bluuebunny/crossref_metadata_2025_split huggingface dataset:
The post-translational modification landscape of commercial beers
Authors: Kerr Edward D. , Caboche Christopher H. , Pegg Cassandra L. , Phung Toan K. , Viejo Claudia Gonzalez , Fuentes Sigfredo , Howes Mark T. , Howell Kate , Schulz Benjamin L. 
Published: January 2021

AbstractBeer is one of the most popular beverages worldwide. As a product of variable agricultural ingredients and processes, beer has high molecular complexity. We used DIA/SWATH-MS to investigate the proteomic complexity and diversity of 23 commercial Australian beers. While the overall complexity of the beer proteome was modest, with contributions from barley and yeast proteins, we uncovered a very high diversity of post-translational modifications (PTMs), especially proteolysis, glycation, and glycosylation. Proteolysis was widespread throughout barley proteins, but showed clear site-specificity. Oligohexose modifications were common on lysines in barley proteins, consistent with glycation by maltooligosaccharides released from starch during malting or mashing.O-glycosylation consistent with oligomannose was abundant on secreted yeast glycoproteins. We developed and used data analysis pipelines to efficiently extract and quantify site-specific PTMs from SWATH-MS data, and showed incorporating these features into proteomic analyses extended analytical precision. We found that the key differentiator of the beer glyco/proteome was the brewery, with beer from independent breweries having a distinct profile to beer from multinational breweries. Within a given brewery, beer styles also had distinct glyco/proteomes. Targeting our analyses to beers from a single brewery, Newstead Brewing Co., allowed us to identify beer style-specific features of the glyco/proteome. Specifically, we found that proteins in darker beers tended to have low glycation and high proteolysis. Finally, we objectively quantified features of foam formation and stability, and showed that these quality properties correlated with the concentration of abundant surface-active proteins from barley and yeast.
Ecology drives the evolution of diverse siderophore-production strategies in the opportunistic human pathogenPseudomonas aeruginosa
Authors: Figueiredo Alexandre R.T. , Wagner Andreas , Kümmerli Rolf 
Published: January 2021

AbstractBacteria often cooperate by secreting molecules that can be shared as public goods between cells. Because the production of public goods is subject to cheating by mutants that exploit the good without contributing to it, there has been great interest in elucidating the evolutionary forces that maintain cooperation. However, little is known on how bacterial cooperation evolves under conditions where cheating is unlikely of importance. Here we use experimental evolution to follow changes in the production of a model public good, the iron-scavenging siderophore pyoverdine, of the bacteriumPseudomonas aeruginosa. After 1200 generations of evolution in nine different environments, we observed that cheaters only reached high frequency in liquid medium with low iron availability. Conversely, when adding iron to reduce the cost of producing pyoverdine, we observed selection for pyoverdine hyper-producers. Similarly, hyper-producers also spread in populations evolved in highly viscous media, where relatedness between interacting individuals is higher. Whole-genome sequencing of evolved clones revealed that hyper-production is associated with mutations/deletions in genes encoding quorum-sensing communication systems, while cheater clones had mutations in the iron-starvation sigma factor or in pyoverdine biosynthesis genes. Our findings demonstrate that bacterial social traits can evolve rapidly in divergent directions, with particularly strong selection for increased levels of cooperation occurring in environments where individual dispersal is reduced, as predicted by social evolution theory. Moreover, we establish a regulatory link between pyoverdine production and quorum-sensing, showing that increased cooperation at one trait (pyoverdine) can be associated with the loss (quorum-sensing) of another social trait.
AMPK-dependent phosphorylation is required for transcriptional activation of TFEB/TFE3
Authors: Paquette Mathieu , El-Houjeiri Leeanna , Zirden Linda C. , Puustinen Pietri , Blanchette Paola , Jeong Hyeonju , Dejgaard Kurt , Siegel Peter M. , Pause Arnim 
Published: January 2021

