bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP
Authors: Peter Martin F. , Ruland Jan A. , Kim Yeojin , Hendricks Philipp , Siebrasse Jan Peter , Thomas Gavin H. , Kubitscheck Ulrich , Hagelueken Gregor
Published: March 2023

The tripartite ATP-independent periplasmic (TRAP) transporters use an extra cytoplasmic substrate binding protein (SBP) to transport a wide variety of substrates in bacteria and archaea. The SBP can adopt an ‘open’ or ‘closed’ state depending on the presence of substrate. The two transmembrane domains of TRAP transporters form a monomeric elevator whose function is strictly dependent on the presence of a sodium ion gradient. Insights from experimental structures, structural predictions and molecular modeling have suggested a conformational coupling between the membrane elevator and the substrate binding protein. Here, we use a disulfide engineering approach to lock the TRAP transporter HiSiaPQM fromHaemophilus influenzaein different conformational states. The SBP, HiSiaP, was locked in its substrate-bound form and the transmembrane elevator, HiSiaQM, was locked in either its predicted inward- or outward-facing states. We characterized the disulfide-locked variants and used single-molecule total internal reflection fluorescence (TIRF) microscopy to study their interactions. Our experiments demonstrate that the SBP and the transmembrane elevator are indeed ‘conformationally coupled’, meaning that the open and closed state of the SBP recognize specific conformational states of the transporter and vice versa.
Nodule-specific Cu+-chaperone NCC1 is required for symbiotic nitrogen fixation inMedicago truncatularoot nodules
Authors: Navarro-Gómez Cristina , León-Mediavilla Javier , Küpper Hendrik , Rodríguez-Simón Mario , Paganelli-López Alba , Wen Jiangqi , Burén Stefan , Mysore Kirankumar S. , Hussain Bokhari Syed Nadeem , Imperial Juan , Escudero Viviana , González-Guerrero Manuel
Published: March 2023

Cu+-chaperones are a diverse group of proteins that allocate Cu+ions to specific copper-proteins, creating different copper pools targeted to specific physiological processes. Symbiotic nitrogen fixation carried out in legume root nodules indirectly requires relatively large amounts of copper e.g. for energy delivery via respiration, for which targeted copper deliver systems would be required. MtNCC1 is a nodule-specific Cu+-chaperone encoded in theMedicago truncatulagenome, with a N-terminus Atx1-like domain that can bind Cu+with picomolar affinities. This gene is expressed primarily from the late infection zone to the early fixation zone, and is located in the cytosol, associated to plasma and symbiosome membranes, and within nuclei. Consistent with its key role in nitrogen fixation,ncc1mutants have a severe reduction of nitrogenase activity, and a 50% reduction in copper-dependent cytochromecoxidase activity. A subset of the copper-proteome is also affected in the mutant nodules. Many of these proteins can be pulled-down when using a Cu+-loaded N-terminal MtNCC1 moiety as a bait, indicating a role in nodule copper homeostasis and in copper-dependent physiological processes. Overall, these data suggest a pleiotropic role of MtNCC1 in copper delivery for symbiotic nitrogen fixation.
Beyond analytic solution: analysis of FRAP experiments by spatial simulation of the forward problem
Authors: Cowan Ann E. , Loew Leslie M.
Published: March 2023

Fluorescence redistribution after photobleaching (FRAP) is a commonly used method to understand the dynamic behavior of molecules within cells. Analytic solutions have been developed for specific, well-defined models of dynamic behavior in idealized geometries, but these solutions are inaccurate in complex geometries or when complex binding and diffusion behaviors exist. We demonstrate the use of numerical reaction-diffusion simulation approaches using the easily accessible Virtual Cell (VCell) software, to establish methods for analyzing photobleaching data. We show how multiple simulations employing parameter scans and varying bleaching locations and sizes can help to bracket diffusion coefficients and kinetic rate constants. This approach is applied to problems in membrane surface diffusion, diffusion and binding in cytosolic volumes in complex cell geometries, and analysis of diffusion and binding in intracellular liquid droplets.

Statement of Significance

Fluorescence Redistribution After Photobleaching (FRAP) is a widely used experimental method that can reveal important parameters for reaction/diffusion events within cells. However, analytic methods to analyze FRAP experiments are limited to specific geometries and conditions. We demonstrate how spatial numerical simulation methods using the freely available software Virtual Cell can be used to obtain parameter information from FRAP experiments in situations that are not amenable to analytic solutions and that are accessible to most bench biologists.
ATP1A1-linked diseases require a malfunctioning protein product from one allele
Authors: Spontarelli Kerri , Young Victoria C. , Sweazey Ryan , Padro Alexandria , Lee Jeannie , Bueso Tulio , Hernandez Roberto M. , Kim Jongyeol , Katz Alexander , Rossignol Francis , Turner Clesson , Wilczewski Caralynn M. , Maxwell George L. , Holmgren Miguel , Bailoo Jeremy D. , Yano Sho T. , Artigas Pablo
Published: March 2023

