bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate change effects on plankton recruitment from coastal sediments
Authors: Hedberg Per , Olsson Markus , Höglander Helena , Brüchert Volker , Winder Monika 
Published: February 2024

Abstract
In highly seasonal systems, the emergence of planktonic resting stages from the sediment is a key driver for bloom timing and plankton community composition. The termination of the resting phase is often linked to environmental cues, but the extent to which recruitment of resting stages is affected by climate change remains largely unknown for coastal environments. Here we investigate phyto- and zooplankton recruitment from oxic sediments in the Baltic Sea in a controlled experiment under proposed temperature and light increase during the spring and summer. We find that emergence of resting stage differs between seasons and the abiotic environment. Phytoplankton recruitment from resting stages were high in spring with significantly higher emergence rates at increased temperature and light levels for dinoflagellate and cyanobacteria than for diatoms, which had highest emergence under cold and dark conditions. In comparison, hatching of copepod nauplii was not affected by increased temperature and light levels. These results show that activation of plankton resting stages are affected to different degrees by increasing temperature and light levels, indicating that climate change affects plankton dynamics through processes related to resting stage termination with potential consequences for bloom timing, community composition and trophic mismatch.
PECTIN ACETYLESTERASE12 regulates shoot branching via acetic acid and auxin accumulation in alfalfa shoots
Authors: Fan Nana , Su Liantai , Lv Aimin , Wen Wuwu , Gao Li , You Xiangkai , Zhou Peng , An Yuan 
Published: February 2024

Abstract
Shoot branching is an important biological trait affecting alfalfa (Medicago sativa L.) production, but its development is complicated and the mechanism is not fully clear. In the present study, pectin acetylesterase 12 (MsPAE12) and NAM/ATAF/CUC-domain transcription factor gene (MsNAC73) were isolated from alfalfa. MsPAE12 was highly expressed in shoot apexes, and MsNAC73 was found to be a key transcriptional repressor of MsPAE12 by directly binding to salicylic acid (SA) and jasmonic acid (JA) elements in the MsPAE12 promoter. The biological functions of MsPAE12 and MsNAC73 were studied through overexpression (OE) and down-expression (RNAi) of the 2 genes in alfalfa. The numbers of shoot branches increased in MsPAE12-OE lines but decreased in MsPAE12-RNAi and MsNAC73-OE plants, which was negatively related to their indole-3-acetic acid (IAA) accumulation in shoot apexes. Furthermore, the contents of acetic acid (AA) in shoot apexes decreased in MsPAE12-OE plants but increased in MsPAE12-RNAi and MsNAC73-OE plants. The changes of AA contents were positively related to the expression of TRYPTOPHAN AMINOTRANSFERASE 1 (MsTAA1), TRYPTOPHAN AMINOTRANSFERASE-RELATED 2 (MsTAR2), and YUCCA flavin monooxygenase (MsYUCC4) and the contents of tryptophan (Trp), indole-3-pyruvic acid (IPA), and IAA in shoot apexes of MsPAE12-OE, MsPAE12-RNAi, and MsNAC73-OE plants. Exogenous application of AA to wild type (WT) and MsPAE12-OE plants increased Trp, IPA, and IAA contents and decreased branch number. Exogenous IAA suppressed shoot branching in MsPAE12-OE plants, but exogenous IAA inhibitors increased shoot branching in MsPAE12-RNAi plants. These results indicate that the MsNAC73-MsPAE12 module regulates auxin-modulated shoot branching via affecting AA accumulation in shoot apexes of alfalfa.
RNA-directed DNA methylation mutants reduce histone methylation at the paramutated maize booster1 enhancer
Authors: Hövel Iris , Bader Rechien , Louwers Marieke , Haring Max , Peek Kevin , Gent Jonathan I , Stam Maike 
Published: February 2024

