bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unlocking regeneration potential: harnessing morphogenic regulators and small peptides for enhanced plant engineering
Authors: Youngstrom Christopher , Wang Kan , Lee Keunsub 
Published: December 2024

SUMMARYPlant genetic transformation is essential for understanding gene functions and developing improved crop varieties. Traditional methods, often genotype‐dependent, are limited by plants' recalcitrance to gene delivery and low regeneration capacity. To overcome these limitations, new approaches have emerged that greatly improve efficiency and genotype flexibility. This review summarizes key strategies recently developed for plant transformation, focusing on groundbreaking technologies enhancing explant‐ and genotype flexibility. It covers the use of morphogenic regulators (MRs), stem cell‐based methods, and in planta transformation methods. MRs, such as maize Babyboom (BBM) with Wuschel2 (WUS2), and GROWTH‐REGULATING FACTORs (GRFs) with their cofactors GRF‐interacting factors (GIFs), offer great potential for transforming many monocot species, including major cereal crops. Optimizing BBM/WUS2 expression cassettes has further enabled successful transformation and gene editing using seedling leaves as starting material. This technology lowers the barriers for academic laboratories to adopt monocot transformation systems. For dicot plants, tissue culture‐free or in planta transformation methods, with or without the use of MRs, are emerging as more genotype‐flexible alternatives to traditional tissue culture‐based transformation systems. Additionally, the discovery of the local wound signal peptide Regeneration Factor 1 (REF1) has been shown to enhance transformation efficiency by activating wound‐induced regeneration pathways in both monocot and dicot plants. Future research may combine these advances to develop truly genotype‐independent transformation methods.
Rapid and efficient in planta genome editing in sorghum using foxtail mosaic virus‐mediated sgRNA delivery
Authors: Baysal Can , Kausch Albert P. , Cody Jon P. , Altpeter Fredy , Voytas Daniel F. 
Published: December 2024

SUMMARYThe requirement of in vitro tissue culture for the delivery of gene editing reagents limits the application of gene editing to commercially relevant varieties of many crop species. To overcome this bottleneck, plant RNA viruses have been deployed as versatile tools for in planta delivery of recombinant RNA. Viral delivery of single‐guide RNAs (sgRNAs) to transgenic plants that stably express CRISPR‐associated (Cas) endonuclease has been successfully used for targeted mutagenesis in several dicotyledonous and few monocotyledonous plants. Progress with this approach in monocotyledonous plants is limited so far by the availability of effective viral vectors. We engineered a set of foxtail mosaic virus (FoMV) and barley stripe mosaic virus (BSMV) vectors to deliver the fluorescent protein AmCyan to track viral infection and movement in Sorghum bicolor. We further used these viruses to deliver and express sgRNAs to Cas9 and Green Fluorescent Protein (GFP) expressing transgenic sorghum lines, targeting Phytoene desaturase (PDS), Magnesium‐chelatase subunit I (MgCh), 4‐hydroxy‐3‐methylbut‐2‐enyl diphosphate reductase, orthologs of maize Lemon white1 (Lw1) or GFP. The recombinant BSMV did neither infect sorghum nor deliver or express AmCyan and sgRNAs. In contrast, the recombinant FoMV systemically spread throughout sorghum plants and induced somatic mutations with frequencies reaching up to 60%. This mutagenesis led to visible phenotypic changes, demonstrating the potential of FoMV for in planta gene editing and functional genomics studies in sorghum.
The importin α proteins IMPA1, IMPA2, and IMPA4 play redundant roles in suppressing autoimmunity in Arabidopsis thaliana
Authors: Mori Airi , Nakagawa Shitomi , Suzuki Toshiyuki , Suzuki Takamasa , Gaudin Valérie , Matsuura Takakazu , Ikeda Yoko , Tamura Kentaro 
Published: December 2024

