bluuebunny/crossref_metadata_2025 huggingface dataset:
Biocontrol Efficacy of Bacillus methylotrophicus TA-1 Against Meloidogyne incognita in Tomato
Authors: Liu Huimin , Fu Guanghan , Li Yujie , Zhang Shouan , Ji Xiaoxue , Qiao Kang
Published: February 2023

Root-knot nematodes (RKNs) are harmful plant-parasitic nematodes of tomatoes which can cause significant yield losses. Therefore, there is increasing interest in exploring the application of bacterial nematicides. The bacterium Bacillus methylotrophicus TA-1 is a broad-spectrum biological control agent; however, its effect on RKNs control remains largely unclear. In this study, the toxicity of B. methylotrophicus TA-1 against Meloidogyne incognita was investigated in vitro, and the potential of B. methylotrophicus TA-1 to decrease infection of RKNs in tomato were evaluated in pot and field trials. Results showed that B. methylotrophicus TA-1 exhibited high nematicidal activity against second-stage juveniles (J2s) and eggs of M. incognita with 50% lethal concentration (LC50) values of 5.80 and 7.00 × 108 colony forming units (CFU)/ml, respectively. In the pot experiments and field trials conducted in 2020 and 2021, tomato plants treated with B. methylotrophicus TA-1 soil drench applied once at 3, 6, and 9 × 108 CFU/plant had significantly higher plant height and greater yield compared with the untreated control. Tomato yields of the treated plots with B. methylotrophicus TA-1 in 2 consecutive years’ field trials were between 53.4 to 66.1 and 52.8 to 61.5 t/ha, while they were 49.7 and 48.2 t/ha in the untreated control for each year, respectively. The lowest population densities of M. incognita at 30 and 60 days after treatment were 119 and 135 J2s per 100 g soil in 2020 and 43 and 118 J2s in 2021 in TA-1-treated plots. The lowest gall index of 4.7 and 3.3 in 2020 and 2021, respectively, and the highest yield were all observed in the TA-1 at 9 × 108 CFU/plant treated plants, with no significant differences with the commercial control abamectin. These results provided a basis for further studies of B. methylotrophicus TA-1 formulations, application doses, frequencies, and mechanisms of action, which are necessary before it could be used as a component of integrated management programs to manage RKNs in tomato production.
Establishment of the Recombinase Polymerase Amplification–Lateral Flow Dipstick Detection Technique for Fusarium oxysporum
Authors: Hu Shuodan , Yan Chenyi , Yu Hong , Zhang Yu , Zhang Chuan-Qing
Published: February 2023

Fusarium oxysporum causes crown rot, wilt, root rot, and many other major plant diseases worldwide. During the progression of strawberry crown rot disease, the pathogen is transmitted from the mother plant to the seedling through the stolon, with obvious characteristics of latent infection. Therefore, rapid and timely detection of F. oxysporum is important for efficient disease management. In this study, a recombinase polymerase amplification–lateral flow dipstick (RPA-LFD) detection technique was developed for the rapid detection of F. oxysporum on strawberry plants by targeting the CYP51C gene, which is unique to Fusarium spp. Because this RPA-LFD detection technique was highly specific to F. oxysporum, other Fusarium and non-Fusarium fungi were not detected. The optimal reaction temperature and time for this technique were 39°C and 8 min, respectively. The detection limit was 1 pg of F. oxysporum genomic DNA in a 50-μl reaction system. A total of 46 strawberry plants with or without crown rot symptoms collected from Jiande, Changxing, and Haining in Zhejiang Province were further assessed for F. oxysporum infection using both RPA-LFD and traditional tissue isolation techniques. The RPA-LFD test showed that 32 of the 46 strawberry plants tested were positive for F. oxysporum, while in the traditional isolation technique, F. oxysporum was isolated from 30 of the 46 strawberry plants. These results suggest that our established RPA-LFD method is rapid, sensitive, and highly specific in detecting F. oxysporum infection in strawberry plants.
Chemotaxis and Motility of Spongospora subterranea Zoospores in Response to Potato Root Exudate Constituents and pH
Authors: Amponsah J. , Tegg R. S. , Thangavel T. , Wilson C. R.
Published: February 2023

Spongospora subterranea f. sp. subterranea is an important pathogen of potato responsible for major losses in most potato growing regions of the world. Infection is initiated by biflagellated motile zoospores released from long-lived resting spores. Zoospore chemotaxis to the host plant root is widely believed to be stimulated by host root exudate compounds, although direct evidence is lacking. This study refined the traditional chemotaxis capillary assay, with which we provided the first empirical evidence of S. subterranea zoospore chemotaxis. Individual potato root exudate metabolites were either taxis neutral, inhibitory, or attractant to the zoospores. L-Glutamine was the strongest chemoattractant, while spermine was the most inhibitory. Zoospore motility and chemotaxis were constrained by strongly acidic or alkaline solutions of pH < 5.3 and >8.5, respectively. Beyond pH, ionic constituents of the test solution affected zoospore motility as Sorensen's phosphate buffer stalled zoospore motility, but HEPES buffer at the same concentration and pH had little or no negative motility effect. Zoospore motility, as characterized by several parameters, influenced chemotaxis. Among the parameters measured, total distance traveled was the best predictor of zoospore chemotaxis. The characterization of environmental and ecological effects on zoospore motility and chemotaxis highlights useful targets for S. subterranea disease control through manipulation of zoospore taxis or selection of host resistance traits.
A Compartmental Model for Xylella fastidiosa Diseases with Explicit Vector Seasonal Dynamics
Authors: Giménez-Romero Àlex , Moralejo Eduardo , Matías Manuel A.
Published: February 2023

