bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of hormonal regulation of promoter activities ofCannabis sativaprenyltransferase 1 and 4 and salicylic acid mediated regulation of cannabinoid biosynthesis
Authors: Sands Lauren B. , Haiden Samuel R. , Ma Yi , Berkowitz Gerald A. 
Published: November 2022

AbstractCannabis sativaprenyltransferase 4 (CsPT4) and prenyltransferase 1 (CsPT1) have been shown to catalyze the step in the cannabinoid biosynthetic pathway that generates cannabigerolic acid (CBGA), the substrate for the end-point enzymes that generate cannabidiolic acid (CBDA) and tetrahydrocannabinolic acid (THCA). Prior studies from our lab suggest that CBGA production rate-limits the pathway. There is a lack of understanding concerning how important cannabinoid biosynthetic genes are regulated as cannabinoid synthesis increases during female flower development. BothCsPTgenes were shown to be highly expressed in flowers. The genes were also found to be present in leaves and roots. GUS staining also detected the promoter activities in leaves of seedlings, and the promoter activities were drastically stronger in the section of the sugar leaves where glandular trichomes are formed.In silicoanalysis of the twoCsPTgenes revealed several hormone and transcription factor responsive elements. Dual luciferase assays were conducted to determine whether a hormone could alter the promoter activities ofCsPT1andCsPT4. The results showed thatCsPT4pro was activated following treatment from salicylic acid (SA), gibberellic acid (GA), ethylene, ABA, and cytokinin, while theCsPT1promoter was activated following SA, ethylene, ABA, and auxin treatment. In parallel studies, a correlation was observed between multiple cannabinoid biosynthetic pathway genes and SA application to the cannabis growing medium, along with a correlation between MeSA floral application and an increase in cannabinoid content. The results from all aspects of this study demonstrated an interaction between certain hormones and cannabinoid synthesis.
A primary microcephaly-associatedsas-6mutation perturbs centrosome duplication, dendrite morphogenesis, and ciliogenesis inCaenorhabditis elegans
Authors: Bergwell Mary , Smith Amy , Smith Ellie , Dierlam Carter , Duran Ramon , Haastrup Erin , Napier-Jameson Rebekah , Seidel Rory , Potter William , Norris Adam , Iyer Jyoti 
Published: November 2022

AbstractThe human SASS6(I62T) missense mutation has been linked with the incidence of primary microcephaly in a Pakistani family, although the mechanisms by which this mutation causes disease remain unclear. The SASS6(I62T) mutation corresponds to SAS-6(L69T) inC. elegans. Given that SAS-6 is highly conserved, we modeled this mutation inC. elegansand examinedsas-6(L69T)effect on centrosome duplication, ciliogenesis and dendrite morphogenesis. Our studies revealed that all the above processes are perturbed by thesas-6(L69T)mutation. Specifically,C. eleganscarrying thesas-6(L69T)mutation exhibit an increased failure of centrosome duplication in a sensitized genetic background. Further, worms carrying this mutation also display shortened phasmid cilia, an abnormal phasmid cilia morphology, shorter phasmid dendrites and chemotaxis defects. Our data show that the centrosome duplication defects caused by this mutation are only uncovered in a sensitized genetic background, indicating that these defects are mild. However, the ciliogenesis and dendritic defects caused by this mutation are evident in an otherwise wild-type background, indicating that they are stronger defects. Thus, our studies shed light on the novel mechanisms by which thesas-6(L69T)mutation could contribute to the incidence of primary microcephaly in humans.
Centromere-associated retroelement evolution inDrosophila melanogasterreveals an underlying conflict
Authors: Hemmer Lucas W. , Negm Sherif , Geng Xuewen , Courret Cécile , Navarro-Domínguez Beatriz , Speece Iain , Wei Xiaolu , Altidor Eddyson , Chaffer James , Sproul John S. , Larracuente Amanda M. 
Published: November 2022