SUMMARYProteins in the importin α (IMPA) family play pivotal roles in intracellular nucleocytoplasmic transport. Arabidopsis thaliana possesses nine IMPA members, with diverse tissue‐specific expression patterns. Among these nine IMPAs, IMPA1, IMPA2, and IMPA4 cluster together phylogenetically, suggesting potential functional redundancy. To explore this redundancy, we analyzed single and multiple T‐DNA mutants for these genes and discovered severe growth defects in the impa1 impa2 impa4 triple knockout mutant but not in the single or double mutants. Complementation with IMPA1, IMPA2, or IMPA4 fused to green fluorescent protein (GFP) rescued the growth defects observed in the impa1 impa2 impa4 mutant, indicating the functional redundancy of these three IMPAs. The IMPA‐GFP fusion proteins were localized in the nucleus and nuclear envelope, suggesting their involvement in nucleocytoplasmic transport processes. Comparative transcriptomics revealed that salicylic acid (SA)‐responsive genes were significantly upregulated in the impa1 impa2 impa4 triple mutant. Consistent with this observation, impa1 impa2 impa4 mutant plants accumulated SA and reactive oxygen species to high levels compared with wild‐type plants. We also found enhanced resistance to the anthracnose pathogen Colletotrichum higginsianum in the impa1 impa2 impa4 mutants, suggesting that defense responses were constitutively activated in the impa1 impa2 impa4 mutant. Our findings shed light on the redundant roles of IMPA1, IMPA2, and IMPA4 in suppressing the autoimmune responses and suggest avenues of research to clarify their potentially unique roles.
Elicitron: A Large Language Model Agent-Based Simulation Framework for Design Requirements Elicitation
Authors: Ataei Mohammadmehdi , Cheong Hyunmin , Grandi Daniele , Wang Ye , Morris Nigel , Tessier Alexander 
Published: December 2024

Abstract
Requirement elicitation, a critical, yet time-consuming and challenging step in product development, often fails to capture the full spectrum of user needs. This may lead to products that fall short of user expectations. This article introduces a novel framework that leverages large language models (LLMs) to automate and enhance the requirement elicitation process. LLMs are used to generate a vast array of simulated users (LLM agents), enabling the exploration of a much broader range of user needs and unforeseen use cases. These agents engage in product experience scenarios, explaining their actions, observations, and challenges. Subsequent agent interviews and analysis uncover valuable user needs, including latent ones. We validate our framework with three experiments. First, we explore different methodologies for the challenge of diverse agent generation, discussing their advantages and shortcomings. We measure the diversity of identified user needs and demonstrate that context-aware agent generation leads to greater diversity. Second, we show how our framework effectively mimics empathic lead user interviews, identifying a greater number of latent needs than conventional human interviews. Third, we show that LLMs can be used to analyze interviews, capture needs, and classify them as latent or not. Our work highlights the potential of using LLMs to accelerate early-stage product development with minimal costs and increase innovation.
Malate or Not? Acute Effects of L-Citrulline Versus Citrulline Malate on Neuromuscular Performance in Young, Trained Adults: A Randomized, Double-Blind, Placebo-Controlled Crossover Trial
Authors: Martín-Olmedo Juan J. , Miras-Moreno Sergio , Cuadra-Montes Kevin , García-Ramos Amador , Ruiz Jonatan R. , Jurado-Fasoli Lucas 
Published: December 2024

L-citrulline (CIT) supplementation seems to improve resistance training performance; yet, whether malate has additive ergogenic effects when combined with CIT is unknown. This randomized, double-blind, placebo-controlled crossover trial aimed to compare the acute effects of CIT versus citrulline malate (CMA) supplementation on neuromuscular performance and exertion and emotional perceptions in young, trained men and women. 43 (21 women; 24.2 ± 3.7 years) participants ingested a placebo, CIT (5.3 g of CIT), or CMA (5.3 g of CIT, 2.7 g of malate) 45 min before three experimental sessions in a counterbalanced manner. We evaluated the upper and lower limb maximal neuromuscular and ballistic performance through the two-point method and countermovement jump. Strength-endurance was assessed across three sets of 10 repetitions in the squat and bench press exercises. Exertion and emotional perceptions were evaluated before and after the assessment and during the strength-endurance assessment. CIT and CMA supplementation did not enhance maximal neuromuscular performance (all p ≥ .061, ), or ballistic strength (all p ≥ .348, ). Neither CIT nor CMA supplementation improved strength-endurance as observed in the total number of repetitions (all p ≥ .590, ), repetitions before reaching velocity loss threshold (all p ≥ .623, ), mean velocity (all p ≥ .792, ), mean velocity decline (all p ≥ .293, ), and mean velocity maintenance (all p ≥ .393 ), or exertion and emotional perceptions (both p ≥ .306, ). In conclusion, CIT and CMA supplementation may not increase the neuromuscular performance during low- to moderate-volume resistance training sessions in young, trained adults. This trial was registered at ClinicalTrials.gov (No. NCT05183893).
Association Between Anthropometry and Motor Performance With Competitive Indicators of Women Athletes in the Capoeira World Games: A Cross-Sectional Study
Authors: Barros Lorrana K.S. , Oliveira Ariel C. , Vale Thamires S. , dos Santos Geovani A. , Moreira Débora Vitória S. , Pinheiro Anderson S. , dos Santos Rafael G. , da Silva Ilma Sabrina B. , de Souza Thales Alessandro V.M. , Ribeiro Davi L. , da Silva Priscila , Moreira Sérgio R. 
Published: December 2024