Abstract
Paramutation is the transfer of mitotically and meiotically heritable silencing information between two alleles. With paramutation at the maize (Zea mays) booster1 (b1) locus, the low-expressed B′ epiallele heritably changes the high-expressed B-I epiallele into B′ with 100% frequency. This requires specific tandem repeats and multiple components of the RNA-directed DNA methylation pathway, including the RNA-dependent RNA polymerase (encoded by mediator of paramutation1, mop1), the second-largest subunit of RNA polymerase IV and V (NRP(D/E)2a, encoded by mop2), and the largest subunit of RNA Polymerase IV (NRPD1, encoded by mop3). Mutations in mop genes prevent paramutation and release silencing at the B′ epiallele. In this study, we investigated the effect of mutations in mop1, mop2, and mop3 on chromatin structure and DNA methylation at the B′ epiallele, and especially the regulatory hepta-repeat 100 kb upstream of the b1 gene. Mutations in mop1 and mop3 resulted in decreased repressive histone modifications H3K9me2 and H3K27me2 at the hepta-repeat. Associated with this decrease were partial activation of the hepta-repeat enhancer function, formation of a multi-loop structure, and elevated b1 expression. In mop2 mutants, which do not show elevated b1 expression, H3K9me2, H3K27me2 and a single-loop structure like in wild-type B′ were retained. Surprisingly, high CG and CHG methylation levels at the B′ hepta-repeat remained in all three mutants, and CHH methylation was low in both wild type and mutants. Our results raise the possibility of MOP factors mediating RNA-directed histone methylation rather than RNA-directed DNA methylation at the b1 locus.
Mediator kinase subunit CDK8 phosphorylates transcription factor TCP15 during tomato pollen development
Authors: Xu Rui , Chong Leelyn , Zhu Yingfang 
Published: February 2024

Abstract
Pollen development in flowering plants has strong implications for reproductive success. Pollen DNA can be targeted to improve plant traits for yield and stress tolerance. In this study, we demonstrated that the Mediator subunit CYCLIN-DEPENDENT KINASE 8 (CDK8) is a key modulator of pollen development in tomato (Solanum lycopersicum). SlCDK8 knockout led to significant decreases in pollen viability, fruit yield, and fruit seed number. We also found that SlCDK8 directly interacts with transcription factor TEOSINTE BRANCHED1-CYCLOIDEA-PCF15 (SlTCP15) using yeast two-hybrid screens. We subsequently showed that SlCDK8 phosphorylates Ser 187 of SlTCP15 to promote SlTCP15 stability. Phosphorylated TCP15 directly bound to the TGGGCY sequence in the promoters of DYSFUNCTIONAL TAPETUM 1 (SlDYT1) and MYB DOMAIN PROTEIN 103 (SlMYB103), which are responsible for pollen development. Consistently, disruption of SlTCP15 resembled slcdk8 tomato mutants. In sum, our work identified a new substrate of Mediator CDK8 and revealed an important regulatory role of SlCDK8 in pollen development via cooperation with SlTCP15.
Defying gravity: WEEP promotes negative gravitropism in peach trees by establishing asymmetric auxin gradients
Authors: Kohler Andrea R , Scheil Andrew , Hill Joseph L , Allen Jeffrey R , Al-Haddad Jameel M , Goeckeritz Charity Z , Strader Lucia C , Telewski Frank W , Hollender Courtney A 
Published: February 2024

Abstract
Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The peach (Prunus persica) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Little is known about the function of WEEP despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach trees do not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development. This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster lateral root gravitropic response. This suggests that WEEP moderates root gravitropism and is essential to establishing the set-point angle of lateral roots from the gravity vector. Additionally, size exclusion chromatography indicated that WEEP proteins self-oligomerize, like other proteins with sterile alpha motif domains. Collectively, our results from weeping peach provide insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.
FLOWERING LOCUS T1 and TERMINAL FLOWER1 regulatory networks mediate flowering initiation in apple
Authors: Zuo Xiya , Wang Shixiang , Liu Xiuxiu , Tang Ting , Li Youmei , Tong Lu , Shah Kamran , Ma Juanjuan , An Na , Zhao Caiping , Xing Libo , Zhang Dong 
Published: February 2024

