a second candidate planet in the system, TIC 271971130.02, with a potential orbital period of $P_{02} = 25.60712_{-0.00036}^{+0.00031}$ d and a radius of $R_{02} = 1.066\pm 0.092\, \rm R_{\oplus }$, just inside the outer boundary of the habitable zone, and near a 4:3 orbital period commensurability. Should this second planet be confirmed, it would represent the smallest habitable zone planet discovered by TESS to date.
A morphological analysis of the substructures in radio relics
Authors: Wittor D , Brüggen M , Grete P , Rajpurohit K
Published: May 2023

Recent observations of radio relics – diffuse radio emission in galaxy clusters – have revealed that these sources are not smooth but consist of structures in the form of threads and filaments. We investigate the origin of these filamentary structures and the role of projection effects. To this end, we have developed a tool that extracts the filamentary structures from background emission. Moreover, it is capable of studying both two-dimensional and three-dimensional objects. We apply our structure extractor to both observations and cosmological simulations of radio relics. Using Minkowski functionals, we determine the shape of the identified structures. In our 2D analysis, we find that the brightest structures in the observed and simulated maps are filaments. Our analysis of the 3D simulation data shows that radio relics do not consist of sheets but only of filaments and ribbons. Furthermore, we did not find any measurable projection effect that could hide any sheet-like structures in projection. We find that both the magnetic field and the shock front consist of filaments and ribbons that cause filamentary radio emission.
New constraints on cosmological modified gravity theories from anisotropic three-point correlation functions of BOSS DR12 galaxies
Authors: Sugiyama Naonori S , Yamauchi Daisuke , Kobayashi Tsutomu , Fujita Tomohiro , Arai Shun , Hirano Shin’ichi , Saito Shun , Beutler Florian , Seo Hee-Jong
Published: May 2023

We report a new test of modified gravity theories using the large-scale structure of the Universe. This paper is the first attempt to (1) apply a joint analysis of the anisotropic components of galaxy two- and three-point correlation functions (2 and 3PCFs) to actual galaxy data and (2) constrain the non-linear effects of degenerate higher-order scalar-tensor (DHOST) theories on cosmological scales. Applying this analysis to the Baryon Oscillation Spectroscopic Survey (BOSS) data release 12, we obtain the lower bounds of −1.655 < ξt and −0.504 < ξs at the $95{{\ \rm per\ cent}}$ confidence level on the parameters characterizing the time evolution of the tidal and shift terms of the second-order velocity field. These constraints are consistent with GR predictions of ξt = 15/1144 and ξs = 0. Moreover, they represent a 35-fold and 20-fold improvement, respectively, over the joint analysis with only the isotropic 3PCF. We ensure the validity of our results by investigating various quantities, including theoretical models of the 3PCF, window function corrections, cumulative S/N, Fisher matrices, and statistical scattering effects of mock simulation data. We also find statistically significant discrepancies between the BOSS data and the Patchy mocks for the 3PCF measurement. Finally, we package all of our 3PCF analysis codes under the name hitomi and make them publicly available so that readers can reproduce all the results of this paper and easily apply them to ongoing future galaxy surveys.
Pest Alert Tool—a web-based application for flagging species of concern in metabarcoding datasets
Authors: Zaiko Anastasija , Scheel Maximilian , Schattschneider Jessica , von Ammon Ulla , Scriver Michelle , Pochon Xavier , Pearman John K
Published: May 2023

Advances in high-throughput sequencing (HTS) technologies and their increasing affordability have fueled environmental DNA (eDNA) metabarcoding data generation from freshwater, marine and terrestrial ecosystems. Research institutions worldwide progressively employ HTS for biodiversity assessments, new species discovery and ecological trend monitoring. Moreover, even non-scientists can now collect an eDNA sample, send it to a specialized laboratory for analysis and receive in-depth biodiversity record from a sampling site. This offers unprecedented opportunities for biodiversity assessments across wide temporal and spatial scales. The large volume of data produced by metabarcoding also enables incidental detection of species of concern, including non-indigenous and pathogenic organisms. We introduce an online app—Pest Alert Tool—for screening nuclear small subunit 18S ribosomal RNA and mitochondrial cytochrome oxidase subunit I datasets for marine non-indigenous species as well as unwanted and notifiable marine organisms in New Zealand. The output can be filtered by minimum length of the query sequence and identity match. For putative matches, a phylogenetic tree can be generated through the National Center for Biotechnology Information’s BLAST Tree View tool, allowing for additional verification of the species of concern detection. The Pest Alert Tool is publicly available at https://pest-alert-tool-prod.azurewebsites.net/.
GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex
Authors: Orzeł Urszula , Pasznik Paweł , Miszta Przemysław , Lorkowski Marcin , Niewieczerzał Szymon , Jakowiecki Jakub , Filipek Sławomir
Published: May 2023