Objective: This study aimed to verify the association of anthropometric and motor variables with the competitive indicators of female athletes in the ABADÁ-Capoeira (Associação Brasileira de Apoio e Desenvolvimento da Arte Capoeira) World Games. Methods: Forty-two capoeira athletes from 15 countries (capoeira experience = 15.1 [7.9] y, age = 32.1 [8.8] y, body mass = 63.2 [6.3] kg, and height = 161.8 [4.4] cm) were recruited for anthropometric and motor evaluation of sit and reach, push-up, trunk flexion, countermovement jump (CMJ), and quadrant jump (QDJ). Each athlete’s ranking and stage scores in the competition were obtained as indicators of competitive performance. Results: There were inverse correlations between abdominal circumference, body mass index, body fat percentage, and endomorphy with motor variables (rho = −.36 to −.46; P < .05). Positive correlations of motor performance with competitive performance indicators were evidenced, being between the average increment score with the CMJ (rho = .33; P < .05) and the QDJ (rho = .35; P < .05), and between the competition score with the CMJ (rho = .32; P < .05) and the QDJ (rho = .32; P < .05). Additionally, the motor performance of trunk flexion (β = 0.11; odds ratio = 1.126; 95% CI, 1.025–1.238), QDJ (β = 0.21; odds ratio = 1.239; 95% CI, 1.022–1.503), and CMJ (β = 0.20; odds ratio = 1.230; 95% CI, 1.029–1.471) predicted competition stage advancement. Conclusions: Associations occurred between anthropometry and motor performance, and this was predictive of competitive indicators of female capoeira athletes in international competition. Such information may contribute to an optimized and effective training process aimed at the integral improvement of capoeira practitioners’ body composition and motor skills, especially to improve localized muscular endurance of the upper limbs and abdomen, as well as agility and power of the lower limbs.
From Early Explorers to Restricted Practitioners: A Qualitative Analysis of Coaches’ Development, Context, and Practices Within U.K. Mixed Martial Arts
Authors: Kirk Christopher , Cronin Colum , Langan-Evans Carl , Clark David R. , Morton James P. 
Published: December 2024

Despite its growing popularity and participation rates, mixed martial arts (MMA) coaching has not been the subject of much critical scholarly analysis. Accordingly, knowledge of this activity is limited, and inadequate, as a means of understanding this MMA context, and supporting those coaches who practice in it. To begin to address this gap, we report an initial exploration based upon three interviews with four experienced U.K.-based MMA coaches (12 interviews in total). Via a reflexive thematic analysis we generated four themes: (1) MMA coaches developed their practice via experiential and peer learning; (2) MMA coaches have dual aims of producing competitive athletes while appealing to paying, recreational participants; (3) private event promoters dictate competition dates, meaning preparation time may be suboptimal; and (4) MMA coaches rely on “coach’s eye” and subjective feedback to enact practices in relation to training load, fatigue, and skill development. Coupled with theoretical sensemaking, this novel exploration reveals MMA practices that are grounded in “folk pedagogies,” and shaped by economic imperatives and powerful actors. These findings provide an original and significant analysis of an increasingly prevalent coaching. This approach supplements existing quantitative training studies, thus enabling a pragmatic understanding of the U.K. MMA coaching, while also providing direction for future in-depth studies.
Impact of Reach Height on Estimated Rotator Cuff Compression Risk in Manual Wheelchair Users With Spinal Cord Injury
Authors: Schaffer Kylee M. , Madansingh Stefan I. , Fortune Emma , Morrow Melissa M. , Zhao Kristin D. , Cloud-Biebl Beth A. 
Published: December 2024