Heterozygous germline variants inATP1A1, the gene encoding the α1 subunit of the Na+/K+-ATPase (NKA), have been linked to diseases including primary hyperaldosteronism and the peripheral neuropathy Charcot-Marie-Tooth disease (CMT).ATP1A1variants that cause CMT induce loss-of-function of NKA. This heterodimeric (αβ) enzyme hydrolyzes ATP to establish transmembrane electrochemical gradients of Na+and K+that are essential for electrical signaling and cell survival. Of the 4 catalytic subunit isoforms, α1 is ubiquitously expressed and is the predominant paralog in peripheral axons. Human population sequencing datasets indicate strong negative selection against both missense and protein-nullATP1A1variants. To test whether haploinsufficiency generated by heterozygous protein-null alleles are sufficient to cause disease, we tested the neuromuscular characteristics of heterozygousAtp1a1+/-knockout mice and their wildtype littermates, while also evaluating if exercise increased CMT penetrance. We found thatAtp1a1+/-mice were phenotypically normal up to 18 months of age. Consistent with the observations in mice, we report clinical phenotyping of a healthy adult human who lacks any clinical features of knownATP1A1-related diseases despite carrying a protein-null early truncation variant, p.Y148*. Taken together, these results suggest that a malfunctioning gene product is required for disease induction byATP1A1variants and that if any pathology is associated with protein-null variants, they may display low penetrance or high age of onset.
Induction of T-DNA amplification by retrotransposon-derived sequences
Authors: Dickinson Lauren , Yuan Wenxin , LeBlanc Chantal , Thomson Geoffrey , Wang Siyuan , Jacob Yannick
Published: March 2023

Transformation viaAgrobacterium tumefaciens(Agrobacterium) is the predominant method used to introduce exogenous DNA into plants. Transfer DNA (T-DNA) originating from Agrobacterium can be integrated as a single copy or in concatenated forms in plant genomes, but the mechanisms affecting final T-DNA structure remain unknown. In this study, we demonstrate that the inclusion of retrotransposon (RT)-derived sequences in T-DNA can increase transgene copy number by more than 50-fold inArabidopsis thaliana(Arabidopsis). RT-mediated amplification of T-DNA results in large concatemers in the Arabidopsis genome, which are primarily induced by the long terminal repeats (LTRs) of RTs. T-DNA amplification is dependent on the activity of DNA repair proteins associated with theta-mediated end joining (TMEJ). Finally, we show that T-DNA amplification can increase the frequency of targeted mutagenesis and gene targeting. Overall, this work uncovers molecular determinants that modulate T-DNA copy number in Arabidopsis and demonstrates the utility of inducing T-DNA amplification for plant gene editing.
Movements and habitat selection of a marsupial carnivore in a modified landscape
Authors: Jones Evie M. , Koch Amelia J. , Pay James M. , Mann Dydee F. , Jones Menna E. , Hamede Rodrigo K.
Published: March 2023

Landscape modification is a major threat to carnivores worldwide, but modified landscapes can also provide important habitat for these species, as protected areas alone are insufficient. Understanding how carnivores use modified landscapes, such as production forests, can inform management strategies to improve the value of these landscapes to carnivores. Little is known about habitat selection by marsupial carnivores in production forests, where they occupy a similar ecological niche to their more well-studied eutherian counterparts. We used GPS tracking, Hidden Markov Models, and Manly’s selection ratios to identify the habitat selected in 3 behavioral states by the largest marsupial carnivore, the Tasmanian devil (Sarcophilus harrisii), in a timber plantation-dominated landscape. Behavioral states were approximated as: state 1, resting or feeding at a carcass; state 2, foraging; and state 3, travel. Devils did not show preferences for any of native forest, native grassland, and plantation in any behavioral state. Within plantations, devils preferred a plantation age of 4–7 years (selection ratio [wi] = 1.52). Devils preferred roads (state 1:wi =2.71, state 2:wi= 2.48, state 3:wi= 2.97) and plantation edges (state 1:wi =2.38, state 2:wi= 2.24, state 3:wi= 2.78) in all behavioral states, and moved faster on roads and edges than away from them. Together, our results indicate devils use road and edges for foraging (scavenging and hunting) and travel. No measured habitat variables influenced devil home range size. To support devils in plantation landscapes, we recommend maintaining a heterogeneous landscape of different plantation ages and native remnants and reducing the risk of vehicle collisions by minimizing forestry traffic at night. Tasmanian devils share similar adaptable traits to generalist eutherian carnivore species in their use of modified landscapes. Plantations can provide valuable habitat for this and other threatened predator species.
Common And Distinct Patterns Of Task-Related Neural Activation Abnormalities In Patients With Remitted And Current Major Depressive Disorder: A Systematic Review And Coordinate-Based Meta-Analysis
Authors: Wang Zuxing , Wang Peijia , He Danmei , Yang Lin , Zhu Hongru
Published: March 2023