ABSTRACTCentromeres are chromosomal regions essential for coordinating chromosome segregation during cell division. While centromeres are defined by the presence of a centromere-specific histone H3 variant rather than a particular DNA sequence, they are typically embedded in repeat-dense chromosomal genome regions. In many species, centromeres are associated with transposable elements, but it is unclear if these elements are selfish or if they play a role in centromere specification or function. Here we useDrosophila melanogasteras a model to understand the evolution of centromere-associated transposable elements.G2/Jockey-3is a non-LTR retroelement in theJockeyclade and the only sequence shared by all centromeres. We study the evolution ofG2/Jockey-3using short and long read population genomic data to infer insertion polymorphisms across the genome. We combine estimates of the age, frequency, and location of insertions to infer the evolutionary processes shapingG2/Jockey-3and its association with the centromeres. We find thatG2/Jockey-3is an active retroelement targeted by the piRNA pathway that is enriched in centromeres at least in part due to an insertion bias. We do not detect signatures of positive selection on anyG2/Jockey-3insertions that would suggest than individual copies are favored by natural selection. Instead, we infer that most insertions are neutral or weakly deleterious both inside and outside of the centromeres. Therefore,G2/Jockey-3evolution is consistent with it being a selfish genetic element that targets centromeres. We propose that targeting centromeres helps active retroelements escape host defenses, as the unique centromeric chromatin may prevent targeting by the host silencing machinery. At the same time, centromeric TEs insertions may be tolerated or even beneficial if they also contribute to the transcriptional and chromatin environment. Thus, we suspect centromere-associated retroelements likeG2/Jockey-3reflect a balance between conflict and cooperation at the centromeres.
Quantitative assessment of angioplasty induced vascular inflammation with19F cardiovascular magnetic resonance imaging
Authors: Nienhaus Fabian , Walz Moritz , Rothe Maik , Jahn Annika , Pfeiler Susanne , Busch Lucas , Stern Manuel , Heiss Christian , Vornholz Lilian , Cames Sandra , Cramer Mareike , Schrauwen-Hinderling Vera , Gerdes Norbert , Temme Sebastian , Roden Michael , Flögel Ulrich , Kelm Malte , Bönner Florian 
Published: November 2022

AbstractEarly macrophage rich vascular inflammation is a key feature in the pathophysiology of restenosis after angioplasty.19F MRI with intravenously applied perfluorooctyl bromide-nanoemulsion (PFOB-NE) could offer ideal features for serial imaging of the inflammatory response after angioplasty. We aimed to non-invasively image monocyte/macrophage infiltration in response to angioplasty in pig carotid arteries using Fluorine-19 magnetic resonance imaging (19F MRI) to assess early inflammatory response to mechanical injury. Early macrophage rich vascular inflammation is a key feature in the pathophysiology of restenosis after angioplasty.19F MRI with intravenously applied perfluorooctyl bromide-nanoemulsion (PFOB-NE) could offer ideal features for serial imaging of the inflammatory response after angioplasty. In eight minipigs, injury of the right carotid artery was induced by either balloon oversize angioplasty only (BA, n=4) or in combination with endothelial denudation (BA + ECDN, n=4). PFOB-NE was administered intravenously three days after injury followed by1H and19F MRI to assess vascular inflammatory burden at day six. Vascular response to mechanical injury was validated using immunohistology. Angioplasty was successfully induced in all eight pigs. Response to injury was characterized by positive remodeling with predominantly adventitial wall thickening and adventitial infiltration of monocytes/macrophages.19F signal could be detectedin vivoin four pigs following BA + ECDN with a robust signal-to-noise ratio (SNR) of 14.7 ± 4.8.Ex vivoanalysis revealed a linear correlation of19F SNR to local monocyte/macrophage cell density. Minimum detection limit of infiltrated monocytes/macrophages was as about 400 cells/mm2. Therefore,19F MRI enables quantification of monocyte/macrophage infiltration after vascular injury with sufficient sensitivity. This might open an avenue to non-invasively monitor inflammatory response to mechanical injury after angioplasty and thus to identify individuals with distinct patterns of vascular inflammation promoting restenosis.One Sentence Summary19F MRI enables radiation-free quantification of monocyte/macrophage infiltration after vascular injury with sufficient sensitivity.
Proteomic Landscape of Human Spermatozoa: Optimized Extraction Method and Application
Authors: Luo Mengqi , Su Tao , Wang Shisheng , Chen Jianhai , Lin Tianhai , Cheng Qingyuan , Chen Younan , Gong Meng , Yang Hao , Li Fuping , Zhang Yong 
Published: November 2022

