bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding the LMA needle in the wheat proteome haystack
Authors: Vincent Delphine , Bui AnhDuyen , Ezernieks Vilnis , Shahinfar Saleh , Luke Timothy , Ram Doris , Rigas Nicholas , Panozzo Joe , Rochfort Simone , Daetwyler Hans , Hayden Matthew 
Published: January 2023

AbstractLate maturity alpha-amylase (LMA) is a wheat genetic defect causing the synthesis of high isoelectric point (pI) alpha-amylase in the aleurone as a result of a temperature shock during mid-grain development or prolonged cold throughout grain development leading to an unacceptable low falling numbers (FN) at harvest or during storage. High pI alpha-amylase is normally not synthesized until after maturity in seeds when they may sprout in response to rain or germinate following sowing the next season’s crop. Whilst the physiology is well understood, the biochemical mechanisms involved in grain LMA response remain unclear. We have employed high-throughput proteomics to analyse thousands of wheat flours displaying a range of LMA values. We have applied an array of statistical analyses to select LMA-responsive biomarkers and we have mined them using a suite of tools applicable to wheat proteins. To our knowledge, this is not only the first proteomics study tackling the wheat LMA issue, but also the largest plant-based proteomics study published to date. Logistics, technicalities, requirements, and bottlenecks of such an ambitious large-scale high-throughput proteomics experiment along with the challenges associated with big data analyses are discussed. We observed that stored LMA-affected grains activated their primary metabolisms such as glycolysis and gluconeogenesis, TCA cycle, along with DNA- and RNA binding mechanisms, as well as protein translation. This logically transitioned to protein folding activities driven by chaperones and protein disulfide isomerase, as wellas protein assembly via dimerisation and complexing. The secondary metabolism was also mobilised with the up-regulation of phytohormones, chemical and defense responses. LMA further invoked cellular structures among which ribosomes, microtubules, and chromatin. Finally, and unsurprisingly, LMA expression greatly impacted grain starch and other carbohydrates with the up-regulation of alpha-gliadins and starch metabolism, whereas LMW glutenin, stachyose, sucrose, UDP-galactose and UDP-glucose were down-regulated. This work demonstrates that proteomics deserves to be part of the wheat LMA molecular toolkit and should be adopted by LMA scientists and breeders in the future.
“Self-inhibition of HER2 at fever temperatures may prevent dimerization with HER3”
Authors: Singh Puneet K. , Stan Razvan C. 
Published: January 2023

AbstractBackgroundHER2 receptor is overexpressed in different aggressive and recurrent tumors, and the modulation of its conformational changes has been achieved using immunotherapy or chemotherapy.ObjectiveTo assess the role of fever temperatures on the dynamics of HER2 in the absence of a binding partner.MethodsMolecular dynamics simulations of apo-HER2 were performed at 37□-40□, in order to gauge its intramolecular dynamics.ResultsHER2 assumes an inactive and “bent” conformation at 40□, while it maintains its extended, active conformation that can dimerize with other HER partners, in the 37□-39□ range.ConclusionThese novel results indicate the role of fever temperatures on modulating conformational changes in an essential tumor target. Cancer treatment can leverage the use of thermal therapy at particular fever points, in order to complement existing radio or chemotherapy options.
A New Approach for Active Coronavirus Infection Identification by Targeting the Negative RNA Strand- A Replacement for the Current Positive RNA-based qPCR Detection Method
Authors: Davis Darnell , Ullah Hemayet 
Published: January 2023

AbstractThis manuscript describes the development of an alternative method to detect active coronavirus infection, in light of the current COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic, which was first identified in Wuhan, China in December 2019, has had a significant impact on global health as well as on the economy and daily life in the world. The current positive RNA-based detection systems are unable to discriminate between replicating and non-replicating viruses, complicating decisions related to quarantine and therapeutic interventions. The proposed method targets the negative strand of the virus and has the potential to effectively distinguish between active and inactive infections, which could provide a more accurate means of determining the spread of the virus and guide more effective public health measures during the current pandemic.
Global analysis of aging-related protein structural changes uncovers enzyme polymerization-based control of longevity
Authors: Paukštytė Jurgita , López Cabezas Rosa María , Feng Yuehan , Tong Kai , Schnyder Daniela , Elomaa Ellinoora , Gregorova Pavlina , Doudin Matteo , Särkkä Meeri , Sarameri Jesse , Lippi Alice , Vihinen Helena , Juutila Juhana , Nieminen Anni , Törönen Petri , Holm Liisa , Jokitalo Eija , Krisko Anita , Huiskonen Juha , Sarin L. Peter , Hietakangas Ville , Picotti Paola , Barral Yves , Saarikangas Juha 
Published: January 2023