Despite recent advances in research, the mechanism of Alzheimer's disease is not fully understood yet. Understanding the process of cleavage and then trimming of peptide substrates, can help selectively block γ-secretase (GS) to stop overproduction of the amyloidogenic products. Our GS-SMD server (https://gs-smd.biomodellab.eu/) allows cleaving and unfolding of all currently known GS substrates (more than 170 peptide substrates). The substrate structure is obtained by threading of the substrate sequence into the known structure of GS complex. The simulations are performed in an implicit water-membrane environment so they are performed rather quickly, 2–6 h per job, depending on the mode of calculations (part of GS complex or the whole structure). It is also possible to introduce mutations to the substrate and GS and pull any part of the substrate in any direction using the steered molecular dynamics (SMD) simulations with constant velocity. The obtained trajectories are visualized and analyzed in the interactive way. One can also compare multiple simulations using the interaction frequency analysis. GS-SMD server can be useful for revealing mechanisms of substrate unfolding and role of mutations in this process.
Selection of allosteric dnazymes that can sense phenylalanine by expression-SELEX
Authors: Chen Binfen , Yu Xinmei , Gao Ting , Wu Yaoyao , Zhang Xiaojun , Li Sanshu
Published: May 2023

Aptamers are ligand-binding RNA or DNA molecules and have been widely examined as biosensors, diagnostic tools, and therapeutic agents. The application of aptamers as biosensors commonly requires an expression platform to produce a signal to report the aptamer-ligand binding event. Traditionally, aptamer selection and expression platform integration are two independent steps and the aptamer selection requires the immobilization of either the aptamer or the ligand. These drawbacks can be easily overcome through the selection of allosteric DNAzymes (aptazymes). Herein, we used the technique of Expression-SELEX developed in our laboratory to select for aptazymes that can be specifically activated by low concentrations of l-phenylalanine. We chose a previous DNA-cleaving DNAzyme known as II-R1 as the expression platform for its low cleavage rate and used stringent selection conditions to drive the selection of high-performance aptazyme candidates. Three aptazymes were chosen for detailed characterization and these DNAzymes were found to exhibit a dissociation constant for l-phenylalanine as low as 4.8 μM, a catalytic rate constant improvement as high as 20 000-fold in the presence of l-phenylalanine, and the ability to discriminate against closely related l-phenylalanine analogs including d-phenylalanine. This work has established the Expression-SELEX as an effective SELEX method to enrich high-quality ligand-responsive aptazymes.
Dynamic accumulation of cyclobutane pyrimidine dimers and its response to changes in DNA conformation
Authors: Moirangthem Ravina , Gamage Manusha N , Rokita Steven E
Published: May 2023

Photochemical dimerization of adjacent pyrimidines is fundamental to the creation of mutagenic hotspots caused by ultraviolet light. Distribution of the resulting lesions (cyclobutane pyrimidine dimers, CPDs) is already known to be highly variable in cells, and in vitro models have implicated DNA conformation as a major basis for this observation. Past efforts have primarily focused on mechanisms that influence CPD formation and have rarely considered contributions of CPD reversion. However, reversion is competitive under the standard conditions of 254 nm irradiation as illustrated in this report based on the dynamic response of CPDs to changes in DNA conformation. A periodic profile of CPDs was recreated in DNA held in a bent conformation by λ repressor. After linearization of this DNA, the CPD profile relaxed to its characteristic uniform distribution over a similar time of irradiation to that required to generate the initial profile. Similarly, when a T tract was released from a bent conformation, its CPD profile converted under further irradiation to that consistent with a linear T tract. This interconversion of CPDs indicates that both its formation and reversion exert control on CPD populations long before photo-steady-state conditions are achieved and suggests that the dominant sites of CPDs will evolve as DNA conformation changes in response to natural cellular processes.
Atherosclerotic renovascular disease: a clinical practice document by the European Renal Best Practice (ERBP) board of the European Renal Association (ERA) and the Working Group Hypertension and the Kidney of the European Society of Hypertension (ESH)
Authors: Sarafidis Pantelis A , Theodorakopoulou Marieta , Ortiz Alberto , Fernandez-Fernández Beatriz , Nistor Ionut , Schmieder Roland , Arici Mustafa , Saratzis Athanasios , Van der Niepen Patricia , Halimi Jean-Michel , Kreutz Reinhold , Januszewicz Andrzej , Persu Alexandre , Cozzolino Mario
Published: May 2023