The bacterium Xylella fastidiosa is mainly transmitted by the meadow spittlebug Philaenus spumarius in Europe, where it has caused significant economic damage to olive and almond trees. Understanding the factors that determine disease dynamics in pathosystems that share similarities can help to design control strategies focused on minimizing transmission chains. Here, we introduce a compartmental model for X. fastidiosa-caused diseases in Europe that accounts for the main relevant epidemiological processes, including the seasonal dynamics of P. spumarius. The model was confronted with epidemiological data from the two major outbreaks of X. fastidiosa in Europe, the olive quick disease syndrome in Apulia, Italy, caused by the subspecies pauca, and the almond leaf scorch disease in Mallorca, Spain, caused by subspecies multiplex and fastidiosa. Using a Bayesian inference framework, we show how the model successfully reproduces the general field data in both diseases. In a global sensitivity analysis, the vector-to-plant and plant-to-vector transmission rates, together with the vector removal rate, were the most influential parameters in determining the time of the infectious host population peak, the incidence peak, and the final number of dead hosts. We also used our model to check different vector-based control strategies, showing that a joint strategy focused on increasing the rate of vector removal while lowering the number of annual newborn vectors is optimal for disease control.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
The Leucine-Rich Repeat Receptor-Like Kinase Protein TaSERK1 Positively Regulates High-Temperature Seedling Plant Resistance to Puccinia striiformis f. sp. tritici by Interacting with TaDJA7
Authors: Shi Yifeng , Bao Xiyue , Song Xiaopan , Liu Yuyang , Li Yuxiang , Chen Xianming , Hu Xiaoping
Published: February 2023

Somatic embryogenesis receptor kinases (SERKs) belong to the leucine-rich repeat receptor-like kinase (LRR-RLK) subfamily, and many LRR-RLKs have been proven to play a key role in plant immune signal transmission. However, the functions of SERKs in resistance to stripe rust caused by Puccinia striiformis f. sp. tritici remains unknown. Here, we identified a gene, TaSERK1, from Xiaoyan 6, a wheat cultivar possessing high-temperature seedling-plant (HTSP) resistance to the fungal pathogen P. striiformis f. sp. tritici and expresses its resistance at the seedling stage. The expression level of TaSERK1 was upregulated upon P. striiformis f. sp. tritici inoculation under relatively high temperatures. The transcriptional level of TaSERK1 was significantly increased under exogenous salicylic acid and brassinosteroids treatments. The barley stripe mosaic virus-induced gene silencing assay indicated that TaSERK1 positively regulated the HTSP resistance to stripe rust. The transient expression of TaSERK1 in tobacco leaves confirmed its subcellular localization on the plasma membrane. Furthermore, TaSERK1 interacted with and phosphorylated the chaperone protein TaDJA7, which belongs to the heat shock protein 40 subfamily. Silencing TaDJA7 compromised the HTSP resistance to stripe rust. The results indicated that when the membrane immune receptor TaSERK1 perceives the P. striiformis f. sp. tritici infection under relatively high temperatures, it transmits the signal to TaDJA7 to activate HTSP resistance to the pathogen.
The remarkable complexity of the brain microbiome in health and disease
Authors: Hu Xinyue , Mckenzie Chris-Anne , Smith Colin , Haas Juergen G. , Lathe Richard
Published: February 2023

Microbes in human brain and their potential contribution to neurodegenerative conditions such as Alzheimer’s disease (AD) have long been debated. We recently developed a new method (the electronic tree of life, eToL) based on small subunit ribosomal RNA (rRNA) probes, further confirmed by large subunit rRNA analysis, to comprehensively address the spectrum of microorganisms in control and AD brain. We report a remarkable diversity of brain microbes in control brain. The most abundant are fungi, bacteria, and chloroplastida, and we report detailed identification of representative microbial species. The pattern is substantially conserved across different bilateran species fromDrosophilato human. In terms of diversity, the human brain microbiome appears to be a subset (~20%) of the gut microbiome. Adenovirus type C was the major virus found in human brain; other viruses were not well represented. However, the spectrum of brain microbes differed between individuals as well as between brain regions examined from single individuals (amygdala, cingulate cortex, hippocampus, hypothalamus); of these four regions, the highest microbial burden was in cingulate cortex. There was evidence of spreading of pathogens between brain regions in single individuals. Some microbes are over-represented in AD brain according to two measures: (i) absolute number of microbes normalized to endogenous human transcripts, and (ii) the number of brain specimens showing overabundance versus control. Species over-represented in AD brain according to both measures notably include bacteria (Streptococcus,Staphylococcus/Bacillus,Sphingomonas/Ralstonia) and fungi (Acrocalymma/Altenaria/Aureobasidiumof theAspergillusgroup;Komagataellaof theCandidagroup,Cortinariusof theSchizophyllumgroup, andTausoniaof theCryptococcusgroup), that are all related to known human pathogens. In addition, an uncharacterized chloroplastida (algae-related) species was more abundant in AD brain samples. Although these findings point to diverse microbial species, indicative of multiple causation, similar absolute levels of bacteria and fungi in AD brain samples could suggest synergy between pathogens. However, it is important to stress that not all AD samples were positive for these microbes, but this could be because the affected brain region(s) was not examined. These findings support the contention that infection, perhaps associated with declining immunity with age, may contribute to AD development.
Aortic regurgitation provokes phenotypic modulation of smooth muscle cells in the normal ascending aorta
Authors: Balint Brittany , Bernstorff Inés García Lascurain , Schwab Tanja , Schäfers Hans-Joachim
Published: February 2023

Background

Aortic complications are more likely to occur in patients with ascending aortic aneurysms and concomitant aortic regurgitation (AR). AR may have a negative impact on the aortic wall structure even in patients with tricuspid aortic valves and absence of aortic dilatation. It is unknown whether smooth muscle cell (SMC) changes are a feature of AR-associated aortic remodeling.