Whether remitted major depressive disorder (rMDD) and MDD present common or distinct neuropathological mechanisms remains unclear. We performed a meta-analysis of task-related whole-brain functional magnetic resonance imaging (fMRI) using anisotropic effect-size signed differential mapping software to compare brain activation between rMDD/MDD patients and healthy controls (HCs). We included 18 rMDD studies (458 patients and 476 HCs) and 120 MDD studies (3746 patients and 3863 HCs). The results showed that MDD and rMDD patients shared increased neural activation in the right temporal pole and right superior temporal gyrus. Several brain regions, including the right middle temporal gyrus, left inferior parietal, prefrontal cortex, left superior frontal gyrus and striatum, differed significantly between MDD and rMDD. Meta-regression analyses revealed that the percentage of females with MDD was positively associated with brain activity in the right lenticular nucleus/putamen. Our meta-analysis provides useful insights for understanding the potential neuropathology of brain dysfunction in MDD, developing more targeted and efficacious treatment and intervention strategies, and more importantly, providing potential neuroimaging targets for early screening of MDD.
Association between types of physical activity and risk of ischemic heart disease based on US Guidelines: A systematic review and meta-analysis
Authors: Cha Jaewoo , Kim Jeehyun , Hong Kwan
Published: March 2023

Background

Mortality from ischemic heart disease (IHD) is increasing worldwide. There is no available literature regarding the validity of US guidelines for IHD risk reduction through physical exercise. In this meta-analysis, we aimed to measure the effectiveness of US guidelines for physical activity in reducing IHD risk based on the types of exercise.

Methods

Six databases, including MEDLINE, EMBASE, Cochrane Library, CINAHL, Scopus, and Web of Science, were searched from January 1, 2000, to November 6, 2022. The most recent literature search was conducted on November 6, 2022, and only English-language articles were included. Studies designed and conducted on humans on any type of IHD-related physical activity were included. Study outcomes included heterogeneity among the studies, overall effects of all types of physical activity, and IHD risk. The random effects model was measured. A funnel plot was used to assess publication bias.

Results

When the US guidelines for physical activity were not applied, there was a high level of heterogeneity in the effects of physical activity by type, with overall effects of 0.764 (odds ratio [OR], 95% confidence interval [CI]: 0.737–0.795). The effect of physical activity on IHD was 0.593 (OR, 95% CI: 0.489–0.720). No publication bias was observed. After applying the US guidelines for physical activity, there was a low level of heterogeneity in the effects of physical activity by type and an observed OR of 0.515 (95% CI: 0.401–0.662) for myocardial infarction.

Discussion

Each type of exercise had different effects on reducing IHD, and there were certain beneficial results if the US guidelines for physical activity were satisfied.
Unraveling the Interactions between Human DPP4 Receptor, SARS-CoV-2 Variants, and MERS-CoV, converged for Pulmonary Disorders Integrating through Immunoinformatics and Molecular Dynamics
Authors: Roy Arpan Narayan , Mallick Gupta Aayatti , Banerjee Deboshmita , Chakraborty Jaydeb , Raghavendra Pongali B
Published: March 2023

Human coronaviruses like MERS CoV are known to utilize dipeptidyl peptidase 4 (DPP4), apart from angiotensin-converting enzyme 2(ACE2) as potential co-receptor for viral cell entry. DPP4, ubiquitous membrane-bound aminopeptidase is closely associated with elevation of disease severity in comorbidities. In SARS-CoV-2, there is inadequate evidence for combination of spike protein variants with DPP4, and underlying adversity in COVID19. To elucidate this mechanistic basis, we have investigated interaction of spike protein variants with DPP4 through molecular docking and simulation studies. The possible binding interactions between receptor binding domain (RBD) of different spike variants of SARS-CoV-2 and DPP4 have been compared with interactions observed in experimentally determined structure of complex of MERS-CoV with DPP4. Comparative binding affinity confers that Delta-CoV-2:DPP4 shows close proximity with MERS-CoV:DPP4, as depicted from accessible surface area, radius of gyration, number of hydrogen bonding and energy of interactions. Mutation in delta variant, L452R and T478K, directly participate in DPP4 interaction enhancing DPP4 binding. E484K in alpha and gamma variant of spike protein is also found to interact with DPP4. Hence, DPP4 interaction with spike protein gets more suitable due to mutation especially due to L452R, T478K and E484K. Furthermore, perturbation in the nearby residues Y495, Q474 and Y489 is evident due to L452R, T478K and E484K respectively. Virulent strains of spike protein are more susceptible to DPP4 interaction and are prone to be victimized in patients due to comorbidities. Our results will aid the rational optimization of DPP4 as a potential therapeutic target to manage COVID-19 disease severity.
A transcriptional activator effector ofUstilago maydisregulates hyperplasia in maize during pathogen-induced tumor formation
Authors: Zuo Weiliang , Depotter Jasper R. L. , Stolze Sara Christina , Nakagami Hirofumi , Doehlemann Gunther
Published: March 2023