Atherosclerotic renovascular disease (ARVD) is the most common type of renal artery stenosis. It represents a common health problem with clinical presentations relevant to many medical specialties and carries a high risk for future cardiovascular and renal events, as well as overall mortality. The available evidence regarding the management of ARVD is conflicting. Randomized controlled trials failed to demonstrate superiority of percutaneous transluminal renal artery angioplasty (PTRA) with or without stenting in addition to standard medical therapy compared with medical therapy alone in lowering blood pressure levels or preventing adverse renal and cardiovascular outcomes in patients with ARVD, but they carried several limitations and met important criticism. Observational studies showed that PTRA is associated with future cardiorenal benefits in patients presenting with high-risk ARVD phenotypes (i.e. flash pulmonary oedema, resistant hypertension or rapid loss of kidney function). This clinical practice document, prepared by experts from the European Renal Best Practice (ERBP) board of the European Renal Association (ERA) and from the Working Group on Hypertension and the Kidney of the European Society of Hypertension (ESH), summarizes current knowledge in epidemiology, pathophysiology and diagnostic assessment of ARVD and presents, following a systematic literature review, key evidence relevant to treatment, with an aim to support clinicians in decision making and everyday management of patients with this condition.
A novel prognostic nomogram predicts premature failure of kidney allografts with IgA nephropathy recurrence
Authors: Bednarova Kamila , Mjøen Geir , Hruba Petra , Modos Istvan , Voska Ludek , Kollar Marek , Viklicky Ondrej
Published: May 2023

Background

Recurrence of immunoglobulin A nephropathy (IgAN) limits graft survival in kidney transplantation. However, predictors of a worse outcome are poorly understood.

Methods

Among 442 kidney transplant recipients (KTRs) with IgAN, 83 (18.8%) KTRs exhibited biopsy-proven IgAN recurrence between 1994 and 2020 and were enrolled in the derivation cohort. A multivariable Cox model predicting allograft loss based on clinical data at the biopsy and a web-based nomogram were developed. The nomogram was externally validated using an independent cohort (n = 67).

Results

Patient age <43 years {hazard ratio [HR] 2.20 [95% confidence interval (CI) 1.41–3.43], P < .001}, female gender [HR 1.72 (95% CI 1.07–2.76), P = .026] and retransplantation status [HR 1.98 (95% CI 1.13–3.36), P = .016] were identified as independent risk factors for IgAN recurrence. Patient age <43 years [HR 2.77 (95% CI 1.17–6.56), P = .02], proteinuria >1 g/24 hours [HR 3.12 (95% CI 1.40–6.91), P = .005] and C4d positivity [HR 2.93 (95% CI 1.26–6.83), P = .013] were found to be associated with graft loss in patients with IgAN recurrence. A nomogram predicting graft loss was constructed based on clinical and histological variables, with a C statistic of 0.736 for the derivation cohort and 0.807 for the external validation cohort.

Conclusions

The established nomogram identified patients with recurrent IgAN at risk for premature graft loss with good predictive performance.
Anti-inflammatory pathways of kefir in murine model: a systematic review
Authors: Albuquerque Pereira Mariana de Fátima , Matias Albuini Fernanda , Gouveia Peluzio Maria do Carmo
Published: May 2023

Context

Kefir consumption has been associated with immune response modulation, antioxidant, and anti-inflammatory effects.

Objective

The objective of this systematic review was to investigate the role of kefir against inflammation and the main response mechanisms involved in this process in a murine model.

Data Sources

The searches were searched in the PubMed, Science Direct, and LILACS databases. Only murine model studies, according to PRISMA guidelines, published in the past 10 years were included.

Study Selection

Only articles about original and placebo-controlled experiments in murine models used to investigate the anti-inflammatory mechanisms of kefir were considered. Of the articles found, 349 were excluded according to the following criteria: duplicate articles (n = 99), off-topic title and abstract (n = 157), reviews (n = 47), studies in vitro (n = 29), and studies with humans (n = 17). In total, 23 studies were included in this review.

Data Extraction

Two independently working authors assessed the risk of bias and extracted data from the included studies.

Results

Kefir consumption had positive effects on inflammation modulation. The main mechanisms involved were the reduction of pro-inflammatory and molecular markers; reduction in inflammatory infiltrate in tissues, serum biomarkers, risk factors for chronic diseases, and parasitic infection; composition and metabolic activity change of intestinal microbiota and mycobiota; activation of humoral and cellular immunity; and modulation of oxidative stress.