Methods

Non-dilated aortic samples were harvested intra-operatively from individuals with normal aortic valves (n=10) or those with either predominant aortic stenosis (AS; n=20) or AR (n=35). Tissue from each patient was processed for immunohistochemistry or used for the extraction of medial SMCs. Tissue and cells were stained for markers of SMC contraction (alpha-smooth muscle actin; ASMA), synthesis (vimentin) and senescence (p16/p21). Replicative capacity was analyzed in cultured SMCs from AS- and AR-associated aortas. A sub-analysis compared SMCs from individuals with either TAVs or BAVs to rule out the effect of aortic valve morphology.

Results

In aortic tissue samples, AR was associated with decreased ASMA and increased vimentin, p16 and p21 compared to normal aortic valves and AS. In cell culture, SMCs from AR-aortas had decreased ASMA and increased vimentin compared to SMCs from AS-aortas. AR-associated SMCs had increased p16 and p21 expression, and they reached senescence earlier than SMCs from AS-aortas. In AR, SMC changes were more pronounced with the presence of a BAV.

Conclusions

AR itself negatively impacts SMC phenotype in the ascending aortic wall, which is independent of aortic diameter and aortic valve morphology. These findings provide insight into the mechanisms of AR-related aortic remodeling, and they provide a model for studying SMC-specific therapies in culture.
Hypoxia-inducible factor (HIF) activation promotes osteogenic transition of valve interstitial cells and accelerates heart valve calcification in chronic kidney disease (CKD)
Authors: Csiki Dávid Máté , Ababneh Haneen , Tóth Andrea , Lente Gréta , Szöőr Árpád , Tóth Anna , Fillér Csaba , Juhász Tamás , Nagy Béla , Balogh Enikő , Jeney Viktória
Published: February 2023

Aims

Valve calcification (VC) is a widespread complication in chronic kidney disease (CKD) patients on hemodialysis. VC is an active process with the involvement ofin situosteogenic transition of valve interstitial cells (VICs). VC is accompanied by the activation of hypoxia inducible factor (HIF) pathway, but the role of HIF activation in the calcification process remains undiscovered.

Methods and result

Usingin vitroandin vivoapproaches we addressed the role of HIF activation in osteogenic transition of VICs and CKD-associated VC. Elevation of osteogenic (Runx2, Sox9) and HIF activation markers (HIF-1α and HIF-2α) and VC occurred in adenine-induced CKD mice. High phosphate (Pi) induced upregulation of osteogenic (Runx2, alkaline-phosphatase, Sox9, osteocalcin) and hypoxia markers (HIF-1α, HIF-2α, Glut-1), and calcification in VICs. Down-regulation of HIF-1α and HIF-2α inhibited, whereas further activation of HIF pathway by hypoxic exposure (1% O2) or hypoxia mimetics (desferrioxamine, CoCl2, Daprodustat (DPD)) promoted Pi-induced calcification of VICs. Pi augmented the formation of reactive oxygen species (ROS) and decreased viability of VICs, whose effects were further exacerbated by hypoxia. N-acetyl cysteine inhibited Pi-induced ROS production, cell death and calcification under both normoxic and hypoxic conditions. DPD treatment corrected anemia but promoted VC in the CKD mice model.

Conclusions

HIF activation plays a fundamental role in Pi-induced osteogenic transition of VICs and CKD-induced VC. The cellular mechanism involves stabilization of HIF-1α and HIF-2α, increased ROS production and cell death. Targeting the HIF pathways may thus be investigated as a therapeutic approach to attenuate VC.

Translational perspective

One in four hemodialysis-dependent CKD patients on DPD treatment experience a major cardiovascular event during a 2.5-year follow-up period. This work provides a possible explanation for this phenomenon and should initiate further studies to address whether DPD-mediated acceleration of valve calcification triggers the unbeneficial effect of DPD.
Cryo-EM Structure of a Human LECT2 Amyloid Fibril Reveals a Network of Polar Ladders at its Core
Authors: Richards Logan S. , Flores Maria D. , Zink Samantha , Schibrowsky Natalie A. , Sawaya Michael R. , Rodriguez Jose A.
Published: February 2023

ALECT2 is a type of systemic amyloidosis caused by deposition of the leukocyte cell-derived chemotaxin-2 (LECT2) protein in the form of fibrils. In ALECT2, LECT2 fibril deposits can be found in the glomerulus, resulting in renal failure. Affected patients lack effective treatment options outside of renal transplant or dialysis. While the structure of LECT2 in its globular form has been determined by X-ray crystallography, structures of LECT2 amyloid fibrils remain unknown. Using single particle cryo-EM, we now find that human LECT2 forms robust twisting fibrils with canonical amyloid features. At their core, LECT2 fibrils contain two mating protofilaments, the ordered core of each protofilament spans residues 55-75 of the LECT2 sequence. The overall geometry of the LECT2 fibril displays features in line with other pathogenic amyloids. Its core is tightly packed and stabilized by a network of hydrophobic contacts and hydrogen-bonded uncharged polar residues, while its outer surface displays several charged residues. The robustness of LECT2 fibril cores is illustrated by their limited dissolution in 3M urea and their persistence after treatment with proteinase K. As such, the LECT2 fibril structure presents a potential new target for treatments against ALECT2.
Multiplexed Subspaces Route Neural Activity Across Brain-wide Networks
Authors: MacDowell Camden J. , Libby Alexandra , Jahn Caroline I. , Tafazoli Sina , Buschman Timothy J.
Published: February 2023