AbstractAging is associated with progressive phenotypic changes over time. Virtually all cellular phenotypes are produced by proteins and structural alterations in proteins can lead to age-related diseases. Nonetheless, comprehensive knowledge of proteins undergoing structural-functional changes during cellular aging and their contribution to age-related phenotypes is lacking. Here, we conducted proteome-wide analysis of early age-related protein structural changes in budding yeast using limited proteolysis-mass spectrometry. The results, compiled in online ProtAge-catalog, unravelled age-related functional changes in regulators of translation, protein folding and amino acid metabolism. Mechanistically, we found that folded glutamate synthase Glt1 polymerizes into supramolecular self-assemblies during aging causing breakdown of cellular amino acid homeostasis. Inhibiting Glt1 polymerization by mutating the polymerization interface restored amino acid levels in aged cells, attenuated mitochondrial dysfunction and led to life span extension. Altogether, this comprehensive map of protein structural changes enables identifying novel mechanisms of age-related phenotypes and offers opportunities for their reversal.
A planar-polarized MYO6-DOCK7-RAC1 axis promotes tissue fluidification in mammary epithelia
Authors: Menin Luca , Weber Janine , Villa Stefano , Martini Emanuele , Maspero Elena , Cancila Valeria , Maiuri Paolo , Palamidessi Andrea , Frittoli Emanuela , Bianchi Fabrizio , Tripodo Claudio , Walters Kylie J. , Giavazzi Fabio , Scita Giorgio , Polo Simona 
Published: January 2023

Tissue fluidification and collective motility are pivotal in regulating embryonic morphogenesis, wound healing and tumor metastasis. These processes frequently require that each cell constituent of a tissue coordinates its migration activity and directed motion through the oriented extension of lamellipodia cell protrusions, promoted by RAC1 activity. While the upstream RAC1 regulators in individual migratory cells or leader cells during invasion or wound healing are well characterized, how RAC1 is controlled in follower cells remains unknown. Here, we identify a novel MYO6-DOCK7 axis that is critical for spatially restriction of RAC1 activity in a planar polarized fashion in model tissue monolayers. The MYO6-DOCK7 axis specifically controls the extension of cryptic lamellipodia required to drive tissue fluidification and cooperative mode motion in otherwise solid and static carcinoma cell collectives.HighlightsCollective motion of jammed epithelia requires myosin VI activityThe MYO6-DOCK7 axis is critical to restrict the activity of RAC1 in a planar polarized fashionMYO6-DOCK7-RAC1 activation ensures long-range coordination of movements by promoting orientation and persistence of cryptic lamellipodiaMyosin VI overexpression is exploited by infiltrating breast cancer cells
Assessing HLA imputation accuracy in a West African population
Authors: Nanjala Ruth , Mbiyavanga Mamana , Hashim Suhaila , de Villiers Santie , Mulder Nicola 
Published: January 2023