Ustilago maydiscauses common smut in maize, which is characterized by tumor formation in aerial parts of the host. Tumors result from thede novocell division of highly developed bundle sheath and subsequent cell enlargement. However, the molecular mechanisms underlying tumorigenesis are still largely unknown. Here, we characterize theU. maydiseffector Sts2 (Smalltumor onseedlings 2), which promotes the division of hyperplasia tumor cells. Upon infection, Sts2 is translocated into the maize cell nucleus, where it acts as a transcriptional activator, and the transactivation activity is crucial for its virulence function. Sts2 interacts with ZmNECAP1, a yet undescribed plant transcriptional activator, and it activates the expression of several leaf developmental regulators to potentiate tumor formation. Contrary, fusion of a suppressive SRDX-motif to Sts2 causes dominant negative inhibition of tumor formation, underpinning the central role of Sts2 for tumorigenesis. Our results not only disclose the virulence mechanism of a tumorigenic effector, but also reveal the essential role of leaf developmental regulators in pathogen-induced tumor formation.
Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning
Authors: Mahinthichaichan Paween , Liu Ruibin , Vo Quynh N , Ellis Christopher R , Stavitskaya Lidiya , Shen Jana
Published: March 2023

The nation's opioid overdose deaths reached an all-time high in 2021. The majority of deaths are due to synthetic opioids represented by fentanyl. Naloxone, which is an FDA-approved reversal agent, antagonizes opioids through competitive binding at the mu-opioid receptor (mOR). Thus, knowledge of opioid's residence time is important for assessing the effectiveness of naloxone. Here we estimated the residence times of 15 fentanyl and 4 morphine analogs using metadynamics, and compared them with the most recent measurement of the opioid kinetic, dissociation, and naloxone inhibitory constants (Mann, Li et al, Clin. Pharmacol. Therapeut. 2022). Importantly, the microscopic simulations offered a glimpse at the common binding mechanism and molecular determinants of dissociation kinetics for fentanyl analogs. The insights inspired us to develop a machine learning (ML) approach to analyze the kinetic impact of fentanyl's substituents based on the interactions with mOR residues. This proof-of-concept approach is general; for example, it may be used to tune ligand residence times in computer-aided drug discovery.
Myosin VIII and XI isoforms interact withAgrobacteriumVirE2 protein and help direct transport from the plasma membrane to the perinuclear region during plant transformation
Authors: Liu Nana , Lee Lan-Ying , Yu Yanjun , Gelvin Stanton B.
Published: March 2023

VirulentAgrobacteriumstrains transfer single-strand T-DNA (T-strands) and virulence effector proteins into plant cells. VirE2, one of these virulence effectors, enters the plant cell and is thought to bind T-strands, protecting them from nuclease degradation and helping guide them to the nucleus. How VirE2 is trafficked inside the plant cell is not fully understood. Using bimolecular fluorescence complementation,in vitropull-down, yeast two-hybrid, andin vivoco-immunoprecipitation assays, we found that VirE2 binds directly to the cargo binding domains of several myosin VIII family members, and to myosin XI-K. We observed reduced susceptibility of severalArabidopsisactin mutants and a myosinVIII-1/2/a/bquadruple mutant toAgrobacterium-mediated transformation. Expression of cargo binding domains of myosin VIII-1, VIII-2, VIII-A, or VIII-B in transgenic plants inhibitsArabidopsisroot transformation. However, none of the myosin VIII proteins contribute to the intracellular trafficking of VirE2. Expression of myosinVIII-2,-A,-B, but notVIII-1, cDNAs in the myosinVIII-1/2/a/bmutant partially restored transformation. Furthermore, functional fluorescently-tagged VirE2, synthesized in plant cells, relocalized from the cellular periphery into the cytoplasm after delivery of T-strands fromAgrobacterium. Surprisingly, mutation of myosinXI-kand expression of the myosin XI-K cargo binding domain had no effect on transformation, although it blocked VirE2 movement along actin filaments. We hypothesize that myosin VIII proteins facilitate VirE2 tethering to the plasma membrane and are required for efficient localization of VirE2 to membrane sites from which they bind incoming T-strands. Myosin XI-K is important for VirE2 movement through the cytoplasm towards the nucleus.
A rapid method to quantify vein density in C4plants using starch staining
Authors: Simpson Conor J. C. , Singh Pallavi , Sogbohossou Deedi E.O. , Schranz M. Eric , Hibberd Julian M.
Published: March 2023

C4photosynthesis has evolved multiple times in the angiosperms and typically involves alterations to the biochemistry, cell biology and development of leaves. One common modification found in C4plants compared with the ancestral C3state is an increase in vein density such that the leaf contains a larger proportion of bundle sheath cells. Recent findings indicate that there may be significant intra-specific variation in traits such as vein density in C4plants but to use such natural variation for trait-mapping, rapid phenotyping would be required. Here we report a high-throughput method to quantify vein density that leverages the bundle sheath specific accumulation of starch found in C4species. Starch staining allowed high-contrast images to be acquired that permitted image analysis using a MATLAB-based program. The method works for the dicotyledonGynandropsis gynandrawhere significant variation in vein density was detected between natural accessions, and the monocotyledonZea mayswhere no variation was apparent in the genotypically diverse lines assessed. We anticipate this approach will be useful to map genes controlling vein density in C4species demonstrating natural variation for this trait.