Conclusions

Kefir modulates the immune system in different experimental models, among other secondary outcomes, to improve overall health. The beverage reduces inflammation through the alternation between innate, Th1, and Th2 responses, reducing levels of pro-inflammatory cytokines while increasing those of anti-inflammatory ones. In addition, it also mediates immunomodulatory and protective effects through the numerous molecular biomarkers and organic acids produced and secreted by kefir in the intestinal microbiota. The health-promoting effects attributed to kefir may help in the different treatments of inflammatory, chronic, and infectious diseases in the population.
Contemporary Class Analysis
Authors: Oesch Daniel
Published: May 2023

A popular thesis in social stratification maintains that the middle class is declining. This chapter argues that this thesis is flawed both conceptually and empirically. Conceptually, it mixes up the middle class and the working class, and empirically, it misrepresents the trends that shape the class structure. The chapter discusses the concept of social class and proposes a model that grasps the class structure of contemporary Western societies. Based on the conceptual distinction between the middle class and the working class, labor force surveys clearly show that the early twenty-first century saw, not the demise, but the expansion of the (salaried) middle class in the Western world. Never in history have so many people worked in managerial, professional, and technical jobs as do so today. By contrast, over the last four decades, the working class has experienced a massive employment decline—with far-reaching consequences. The political clout of the working class has declined, as is illustrated by decreasing trade union density and strike activity and in rising income inequality. Moreover, working-class decline has led to a fundamental realignment of class voting and contributed to growing family instability. Instead of eroding the middle class, the last decades have thus put an end to the working-class century.
The mass of TOI-519 b: A close-in giant planet transiting a metal-rich mid-M dwarf
Authors: Kagetani Taiki , Narita Norio , Kimura Tadahiro , Hirano Teruyuki , Ikoma Masahiro , Ishikawa Hiroyuki Tako , Giacalone Steven , Fukui Akihiko , Kodama Takanori , Gore Rebecca , Schroeder Ashley , Hori Yasunori , Kawauchi Kiyoe , Watanabe Noriharu , Mori Mayuko , Zou Yujie , Ikuta Kai , Krishnamurthy Vigneshwaran , Zink Jon , Hardegree-Ullman Kevin , Harakawa Hiroki , Kudo Tomoyuki , Kotani Takayuki , Kurokawa Takashi , Kusakabe Nobuhiko , Kuzuhara Masayuki , de Leon Jerome P , Livingston John H , Nishikawa Jun , Omiya Masashi , Palle Enric , Parviainen Hannu , Serizawa Takuma , Teng Huan-Yu , Ueda Akitoshi , Tamura Motohide
Published: May 2023

We report on the determination of the mass of TOI-519 b, a transiting substellar object around a mid-M dwarf. We carried out radial velocity measurements using Subaru/InfraRed Doppler (IRD), revealing that TOI-519 b is a planet with a mass of $0.463^{+0.082}_{-0.088}\, M_{\rm Jup}$. We also found that the host star is metal rich ([Fe/H] = 0.27 ± 0.09 dex) and has the lowest effective temperature (Teff = 3322 ± 49 K) among all stars hosting known close-in giant planets based on the IRD spectra and mid-resolution infrared spectra obtained with NASA Infrared Telescope Facility/SpeX. The core mass of TOI-519 b inferred from a thermal evolution model ranges from 0 to ∼30 M⊕, which can be explained by both core accretion and disk instability models as the formation origins of this planet. However, TOI-519 is in line with the emerging trend that M dwarfs with close-in giant planets tend to have high metallicity, which may indicate that they formed in the core accretion model. The system is also consistent with the potential trend that close-in giant planets around M dwarfs tend to be less massive than those around FGK dwarfs.
miR171-targeted SCARECROW-LIKE genes CsSCL2 and CsSCL3 regulate somatic embryogenesis in citrus
Authors: Feng Meng-Qi , Jiang Nan , Wang Peng-Bo , Liu Yue , Xia Qiang-Ming , Jia Hui-Hui , Shi Qiao-Fang , Long Jian-Mei , Xiao Gong-Ao , Yin Zhao-Ping , Xie Kai-Dong , Guo Wen-Wu , Wu Xiao-Meng
Published: May 2023

Somatic embryogenesis (SE) is a key regeneration pathway in various biotechnology approaches to crop improvement, especially for economically important perennial woody crops like citrus. However, maintenance of SE capability has long been a challenge and becomes a bottleneck in biotechnology-facilitated plant improvement. In the embryogenic callus (EC) of citrus, we identified 2 csi-miR171c–targeted SCARECROW-LIKE genes CsSCL2 and CsSCL3 (CsSCL2/3), which exert positive feedback regulation on csi-miR171c expression. Suppression of CsSCL2 expression by RNA interference (RNAi) enhanced SE in citrus callus. A thioredoxin superfamily protein CsClot was identified as an interactive protein of CsSCL2/3. Overexpression of CsClot disturbed reactive oxygen species (ROS) homeostasis in EC and enhanced SE. Chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq identified 660 genes directly suppressed by CsSCL2 that were enriched in biological processes including development-related processes, auxin signaling pathway, and cell wall organization. CsSCL2/3 bound to the promoters of regeneration-related genes, such as WUSCHEL-RELATED HOMEOBOX 2 (CsWOX2), CsWOX13, and Lateral Organ Boundaries Domain 40 (LBD40), and repressed their expression. Overall, CsSCL2/3 modulate ROS homeostasis through the interactive protein CsClot and directly suppress the expression of regeneration-related genes, thus regulating SE in citrus. We uncovered a regulatory pathway of miR171c-targeted CsSCL2/3 in SE, which shed light on the mechanism of SE and regeneration capability maintenance in citrus.
Transcription factor OsSNAC1 positively regulates nitrate transporter gene expression in rice
Authors: Qi（杞金芳） Jinfang , Yu（郁露） Lu , Ding（丁静丽） Jingli , Ji（姬晨晨） Chenchen , Wang（汪社亮） Sheliang , Wang（王创） Chuang , Ding（丁广大） Guangda , Shi（石磊） Lei , Xu（徐芳森） Fangsen , Cai（蔡红梅） Hongmei
Published: May 2023