AbstractThe Human Leukocyte Antigen (HLA) region plays an important role in autoimmune and infectious diseases. HLA is a highly polymorphic region and thus difficult to impute. We therefore sought to evaluate HLA imputation accuracy, specifically in a West African population, since they are understudied and are known to harbor high genetic diversity. The study sets were selected from Gambian individuals within the Gambian Genome Variation Project (GGVP) Whole Genome Sequence datasets. Two different arrays, Illumina Omni 2.5 and Human Hereditary and Health in Africa (H3Africa), were assessed for the appropriateness of their markers, and these were used to test several imputation panels and tools. The reference panels were chosen from the 1000 Genomes dataset (1kg-All), 1000 Genomes African dataset (1kg-Afr), 1000 Genomes Gambian dataset (1kg-Gwd), H3Africa dataset and the HLA Multi-ethnic dataset. HLA-A, HLA-B and HLA-C alleles were imputed using HIBAG, SNP2HLA, CookHLA and Minimac4, and concordance rate was used as an assessment metric. Overall, the best performing tool was found to be HIBAG, with a concordance rate of 0.84, while the best performing reference panel was the H3Africa panel with a concordance rate of 0.62. Minimac4 (0.75) was shown to increase HLA-B allele imputation accuracy compared to HIBAG (0.71), SNP2HLA (0.51) and CookHLA (0.17). The H3Africa and Illumina Omni 2.5 array performances were comparable, showing that genotyping arrays have less influence on HLA imputation in West African populations. The findings show that using a larger population-specific reference panel and the HIBAG tool improves the accuracy of HLA imputation in West African populations.Author SummaryFor studies that associate a particular HLA type to a phenotypic trait for instance HIV susceptibility or control, genotype imputation remains the main method for acquiring a larger sample size. Genotype imputation, process of inferring unobserved genotypes, is a statistical technique and thus deals with probabilities. Also, the HLA region is highly variable and therefore difficult to impute. In view of this, it is important to assess HLA imputation accuracy especially in African populations. This is because the African genome has high diversity, and such studies have hardly been conducted in African populations. This work highlights that using HIBAG imputation tool and a larger population-specific reference panel increases HLA imputation accuracy in an African population.
PNAG exopolysaccharide eradication gives neutrophils access toStaphylococcus aureusbiofilm infections
Authors: Kratofil Rachel M. , Randall Trevor E. , Hommes Josefien W. , Sejuty Rehnuma , Chisholm Jessica , Raju Deepa , Vargas Mario , Howell P. Lynne , Pier Gerald B. , Morck Douglas W. , Harrison Joe J. , Kubes Paul 
Published: January 2023

AbstractStaphylococcus aureus(S. aureus) can form biofilms on biotic or abiotic surfaces making biofilm infections a relevant clinical problem. Biofilms can evade immunity and resist antimicrobial treatment, and as such an understanding of biofilm infectionin vivois necessary to inform new therapeutics. Using a mouse model ofS. aureusforeign-body skin infection and intravital microscopy, we imaged the interactions between neutrophils andS. aureusbiofilm. We observed that neutrophils were separated from bacteria by a biofilm matrix composed of the polysaccharide intercellular adhesin (PIA), an exopolysaccharide chemically designated as poly-N-acetylglucosamine (PNAG) that is produced by enzymatic machinery encoded by theicaADBCoperon. Infection withicaADBC-deficient S. aureusstrains led to increased neutrophil infiltration and access to bacteria and resulted in full clearance of infection by 7 days. Moreover, enzymatic treatment with PgaB, which hydrolyzes partially deacetylated PNAG, was shown to disaggregate the biofilm giving neutrophils access into the infection site to improve clearance. Taken together, our results show that PNAG sheltersS. aureusbiofilms from innate host defense, and that targeting the biofilm matrix with glycoside hydrolases is a promising therapeutic avenue to treatS. aureusbiofilm infections.Author SummaryStaphylococcus aureusis a major cause of biofilm-associated infections, which pose a major threat to human health. A biofilm is difficult to treat since bacteria are protected from antimicrobials within an extracellular matrix. This study is the first to show that the PgaB enzyme, a glycoside hydrolase, can disrupt theS. aureusbiofilm matrix in vivo. Disrupting the biofilm matrix with PgaB gives neutrophils access to bacteria for elimination.
YTHDC2 serves a distinct late role in spermatocytes during germ cell differentiation
Authors: Bailey Alexis S. , Fuller Margaret T. 
Published: January 2023