AbstractIncreased autophagy and lysosomal activity promote tumor growth, survival and chemo-resistance. During acute starvation, autophagy is rapidly engaged by AMPK activation and mTORC1 inhibition to maintain energy homeostasis and cell survival. TFEB and TFE3 are master transcriptional regulators of autophagy and lysosomal activity and their cytoplasm/nuclear shuttling is controlled by mTORC1-dependent multisite phosphorylation. However, it is not known whether and how the transcriptional activity of TFEB or TFE3 is regulated. We show that AMPK mediates phosphorylation of TFEB and TFE3 on three serine residues, leading to TFEB/TFE3 transcriptional activity upon nutrient starvation, FLCN depletion and pharmacological manipulation of mTORC1 or AMPK. AMPK loss does not affect TFEB/TFE3 nuclear localization nor protein levels but reduces their transcriptional activity. Collectively, we show that mTORC1 specifically controls TFEB/TFE3 cytosolic retention whereas AMPK is essential for TFEB/TFE3 transcriptional activity. This dual and opposing regulation of TFEB/TFE3 by mTORC1 and AMPK is reminiscent of the regulation of another critical regulator of autophagy, ULK1. Surprisingly, we show that chemoresistance is mediated by AMPK-dependent activation of TFEB, which is abolished by pharmacological inhibition of AMPK or mutation of serine 466/467/469 to alanine residues within TFEB. Altogether, we show that AMPK is a key regulator of TFEB/TFE3 transcriptional activity, and we validate AMPK as a promising target in cancer therapy to evade chemotherapeutic resistance.
Baseline Lateral Habenula Firing Rate Negatively Correlates with Increase in Ethanol Intake over Days in Adult Long Evans Rats
Authors: Tandon Shashank 
Published: January 2021

AbstractWhile many adults consume alcohol, yet only some individuals are at a risk to develop alcohol use disorder (AUD). Variability in the risk for alcohol abuse is multifactorial and includes differences in behavioral and neuronal traits. The lateral habenula (LHb) has been shown to mediate aversive state-related behavioral responses. Interestingly, in both humans and rodents, depression-like symptoms are associated with high LHb activity. Additionally, there is a high co-morbidity between major depressive disorder and AUD. However, LHb lesions in rodents increase ethanol intake over time. Thus, we wanted to determine how baseline LHb activity correlates with ethanol intake over days. Specifically, we wanted to test whether individual variation in baseline LHb activity in ethanol-naive rats is related to home-cage ethanol drinking patterns. Hence, in this study, we determined the correlation between individual variability in baseline LHb neural activity, the negative-affective state-related ultrasonic vocalizations (USVs; 22-28 kHz), and the extent of ethanol intake over days. We first surgically implanted a unilateral 16-wire electrode array in the LHb of adult male Long Evans rats (n=11). Following recovery from surgery, rats were placed in sound-insulated chambers for two hours, where they were free to explore while we simultaneously recorded neuronal signals from their LHb and the USVs emitted by them. Next, these rats underwent an intermittent access to ethanol (IAE) paradigm, where they received 20% ethanol for 24 hours on alternate days (Monday-Wednesday-Friday) and ad-libitum water in their home cages for four weeks. The change in ethanol intake over days differed between rats, with some rats escalating their ethanol intake in the four weeks, while other rats showing no meaningful change in ethanol intake over days as compared to the first session. We found a significant negative correlation between average baseline LHb firing rates in rats and the changes in ethanol intake in the first week of IAE. Specifically, rats with higher baseline LHb firing rats, unlike rats with lower baseline firing rates, did not escalate their ethanol intake from the first session to the second and fourth ethanol sessions of the IAE paradigm. We also found a moderate positive correlation between the number of 22-28 kHz USVs and the average LHb firing rates of these rats. These results indicate that higher baseline LHb neuronal activity in normal adult ethanol naive rats is associated with decreased motivation to seek and consume ethanol during the early stages of ethanol consumption.
A noncanonical FLT3 gatekeeper mutation disrupts gilteritinib binding and confers resistance
Authors: Joshi Sunil K. , Sharzehi Setareh , Pittsenbarger Janét , Bottomly Daniel , Tognon Cristina E. , McWeeney Shannon K. , Druker Brian J. , Traer Elie 
Published: January 2021