Cognition is flexible. Behaviors can change on a moment-by-moment basis. Such flexibility is thought to rely on the brain’s ability to route information through different networks of brain regions in order to support different cognitive computations. However, the mechanisms that determine which network of brain regions is engaged are unknown. To address this, we combined cortex-wide calcium imaging with high-density electrophysiological recordings in eight cortical and subcortical regions of mice. Different dimensions within the population activity of each brain region were functionally connected with different cortex-wide ‘subspace networks’ of regions. These subspace networks were multiplexed, allowing a brain region to simultaneously interact with multiple independent, yet overlapping, networks. Alignment of neural activity within a region to a specific subspace network dimension predicted how neural activity propagated between regions. Thus, changing the geometry of the neural representation within a brain region could be a mechanism to selectively engage different brain-wide networks to support cognitive flexibility.
Transcriptomic profiles of stress susceptibility and resilience in the amygdala and hippocampus
Authors: Long Kimberly L. P. , Muroy Sandra E. , Sorooshyari Siamak K. , Ko Mee Jung , Jaques Yanabah , Sudmant Peter , Kaufer Daniela
Published: February 2023

A single, severe episode of stress can bring about myriad responses amongst individuals, ranging from cognitive enhancement to debilitating and persistent anxiety; however, the biological mechanisms that contribute to resilience versus susceptibility to stress are poorly understood. The dentate gyrus (DG) of the hippocampus and the basolateral nucleus of the amygdala (BLA) are key limbic regions that are susceptible to the neural and hormonal effects of stress. Previous work has also shown that these regions contribute to individual variability in stress responses; however, the molecular mechanisms underlying the role of these regions in susceptibility and resilience are unknown. In this study, we profiled the transcriptomic signatures of the DG and BLA of rats with divergent behavioral outcomes after a single, severe stressor. We subjected rats to three hours of immobilization with exposure to fox urine and conducted a behavioral battery one week after stress to identify animals that showed persistent, high anxiety-like behavior. We then conducted bulk RNA sequencing of the DG and BLA from susceptible, resilient, and unexposed control rats. Differential gene expression analyses revealed that the molecular signatures separating each of the three groups were distinct and non-overlapping between the DG and BLA. In the amygdala, key genes associated with insulin and hormonal signaling corresponded with vulnerability. Specifically,Inhbb, Rab31, andNcoa3were upregulated in the amygdala of stress-susceptible animals compared to resilient animals. In the hippocampus, increased expression ofCartpt -which encodes a key neuropeptide involved in reward, reinforcement, and stress responses - was strongly correlated with vulnerability to anxiety-like behavior. However, few other genes distinguished stress-susceptible animals from control animals, while a larger number of genes separated stress-resilient animals from control and stress-susceptible animals. Of these,Rnf112, Tbx19, andUBALD1distinguished resilient animals from both control and susceptible animals and were downregulated in resilience, suggesting that an active molecular response in the hippocampus facilitates protection from the long-term consequences of severe stress. These results provide novel insight into the mechanisms that bring about individual variability in the behavioral responses to stress and provide new targets for the advancement of therapies for stress-induced neuropsychiatric disorders.
Long-term epidemiology and evolution of swine influenza viruses in Vietnam
Authors: Cheung Jonathan , Bui Anh Ngoc , Younas Sonia , Edwards Kimberly M. , Nguyen Huy Quang , Pham Ngoc Thi , Bui Vuong Nghia , Peiris Malik , Dhanasekaran Vijaykrishna
Published: February 2023

Swine influenza virus (SwIV) surveillance in Hanoi, Vietnam from 2013–2019 found gene pool enrichment from imported swine from Asia and North America. Long-term maintenance, persistence and reassortment of SwIV lineages was observed. Co-circulation of H1-δ1a viruses with other SwIV genotypes raises concern due to its zoonotic potential.
Rapid lethality of mice lacking the phagocyte oxidase and Caspase1/11 followingMycobacterium tuberculosisinfection
Authors: Thomas Sean M. , Olive Andrew J.
Published: February 2023