Nitrogen (N) is a critical factor for crop growth and yield. Improving N use efficiency (NUE) in agricultural systems is crucial for sustainable food production. However, the underlying regulation of N uptake and utilization in crops is not well known. Here, we identified OsSNAC1 (stress-responsive NAC 1) as an upstream regulator of OsNRT2.1 (nitrate transporter 2.1) in rice (Oryza sativa) by yeast 1-hybridization screening. OsSNAC1 was mainly expressed in roots and shoots and induced by N deficiency. We observed similar expression patterns of OsSNAC1, OsNRT2.1/2.2, and OsNRT1.1A/B in response to NO3− supply. Overexpression of OsSNAC1 resulted in increased concentrations of free NO3− in roots and shoots, as well as higher N uptake, higher NUE, and N use index (NUI) in rice plants, which conferred increased plant biomass and grain yield. On the contrary, mutations in OsSNAC1 resulted in decreased N uptake and lower NUI, which inhibited plant growth and yield. OsSNAC1 overexpression significantly upregulated OsNRT2.1/2.2 and OsNRT1.1A/B expression, while the mutation in OsSNAC1 significantly downregulated OsNRT2.1/2.2 and OsNRT1.1A/B expression. Y1H, transient co-expression, and ChIP assays showed OsSNAC1 directly binds to the upstream promoter regions of OsNRT2.1/2.2 and OsNRT1.1A/1.1B. In conclusion, we identified a NAC transcription factor in rice, OsSNAC1, with a positive role in regulating NO3− uptake through direct binding to the upstream promoter regions of OsNRT2.1/2.2 and OsNRT1.1A/1.1B and activating their expression. Our results provide a potential genetic approach for improving crop NUE in agriculture.
PmAGAMOUS recruits polycomb protein PmLHP1 to regulate single-pistil morphogenesis in Japanese apricot
Authors: Shi Ting , Bai Yang , Wu Xinxin , Wang Yike , Iqbal Shahid , Tan Wei , Ni Zhaojun , Gao Zhihong
Published: May 2023

Japanese apricot (Prunus mume Sieb. et Zucc.) is a traditional fruit tree with a long history. Multiple pistils (MP) lead to the formation of multiple fruits, decreasing fruit quality and yield. In this study, the morphology of flowers was observed at 4 stages of pistil development: undifferentiated stage (S1), predifferentiation stage (S2), differentiation stage (S3), and late differentiation stage (S4). In S2 and S3, the expression of PmWUSCHEL (PmWUS) in the MP cultivar was significantly higher than that in the single-pistil (SP) cultivar, and the gene expression of its inhibitor, PmAGAMOUS (PmAG), also showed the same trend, indicating that other regulators participate in the regulation of PmWUS during this period. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) showed that PmAG could bind to the promoter and the locus of PmWUS, and H3K27me3 repressive marks were also detected at these sites. The SP cultivar exhibited an elevated level of DNA methylation in the promoter region of PmWUS, which partially overlapped with the region of histone methylation. This suggests that the regulation of PmWUS involves both transcription factors and epigenetic modifications. Also, the gene expression of Japanese apricot LIKE HETEROCHROMATIN PROTEIN (PmLHP1), an epigenetic regulator, in MP was significantly lower than that in SP in S2 to 3, contrary to the trend in expression of PmWUS. Our results showed that PmAG recruited sufficient PmLHP1 to maintain the level of H3K27me3 on PmWUS during the S2 of pistil development. This recruitment of PmLHP1 by PmAG inhibits the expression of PmWUS at the precise time, leading to the formation of 1 normal pistil primordium.
GmGAMYB-BINDING PROTEIN 1 promotes small auxin-up RNA gene transcription to modulate soybean maturity and height
Authors: Sun Jingzhe , Zheng Yuhong , Guo Jinpeng , Zhang Yuntong , Liu Ying , Tao Yahan , Wang Mengyuan , Liu Tianmeng , Liu Yangyang , Li Xin , Zhang Xiaoming , Zhao Lin
Published: May 2023