One sentence summary

Preferential accumulation of starch in bundle sheath cells of C4plants allows high-throughput phenotyping of vein density.
Knockout of endoplasmic reticulum localized molecular chaperone HSP90.7 impairs seeding development and cellular auxin homeostasis in Arabidopsis
Authors: Noureddine Jenan , Mu Bona , Hamidzada Homaira , Mok Wai Lam , Bonea Diana , Nambara Eiji , Zhao Rongmin
Published: March 2023

The Arabidopsis endoplasmic reticulum localized heat shock protein HSP90.7 modulates tissue differentiation and stress responses; however, complete knockout lines have not been previously reported. In this study, we identified and analyzed a mutant allele,hsp90.7-1, which did not express any protein and showed seedling lethality. Microscopic analyses revealed its essential role in male and female fertility, trichomes and root hairs development, proper chloroplast function, and in apical meristem maintenance and differentiation. Comparative transcriptome and proteome analyses also revealed a role of the protein in a multitude of cellular processes. Particularly, the auxin responsive pathway was specifically down-regulated in thehsp90.7-1mutant seedlings. We measured a much-reduced auxin content in both root and shoot tissues. Through comprehensive histological and molecular analyses, we demonstrated PIN1 and PIN5 expressions were dramatically reduced in the mutant, and the TAA-YUCCA primary auxin biosynthesis pathway was also down-regulated, thus revealing a critical new role of HSP90.7 in the regulation of auxin responses. This study therefore not only fulfilled a gap in understanding the essential role of HSP90 paralogs in eukaryotes, but also provided a mechanistic insight on this molecular chaperone in regulating plant growth and development via modulating cellular auxin homeostasis.
Comparative transcriptomics reveals divergence in pathogen response gene families amongst 20 forest tree species
Authors: Lu Mengmeng , Cao Min , Yang Jie , Swenson Nathan G.
Published: March 2023

Forest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity is key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, we used the RNA-seq data of twenty co-occurring forest trees species from genera includingAcer,Alnus,Amelanchier,Betula,Cornus,Corylus,Dirca,Fraxinus,Ostrya,Populus,Prunus,Quercus,Ribes,Tilia, andUlmussampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant-pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies.
Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem
Authors: Coclet Clement , Sorensen Patrick O. , Karaoz Ulas , Wang Shi , Brodie Eoin L. , Eloe-Fadrosh Emiley A. , Roux Simon
Published: March 2023

Viruses, including phages, impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time, and their response to strong seasonal change in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental DNA and RNA viruses, including phages, across dynamics seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of RNA viruses target fungal hosts and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active phages which changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example replication and host lysis, is sequentially triggered by changes in environmental conditions. Zooming in at the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly it is more beneficial to remain in a lysogenic state. The former was associated with summer months of high and rapid microbial activity, and the latter to winter months of limited and slow host growth. Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. Moving forward, while as our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.
Leaf traits predict performance under varying levels of drought stress in cultivated sunflower (Helianthus annuusL.)
Authors: Earley Ashley M. , Nolting Kristen M. , Burke John M.
Published: March 2023

Drought is a major agricultural challenge and is expected to worsen with climate change. Exploring plant traits and how they respond to drought has the potential to improve understanding of drought tolerance and inform breeding efforts to develop more drought tolerant plants. Given their importance in plant-water relations, we explored variation and plasticity in leaf traits in response to water limitation in cultivated sunflower (Helianthus annuusL.). A set of four sunflower genotypes was grown under four different levels of water availability and leaf vein and stomatal traits were measured along with total biomass (as an indicator of performance), leaf mass per area (LMA), chlorophyll content, and various mass fraction traits related to resource allocation (e.g., leaf, root, and stem mass fraction). Traits exhibited numerous bivariate correlations within treatments that generally followed expectations based on the literature. For example, stomatal size and density were negatively correlated while stomatal density and vein length per area (VLA) were positively correlated. Most traits exhibited substantial plasticity, as evidenced by significant shifts in trait values across environments and multivariate analyses revealed differentiation in trait space across treatment levels. This included an overall reduction in growth/productivity in response to stress, accompanied by a shift in traits relating to gas exchange and hydraulics including stomatal and vein density (increased), stomatal size (decreased), and theoretical gsmax (increased). We found that variation in performance across treatments (estimated as total biomass) can be largely explained by a small number of putatively size-independent traits (i.e., VLA, stomatal length and density and LMA;R2= 0.74). Moreover, on average, more extreme changes in VLA were associated with more extreme decreases in performance across environments. A small number of leaf traits can predict plant performance, with plasticity in VLA being the best predictor of changes in productivity.
Distinct activation mechanisms of β-arrestin 1 revealed by19F NMR spectroscopy
Authors: Zhai Ruibo , Wang Zhuoqi , Chai Zhaofei , Li Conggang , Jin Changwen , Hu Yunfei
Published: March 2023