Immune networks that control antimicrobial and inflammatory mechanisms have overlapping regulation and functions to ensure effective host responses. Genetic interaction studies of immune pathways that compare host responses in single and combined knockout backgrounds are a useful tool to identify new mechanisms of immune control during infection. For disease caused by pulmonaryMycobacterium tuberculosisinfections, which currently lacks an effective vaccine, understanding genetic interactions between protective immune pathways may identify new therapeutic targets or disease-associated genes. Previous studies suggested a direct link between the activation of NLRP3-Caspase1 inflammasome and the NADPH-dependent phagocyte oxidase complex during Mtb infection. Loss of the phagocyte oxidase complex alone resulted in increased activation of Caspase1 and IL1β production during Mtb infection, resulting in failed disease tolerance during the chronic stages of disease. To better understand this interaction, we generated mice lacking bothCybb, a key subunit of the phagocyte oxidase, andCaspase1/11. We found thatex vivoMtb infection ofCybb-/-Caspase1/11-/-macrophages resulted in the expected loss of IL1β secretion but an unexpected change in other inflammatory cytokines and bacterial control. Mtb infectedCybb-/-Caspase1/11-/-mice rapidly progressed to severe TB, succumbing within four weeks to disease characterized by high bacterial burden, increased inflammatory cytokines, and the recruitment of granulocytes that associated with Mtb in the lungs. These results uncover a key genetic interaction between the phagocyte oxidase complex and Caspase1/11 that controls protection against TB and highlight the need for a better understanding of the regulation of fundamental immune networks during Mtb infection.
Human Tear Film Protein Sampling Using Soft Contact Lenses
Authors: Roden Robert K. , Zuniga Nathan , Wright Joshua C. , Parkinson David H. , Patil Leena M. , Jiang Fangfang , Burlett Rebecca S. , Rogers Joshua J. , Pittman Jarett T. , Roper Connor O. , Virgin Kenneth L. , Ackroyd P. Christine , Price John C. , Christensen Kenneth A.
Published: February 2023

Human tear protein biomarkers are useful for detecting both ocular and systemic diseases. Unfortunately, existing tear film sampling methods (Schirmer strips [SS] and microcapillary tubes [MCT]) have significant drawbacks. Here we present an alternative tear protein sampling method using soft contact lenses (SCLs). First, we optimized SCL protein samplingin vitro, then performedin vivostudies in 6 human subjects. Using Etafilcon A SCLs and 4M guanidine-HCl for protein removal, we sampled an average of 60±31 μg of protein per eye. We also performed objective and subjective assessments of all sampling methods. Proteomic analysis by mass spectrometry (MS) revealed the majority of proteins were sampled by all methods. However, smaller subsets of unique and shared proteins were identified, particularly for SS and MCT. Additionally, SCLs had reduced levels of reflex tear protein zymogen granule protein 16 homolog B (ZG16B) versus SS and MCT. These experiments demonstrate SCLs as an accessible tear sampling method which may minimize reflex tearing and potentially aid biomarker discovery.

Abstract Figure
Evaluation of Kernel Low-Rank Compressed Sensing in preclinical Diffusion Magnetic Resonance Imaging
Authors: Alves Rodrigues De Souza Diego , Mathieu Hervé , Deloulme Jean-Christophe , Barbier Emmanuel L.
Published: February 2023

Compressed Sensing (CS) is widely used to accelerate clinical diffusion MRI acquisitions, but it remains under-utilized in preclinical settings. In this study, we optimized and compared several CS reconstruction methods for diffusion imaging.

Different undersampling patterns and two reconstruction approaches were evaluated: conventional CS, based on Berkeley Advanced Reconstruction Toolbox (BART-CS) toolbox, and a new Kernel Low-Rank (KLR)-CS, based on Kernel Principal Component Analysis and low-resolution-phase maps. 3D CS acquisitions were performed at 9.4T using a 4-element cryocoil on mice (wild type and aMAP6knockout). Comparison metrics were error and Structural Similarity Index Measure (SSIM) on fractional anisotropy (FA) and mean diffusivity (MD), as well as reconstructions of the anterior commissure and fornix. Acceleration factors (AF) up to 6 were considered.

In the case of retrospective undersampling, the proposed KLR-CS outperformed BART-CS up to AF=6 for FA and MD maps and tractography. For instance, for AF=4, the maximum errors were respectively 8.0% for BART-CS and 4.9% for KLR-CS, considering both FA and MD in the corpus callosum. Regarding undersampled acquisitions, these maximum errors became respectively 10.5% for BART-CS and 7.0% for KLR-CS. This difference between simulations and acquisitions arose mainly from repetition noise, but also from differences in resonance frequency drift, signal-to-noise ratio, and in reconstruction noise. Despite this increased error, fully sampled and AF=2 yielded comparable results for FA, MD and tractography, and AF=4 showed minor faults. Altogether, KLR-CS based on low-resolution-phase maps seems a robust approach to accelerate preclinical diffusion MRI.
Functional binding of PD1 ligands predicts response to anti-PD1 treatment in cancer patients
Authors: Kaufman Bar , Abramov Orli , Yevko Anna , Apple Daria , Shlapobersky Mark , Greenshpan Yariv , Shaco-Levy Ruthy , Roubinov Keren , Liboff Alejandro , Elkabets Moshe , Porgador Angel
Published: February 2023

Accurate predictive biomarkers of response to immune checkpoint inhibitors (ICIs) are required for better stratifying cancer patients to ICI treatments. Here, we present a new concept for a bioassay to predict the response to anti-PD1 therapies, which is based on measuring the binding functionality of PDL1 and PDL2 to their receptor, PD1. In detail, we developed a cell-based reporting system, called the Immuno-checkpoint Artificial Reporter with overexpression of PD1 (IcAR-PD1) and evaluated the PDL1 and PDL2 binding functionality in tumor cell lines, patient-derived xenografts, and in fixed-tissue tumor samples obtained from cancer patients. In a retrospective clinical study, we found that the functionality of PDL1 and PDL2 predicts response to anti-PD1, and functionality of PDL1 binding is a more effective predictor than PDL1 protein expression alone. Our findings suggest that assessing the functionality of ligand binding is superior to staining of protein expression for predicting response to ICIs.