Flowering time, maturity, and plant height are crucial agronomic traits controlled by photoperiod that affect soybean (Glycine max [L.] Merr.) yield and regional adaptability. It is important to cultivate soybean cultivars of earlier maturity that adapt to high latitudes. GAMYB-binding protein 1 (GmGBP1), a member of the SNW/SKIP family of transcriptional coregulators in soybean, is induced by short days and interacts with transcription factor GAMYB (GmGAMYB) during photoperiod control of flowering time and maturity. In the present study, GmGBP1:GmGBP1 soybean showed the phenotypes of earlier maturity and higher plant height. Chromatin immunoprecipitation sequencing (ChIP-seq) assays of GmGBP1-binding sites and RNA sequencing (RNA-seq) of differentially expressed transcripts in GmGBP1:GmGBP1 further identified potential targets of GmGBP1, including small auxin-up RNA (GmSAUR). GmSAUR:GmSAUR soybean also showed earlier maturity and higher plant height. GmGBP1 interacted with GmGAMYB, bound to the promoter of GmSAUR and promoted the expression of FLOWER LOCUS T homologs 2a (GmFT2a) and FLOWERING LOCUS D LIKE 19 (GmFDL19). Flowering repressors such as GmFT4 were negatively regulated, resulting in earlier flowering and maturity. Furthermore, the interaction of GmGBP1 with GmGAMYB increased the gibberellin (GA) signal to promote height and hypocotyl elongation by activating GmSAUR and GmSAUR bound to the promoter of the GA-positive activating regulator gibberellic acid-stimulated Arabidopsis 32 (GmGASA32). These results suggested a photoperiod regulatory pathway in which the interaction of GmGBP1 with GmGAMYB directly activated GmSAUR to promote earlier maturity and plant height in soybean.
Vitamin A deficiency compromises the barrier function of the retinal pigment epithelium
Authors: Moon Jean , Zhou Gao , Jankowsky Eckhard , von Lintig Johannes
Published: May 2023

A major cause for childhood blindness worldwide is attributed to nutritional vitamin A deficiency. Surprisingly, the molecular basis of the ensuing retinal degeneration has not been well defined. Abundant expression of the retinoid transporter STRA6 in the retinal pigment epithelium (RPE) and homeostatic blood levels of retinol-binding protein delay vitamin A deprivation of the mouse eyes. Hence, genetic dissection of STRA6 makes mice susceptible to nutritional manipulation of ocular retinoid status. We performed RNA-seq analyses and complemented the data with tests of visual physiology, ocular morphology, and retinoid biochemistry to compare eyes with different vitamin A status. Mild ocular vitamin A deficiency decreased transcripts of photoreceptor transduction pathway-related genes and increased transcripts of oxidative stress pathways. The response was associated with impaired visual sensitivity and an accumulation of fluorescent debris in the retina. Severe vitamin A deficiency did not only impair visual perception but also decreased transcripts of genes encoding cell adhesion and cellular junction proteins. This response altered cell morphology, resulted in significant changes in transport pathways of small molecules, and compromised the barrier function of the RPE. Together, our analyses characterize the molecular events underlying nutritional blindness in a novel mouse model and indicate that breakdown of the outer blood–retinal barrier contributes to retinal degeneration and photoreceptor cell death in severe vitamin A deficiency.
Global quantification of newly synthesized proteins reveals cell type- and inhibitor-specific effects on protein synthesis inhibition
Authors: Yin Kejun , Tong Ming , Suttapitugsakul Suttipong , Xu Senhan , Wu Ronghu
Published: May 2023

Manipulation of protein synthesis is commonly applied to uncover protein functions and cellular activities. Multiple inhibitors with distinct mechanisms have been widely investigated and employed in bio-related research, but it is extraordinarily challenging to measure and evaluate the synthesis inhibition efficiencies of individual proteins by different inhibitors at the proteome level. Newly synthesized proteins are the immediate and direct products of protein synthesis, and thus their comprehensive quantification provides a unique opportunity to study protein inhibition. Here, we systematically investigate protein inhibition and evaluate different popular inhibitors, i.e. cycloheximide, puromycin, and anisomycin, through global quantification of newly synthesized proteins in several types of human cells (A549, MCF-7, Jurkat, and THP-1 cells). The inhibition efficiencies of protein synthesis are comprehensively measured by integrating azidohomoalanine-based protein labeling, selective enrichment, a boosting approach, and multiplexed proteomics. The same inhibitor results in dramatic variation of the synthesis inhibition efficiencies for different proteins in the same cells, and each inhibitor exhibits unique preferences. Besides cell type- and inhibitor-specific effects, some universal rules are unraveled. For instance, nucleolar and ribosomal proteins have relatively higher inhibition efficiencies in every type of cells treated with each inhibitor. Moreover, proteins intrinsically resistant or sensitive to the inhibition are identified and found to have distinct functions. Systematic investigation of protein synthesis inhibition in several types of human cells by different inhibitors provides valuable information about the inhibition of protein synthesis, advancing our understanding of inhibiting protein synthesis.
Searching for quasi-periodic eruptions using machine learning
Authors: Webbe Robbie , Young A J
Published: May 2023