ABSTRACTThe recent FDA approval of the FLT3 inhibitor, gilteritinib, for AML represents a major breakthrough for treatment of FLT3 mutated AML. However, patients only respond to gilteritinib for 6-7 months due to the emergence of drug resistance. Clinical resistance to gilteritinib is often associated with expansion of NRAS mutations, and less commonly via gatekeeper mutations in FLT3, with F691L being the most common. We developed anin vitromodel that charts the temporal evolution of resistance to gilteritinib from early microenvironmental-mediated resistance to late intrinsic resistance mutations. Our model system accurately recapitulates the expansion of NRAS mutations and the F691L gatekeeper mutations found in AML patients. As part of this study, we also identified a novel FLT3N701Kmutation that also appeared to promote resistance to gilteritinib. Using the Ba/F3 system, we demonstrate that N701K mutations effectively act like a gatekeeper mutation and block gilteritinib from binding to FLT3, thereby promoting resistance. Structural modeling of FLT3 reveals how N701K, and other reported gilteritinib resistance mutations, obstruct the gilteritinib binding pocket on FLT3. Interestingly, FLT3N701Kdoes not block quizartinib binding, suggesting that FLT3N701Kmutations are more specific for type 1 FLT3 inhibitors (gilteritinib, midostaurin, and crenolanib). Thus, our data suggests that for the FLT3N701Kmutation, switching classes of FLT3 inhibitors may restore clinical response. As the use of gilteritinib expands in the clinic, this information will become critical to define clinical strategies to manage gilteritinib resistance.
Production of functional oocytes requires maternally expressedPIWIgenes and piRNAs in golden hamsters
Authors: Hasuwa Hidetoshi , Iwasaki Yuka W. , Wan Kin Au Yeung , Ishino Kyoko , Masuda Harumi , Sasaki Hiroyuki , Siomi Haruhiko 
Published: January 2021

AbstractMany animals have a conserved adaptive genome defense system known as the Piwi-interacting RNA (piRNA) pathway which is essential for germ cell development and function. Disruption of individual mousePiwigenes results in male but not female sterility, leading to the assumption thatPIWIgenes play little or no role in mammalian oocytes. Here, we report generation ofPIWI-defective golden hamsters, which reveals defects in the production of functional oocytes. The mechanisms involved vary among the hamsterPIWIgenes; lack ofPIWIL1has a major impact on gene expression, including hamster-specific young transposon de-silencing, whereasPIWIL3deficiency has little impact on gene expression in oocytes, although DNA methylation was found to be reduced to some extent inPIWIL3-defecient oocytes. Our findings serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes, including humans, which is not possible with mice.
Selection and Validation of Reference Genes Desirable for Gene Expression Analysis by qRT-PCR on Seed Germination ofCastanea henryi
Authors: Liu Bin , Jiang Yuting , Lin Ruqiang , Xiong Yuanfang , Jiang Shuzhen , Lian Hui , Liu Xuedie , Liu Zhong-Jian , Chen Shipin 
Published: January 2021

AbstractSeed germination is the beginning of the plant’s life cycle, and seed biology is one of the most extensively researched areas in plant physiology, however,Castanea henryias an important seed plant, the stable internal reference gene during germination is not clear. In this study, seven candidate genes (TUA, TUB, TIF, UBC, RPL21, RPL30, RPL34) were screened out from transcriptome data, we analyzed the expression of seven candidate reference genes inC. henryiat different germination stages with RT–qPCR, and using common algorithms including NormFinder, geNorm and BestKeeper to evaluate the candidate genes stability. The results showed that RPL34 and RPL30 were selected as the most stable genes by NormFinder; TIF was the most stable gene identified by BestKeeper; RPL34 and RPL21 were the most stable genes ranked by geNorm, and TUB was the most unstable gene identified by all of the three software. The RPL34 gene was used as the reference gene, to detected the expression trend of two starch synthetase genes SS1 and SS2 during germination by RT–qPCR, the results of RT–qPCR and transcriptome sequencing were basically consistent, which verified the stability of RPL34 candidate gene. Our result is not only showed functional genes for germination ofC. henryiseeds and provide useful guidelines for the selection of reliable reference genes for the normalization of RT– qPCR data for germination of seed plants.
Gas6 drives Zika virus-induced neurological complications in humans and congenital syndrome in immunocompetent mice
Authors: Silva-Filho Joao Luiz , de Oliveira Lilian Gomes , Monteiro Leticia , Parise Pierina L. , Zanluqui Nagela G. , Polonio Carolina M. , de Freitas Carla Longo , Toledo-Teixeira Daniel A. , Souza William M. , Bittencourt Najara , Amorim Mariene R. , Forato Julia , Muraro Stéfanie Primon , de Souza Gabriela Fabiano , Martini Matheus Cavalheiro , Bispos-dos-Santos Karina , Judice Carla C. , Costa Maria Laura , Angerami Rodrigo N. , Freitas André R. R. , Resende Mariangela R. , Garcia Márcia T. , Moretti Maria Luiza ,   The Zika-Unicamp Network, Renia Laurent , Ng Lisa F. P. , Rothlin Carla V. , Costa Fabio TM , Schatzmann Peron Jean Pierre , Proença-Modena José Luiz 
Published: January 2021

