bluuebunny/crossref_metadata_2025_split huggingface dataset:
A WAX INDUCER1/SHINE transcription factor controls cuticular wax in barley
Authors: McAllister Trisha , Campoli Chiara , Eskan Mhmoud , Liu Linsan , McKim Sarah M. 
Published: March 2022

AbstractAll land plants seal their above ground body parts with a lipid-rich hydrophobic barrier called the cuticle that protects tissues from dehydration and other terrestrial threats. Mutational studies in several model species, including barley, have resolved multiple loci regulating cuticular metabolism and development. Of particular importance are the eceriferum (cer) mutants characterized by visual alterations in cuticular wax. In barley, some cer mutants, such as cer-x lines, show defects in the distinctive β-diketone-enriched wax bloom on reproductive stage leaf sheaths, stems and spikes. In our study we exploited extensive allelic populations, near-isogenic lines and powerful genotyping platforms to identify variation in the HvWAX INDUCER1 (HvWIN1) gene as causal for cer-x mutants. We show that HvWIN1 function reduces cuticular permeability, promotes the accumulation of β-diketones, and regulates cuticular metabolic gene expression. Analyses across the barley pangenome and hundreds of exome-capture datasets revealed high sequence conservation of HvWIN1 but also two non-synonymous variants exclusive to cultivated germplasm. Taken together, we suggest that variation in HvWIN1 controls multiple cuticular features in barley by controlling the expression of genes involved in cuticle development.
Robust high-throughput phenotyping with deep segmentation enabled by a web-based annotator
Authors: Yuan Jialin , Kaur Damanpreet , Zhou Zheng , Nagle Michael , Kiddle Nicholas George , Doshi Nihar A. , Behnoudfar Ali , Peremyslova Ekaterina , Ma Cathleen , Strauss Steven H. , Fuxin Li 
Published: March 2022

AbstractThe abilities of plant biologists and breeders to characterize the genetic basis of physio-logical traits is limited by their abilities to obtain quantitative data representing precise details of trait variation, and particularly to collect this data at a high-throughput scale at low cost. Although deep learning methods have demonstrated unprecedented potential to automate plant phenotyping, these methods commonly rely on large training sets that can be time-consuming to generate. Intelligent algorithms have therefore been proposed to enhance the productivity of these annotations and reduce human efforts. We propose a high-throughput phenotyping system which features a Graphical User Interface (GUI) and a novel interactive segmentation algorithm: Semantic-Guided Interactive Object Segmentation (SGIOS). By providing a user-friendly interface and intelligent assistance with annotation, this system offers potential to streamline and accelerate the generation of training sets, reducing the effort required by the user. Our evaluation shows that our proposed SGIOS model requires fewer user inputs compared to the state-of-art models for interactive segmentation. As a case study in the use of the GUI applied for genetic discovery in plants, we present an example of results from a preliminary genome-wide association study (GWAS) ofin plantaregeneration inPopulus trichocarpa(poplar). We further demonstrate that the inclusion of semantic prior map with SGIOS can accelerate the training process for future GWAS, using a sample of a dataset extracted from a poplar GWAS ofin vitroregeneration. The capabilities of our phenotyping system surpass those of humans unassisted to rapidly and precisely phenotype our traits of interest. The scalability of this system enables large-scale phenomic screens that would otherwise be time-prohibitive, thereby providing increased power for GWAS, mutant screens, and other studies relying on large sample sizes to characterize the genetic basis of trait variation. Our user-friendly system can be used by researchers lacking a computational background, thus helping to democratize the use of deep segmentation as a tool for plant phenotyping.
Oligomer-to-Monomer Transition Underlies the Chaperone Function of AAGAB in AP1/AP2 Assembly
Authors: Tian Yuan , Datta Ishara , Yang Rui , Wan Chun , Wang Bing , He Huan , Li Suzhao , Shen Jingshi , Yin Qian 
Published: March 2022