Quasi-periodic eruption (QPE) is a rare phenomenon in which the X-ray emission from the nuclei of galaxies shows a series of large amplitude flares. Only a handful of QPEs have been observed but the possibility remains that there are as yet undetected sources in archival data. Given the volume of data available a manual search is not feasible, and so we consider an application of machine learning to archival data to determine whether a set of time-domain features can be used to identify further light curves containing eruptions. Using a neural network and 14 variability measures we are able to classify light curves with accuracies of greater than $94{{\ \rm per\ cent}}$ with simulated data and greater than $98{{\ \rm per\ cent}}$ with observational data on a sample consisting of 12 light curves with QPEs and 52 light curves without QPEs. An analysis of 83 531 X-ray detections from the XMM Serendipitous Source Catalogue allowed us to recover light curves of known QPE sources and examples of several categories of variable stellar objects.
Association between knee magnetic resonance imaging markers and knee symptoms over 6–9 years in young adults
Authors: Singh Ambrish , Venn Alison , Blizzard Leigh , March Lyn , Eckstein Felix , Jones Graeme , Wirth Wolfgang , Cicuttini Flavia , Ding Changhai , Antony Benny
Published: May 2023

Objectives

To describe associations between MRI markers with knee symptoms in young adults.

Methods

Knee symptoms were assessed using the WOMAC scale during the Childhood Determinants of Adult Health Knee Cartilage study (CDAH-knee; 2008–2010) and at the 6- to 9-year follow-up (CDAH-3; 2014–2019). Knee MRI scans obtained at baseline were assessed for morphological markers (cartilage volume, cartilage thickness, subchondral bone area) and structural abnormalities [cartilage defects and bone marrow lesions (BMLs)]. Univariable and multivariable (age, sex, BMI adjusted) zero-inflated Poisson (ZIP) regression models were used for analysis.

Results

The participants’ mean age in CDAH-knee and CDAH-3 were 34.95 (s.d. 2.72) and 43.27 (s.d. 3.28) years, with 49% and 48% females, respectively. Cross-sectionally, there was a weak but significant negative association between medial femorotibial compartment (MFTC) [ratio of the mean (RoM) 0.99971084 (95% CI 0.9995525, 0.99986921), P < 0.001], lateral femorotibial compartment (LFTC) [RoM 0.99982602 (95% CI 0.99969915, 0.9999529), P = 0.007] and patellar cartilage volume [RoM 0.99981722 (95% CI 0.99965326, 0.9999811), P = 0.029] with knee symptoms. Similarly, there was a negative association between patellar cartilage volume [RoM 0.99975523 (95% CI 0.99961427, 0.99989621), P = 0.014], MFTC cartilage thickness [RoM 0.72090775 (95% CI 0.59481806, 0.87372596), P = 0.001] and knee symptoms assessed after 6–9 years. The total bone area was negatively associated with knee symptoms at baseline [RoM 0.9210485 (95% CI 0.8939677, 0.9489496), P < 0.001] and 6–9 years [RoM 0.9588811 (95% CI 0.9313379, 0.9872388), P = 0.005]. The cartilage defects and BMLs were associated with greater knee symptoms at baseline and 6–9 years.

Conclusion

BMLs and cartilage defects were positively associated with knee symptoms, whereas cartilage volume and thickness at MFTC and total bone area were weakly and negatively associated with knee symptoms. These results suggest that the quantitative and semiquantitative MRI markers can be explored as a marker of clinical progression of OA in young adults.
COVID-19 Pandemic in Ireland and the Gendered Division of Care Work: The Impact of the Pandemic on Childcare Policy
Authors: Bobek Alicja , Clavero Sara , Gavigan Sylvia , Ryan Mark
Published: May 2023