ABSTRACTZika virus (ZIKV) has the ability to cross placental and brain barriers, causing congenital malformations in neonates and neurological disorders in adults. However, the pathogenic mechanisms of ZIKV-induced neurological complications in adults and congenital malformations remain unknown. Gas6 is a soluble TAM receptor ligand able to promote flavivirus internalization and downregulation of immune responses. Here we demonstrate high Gas6 levels in the serum of patients with neurological complications which correlated with downregulation of genes associated with the type I IFN responses as consequence ofSocs1upregulation. Gas6 gamma-carboxylation is essential for ZIKV replication in monocytes, the main source of this protein. Gas6 also facilitates ZIKV replication in adult immunocompetent mice enabled susceptibility to transplacental infection and congenital malformations. Our data thus indicate that ZIKV promotes the upregulation of its ligand Gas6, which contributes to viral infectivity and drives the development of severe adverse outcomes during ZIKV infection.
Enhanced Cas12a multi-gene regulation using a CRISPR array separator
Authors: Magnusson Jens P. , Rios Antonio R. , Wu Lingling , Qi Lei S. 
Published: January 2021

AbstractThe type V-A Cas12a protein can process its CRISPR array, a feature useful for multiplexed gene editing and regulation. However, CRISPR arrays often exhibit unpredictable performance due to interference between multiple crRNAs. Here, we report that Cas12a array performance is hypersensitive to the GC content of crRNA spacers, as high-GC spacers can impair activity of the downstream crRNA. We analyzed naturally occurring CRISPR arrays and observed that repeats always contain an AT-rich fragment that separates crRNAs; we term this fragment aCRISPR separator.Inspired by this observation, we designed short, AT-rich synthetic separators (synSeparators) that successfully removed the disruptive effects between crRNAs. We demonstrate enhanced simultaneous activation of seven endogenous genes in human cells using an array containing the synSeparator. These results elucidate a previously unknown feature of natural CRISPR arrays and demonstrate how nature-inspired engineering solutions can improve multi-gene control in mammalian cells.
A robust method to isolateDrosophilafat body nuclei for transcriptomic analysis
Authors: Gupta Vanika , Lazzaro Brian P. 
Published: January 2021

ABSTRACTGene expression profiles are typically described at the level of the tissue or, often inDrosophila, at the level of the whole organism. Collapsing the gene expression of entire tissues into single measures averages over potentially important heterogeneity among the cells that make up that tissue. The advent of single-cell RNA-sequencing technology (sc-RNAseq) allows transcriptomic evaluation of the individual cells that make up a tissue. However, sc-RNAseq requires a high-quality suspension of viable cells or nuclei, and cell dissociation methods that yield healthy cells and nuclei are still lacking for many important tissues. The insect fat body is a polyfunctional tissue responsible for diverse physiological processes and therefore is an important target for sc-RNAseq. TheDrosophilaadult fat body consists of fragile cells that are difficult to dissociate while maintaining cell viability. As an alternative, we developed a method to isolate single fat body nuclei for RNA-seq. Our isolation method is largely free of mitochondrial contamination and yields higher capture of transcripts per nucleus compared to other nuclei preparation methods. Our method works well for single cell nuclei sequencing and potentially can be implemented for bulk RNA-seq.
Targeted knockdown of the PAF49 component of the PAF53/PAF49 heterodimer causes the degradation of PAF53
Authors: McNamar Rachel , Rothblum Katrina , Rothblum Lawrence I. 
Published: January 2021