Teaser

Positive clinical response of cancer patients to anti-PD1 therapy can be predicted by measuring the binding activity of PDL1 and PDL2.
Pathogen genetics identifies avirulence/virulence loci associated with barley chromosome 6H resistance in thePyrenophora teresf.teres– barley interaction
Authors: Li Jinling , Wyatt Nathan A. , Skiba Ryan M. , Kariyawasam Gayan K. , Richards Jonathan K. , Effertz Karl , Rehman Sajid , Brueggeman Robert S. , Friesen Timothy L.
Published: February 2023

Barley net form net blotch (NFNB) is a foliar disease caused byPyrenophora teresf.teres. Barley line CIho5791, which harbors the chromosome 6H broad spectrum resistance geneRpt5, displays dominant resistance toP. teresf.teres. To genetically characterizeP. teresf.teresavirulence/virulence on the barley line CIho5791, we generated aP. teresf.teresmapping population using a cross between the Moroccan CIho5791-virulent isolate MorSM40-3, and the avirulent reference isolate 0-1. Genetic maps were generated for all 12 chromosomes (Ch) and quantitative trait locus (QTL) mapping identified two significant QTL associated withP. teresf.teresavirulence/virulence on CIho5791. The most significant QTL mapped toP. teresf.teresCh1 where the virulent allele was contributed by MorSM40-3. A second QTL mapped to Ch8, however, this virulent allele was contributed by 0-1. The Ch1 and Ch8 loci accounted for 27 and 15% of the disease variation, respectively and the avirulent allele at the Ch1 locus was shown to be epistatic over the virulent allele at the Ch8 locus. Additionally, we used 177 sequencedP. teresf.teresisolates in a genome wide association study that identified the same Ch1 and Ch8 loci as the two most significant associations. Within the identified genomic regions, we identified several genes that encoded small secreted proteins, one or more of which may be responsible for overcoming the CIho5791 resistance. Results presented here demonstrate the complexity of avirulence/virulence in theP. teresf.teres- barley interaction.
PI3Kδ inhibition potentiates glucocorticoids in B-lymphoblastic leukemia by decreasing receptor phosphorylation and enhancing gene regulation
Authors: Zimmerman Jessica A.O. , Fang Mimi , Pufall Miles A.
Published: February 2023

Glucocorticoids, including dexamethasone and prednisone, are the cornerstone of B-lymphoblastic leukemia (B-ALL) therapy. Because response to glucocorticoids alone predicts overall outcomes for B-ALL, enhancing glucocorticoid potency is a route to improving outcomes. However, systematic toxicities prevent the use of higher dose and more potent glucocorticoids. We therefore took a functional genomic approach to identify targets to enhance glucocorticoid activity specifically in B-ALL cells. Here we show that inhibition of the lymphoid-restricted PI3Kδ, signaling through the RAS/MAPK pathway, enhances both prednisone and dexamethasone activity in almost allex vivoB-ALL specimens tested. This potentiation is most synergistic at sub-saturating doses of glucocorticoids, approaching the EC50. Potentiation correlates with global enhancement of glucocorticoid-induced gene regulation, including regulation of effector genes that drive B-ALL cell death. Idelalisib reduces phosphorylation of the glucocorticoid receptor (GR) at MAPK1/ERK2 targets S203 and S226, and ablation of these phospho-acceptor sites enhances glucocorticoid potency. We further show that phosphorylation of S226 reduces the affinity of GR for DNAin vitro, which impairs DNA binding. We therefore propose that PI3Kδinhibition improves glucocorticoid efficacy in B-ALL in part by decreasing GR phosphorylation, increasing DNA binding affinity, and enhancing downstream gene regulation. The overall enhancement of GR function suggests that idelalisib will provide benefit to most patients with B-ALL by improving outcomes for patients whose disease is less responsive to glucocorticoid-based therapy, including high-risk disease, and allowing less toxic glucocorticoid-sparing strategies for patients with standard-risk disease.
Mechanically activated bone cells drive vessel formation via an extracellular vesicle mediated mechanism
Authors: Shen N. , Maggio M. , Woods I. , Lowry M. , Eichholz K.F , Stavenschi E. , Hokamp K. , Roche F.M. , O’Driscoll L. , Hoey D.A.
Published: February 2023

Blood vessel formation is an important initial step for bone formation during development as well as during remodelling and repair in the adult skeleton. This results in a heavily vascularized tissue where endothelial cells and skeletal cells are constantly in crosstalk to facilitate homeostasis, a process that is mediated by numerous environment signals, including mechanical loading. Breakdown in this communication can lead to disease and/or poor fracture repair. Therefore, this study aimed to determine the role of mature bone cells in regulating angiogenesis, how this is influenced by a dynamic mechanical environment, and understand the mechanism by which this could occur. Herein, we demonstrate that both osteoblasts and osteocytes coordinate endothelial cell proliferation, migration, and blood vessel formation via a mechanically dependent paracrine mechanism. Moreover, we identified that this process is mediated via the secretion of extracellular vesicles (EVs), as isolated EVs from mechanically stimulated bone cells elicited the same response as seen with the full secretome, while the EV depleted secretome did not elicit any effect. Despite mechanically activated bone cell derived EVs (MA-EVs) driving a similar response to VEGF treatment, MA-EVs contain minimal quantities of this angiogenic factor. Lastly, a miRNA screen identified mechanoresponsive miRNAs packaged within MA-EVs which are linked with angiogenesis. Taken together, this study has highlighted an important mechanism in osteogenic-angiogenic coupling in bone and has identified the mechanically activated bone cell derived EVs as a therapeutic to promote angiogenesis and potentially bone repair.
Clinorotation inhibits myotube formation by fluid motion, not by simulated microgravity
Authors: Mansour Janet , Berwanger Carolin , Jung Marcel , Eichinger Ludwig , Fabry Ben , Clemen Christoph S.
Published: February 2023