Abstract
Flower bud formation is a critical process that directly determines yield and fruit quality in fruit crops. Floral induction is modulated by the balance between 2 flowering-related proteins, FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1); however, the mechanisms underlying the establishment and maintenance of this dynamic balance remain largely elusive. Here, we showed that in apple (Malus × domestica Borkh.), MdFT1 is predominantly expressed in spur buds and exhibits an increase in expression coinciding with flower induction; in contrast, MdTFL1 exhibited downregulation in apices during flower induction, suggesting that MdTFL1 has a role in floral repression. Interestingly, both the MdFT1 and MdTFL1 transcripts are directly regulated by transcription factor basic HELIX–LOOP–HELIX48 (MdbHLH48), and overexpression of MdbHLH48 in Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum) results in accelerated flowering. Binding and activation analyses revealed that MdbHLH48 functions as a positive regulator of MdFT1 and a negative regulator of MdTFL1. Further studies established that both MdFT1 and MdTFL1 interact competitively with MdWRKY6 protein to facilitate and inhibit, respectively, MdWRKY6-mediated transcriptional activation of target gene APPLE FLORICAULA/LFY (AFL1, an apple LEAFY-like gene), ultimately regulating apple flower bud formation. These findings illustrate the fine-tuned regulation of flowering by the MdbHLH48-MdFT1/MdTFL1-MdWRKY6 module and provide insights into flower bud formation in apples.
Far-red light-enhanced apical dominance stimulates flower and fruit abortion in sweet pepper
Authors: Chen Sijia , Marcelis Leo F M , Offringa Remko , Kohlen Wouter , Heuvelink Ep 
Published: February 2024

Abstract
Far-red radiation affects many plant processes, including reproductive organ abortion. Our research aimed to determine the role of apical dominance in far-red light-induced flower and fruit abortion in sweet pepper (Capsicum annuum L.). We conducted several climate room experiments where plants were grown under white- or red-rich LED light, with or without additional far-red light. Additional far-red light enhanced apical dominance: it increased auxin levels in the apices of dominant shoots, and caused a greater difference in internode length and apical auxin levels between dominant and subordinate shoots. Additional far-red light stimulated fruit abortion in intact plants but not in decapitated plants, suggesting a crucial role of shoot apices in this effect. However, reducing basipetal auxin transport in the stems with N-1-naphthylphthalamic acid did not influence far-red light-stimulated fruit abortion, although auxin levels in the stem were largely reduced. Applying the synthetic auxin 1-naphthaleneacetic acid on decapitated apices did not influence fruit abortion. However, applying the auxin biosynthesis inhibitor yucasin to shoot apices reduced fruit abortion regardless of the light conditions, accompanied by slight shoot growth retardation. These findings suggest that the basipetal auxin stream does not mediate far-red light-stimulated fruit abortion. Far-red light-stimulated fruit abortion was associated with reduced sucrose accumulation and lower invertase activities in flowers. We suggest that under additional far-red light conditions, increased auxin levels in shoot apices promote fruit abortion probably through enhanced competition for assimilates between apices and flowers, which limits assimilate import into flowers.
Distinct senescence mechanisms restrain progression of dysplastic nevi
Authors: Lorbeer Franziska K , Rieser Gabrielle , Goel Aditya , Wang Meng , Oh Areum , Yeh Iwei , Bastian Boris C , Hockemeyer Dirk 
Published: February 2024