AbstractAssembly of protein complexes is facilitated by assembly chaperones. Alpha and gamma adaptin binding protein (AAGAB) is a chaperone governing the assembly of the heterotetrameric adaptor complexes 1 and 2 (AP1 and AP2) involved in clathrin-mediated membrane trafficking. Here, we found that before AP1/2 binding, AAGAB exists as a homotetramer. AAGAB tetramerization is mediated by its C-terminal domain, which is critical for AAGAB stability and is missing in mutant proteins found in patients with the skin disease punctate palmoplantar keratoderma type 1 (PPKP1). We solved the crystal structure of the tetramerization domain (TD), revealing a dimer of dimer assembly. Interestingly, AAGAB uses the same TD to recognize and stabilize the γ subunit in the AP1 complex and the α subunit in the AP2 complex, forming binary complexes containing only one copy of AAGAB. These findings demonstrate a dual role of TD in stabilizing resting AAGAB and binding to substrates, providing a molecular explanation for disease-causing AAGAB mutations. The oligomerization state transition mechanism may also underlie the functions of other assembly chaperones.
In vitro susceptibility to β-lactam antibiotics and viability of Neisseria gonorrhoeae strains producing plasmid-mediated broad- and extended-spectrum β-lactamases
Authors: Kandinov Ilya , Gryadunov Dmitry , Vinokurova Alexandra , Antonova Olga , Kubanov Alexey , Solomka Victoria , Shagabieva Julia , Deryabin Dmitry , Shaskolskiy Boris 
Published: March 2022

ABSTRACTN. gonorrhoeae strains producing plasmid-mediated broad- and extended-spectrum β-lactamases (ESBLs) have been obtained in vitro and studied for their viability and susceptibility to β-lactam antibiotics. The artificial pblaTEM-1 and pblaTEM-20 plasmids were constructed by site-directed mutagenesis from a pblaTEM-135 plasmid of the Toronto/Rio type, which was extracted from the clinical isolate. MIC values were determined for a series of β-lactam antibiotics, including benzylpenicillin, ampicillin, cefuroxime, ceftriaxone, cefixime, cefotaxime, cefepime, meropenem, imipenem, and doripenem. The N. gonorrhoeae strain carrying the pblaTEM-20 plasmid exhibited a high level of resistance to penicillins and II-IV generation cephalosporins (MIC ≥ 2 mg/L) but not to carbapenems (MIC ≤ 0.008 mg/L). However, this strain stopped growing after 6 hours of cultivation. The reduced viability was not associated with the plasmid loss but can be explained by the following factors: the presence of the plasmid itself, which requires additional costs for its reproduction, and the expression of ESBL, which can affect the structure of the peptidoglycan layer in the cell membrane. The cell growth was mathematically modeled using the generalized Verhulst equation. The parameter, characterizing the maximum possible number of cells grown under given conditions, decreased within the wild type (without plasmids) - pblaTEM-135 - pblaTEM-1 - pblaTEM-20 series, i.e., the plasmid-bearing strains had reduced viability compared to that of the wild-type strain. The kinetics for the cell death of N. gonorrhoeae strains without the pblaTEM-20 plasmid in the presence of ceftriaxone can be described by a modified Chick-Watson law. For the N. gonorrhoeae strain that harbors the pblaTEM-20 plasmid, the kinetics for cell number changes with time reflected several processes: the hydrolysis of ceftriaxone by TEM-20 β-lactamase, growth and gradual death of cells. The demonstrated reduced viability of N. gonorrhoeae strains with the pblaTEM-20 plasmid probably explains the absence of clinical isolates of N. gonorrhoeae that produce ESBL.
Adipocyte-specific ablation of the Ca2+ pump SERCA2 impairs whole-body metabolic function and reveals the diverse metabolic flexibility of white and brown adipose tissue
Authors: Bauzá-Thorbrügge Marco , Banke Elin , Chanclón Belén , Peris Eduard , Wu Yanling , Musovic Saliha , Jönsson Cecilia , Strålfors Peter , Rorsman Patrik , Olofsson Charlotta S. , Asterholm Ingrid Wernstedt 
Published: March 2022