To study processes related to weightlessness in ground-based cell biological research, a theoretically assumed microgravity environment is typically simulated using a clinostat – a small laboratory device that rotates cell culture vessels with the aim of averaging out the vector of gravitational forces. Here, we report that the rotational movement during fast clinorotation induces complex fluid motions in the cell culture vessel, which can trigger unintended cellular responses. Specifically, we demonstrate that suppression of myotube formation by 2D-clinorotation at 60 rpm is not an effect of the assumed microgravity but instead is a consequence of fluid motion. Therefore, cell biological results from fast clinorotation cannot be attributed to microgravity unless alternative explanations have been rigorously tested and ruled out. We consider two control experiments mandatory, i) a static, non-rotating control, and ii) a control for fluid motion. These control experiments are also highly recommended for other rotation speed settings and experimental conditions. Finally, we discuss strategies to minimize fluid motion in clinorotation experiments.
Stabilisation of β-Catenin-WNT signalling by USP10 in APC-truncatedcolorectal cancer drives cancer stemness and enables super-competitor signalling
Authors: Reissland Michaela , Hartmann Oliver , Tauch Saskia , Prieto-Garcia Cristian , Schulte Clemens , Solvie Daniel , Loebbert Sinah , Jacomin Anne-Claire , Pesic Marina , Bugter Jeroen M. , Schuelein-Voelk Christina , Fuss Carmina T. , Pahor Nikolet , Ade Carsten , Buck Viktoria , Potente Michael , Li Vivian , Beliu Gerti , Wiegering Armin , Bitman-Lotan Eliya , Grossmann Tom , Rosenfeldt Mathias , Eilers Martin , Maric Hans , Maurice Madelon M. , Greten Florian , Dikič Ivan , Orian Amir , Gallant Peter , Diefenbacher Markus E.
Published: February 2023

The contribution of deubiquitylating enzymes to β-Catenin stabilisation in intestinal stem cells and colorectal cancer (CRC) is poorly understood. Here, we report the deubiquitylase USP10 as an APC-truncation- specific enhancer of β-Catenin stability, potentiating WNT signalling in CRC and cancer stem cells. Mechanistically, interaction studies in various CRC cell lines and in vitro binding studies, together with computational modelling, revealed that USP10 binding to β-Catenin is mediated via the unstructured N-terminus of USP10 and requires the absence of full-length APC. Notably, loss of USP10 in CRISPR engineered intestinal organoids reduces tumorigenic properties of CRC and blocks the super competitor-signalling of APC-mutated CRC. Furthermore, reduction of USP10 induces the expression of differentiation genes, and opposes the APC-truncated phenotype in an intestinal hyperplasia model ofD.melanogaster.

Taken together, our findings reveal USP10s role in intestinal tumourigenesis by stabilising β-Catenin, leading to aberrant WNT signalling, enhancing cancer cell stemness and implicate the DUB USP10 as a cancer specific therapeutic vulnerability inApctruncated CRC.
The ecdysone receptor promotes or suppresses proliferation according to ligand level
Authors: Perez-Mockus Gantas , Cocconi Luca , Alexandre Cyrille , Aerne Birgit , Salbreux Guillaume , Vincent Jean-Paul
Published: February 2023

Steroid hormones control various cellular activities in a context-dependent manner. For example, ecdysone, which acts through a type II nuclear receptor, has seemingly opposite effects in Drosophila wing precursors, promoting proliferation during larval stages, and triggering proliferation arrest at pupariation. We find that wing precursors proliferate normally in the complete absence of the ecdysone receptor (EcR), whether ecdysone is present or not, suggesting that ecdysone overrides a default antiproliferative activity of the receptor. By contrast, termination of proliferation by high concentration of 20E at the end of larval life involves conventional gene regulation by the ligand-receptor complex. The switch from one mode of regulation to the other is determined by ligand level, as measured with a calibrated EcR transcriptional reporter andex vivoproliferation assays. Accordingly, RNA Seq analysis uncovers distinct transcriptional responses to different doses of ecdysone. Some genes are only activated at high doses (high threshold targets) and likely to comprise genes that stop proliferation at pupariation, when ecdysone titres are high. We find that other target genes respond to all physiological concentrations of ecdysone. Some of these genes are known to promote proliferation and could therefore contribute to the pro-proliferation activity of low-level ecdysone. Finally, we show mathematically and with synthetic reporters that relatively simple combinations of regulatory elements can recapitulate the behaviour of both types of target genes.
Proteins with anti-apoptotic action in the hemolymph of caterpillars of the Megalopygidae family acts by maintaining the structure of the cellular cytoskeleton
Authors: de Carvalho Nathalia Delazeri , Rofatto Henrique Krambeck , de Senna Villar Karina , Magnelli Roberta Fiusa , da Silva Junior PI , Mendonça Ronaldo Zucatelli
Published: February 2023