Abstract
Telomerase reverse transcriptase (TERT) promoter mutations (TPMs) are frequently found in different cancer types, including ∼70% of sun-exposed skin melanomas. In melanoma, TPMs are among the earliest mutations and can be present during the transition from nevus to melanoma. However, the specific factors that contribute to the selection of TPMs in certain nevi subsets are not well understood. To investigate this, we analyzed a group of dysplastic nevi (DN) by sequencing genes commonly mutated in melanocytic neoplasms. We examined the relationship between the identified mutations, patient age, telomere length, histological features, and the expression of p16. Our findings reveal that TPMs are more prevalent in DN from older patients and are associated with shorter telomeres. Importantly, these TPMs were not found in nevi with BRAF V600E mutations. Conversely, DN with BRAF V600E mutations were observed in younger patients, had longer telomeres and a higher proportion of p16-positive cells. This suggests that these nevi arrest growth independently of telomere shortening through a mechanism known as oncogene-induced senescence (OIS). These characteristics extend to melanoma-sequencing datasets, where melanomas with BRAF V600E mutations were more likely to have a CDKN2A inactivation, overriding OIS. In contrast, melanomas without BRAF V600E mutations showed a higher frequency of TPMs. Our data imply that TPMs are selected to bypass replicative senescence (RS) in cells that were not arrested by OIS. Overall, our results indicate that a subset of melanocytic neoplasms face constraints from RS, while others encounter OIS and RS. The order in which these barriers are overcome during progression to melanoma depends on the mutational context.
Estimating the loss of economic predictability from aggregating firm-level production networks
Authors: Diem Christian , Borsos András , Reisch Tobias , Kertész János , Thurner Stefan 
Published: February 2024

Abstract
To estimate the reaction of economies to political interventions or external disturbances, input–output (IO) tables—constructed by aggregating data into industrial sectors—are extensively used. However, economic growth, robustness, and resilience crucially depend on the detailed structure of nonaggregated firm-level production networks (FPNs). Due to nonavailability of data, little is known about how much aggregated sector-based and detailed firm-level-based model predictions differ. Using a nearly complete nationwide FPN, containing 243,399 Hungarian firms with 1,104,141 supplier–buyer relations, we self-consistently compare production losses on the aggregated industry-level production network (IPN) and the granular FPN. For this, we model the propagation of shocks of the same size on both, the IPN and FPN, where the latter captures relevant heterogeneities within industries. In a COVID-19 inspired scenario, we model the shock based on detailed firm-level data during the early pandemic. We find that using IPNs instead of FPNs leads to an underestimation of economic losses of up to 37%, demonstrating a natural limitation of industry-level IO models in predicting economic outcomes. We ascribe the large discrepancy to the significant heterogeneity of firms within industries: we find that firms within one sector only sell 23.5% to and buy 19.3% from the same industries on average, emphasizing the strong limitations of industrial sectors for representing the firms they include. Similar error levels are expected when estimating economic growth, CO2 emissions, and the impact of policy interventions with industry-level IO models. Granular data are key for reasonable predictions of dynamical economic systems.
Tailbeat perturbations improve swimming efficiency by reducing the phase lag between body motion and the resulting fluid response
Authors: Chao Li-Ming , Jia Laibing , Wang Siyuan , Liberzon Alexander , Ravi Sridhar , Couzin Iain D , Li Liang 
Published: February 2024

Abstract
Understanding how animals swim efficiently and generate high thrust in complex fluid environments is of considerable interest to researchers in various fields, including biology, physics, and engineering. However, the influence of often-overlooked perturbations on swimming fish remains largely unexplored. Here, we investigate the propulsion generated by oscillating tailbeats with superimposed rhythmic perturbations of high frequency and low amplitude. We reveal, using a combination of experiments in a biomimetic fish-like robotic platform, computational fluid dynamics simulations, and theoretical analysis, that rhythmic perturbations can significantly increase both swimming efficiency and thrust production. The introduction of perturbations increases pressure-induced thrust, while reduced phase lag between body motion and the subsequent fluid dynamics response improves swimming efficiency. Moreover, our findings suggest that beneficial perturbations are sensitive to kinematic parameters, resolving previous conflicts regarding the effects of such perturbations. Our results highlight the potential benefits of introducing perturbations in propulsion generators, providing potential hypotheses for living systems and inspiring the design of artificial flapping-based propulsion systems.
Quantitative description of the phase-separation behavior of the multivalent SLP65–CIN85 complex
Authors: Maier Joachim , Sieme Daniel , Wong Leo E , Dar Furqan , Wienands Jürgen , Becker Stefan , Griesinger Christian 
Published: February 2024