β-Arrestins (βarrs) are functionally versatile proteins that play critical roles in the G-protein-coupled receptor (GPCR) signaling pathways. While the classical theory of GPCR-mediated βarr activation centers around the formation of a stable complex between βarr and the phosphorylated receptor tail, emerging evidences highlight the indispensable contribution from membrane lipids for many receptors. Due to the intrinsic complexity of βarr conformational dynamics, detailed molecular mechanisms of its activation by different binding partners remain elusive. Herein we present a comprehensive study of the structural changes of βarr1 in critical structural regions during activation using19F NMR method. We demonstrate that phosphopeptides derived from different classes of GPCRs show distinct abilities in inducing βarr1 activation. We further show that the membrane phosphoinositide PIP2independently modulates βarr1 conformational dynamics without displacing its autoinhibitory carboxyl tail, leading to a distinct partially activated state. Our results delineate two activation mechanisms of βarr1 by different binding partners, uncovering a highly multifaceted conformational energy landscape for this protein family.
EhrlichiaWnt short linear motif ligand mimetic deactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis
Authors: Byerly Caitlan D. , Patterson LaNisha L. , Pittner Nicholas A. , Solomon Regina N. , Patel Jignesh G. , Rogan Madison R. , McBride Jere W.
Published: March 2023

Ehrlichia chaffeensisTRP120 effector has evolved short linear motif (SLiM) ligand mimicry to repurpose multiple evolutionarily conserved cellular signaling pathways including Wnt, Notch and Hedgehog. In this investigation, we demonstrate thatE. chaffeensisand recombinant TRP120 deactivate Hippo signaling resulting in activation of Hippo transcription coactivator Yap and target gene expression. Moreover, a homologous 6 amino acid (QDVASH) SLiM shared by TRP120 and Wnt3a/5a ligands phenocopied Yap and β-catenin activation induced byE. chaffeensis,rTRP120 and Wnt5a. Similar Hippo gene expression profiles were also stimulated byE. chaffeensis,rTRP120, SLiM and Wnt5a. Single siRNA knockdown of Hippo transcription co-activator/factors (Yap and TEAD) significantly decreasedE. chaffeensisinfection. Yap activation was abolished in THP-1 Wnt Frizzled-5 (Fzd5) receptor knockout cells (KO), demonstrating Fzd5 receptor dependence. In addition, TRP120 Wnt-SLiM antibody blocked Hippo deactivation (Yap activation). Expression of anti-apoptotic Hippo target geneSLC2A1(encodes glucose transporter 1; GLUT1) was upregulated byE. chaffeensisand corresponded to increased levels of GLUT1. Conversely, siRNA knockdown ofSLC2A1significantly inhibited infection. Higher GLUT1 levels correlated with increased BCL-xL and decreased Bax levels. Moreover, blocking Yap activation with the inhibitor Verteporfin induced apoptosis that corresponded to significant reductions in levels of GLUT1 and BCL-xL, and activation of Bax and Caspase-3 and -9. This study identifies a novel shared Wnt/Hippo SLiM ligand mimetic and demonstrates thatE. chaffeensisdeactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis.
Distinguishing integrated sub-viral fragments from infectious Rubus yellow net virus in Scottish commercial red raspberry cultivars
Authors: McGavin Wendy , Jones Sue , MacFarlane Stuart
Published: March 2023

Short read sequencing of two field-grown plants of red raspberry cv Glen Dee identified sequences derived from Rubus yellow net virus (RYNV). Surprisingly, PCR primers designed to target these sequences amplified RYNV-specific DNA fragments from some high health nuclear stock raspberry plants, previously tested as free from RYNV infection. The complete sequence of a Scottish isolate of RYNV (RYNV LG) was determined and a panel of primers covering the entire virus genome was designed to demonstrate that nuclear stock plants of cultivars Glen Dee, Glen Ericht, Glen Fyne and Glen Moy all contain partial fragments of the RYNV genome as integrated elements but do not contain the entire RYNV genome.

The complete, circular genome of RYNV could be detected in RYNV LG-infected plants by rolling circle amplification but was not detected in Glen Dee plants. Grafting experiments showed that infectious RYNV could be transferred from RYNV LG plants but not from Glen Dee or Glen Moy plants, further demonstrating that these cultivars contain only partial, integrated RYNV elements. Grafting of RYNV LG to the certification-approved indexing speciesR. occidentalis(black raspberry) andR. macraei, showed that RYNV LG induced recognisable symptoms in both plants but thatR. macraeiwas more susceptible and produced more recognizable symptoms. Effective testing for RYNV in high health certified raspberry plants can be achieved by combining graft testing with multifragment PCR.
The zero-leverage policy and family firms
Authors: Fardnia Pedram , Kooli Maher , Kumar Sonal
Published: March 2023

Purpose

The purpose of the study is to examine the zero-leverage (ZL) phenomenon in family and non-family firms.

Design/methodology/approach

The authors consider three hypotheses and empirically test them using a sample of the largest US firms over the 2001–2016 period.