Brazil has a very large biological variety, which is an almost inexhaustible source of substances of pharmacological and biotechnological interest. Several studies have demonstrated the presence of bioactive peptides in insect hemolymph and their potential use as therapeutic agents. However, few data are available regarding molecules extracted from insects with anti-apoptotic action. The objective of this work was to identify and isolate proteins from the hemolymph of caterpillars of theMegalopygidaefamily with pharmacological and biotechnological interest. Two species of this family were studied,Podalia sp and Megalopyge albicolis. Cytotoxicity tests on Vero and Sf-9 cells revealed that the hemolymph of both caterpillars was cytotoxic only at concentrations greater than 5%v/v. In the anti-apoptotic activity assays, it was verified that the supplementation of cell cultures with only 1% of hemolymph v/v is sufficient to inhibit cell death by apoptosis induced by different inducers such as terbutyl, actinomycin D, hydrogen peroxide, or even by nutrient depletion. For this study, cells were stained with trypan blue, crystal violet, and fluorescent markers to cytoskeleton (actin and tubulin), mitochondria membrane electric potential (JC-1), and apoptosis marker (acridine orange and ethidium). The protein responsible for anti-apoptotic action was isolated through gel filtration chromatography, using an AKTA purifier high-resolution liquid chromatography system. The hemolymph was fractionated into 3 pools forPodalia spand 6 pools forM. abicolis. In the antiapoptotic tests, semi-purified hemolymph from both caterpillars showed anti-apoptotic effect in VERO and SF-9 cells, pre-treated with only 1% v/v of hemolymph and induced to death by different and apoptotic inductors. Was observed that the molecule with anti-apoptotic effect is present in pool 3 in both hemolymphs. This protector effect blocked and attenuated the disruption of the cytoskeleton (actin filaments), being that the protective effect also was observed on the integrity of the mitochondrial membrane of SF-9 cells pre-treated with both hemolymphs and treated with the apoptosis inducer Terbutil at concentrations of 25 to 100μM. By acting on the mitochondrial pathway of death by apoptosis, a pathway that can cause disorders and diseases neurodegenerative such as Parkinson’s and Alzheimer’s diseases, substances present in the hemolymph of these and others caterpillars could be good candidates in studies for the treatment of these diseases.
Mitochondrial genome sequencing and analysis of the invasiveMicrostegium vimineum: a resource for systematics, invasion history, and management
Authors: Barrett Craig F. , Ramachandran Dhanushya , Chen Chih-Hui , Corbett Cameron W. , Huebner Cynthia D. , Sinn Brandon T. , Yu Wen-Bin , Suetsugu Kenji
Published: February 2023

Premise of the Research

Plants remain underrepresented among species with sequenced mitochondrial genomes (mitogenomes), due to the difficulty in assembly with short-read technology. Invasive species lag behind crops and other economically important species in this respect, representing a lack of tools for management and land conservation efforts.

Methodology

The mitogenome ofMicrostegium vimineum, one of the most damaging invasive plant species in North America, was sequenced and analyzed using long-read data, providing a resource for biologists and managers. We conducted analyses of genome content, phylogenomic analyses among grasses and relatives based on mitochondrial coding regions, and an analysis of mitochondrial single nucleotide polymorphism in this invasive grass species.

Pivotal Results

The assembly is 478,010 bp in length and characterized by two large, inverted repeats, and a large, direct repeat. However, the genome could not be circularized, arguing against a “master circle” structure. Long-read assemblies with data subsets revealed several alternative genomic conformations, predominantly associated with large repeats. Plastid-like sequences comprise 2.4% of the genome, with further evidence of Class I and Class II transposable element-like sequences. Phylogenetic analysis placedM. vimineumwith otherMicrostegiumspecies, excludingM. nudum, but with weak support. Analysis of polymorphic sites across 112 accessions ofM. vimineumfrom the native and invasive ranges revealed a complex invasion history.

Conclusions

We present an in-depth analysis of mitogenome structure, content, phylogenetic relationships, and range-wide genomic variation inM. vimineum’sinvasive US range. The mitogenome ofM. vimineumis typical of other andropogonoid grasses, yet mitochondrial sequence variation across the invasive and native ranges is extensive. Our findings suggest multiple introductions to the US over the last century, with subsequent spread, secondary contact, long-distance dispersal, and possibly post-invasion selection on awn phenotypes. Efforts to produce genomic resources for invasive species, including sequenced mitochondrial genomes, will continue to provide tools for their effective management, and to help predict and prevent future invasions.
Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance
Authors: Li Fei , Wang Yizhe , Hwang Inah , Jang Ja-Young , Xu Libo , Deng Zhong , Yu Eun Young , Cai Yiming , Wu Caizhi , Han Zhenbo , Huang Yu-Han , Huang Xiangao , Zhang Ling , Yao Jun , Lue Neal F. , Lieberman Paul M. , Ying Haoqiang , Paik Jihye , Zheng Hongwu
Published: February 2023

Telomere length maintenance is essential for cellular immortalization and tumorigenesis. 5% - 10% of human cancers rely on a recombination-based mechanism termed alternative lengthening of telomeres (ALT) to sustain their replicative immortality, yet there are currently no targeted therapies. Through CRISPR/Cas9-based genetic screens in an ALT-immortalized isogenic cellular model, here we identify histone lysine demethylase KDM2A as a molecular vulnerability selectively for cells contingent on ALT-dependent telomere maintenance. Mechanistically, we demonstrate that KDM2A is required for dissolution of the ALT-specific telomere clusters following homology-directed telomere DNA synthesis. We show that KDM2A promotes de-clustering of ALT multitelomeres through facilitating isopeptidase SENP6-mediated SUMO deconjugation at telomeres. Inactivation of KDM2A or SENP6 impairs post-recombination telomere de-SUMOylation and thus dissolution of ALT telomere clusters, leading to gross chromosome missegregation and mitotic cell death. These findings together establish KDM2A as a selective molecular vulnerability and a promising drug target for ALT-dependent cancers.