AbstractObjectiveSarco/endoplasmic reticulum Ca2+-ATPase (SERCA) transports Ca2+ from the cytosol into the ER and is essential for appropriate regulation of intracellular Ca2+ homeostasis. The objective of this study was to test the hypothesis that SERCA pumps are involved in the regulation of white adipocyte hormone secretion and other aspects of adipose tissue function and that this control is disturbed in obesity-induced type-2 diabetes.MethodsSERCA expression was measured in isolated human and mouse adipocytes as well as in whole mouse adipose tissue by Western blot and RT-qPCR. To test the significance of SERCA2 in adipocyte functionality and whole-body metabolism, we generated adipocyte-specific SERCA2 knockout mice. The mice were metabolically phenotyped by glucose tolerance and tracer studies, histological analyses, measurements of glucose- stimulated insulin release in isolated islets, and gene/protein expression analyses. We also tested the effect of pharmacological SERCA inhibition and genetic SERCA2 ablation in cultured adipocytes. Intracellular and mitochondrial Ca2+ levels were recorded with dual-wavelength ratio imaging and mitochondrial function was assessed by Seahorse technology.ResultsWe demonstrate that SERCA2 is downregulated in white adipocytes from patients with obesity and type-2 diabetes as well as in adipocytes from diet-induced obese mice. SERCA2-ablated adipocytes display disturbed Ca2+ homeostasis associated with upregulated ER stress markers and impaired hormone release. These adipocyte alterations are linked to mild lipodystrophy, reduced adiponectin levels, and impaired glucose tolerance. Interestingly, adipocyte-specific SERCA2 ablation leads to increased glucose uptake in white adipose tissue while glucose uptake is reduced in brown adipose tissue. This dichotomous effect on glucose uptake is due to differently regulated mitochondrial function. In white adipocytes, SERCA2 deficiency triggers an adaptive increase in Fgf21, increased mitochondrial UCP1 levels, and increased oxygen consumption rate (OCR). In contrast, brown SERCA2 null adipocytes display reduced OCR despite increased mitochondrial content and UCP1 levels compared to wild type controls.ConclusionsOur data suggest causal links between reduced white adipocyte SERCA2 levels, deranged adipocyte Ca2+ homeostasis, adipose tissue dysfunction and type-2 diabetes.Graphical abstractHighlightsAdipocyte SERCA2 is downregulated in human subjects with type-2 diabetesLoss of SERCA2 disturbs the intracellular Ca2+ homeostasis in adipocytesImpaired metabolism and altered adipokine levels in adipocyte-SERCA2 null miceLoss of SERCA2 accelerates metabolic processes in white adipocytesLoss of SERCA2 impairs the mitochondrial function of brown adipocytes
Structure and function of diadenylate cyclase DacM fromMycoplasma ovipneumoniae
Authors: Hao Xiujing , Zhou Xinhui , Zhang Ying , Han Yang , Xu Zhaokun , Ma Chunji , Luo Haixia , Qi Kemin , Fan Shilong , Li Min 
Published: March 2022

AbstractCyclic diadenosine monophosphate (c-di-AMP) is a second-messenger nucleotide that is produced by many bacteria. C-di-AMP can not only regulate bacterial growth, cell-wall homeostasis, ion transport and gene transcription, but can also be recognized by multiple sensor / receptor proteins in infected host cells to trigger an innate immune response.Mycoplasma ovipneumoniaecauses non-progressive pneumonia in both sheep and goats. Here, we analyzed c-di-AMP signaling inM. ovipneumoniae, which is a genome-reduced obligately pathogenic bacterium. Our results demonstrate that these bacteria can produce c-di-AMP, and we could identify the diadenylate cyclase, which was named DacM. The enzyme was found to utilize both ATP and ADP to synthesize c-di-AMP, resembling CdaM from a novel family of diadenylate cyclases first found inMycoplasma pneumoniae. Furthermore, we present the crystal structures of DacM in the apo state and substrate-bound state at 3 Å and 1.9 Å resolution, respectively. Mutation of residues Asp112, Gly113, Tyr128, Phe129, and Arg143 surrounding the active sites to Ala were lethal to DacM enzymatic activity. These structures provide valuable insights into the biochemistry of c-di-AMP, and offer a basis for the structure-based design of new drugs for animal husbandry.
Alpha-1-antitrypsin binds to the glucocorticoid receptor with biological significance in macrophages
Authors: Bai Xiyuan , Bai An , Tomasicchio Michele , Hagman James R. , Buckle Ashley M. , Gupta Arnav , Kadiyala Vineela , Bevers Shaun , Serban Karina A. , Kim Kevin , Feng Zhihong , Spendier Kathrin , Hagen Guy , Fornis Lorelenn , Griffith David E. , Dzieciatkowska Monika , Sandhaus Robert A. , Gerber Anthony N. , Chan Edward D. 
Published: March 2022