Findings

The authors find that, on average, 19.20% of family firms have zero debt vs 10.42% for non-family firms. The authors also find that family firms strategically choose to be ZL to maintain financial flexibility for future investments and exercise control over the decision-making process, consistent with the hypotheses of financial flexibility and control considerations. However, non-family firms are more likely to have zero debt if they have financial constraints and the credit market does not lend them money at affordable credit rates, consistent with the financial constraint hypothesis.

Originality/value

This paper contributes to different strands of literature. First, the authors contribute to the literature examining family firms' financial decisions. Second, the authors complement previous studies by exploring the reasons for the ZL behavior of family firms compared to non-family firms. The authors also examine the previously unexplored impact of ownership concentration on the ZL question.
Non‐destructive characterization of pulse flours—A review
Authors: Sivakumar Chitra , Findlay Catherine Rui Jin , Karunakaran Chithra , Paliwal Jitendra
Published: March 2023

The consumption of plant‐based proteins sourced from pulses is sustainable from the perspective of agriculture, environment, food security, and nutrition. Increased incorporation of high‐quality pulse ingredients into foods such as pasta and baked goods is poised to produce refined food products to satisfy consumer demand. However, a better understanding of pulse milling processes is required to optimize the blending of pulse flours with wheat flour and other traditional ingredients. A thorough review of the state‐of‐the‐art on pulse flour quality characterization reveals that research is required to elucidate the relationships between the micro‐ and nanoscale structures of these flours and their milling‐dependent properties, such as hydration, starch and protein quality, components separation, and particle size distribution. With advances in synchrotron‐enabled material characterization techniques, there exist a few options that have the potential to fill knowledge gaps. To this end, we conducted a comprehensive review of four high‐resolution nondestructive techniques (i.e., scanning electron microscopy, synchrotron X‐ray microtomography, synchrotron small‐angle X‐ray scattering, and Fourier‐transformed infrared spectromicroscopy) and a comparison of their suitability for characterizing pulse flours. Our detailed synthesis of the literature concludes that a multimodal approach to fully characterize pulse flours will be vital to predicting their end‐use suitability. A holistic characterization will help optimize and standardize the milling methods, pretreatments, and post‐processing of pulse flours. Millers/processors will benefit by having a range of well‐understood pulse flour fractions to incorporate into food formulations.
Thrombocytopenia during avacopan administration: A case report
Authors: Morimoto Nobuhisa , Mori Takayasu , Shioji Shingo , Watanabe Hatsumi , Sakai Keigo , Mori Katsuo , Yamamura Ayumi , Hanioka Asami , Akagi Yuichiro , Fujiki Tamami , Mandai Shintaro , Mori Yutaro , Ando Fumiaki , Susa Koichiro , Iimori Soichiro , Naito Shotaro , Sohara Eisei , Uchida Shinichi
Published: March 2023

Avacopan is a novel C5a receptor antagonist recently approved for the treatment of microscopic polyangiitis and granulomatosis with polyangiitis. To our knowledge, thrombocytopenia induced by avacopan has not been reported. We report a case of a 78‐year‐old man with microscopic polyangiitis who developed rapidly progressive glomerulonephritis (RPGN) and vasculitis neuropathy. After developing RPGN, he was treated with prednisolone, which was ineffective. As the dosage of corticosteroids was decreased, he developed impaired dorsiflexion of the left ankle, tingling and numbness in his feet, consistent with vasculitis neuropathy. After a 3‐day administration of methylprednisolone, we started avacopan and prednisolone 20 mg/d to reduce the corticosteroid dosage. One week after starting avacopan, platelet counts began to decrease, eventually leading to the cessation of the drug. The possibility of thrombotic microangiopathy and heparin‐induced thrombocytopenia was considered unlikely given the clinical course and laboratory studies. After 3 weeks of avacopan cessation, platelet counts began to increase, suggesting avacopan as the most probable cause of thrombocytopenia. Our case highlights the importance of postmarketing surveillance of avacopan to identify its adverse events that were not reported in clinical trials to ensure its safe use. Clinicians should carefully monitor platelet counts when using avacopan.
Systemic lupus erythematosus flare during SARS‐CoV‐2 infection: Report of 3 cases presented during the fourth wave of the pandemic in Colombia
Authors: Naranjo‐Millán Julián Alberto , Bedoya‐Joaqui Vanessa , Cañas Carlos A.
Published: March 2023

Background

The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus has become a worldwide pandemic since first discovered in 2019. Systemic lupus erythematosus (SLE) flare has been reported in the post‐infectious period. In Colombia, the fourth pandemic wave started at the beginning of 2022 when we observed flare of 3 SLE patients during active infection.

Case presentation

We describe 3 patients with inactive SLE, who presented coronavirus disease 2019 and severe flare in early 2022, 2 patients with nephritis and 1 with severe thrombocytopenia. All patients had increase of antinuclear and anti‐DNA antibody titers and complement consumption.