This article addresses the gendered impacts of the COVID-19 pandemic on the policy domains of care, with a particular focus on childcare. By using historical institutionalism as a conceptual framework, and Ireland as a case study, the article examines the extent to which the pandemic constituted a “critical juncture” leading to change in childcare policy in the country. The study is based on data collected in Ireland as part of the RESISTIRÉ project (Responding to outbreaks through co-creative inclusive equality strategies and collaboration), which investigates the impact of COVID-19 on equality in thirty-one countries, specifically through a gender+ approach that focuses on analyzing the impact of policy responses to COVID-19 on existing inequalities. The analysis carried out in this article reveals that changes in childcare policy were more adaptive than transformative, and that the underlying gender logic of the Irish welfare state regime remained unchanged.
Role of PPARγ in dyslipidemia and altered pulmonary functioning in mice following ozone exposure
Authors: Smith Ley Cody , Gow Andrew J , Abramova Elena , Vayas Kinal , Guo Changjiang , Noto Jack , Lyman Jack , Rodriquez Jessica , Gelfand-Titiyevskiy Benjamin , Malcolm Callum , Laskin Jeffrey D , Laskin Debra L
Published: May 2023

Exposure to ozone causes decrements in pulmonary function, a response associated with alterations in lung lipids. Pulmonary lipid homeostasis is dependent on the activity of peroxisome proliferator activated receptor gamma (PPARγ), a nuclear receptor that regulates lipid uptake and catabolism by alveolar macrophages (AMs). Herein, we assessed the role of PPARγ in ozone-induced dyslipidemia and aberrant lung function in mice. Exposure of mice to ozone (0.8 ppm, 3 h) resulted in a significant reduction in lung hysteresivity at 72 h post exposure; this correlated with increases in levels of total phospholipids, specifically cholesteryl esters, ceramides, phosphatidylcholines, phosphorylethanolamines, sphingomyelins, and di- and triacylglycerols in lung lining fluid. This was accompanied by a reduction in relative surfactant protein-B (SP-B) content, consistent with surfactant dysfunction. Administration of the PPARγ agonist, rosiglitazone (5 mg/kg/day, i.p.) reduced total lung lipids, increased relative amounts of SP-B, and normalized pulmonary function in ozone-exposed mice. This was associated with increases in lung macrophage expression of CD36, a scavenger receptor important in lipid uptake and a transcriptional target of PPARγ. These findings highlight the role of alveolar lipids as regulators of surfactant activity and pulmonary function following ozone exposure and suggest that targeting lipid uptake by lung macrophages may be an efficacious approach for treating altered respiratory mechanics.
Skin-to-skin contact and its effect on mothers’ postpartum psychological distress and their full-term neonate in Egypt
Authors: El Sehmawy Asmaa A , Younes Abd Elaziz Shaimaa , Elwahed Rania Mahfouz Abd , Elsheikh Asmaa Abdelghany
Published: May 2023

Design

A randomized controlled study was conducted on 400 mothers, who were divided into two groups: 200 mothers who applied skin-to-skin infant care (SSC) for at least 1 h daily for 12 weeks and 200 mothers who performed the usual mother–infant care. The mothers were recruited from the Obstetric Department of Al-Zahraa University Hospital in Cairo, Egypt. The enrolled mothers' infants were assessed for body weight. Sleep hours and frequency of breast milk feeding were evaluated by the mother during the day. All of the mothers who took part in the study were assessed for postoperative pain, wound healing, postpartum depression, anxiety, sleep quality and newborn maternal bonding.

Results

There was a significant increase in frequencies of breastfeeding and the body weight at 12 weeks’ postnatal age and also an increase in sleep hours in the infants who had SSC. The mothers who performed SSC had good sleep quality in comparison with those who performed the usual infant care; in addition, they had less postoperative pain intensity and proper wound healing apart from better maternal–infant bond, decreased anxiety and decreased depression frequency.

Conclusion

SSC was associated with better infant breastfeeding, increased sleep hours in infants and less postpartum psychological burden in mothers.
Ride-hailing origin-destination demand prediction with spatiotemporal information fusion
Authors: Wang Ning , Zheng Liang , Shen Huitao , Li Shukai
Published: May 2023

Accurate demand forecasting for online ride-hailing contributes to balancing traffic supply and demand, and improving the service level of ride-hailing platforms. In contrast to previous studies, which have primarily focused on the inflow or outflow demands of each zone, this study proposes a conditional generative adversarial network with a Wasserstein divergence objective (CWGAN-div) to predict ride-hailing origin-destination (OD) demand matrices. Residual blocks and refined loss functions help to enhance the stability of model training. Interpretable conditional information is employed to capture external spatiotemporal dependencies and guide the model towards generating more precise results. Empirical analysis using ride-hailing data from Manhattan, New York City, demonstrates that our proposed CWGAN-div model can effectively predict the network-wide OD matrix and exhibits strong convergence performance. Comparative experiments also show that the CWGAN-div outperforms other benchmarking methods. Consequently, the proposed model displays potential for network-wide ride-hailing OD demand prediction.