ABSTRACTAlpha-1-antitrypsin (AAT), a serine protease inhibitor produced mainly by the liver, is the third most abundant protein in plasma. While a canonical receptor for AAT has not been identified, AAT can be internalized into the cytoplasm and is known to affect gene regulation. Since AAT has significant anti-inflammatory properties affecting many cell types including macrophages, we examined whether AAT binds the cytoplasmic glucocorticoid receptor (GR) in macrophages. We report the novel finding that AAT binds to GR in macrophages using several approaches, including co-immunoprecipitation, mass spectrometry, microscale thermophoresis, and molecular modeling. The mass spectrometry data are availableviaProteomeXchange with identifier PXD030989. We further demonstrate that AAT induction of angiopoietin-like 4 protein and AAT inhibition of lipopolysaccharide-induced nuclear factor-kappa B activation and interleukin-8 production are mediated, in part, through AAT–GR interaction. Furthermore, this interaction contributes to a host-protective role against mycobacteria in macrophages. The interaction of AAT and GR described in this study identifies a mechanism for the antiinflammatory and host-defense properties of AAT.
The role of Cycloastragenol at the intersection of Nrf-2/ARE, telomerase, and proteasome activity
Authors: Yılmaz Sinem , Bedir Erdal , Kırmızıbayrak Petek Ballar 
Published: March 2022

AbstractAging is well-characterized by the gradual decline of cellular functionality. As redox balance, proteostasis, and telomerase systems have been found to be associated with aging and age-related diseases, targeting these systems by small compounds has been considered as a promising therapeutic approach. Cycloastragenol (CA), a small molecule telomerase activator obtained fromAstragalusspecies, has been reported to have positive effects on several age-related pathophysiologies, including ischemia, glucose intolerance, diabetes, and neurodegenerative diseases. Although CA has received intense attention as a promising compound for aging and age-related diseases, the mechanisms underlying CA activity related to redox balance, proteasome, and telomerase has not yet been reported. Here, we presented that CA increased Nrf-2 activity leading to upregulation of cytoprotective enzymes and attenuation of oxidative stress-induced ROS levels. Furthermore, CA enhanced telomerase activity by increasing not only the expression of hTERT but also its nuclear localization via the Hsp90-chaperon complex. CA alleviated the oxidative stress-induced mitochondrial hTERT levels while increasing the nuclear hTERT levels. Additionally, the proteasome activity and assembly were increased by CA. Strikingly, our data revealed that CA-mediated neuroprotection requires both Nrf-2 and hTERT induction. In conclusion, this study is the first report describing the effect of CA on these aging-related three major cellular pathways and their interrelationships. As the proteasome activator effect of CA is dependent on induction of telomerase activity, which is mediated by Nrf-2 system, CA has a great potential for healthier aging and prevention or treatment of age-related diseases by positively affecting these three cellular pathways.
Double NPY motifs at the N-terminus of Sso2 synergistically bind Sec3 to promote membrane fusion
Authors: Peer Maximilian , Yuan Hua , Zhang Yubo , Korbula Katharina , Novick Peter J. , Dong Gang 
Published: March 2022