Conclusions

Three cases with SLE flare concomitant with active SARS‐CoV‐2 infection were different from others reported earlier in the pandemic with post‐infectious flare.
What type of rainforest burnt in the South East Queensland's 2019/20 bushfires and how might this impact biodiversity
Authors: Thorley James , Srivastava Sanjeev Kumar , Shapcott Alison
Published: March 2023

Bushfires burnt over 18 million hectares across Australia's east coast, including rainforests, over the spring and summer 2019/2020 period. Rainforest harbours a large percentage of Australia's biodiversity and does not usually burn and therefore understanding the extent and biodiversity implications was a priority. The National Indicative Aggregated Fire Extent Dataset (NIAFED) combined with detailed regional ecosystem (RE) mapping was used to estimate the perimeter and area of each of the burnt rainforest types within South East Queensland (SEQ). Previous biodiversity estimates for each rainforest regional ecosystem type combined with remnant ecosystem mapping data then enabled an assessment of the potential biodiversity impacts of the fires for SEQ rainforest. We found that 12% of the rainforest estate in SEQ was within the burn footprint (29 031 ha) including parts of the UNESCO World Heritage Gondwana Rainforests of Australia. Fifty per cent of the total remnant area of the Endangered rainforest type, semi‐evergreen vine thicket on Mesozoic to Proterozoic igneous rocks (RE: 12.12.17) was potentially burnt. This rainforest type has high diversity. Burn severity analysis found that the rainforest primarily burnt with low severity, however, there were patches of high severity. Accuracy assessment of severity mapping resulted in a weak correlation (0.57) due to the underestimation of ground fires in rainforest. As expected, we found rainforest‐suppressed fires. However, in contrast to expectations, we found the wettest rainforest types and putative past refugia burnt more than other rainforest types. These results suggest that given drought conditions any rainforest could burn, and we can expect that the area of rainforest will contract if both incidences of drought and wildfires increase due to climate change.
Unmet mental health need and subsequent substance use in individuals with a history of depression: Are there differences between metro and nonmetro areas?
Authors: Danek Robin , Blackburn Justin , Greene Marion , Mazurenko Olena , Menachemi Nir
Published: March 2023

Background and Objectives

More than nine million U.S. adults have a co‐occurring mental health and substance use disorder. The self‐medication hypothesis suggests that individuals with unmet need may alleviate the symptoms of their mental illness by using alcohol or drugs. We examine the relationship between unmet mental health need and subsequent substance use among individuals with a history of depression as well as differences in metro and nonmetro areas.

Methods

We used repeated cross‐sectional data from the National Survey on Drug Use and Health (NSDUH), 2015–2018 after identifying individuals with depression in the past year (n = 12,211). We used logistic regressions with interaction terms to examine the association between unmet need for mental health care and substance use by geographic location.

Results

Unmet mental health need was associated with increased use of marijuana (odds ratio [OR] = 1.32, 95% confidence interval [CI]: 1.08–1.64), illicit drugs (OR = 1.75, 95% CI: 1.19–2.58), and prescription drugs (OR = 1.89, 95% CI: 1.19–3.00) among individuals with depression, which did not vary by geographic location. Unmet need was not associated with increased heavy alcohol drinking (OR = 0.87, 95% CI: 0.60–1.26).

Discussion and Conclusions

No differences in substance usage between metro and nonmetro populations were observed for those with an unmet need for mental health care. We found support for the self‐medication hypothesis among individuals with depression with respect to alcohol.

Scientific Significance

We examine whether individuals with depression and unmet care needs are more likely to self‐medicate with substances including prescription drugs. Due to higher unmeet needs in nonmetro areas, we examine whether the likelihood of self‐medication differs in metro and nonmetro areas.
Occupancy and abundance of a West African mangabey species (Cercocebus atysAudebert, 1797) in forest patch habitat
Authors: Laity Kellie , Conway April , Hernandez Sonia M. , Carroll John P. , Ejigu Dessalegn
Published: March 2023

Sooty mangabeys are Old World primates from the Upper Guinea Rainforests of West Africa. They suffer from habitat degradation due to deforestation and hunting for the bush‐meat trade. Tiwai Island and adjacent small islands are a small protected area surrounded by the Moa River that is known for its high diversity of primate species. We evaluated the occupancy and abundance of sooty mangabeys on Tiwai Island and the surrounding islands using camera traps during 2008–2011. Over two seasons, we obtained a naïve occupancy rate of 0.77 for Tiwai Island but only 0.19 for surrounding smaller islands. We used Abundance‐Induced Heterogeneity Model and Royle Repeated Count Model to estimate the abundance of 326 ± 92 (SE) and 530 ± 102 (SE) individuals of sooty mangabeys respectively. Based on these occurrences, sooty mangabeys usually appeared in riparian, mature and young secondary forests. Activity patterns of sooty mangabeys based on circadian patterns of detections confirmed that they were diurnal with several activity peaks during the daylight hours. The results of this study suggest that a viable population of sooty mangabeys still inhabits Tiwai Island and its vicinity, but that their core population is primarily limited to the Tiwai Island reserve. Thus, there is a need to protect the island and its adjacent habitats to ensure the conservation of sooty mangabeys in particular and other primate species in general.