AbstractThere are significant differences in the components of the ribosomal DNA transcription apparatuses of yeast and mammals. Moreover, the patterns of regulation between mammals and yeast are also different. To overcome, deficits in our understanding of mammalian rDNA transcription, we have developed a system to introduce an inducible degron into the endogenous genes of mammalian cells. This allows us to combine a knock out the endogenous gene product and replace it with mutant proteins in order to study their function in ribosomal DNA transcription. Using this system, we show that the knockout of PAF49, the mammalian ortholog of yeast A34, results in the relatively rapid degradation of PAF53, the ortholog of yeast A49. Interestingly, the steady-state levels of the core subunits of RNA polymerase I are unaffected.
Evaluation of solubility and histological effect of 11-keto-β-Boswellic acid on the diabetic mice liver using FTIR-PCA analysis and microscopy
Authors: Al-Amri I.S. , Mabood F. , Kadim I.T. , Alkindi A.Y. , Al-Harrasi A. , Al-Hashmi S. , Abbas G. , Ahmed B. , Al-Shuhaimi J. , Khalaf S.K. , Shaikh J. 
Published: January 2021

ABSTRACTThis study was designed to develop a rapid, sensitive, accurate, and inexpensive Fourier Transform Infrared Reflectance (FT-IR) Spectroscopy coupled with Principle Component Analysis (PCA) as a detection technique to evaluate the solubility of 11-Keto-β-Boswellic acid (KBA), from the gum resin extracted from the Omani frankincense, (Boswellia sacra) in the liver of STZ induced diabetic mice. This study also investigated the effect of KBA on the histological changes of hepatocytes of diabetic mice. Liver tissue samples from three groups of mice included normal control group, diabetic control group and diabetic group treated IP with KBA were scanned with FT-IR spectrophotometer in the reflection mode. FT-IR Spectra were collected in the wavenumber range from 400 to 4000cm-1using ATR accessorry. The results of FT-IR Spectra were analyzed by using multivariate method Principle Component Analysis. The PCA score plot is an exploratory multivariate method indicated that there was a complete segregation among the three groups of liver samples based on change in variation of position of wavenumber in FT-IR spectra, which revealed that there is a clear effect of KBA solubility on treatments. The histological features showed an improvement in the liver tissues with normal structures of hepatocytes with exhibiting mild vacuolations in their cytoplasm. In conclusion, reflectance FT-IR spectroscopy coupled with PCA could be deployed as a new detection method for rapid, low cost and non-destructive method for evaluating of treatment effects in diseased liver tissue based on the solubility of KBA. Histological findings demonstrated the protective effective of KBA on improving the morphology of liver tissue in diabetic mice which resulted in complete recovery to the damage observed in diabetic control group.Summary StatementReflectance FT-IR spectroscopy coupled with PCA has been deployed as a new rapid, inexpensive and non-destructive detection method to examine the solubility of 11-keto-β-Boswellic acid (KBA) in streptozotocin (STZ) induced-diabetes mice liver tissue following intraperitoneal treatment. Moreover, microscopic study of liver tissue histopathology revealed that KBA has a protecting effect against STZ damage.
Aureochromes are necessary for maintaining polyunsaturated fatty acid content inNannochloropsis oceanica
Authors: Poliner Eric , Busch Andrea W. U. , Newton Linsey , Kim Young Uk , Clark Rachel , Gonzalez-Martinez Sofía C. , Jeong Byeong-ryool , Montgomery Beronda L. , Farré Eva M. 
Published: January 2021

ABSTRACTNannochloropsis oceanica, as other stramenopile microalgae, is rich in long-chain polyunsaturated fatty acids (LC-PUFA) such as eiconsapentaenoic acid (EPA). We observed that fatty acid desaturases (FAD) involved in LC-PUFA biosynthesis were among the strongest blue light induced genes inN. oceanicaCCMP1779. Blue light was also necessary for maintaining LC-PUFA levels in CCMP1779 cells, and growth under red light led to a reduction in EPA content. Aureochromes are stramenopile specific proteins that contain a light-oxygen-voltage-sensing (LOV) domain that associates with a flavin mononucleotide and is able to sense blue light. These proteins also contain a bZIP DNA binding motif and can act as blue light regulated transcription factors by associating with a E-box like motif, which we found enriched in the promoters of blue light induced genes. We demonstrated that,in vitro, two CCMP1779 aureochromes were able to absorb blue light. Moreover, the loss or reduction of any of the three aureochromes led to a decrease in the blue light specific induction of several FADs in CCMP1779. EPA content was also significantly reduced inNoAureo2 andNoAureo4 mutants. Taken together, our results indicate that aureochromes mediate blue light dependent regulation of LC-PUFA content inN. oceanicaCCMP1779 cells.