ABSTRACTPost-transcriptional regulation of gene expression by RNA-binding proteins can enhance the speed and robustness of cell state transitions by controlling RNA stability, localization, or if, when or where mRNAs are translated. The RNA helicase YTHDC2 is required to shut down components of the mitotic program to facilitate a proper switch from mitosis to meiosis in mouse germ cells. Here we show that YTHDC2 has a second essential role in promoting meiotic progression in late spermatocytes. Inducing conditional knockout ofYthdc2during the first wave of spermatogenesis, after initiation of meiotic prophase, allowedYthdc2-deficient germ cells to advance to the pachytene stage and properly express many meiotic markers. However, theYthdc2-deficient spermatocytes mis-expressed a number of genes, some up-regulated and some down-regulated, failed to transition to the diplotene stage, then quickly died. Co-immunoprecipitation experiments revealed that YTHDC2 interacts with several RNA-binding proteins in early or late spermatocytes, with many of the interacting proteins, including MEIOC, localizing to granules, similar to YTHDC2. Our findings suggest that YTHDC2 collaborates with other RNA granule components to facilitate proper progression of germ cells through multiple steps of meiosis via mechanisms influencing post-transcriptional regulation of RNAs.SIGNIFICANCE STATEMENTAn effective, robust switch from mitosis to meiosis is essential for the production of gametes in sexually reproducing organisms. The RNA helicase YTHDC2 is required for germ cells to shut down aspects of the mitotic program as they initiate meiotic prophase in the mouse male germline. Here we utilize a timed conditional knockout strategy to show that, in addition to its conserved function in the mitosis-to-meiosis transition, YTHDC2 has a second critical role in promoting the pachytene-to-diplotene transition late in male meiotic prophase. YTHDC2 interacts with several proteins that are also present in RNA granules, including MEIOC, suggesting that YTHDC2 collaborates with RNA granule components to regulate RNAs as germ cells progress from one cell state to the next.
MHC class II antigen presentation by intestinal epithelial cells fine-tunes bacteria-reactive CD4 T cell responses
Authors: Heuberger C. E. , Janney A. , Ilott N. , Bertocchi A. , Pott S. , Gu Y. , Pohin M. , Friedrich M. , Mann E. H. , Pearson C. , Powrie F. M. , Pott J. , Thornton E. , Maloy K. J. 
Published: January 2023

AbstractAlthough intestinal epithelial cells (IECs) can express major histocompatibility complex class II (MHC II), especially during intestinal inflammation, it remains unclear if antigen presentation by IECs favours pro- or anti-inflammatory CD4+T cell responses. Using selective gene ablation of MHC II in IECs and IEC organoid cultures, we assessed the impact of MHC II expression by IECs on CD4+T cell responses and disease outcomes in response to enteric bacterial pathogens. We found that intestinal bacterial infections elicit inflammatory cues that greatly increase expression of MHC II processing and presentation molecules in colonic IECs. Whilst IEC MHC II expression had little impact on disease severity followingCitrobacter rodentiumorHelicobacter hepaticusinfection, using a colonic IEC organoid-CD4+T cell co-culture system, we demonstrate that IECs can activate antigen-specific CD4+T cells in an MHC II-dependent manner, modulating both regulatory and effector Th cell subsets. Furthermore, we assessed adoptively transferredH. hepaticus-specific CD4+T cells during intestinal inflammationin vivoand report that IEC MHC II expression dampens pro-inflammatory effector Th cells. Our findings indicate that IECs can function as non-conventional antigen presenting cells and that IEC MHC II expression fine-tunes local effector CD4+T cell responses during intestinal inflammation.
A network pharmacology approach to assess the comparative pharmacodynamics of pharmaceutical excipient trehalose in human, mouse and rat
Authors: Friend Jack , Kumar Arun HS 
Published: January 2023

AbstractBackgroundTrehalose is used as a pharmaceutical excipient due to its several desirable pharmacokinetic and historically evident safety features. However, information on the pharmacodynamic properties of trehalose is lacking. Hence this study evaluated the comparative pharmacodynamic properties of trehalose using a network pharmacology approach.Materials and methodsThe specific targets of trehalose in human, mouse and rat were identified from the SwissTargetPrediction database, categorised and compared. The expression profile and subcellular localisation of the targets of trehalose in human was identified and correlated with the affinity of trehalose to these targets to assess its impact on the pharmacodynamic properties of trehalose. The affinity of trehalose to its metabolising enzyme in human, mouse, and rat was assessed by molecular docking and compared.ResultsA significant difference in the target categories and target types of trehalose was observed in human, mouse, and rat. The affinity of trehalose to human (66.03 ± 5.1 μM), rat (102.53 ± 11.3 μM) and mouse (42.07 ± 5.3 μM) trehalase was significantly different. Family A G protein coupled receptors were identified as the major target category of trehalose and cyclin dependent kinase 1 was observed as the high affinity target of trehalose in human and mouse. The correlation of target expression and affinity indicated minimal pharmacodynamic influence under physiological conditions.ConclusionThis study reports the selective targets of trehalose relevant to drug discovery and development protocols and highlights the limitations of rodent models in translating pharmacodynamic analysis of trehalose for development of human therapeutics.
Insights into the mechanism of oligodendrocyte protection and remyelination enhancement by the integrated stress response
Authors: Chen Yanan , Quan Songhua , Patil Vaibhav , Kunjamma Rejani B. , Tokars Haley M. , Leisten Eric D. , Chan Jonah , Wong Yvette , Popko Brian 
Published: January 2023