Reaching is a common daily activity requiring a range of humeral elevation that contributes to rotator cuff compression. The purpose of this study was to estimate supraspinatus and infraspinatus tendon compression risk relative to the acromion and coracoacromial ligament during reaching by manual wheelchair users with spinal cord injury. A cross-sectional design was used to evaluate 8 participants (7 males, median [range] age 36 y [23–61]). Electromagnetic motion capture recorded shoulder kinematics while participants reached for a can at 2 heights: low (0.91 m) and high (1.37 m). Using 1 set of computed tomographic-based bone models and individual glenohumeral kinematics, compression risk was evaluated as the percentage of the reach activity and number of seconds that tendon insertions were less than 5 mm from scapular landmarks. Reach conditions were compared using a Wilcoxon signed-rank test (α = .05). Although not statistically significant, the supraspinatus and infraspinatus relative to the acromion had approximately 40% of the activity duration or 0.8 seconds more time under 5 mm in low versus high reach, indicating increased risk of compression. Compression risk estimates were consistent with prior publications on planar arm movements. Estimating the risk of tendon compression using absolute time may help with understanding cumulative exposure during day-to-day activity.
Prevalence and features of hypervirulent
Klebsiella pneumoniae
in respiratory specimens at a US hospital system
Authors: McElheny Christi L. , Iovleva Alina , Chen Nathalie , Woods Dominic , Pradhan Akansha , Sonnabend Jonah L. , Matunis Aidan R. , Raabe Nathan J. , Lee Janet S. , Trevejo-Nuñez Giraldina , Van Tyne Daria , Doi Yohei 
Published: December 2024

ABSTRACT

Hypervirulent
Klebsiella pneumoniae
(hvKp) strains are considered to be relatively rare in the United States, but cases are increasingly reported. We prospectively and serially collected
K. pneumoniae
clinical isolates identified in respiratory specimens at a health system in Western Pennsylvania between 2020 and 2022. A total of 273
K
.
pneumoniae
isolates from 216 unique patients were analyzed for markers of hypervirulence by both string test for a hypermucoid phenotype and multiplex PCR to detect isolates carrying cardinal virulence genes
rmpA
,
rmpA2
,
iutA
, and
iro
. Of the 273 isolates, 13 (4.8%) tested positive by string test including 11 nonduplicate
K. pneumoniae
isolates, and two of these (0.7%) were positive by PCR for virulence genes
rmpA
,
rmpA2
,
iutA
, and
iro
. The latter two putative hvKp strains, belonging to sequence types ST23-K1 and ST86-SLV-K2, possessed pLVPK-like plasmids, and were collected from community-associated infections in individuals without known travel histories. Both putative hvKp strains and two additional string test-positive strains were resistant to killing by human serum. The hvKp strains caused significant pneumonia in mice infected by oropharyngeal aspiration, with significantly higher weight loss and increased bacterial burden in the lungs of mice infected with the KL1 (ST23) strain compared to the KL2 (ST86-SLV) strain. We also observed decreased survival of mice infected with the KL1 strain compared to the KL2 strain. These findings add to the growing body of evidence suggesting that hvKp strains, once considered endemic to Asia, may now be circulating in North America.

IMPORTANCE

Certain lineages of
Klebsiella pneumoniae
are increasingly recognized to cause severe community-associated infection, but information on their prevalence in the United States is limited. In a prospective, sequential cohort of 273
K
.
pneumoniae
respiratory isolates, we identified two of them as genetically defined hypervirulent
K. pneumoniae
. The isolates were from local residents who developed community-onset pneumonia, suggesting that hypervirulent
K. pneumoniae
may already be present in the community.
An unusual activity of mycobacterial MutT1 Nudix hydrolase domain as a protein phosphatase regulates nucleoside diphosphate kinase function
Authors: Emam Elhassan Ali Fathi , Roy Koyel , Singh Devendra Pratap , Saini Deepak K. , Varshney Umesh 
Published: December 2024

ABSTRACT

MutT proteins are Nudix hydrolases characterized by the presence of a Nudix box, GX5EX7REUXEEXGU, where U is a bulky hydrophobic residue and X is any residue. Major MutT proteins hydrolyze 8-oxo-(d)GTP (8-oxo-GTP or 8-oxo-dGTP) to the corresponding 8-oxo-(d)GMP, preventing their incorporation into nucleic acids. Mycobacterial MutT1 comprises an N-terminal domain (NTD) harboring the Nudix box motif, and a C-terminal domain (CTD) harboring the RHG histidine phosphatase motif. Interestingly, unlike other MutTs, the MutT1 hydrolyses the mutagenic 8-oxo-(d)GTP to the corresponding 8-oxo-(d)GDP. Nucleoside diphosphate kinase (NDK), a conserved protein, carries out reversible conversion of (d)NDPs to (d)NTPs through phospho-NDK (NDK-
Pi
) intermediate. Recently, we showed that NDK-
Pi
converts 8-oxo-dGDP to 8-oxo-dGTP and escalates A to C mutations in a MutT-deficient
Escherichia coli
. We now show that both
Mycobacterium tuberculosis
MutT1 and
Mycobacterium smegmatis
MutT1, through their NTD (Nudix hydrolase motifs) function as protein phosphatase to regulate the levels of NDK-
Pi
and prevent it from catalyzing conversion of (d)NDPs to (d)NTPs (including conversion of 8-oxo-dGDP to 8-oxo-dGTP). To corroborate this function, we show that
Msm
MutT1 decreases A to C mutations in
E. coli
under the conditions of
Eco
NDK overexpression.