Abstract
Biomolecular condensates play a major role in cell compartmentalization, besides membrane-enclosed organelles. The multivalent SLP65 and CIN85 proteins are proximal B-cell antigen receptor (BCR) signal effectors and critical for proper immune responses. In association with intracellular vesicles, the two effector proteins form phase separated condensates prior to antigen stimulation, thereby preparing B lymphocytes for rapid and effective activation upon BCR ligation. Within this tripartite system, 6 proline-rich motifs (PRMs) of SLP65 interact promiscuously with 3 SH3 domains of the CIN85 monomer, establishing 18 individual SH3–PRM interactions whose individual dissociation constants we determined. Based on these 18 dissociation constants, we measured the phase-separation properties of the natural SLP65/CIN85 system as well as designer constructs that emphasize the strongest SH3/PRM interactions. By modeling these various SLP65/CIN85 constructs with the program LASSI (LAttice simulation engine for Sticker and Spacer Interactions), we reproduced the observed phase-separation properties. In addition, LASSI revealed a deviation in the experimental measurement, which was independently identified as a previously unknown intramolecular interaction. Thus, thermodynamic properties of the individual PRM/SH3 interactions allow us to model the phase-separation behavior of the SLP65/CIN85 system faithfully.
Buckling mediated by mobile localized elastic excitations
Authors: Hutton Robert S , Vitral Eduardo , Hamm Eugenio , Hanna James 
Published: February 2024

Abstract
Experiments reveal that structural transitions in thin sheets are mediated by the passage of transient and stable mobile localized elastic excitations. These “crumples” or “d-cones” nucleate, propagate, interact, annihilate, and escape. Much of the dynamics occurs on millisecond time scales. Nucleation sites correspond to regions where generators of the ideal unstretched surface converge. Additional stable intermediate states illustrate two forms of quasistatic inter-crumple interaction through ridges or valleys. These interactions create pairs from which extended patterns may be constructed in larger specimens. The onset of localized transient deformation with increasing sheet size is correlated with a characteristic stable crumple size, whose measured scaling with thickness is consistent with prior theory and experiment for localized elastic features in thin sheets. We offer a new theoretical justification of this scaling.
Arresting ambitions: Obstacles associated with recruiting college educated women to policing
Authors: Powers Edward L , Skaggs Sherry Lynn , Hardwick Kisha 
Published: February 2024

Abstract
Recruitment and retention are two of the greatest challenges for police agencies, community members, and leaders. Recently, agencies have faced shallow applicant pools and significant declines in retention longevity. Concerns over excessive force, especially fatal incidents in minority communities, have fostered anti-police sentiment, reduced the prestige of police work, and elevated negative perceptions of risk in policing careers. These factors contribute to recruitment and retention woes, especially in women, who often harbour reservations about pursuing careers in a male-dominated work environment. Using data collected from a series of six single-sex focus groups, this study assesses the challenges faced in recruitment of college educated females and their attitudes toward policing as a profession. Findings reveal support for theories of person-vocation fit as primary motivations and barriers to careers in policing for women. Respondent concerns centre around personal interest, family and media pressures, and perceptions about the nature of police work.
Staffing levels are the most important factor influencing police response times
Authors: Mourtgos Scott M , Adams Ian T , Nix Justin 
Published: February 2024

Abstract
We examine the factors influencing police response times, with a particular focus on staffing levels, calls for service (CFS), and proactive police work. We estimate Bayesian Holt-Winters state-space models for each CFS priority level. Using a novel dataset that combines data from the Salt Lake City Police Department's staffing and Computer-Aided Dispatch (CAD) systems at the daily level over seven years, we estimate the effects that staffing, overtime, call volume, and the level of proactive work (e.g., traffic stops, pedestrian stops, business checks) have on police response times. Our findings indicate that the impact of staffing on response times is significantly greater than that of other independent variables in the models. Furthermore, improvements in response times for higher-priority (i.e., more serious) CFS have a lower elasticity response to increases in staffing levels. As police agencies face increasingly complex challenges, the empirical evidence presented herein serves as a cornerstone for making informed decisions in the intricate balancing act of resources, officer well-being, and public safety priorities.