ABSTRACTCNS inflammation triggers activation of the integrated stress response (ISR). We previously reported that prolonging the ISR protects remyelinating oligodendrocytes and promotes remyelination in the presence of inflammation (Chen et al.,eLife, 2021). However, the exact mechanisms through which this occurs remain unknown. Here, we investigated whether the ISR modulator Sephin1 in combination with the oligodendrocyte differentiation enhancing reagent bazedoxifene (BZA) is able to accelerate remyelination under inflammation, and the underlying mechanisms mediating this pathway. We find that the combined treatment of Sephin1 and BZA is sufficient to accelerate early-stage remyelination in mice with ectopic IFN-γ expression in the CNS. IFN-γ, which is a critical inflammatory cytokine in multiple sclerosis (MS), inhibits oligodendrocyte precursor cell (OPC) differentiation in culture and triggers a mild ISR. Mechanistically, we further show that BZA promotes OPC differentiation in the presence of IFN-γ, while Sephin1 enhances the IFN-γ-induced ISR by reducing protein synthesis and increasing RNA stress granule formation in differentiating oligodendrocytes. Finally, the ISR suppressor 2BAct is able to partially lessen the beneficial effect of Sephin1 on disease progression, in an MS mouse model of experimental autoimmune encephalitis (EAE). Overall, our findings uncover distinct mechanisms of action of BZA and Sephin1 on oligodendrocyte lineage cells under inflammatory stress, suggesting that a combination therapy may effectively promote restoring neuronal function in MS patients.
A universal stress protein is essential for the survival ofMycobacterium tuberculosis
Authors: Banerjee Arka , Chakraborty Moubani , Sharma Suruchi , Chaturvedi Ruchi , Bose Avipsa , Biswas Priyanka , Singh Amit , Visweswariah Sandhya S. 
Published: January 2023

ABSTRACTMycobacterium tuberculosisemploys several signaling pathways to regulate its cellular physiology and survival within the host. Mycobacterial genomes encode multiple adenylyl cyclases and cAMP effector proteins, underscoring the diverse ways in which these bacteria utilize cAMP. We have earlier identified universal stress proteins (USP), Rv1636 and MSMEG_3811 inM. tuberculosisandM. smegmatisrespectively, as abundantly expressed, novel cAMP-binding proteins. In this study, we show that these USPs may function to regulate cAMP signaling by direct sequestration of the second messenger. In slow-growing mycobacteria, concentrations of Rv1636 were equivalent to the amounts of cAMP present in the cell, and overexpression of Rv1636 inM. smegmatisincreased levels of ‘bound’ cAMP. Rv1636 is secreted via the SecA2 secretion system inM. tuberculosisbut is not directly responsible for the efflux of cAMP from the cell. Whilemsmeg_3811could be readily deleted from the genome ofM. smegmatis, we find that therv1636gene is essential for growth ofM. tuberculosis, and this functionality depends on the cAMP-binding ability of Rv1636. This is the first evidence of a ‘sink’ for any second messenger in bacterial signaling that would allow mycobacterial cells to regulate the available intracellular ‘free’ pool of cAMP.
Structural and regulatory insights into the glideosome-associated connector fromToxoplasma gondii
Authors: Kumar Amit , Vadas Oscar , Dos Santos Pacheco Nicolas , Zhang Xu , Chao Kin , Darvill Nicolas , Rasmussen Helena Ø. , Xu Yingqi , Lin Gloria , Stylianou Fisentzos A , Pedersen Jan Skov , Rouse Sarah L. , Morgan Marc L. , Soldati-Favre Dominique , Matthews Steve 
Published: January 2023

AbstractThe phylum of Apicomplexa groups intracellular parasites that employ substratedependent gliding motility to invade host cells, egress from the infected cells and cross biological barriers. The glideosome associated connector (GAC) is a conserved protein essential to this process. GAC facilitates the association of actin filaments with surface transmembrane adhesins and the efficient transmission of the force generated by myosin translocation of actin to the cell surface substrate. Here, we present the crystal structure ofToxoplasma gondiiGAC and reveal a unique, supercoiled armadillo repeat region that adopts a closed ring conformation. Characterisation of the membrane binding interface within the C-terminal PH domain as well as an N-terminal fragment necessary for association with F-actin suggest that GAC adopts multiple conformations. A multi-conformational model for assembly of GAC within the glideosome is proposed.