IMPORTANCE

MutT proteins, having a Nudix box domain, hydrolyze the mutagenic 8-oxo-dGTP to 8-oxo-dGMP. However, mycobacterial MutT (MutT1) comprises an N-terminal domain (NTD) harboring a Nudix box, and a C-terminal domain (CTD) harboring an RHG histidine phosphatase. Unlike other MutTs, mycobacterial MutT1 hydrolyses 8-oxo-dGTP to 8-oxo-dGDP. Nucleoside diphosphate kinase (NDK), a conserved protein, converts 8-oxo-dGDP to 8-oxo-dGTP through phospho-NDK (NDK-
Pi
) intermediate and escalates A to C mutations. Here, we show that the mycobacterial MutT1 is unprecedented in that its NTD (Nudix box), functions as protein phosphatase to regulate NDK-
Pi
levels and prevents it from converting dNDPs to dNTPs (including 8-oxo-dGDP to 8-oxo-dGTP conversion). In addition, mycobacterial MutT1 decreases A to C mutations in
Escherichia coli
under the conditions of NDK overexpression.
Lipid a remodeling modulates outer membrane vesicle biogenesis by
Porphyromonas gingivalis
Authors: Alaei Sarah R. , King Alisa J. , Banani Karim , Reddy Angel , Ortiz Joshua , Knight Alexa L. , Haldeman Jessica , Su Thet Hnin , Park Hana , Coats Stephen R. , Jain Sumita 
Published: December 2024

ABSTRACT

Outer membrane vesicles (OMVs) are small membrane enclosed sacs released from bacteria which serve as carriers of biomolecules that shape interactions with the surrounding environment. The periodontal pathogen,
Porphyromonas gingivalis
, is a prolific OMV producer. Here, we investigated how the structure of lipid A, a core outer membrane molecule, influences
P. gingivalis
OMV production, OMV-dependent TLR4 activation, and biofilm formation. We examined mutant strains of
P. gingivalis
33277 deficient for enzymes that alter lipid A phosphorylation and acylation status. The lipid A C4′-phosphatase (
lpxF
)-deficient strain and strains bearing inactivating point mutations in the LpxF active site displayed markedly reduced OMV production relative to WT. In contrast, strains deficient for either the lipid A C1-phosphatase (
lpxE
) or the lipid A deacylase (PGN_1123;
lpxZ
) genes did not display alterations in OMV abundance compared to WT. These data indicate that lipid A C4′-phosphate removal is required for typical OMV formation. In addition, OMVs produced by
ΔlpxF
and
ΔlpxZ
strains, possessing only penta-acylated lipid A, stimulated robust TLR4 activation, whereas OMVs obtained from WT and
ΔlpxE
strains, containing predominantly tetra-acylated lipid A, did not. Hence, lipid A remodeling modulates the capacity of OMVs to engage host TLR4-dependent immunity. Finally, we demonstrate an inverse relationship between OMV abundance and biofilm density, with the
∆lpxF
mutants forming denser biofilms than either WT,
ΔlpxE
, or
ΔlpxZ
strains. Therefore, OMVs may also contribute to pathogenesis by regulating biofilm formation and dispersal.

IMPORTANCE

Porphyromonas gingivalis
is a bacterium strongly associated with periodontitis.
P. gingivalis
exports lipids, proteins, and other biomolecules that contribute to the bacterium’s ability to persist in inflammatory conditions encountered during disease. These biomolecules are exported through several mechanisms, including via outer membrane vesicles (OMVs). Despite their ubiquity, the mechanisms that drive outer membrane vesicle production vary among bacteria and are not fully understood. In this study, we report that C4′ dephosphorylation of lipid A, a major outer membrane molecule, is required for robust outer membrane vesicle production and biological function in
P. gingivalis
. This finding adds to the growing body of evidence that lipid A structure is an important factor in outer membrane vesicle biogenesis in diverse bacterial species.