AbstractExocytosis is an active vesicle trafficking process by which eukaryotes secrete materials to the extracellular environment and insert membrane proteins into the plasma membrane. The final step of exocytosis in yeast involves the assembly of two t-SNAREs, Sso1/2 and Sec9, with the v-SNARE, Snc1/2, on secretory vesicles. The rate-limiting step in this process is the formation of a binary complex of the two t-SNAREs. Despite a previous report of acceleration of binary complex assembly by Sec3, it remains unknown how Sso2 is efficiently recruited to the vesicle-docking site marked by Sec3. Here we report a crystal structure of the pleckstrin homology (PH) domain of Sec3 in complex with a nearly full-length version of Sso2 lacking only its C-terminal transmembrane helix. The structure shows a previously uncharacterized binding site for Sec3 at the N-terminus of Sso2, consisting of two highly conserved triple residue motifs (NPY: Asn-Pro-Tyr). We further reveal that the two NPY motifs bind Sec3 synergistically, which together with the previously reported binding interface constitute dual-site interactions between Sso2 and Sec3 to drive the fusion of secretory vesicles at target sites on the plasma membrane.SignificanceSNARE assembly, which involves one v-SNARE with two t-SNARE proteins, drives the fusion of vesicles to target compartments. The rate-limiting step in SNARE assembly is the assembly of the two t-SNARE proteins on the target membrane. Previous studies in yeast showed that Sec3, a component of the exocyst vesicle tethering complex, directly interacts with the t-SNARE protein Sso2 to promote fast assembly of an Sso2-Sec9 binary t-SNARE complex. This paper presents a new crystal structure of the Sec3 PH domain in complex with a nearly full-length version of Sso2, which reveals a previously unknown binding site for Sec3 at the N-terminus of Sso2. Our work demonstrates that the dual-site interactions between Sso2 and Sec3 plays an essential role in promoting the fusion of secretory vesicles at target sites on the plasma membrane.
Blocking abundant RNA transcripts by high-affinity oligonucleotides during transcriptome library preparation
Authors: Everaert Celine , Verwilt Jasper , Verniers Kimberly , Vandamme Niels , Rubio Alvaro Marcos , Vandesompele Jo , Mestdagh Pieter 
Published: March 2022

ABSTRACTRNA sequencing has become the gold standard for transcriptome analysis but has an inherent limitation of challenging quantification of low-abundant transcripts. In contrast to microarray technology, RNA sequencing reads are proportionally divided in function of transcript abundance. Therefore, low-abundant RNAs compete against highly abundant - and sometimes non-informative - RNA species. We developed an easy-to-use strategy based on high-affinity RNA-binding oligonucleotides to block reverse transcription and PCR amplification of specific RNA transcripts, thereby substantially reducing their abundance in the final sequencing library. To demonstrate the broad application potential of our method, we applied it to different transcripts and library preparation strategies, including YRNAs in small RNA sequencing of human blood plasma, mitochondrial rRNAs in both 3’ end sequencing and long-read sequencing, and MALAT1 in single-cell 3’ end sequencing. We demonstrate that the blocking strategy is highly efficient, reproducible, specific, and generally results in better transcriptome coverage and complexity. Furthermore, our method does not require modifications of the library preparation procedure apart from simply adding blocking oligonucleotides to the RT reaction and can thus be easily integrated into virtually any RNA sequencing library preparation protocol.
Phytochemical-induced mucin accumulation in the gastrointestinal lumen is independent of the microbiota
Authors: Forgie Andrew J. , Ju Tingting , Tollenaar Stephanie L. , Willing Benjamin P. 
Published: March 2022

AbstractThe mucus layer is critical to gastrointestinal health and ecology. Dietary phytochemicals are well documented to stimulate mucus production and secretion, but the underlying mechanism and effects on gut health are poorly understood. We fed germ-free and conventional mice diets containing approximately 0.4% of polyphenols per gram to determine if the phytochemical-induced accumulation of mucin in the gastrointestinal lumen is dependent on the microbiota. In addition, we assess how increased mucin shapes microbial communities in conventional mice. Germ-free mice receiving a pea (Pisum sativuum) seed coat proanthocyanidin-containing diet (PA) had greater levels of fecal mucin compared to the non-proanthocyanidin-containing (NPA) pea seed coat diet control (P < 0.05), confirming that fecal mucin accumulation is independent of the gut microbiota. Conventional mice fed the PA diet and a red osier dogwood (ROD; Cornus sericea) extract diet (DW) had higher mucin levels compared to a control diet without phytochemicals (P < 0.01 and P < 0.05, respectively). The increase in luminal mucin was associated with consistent increases in bacterial taxa belonging to Lachnospiraceae and [Clostridium] leptum species and a decrease in Romboutsia species. We conclude that phytochemicals have the ability to alter gut microbial ecology by increasing the amount of mucin in the gastrointestinal lumen.