AbstractHuman spermatozoa proteomics exposed to some physical, biological or chemical stressors is being explored. However, there is a lack of optimized sample preparation methods to achieve in-depth protein coverage for sperm cells. Meanwhile, it is not clear whether antibiotics can regulate proteins to affect sperm quality. Here, we systematically compared a total of six different protein extraction methods based the combination of three commonly used lysis buffers and physical lysis strategies. The urea buffer combined with ultrasonication (UA_ultrasonication) produced the highest protein extraction rate, leading to the deepest coverage of human sperm proteome (5685 protein groups) from healthy human sperm samples. Since the antibiotics, amoxicillin and clarithromycin, have been widely used againstH. pyloriinfection, we conduct a longitudinal study of sperm proteome via data-independent acquisition tandem mass spectrometry (DIA-MS/MS) on an infected patient during on and off therapy with these two drugs. The semen examination and morphological analysis were performed combined with proteomics analysis. Our results indicated that antibiotics may cause an increase in the sperm concentration and the rate of malformed sperm and disrupt proteome expression in sperm. This work provides an optimized extraction method to characterize the in-depth human sperm proteome and to extend its clinical applications.
A conditional histone H3.3 mutation in mice orthologous to a driver of paediatric diffuse instrinsic pontine glioma
Authors: Mann Jeffrey R. , Tang Michelle C. W. , Wong Lee H. 
Published: November 2022

ABSTRACTMost paediatric diffuse intrinsic pontine gliomas carry a lysine- to methionine-27 (K27M) mutation in the histone variant H3.3 encoded by the ‘H3.3 histone A’ (H3F3A) gene. To establish a pre-clinical model of the disease we made a Cre/loxPconditional H3.3K27M mutation at the orthologousH3f3alocus in mice. Importantly, expression of the mutant transcript is under endogenousH3f3aregulatory control. This system is distinct from others in which H3.3M27 is ectopically expressed, thereby providing a resource for the development of pDIPG models with orthologous regulation of mutant H3.3. Mice in which expression of the mutant transcript was induced with a nestin-cretransgene developed as dwarfs in the presence of intact growth hormone signaling.
Structural and dynamical basis for the interaction of HSP70-EEVD with JDP Sis1
Authors: Matos Carolina O. , Pinheiro Glaucia M.S. , Caruso Icaro P. , Amorim Gisele C. , Almeida Fabio C. L. , Ramos Carlos H. I. 
Published: November 2022

AbstractWe employed NMR spectroscopy to investigate the structure and dynamics of the class B J domain protein (JDP) of S. cerevisiae (Sis1) complexed with an EEVD peptide of HSP70. It is widely recognized that the interactions between the EEVD motif and Sis1 play a crucial role in the chaperone activity. Notably, the deletion of the EEVD impairs the ability of Sis1 to bind with HSP70, while leaving the interaction between the class A JDP Ydj1 and HSP70 unaffected. Leveraging the advantages of NMR, which is particularly suitable for studying transient interactions, we provide compelling evidence that the EEVD motif transiently engages multiple sites on Sis1. Our findings revealed that EEVD binds to two distinct sites within the C-terminal domain I (CTDI) of Sis1. The interaction at these sites plays a crucial role in anchoring HSP70 to Sis1 at site I, as well as displacing the client protein at site II. Notably, site II is also the binding site for the client protein, and its displacement occurs through competition with the binding to site II. In addition to these interactions, we observed that EEVD, as a transient electrostatic binder, also interacts with the J domain and the GF-rich loop located between the J domain and α-helix 6. We propose that the interaction between EEVD and Sis1 facilitates the dissociation of α-helix 6, promoting a conformational state that is more favorable for interaction with HSP70 at the nucleotide-binding domain (NBD) and substrate-binding domain (SBD) interface. We also employed α-synuclein as a substrate to investigate the competitive nature between EEVD and the client protein. Our experimental findings provided evidence supporting the interaction of EEVD with the client protein at multiple sites. Our findings contribute essential insights into the mechanistic cycle of class B JDPs, paving the way toward a more complete understanding of the primary function of Sis1, which is the transfer of the client protein to HSP70, where multiple site transient interactions play a collective role.
Effects of Plastic Ingestion on Blood Chemistry, Gene Expression and Body Condition in Wedge-Tailed Shearwaters (Ardenna Pacifica)
Authors: Mejia Nicole , Garcia Flavia Termignoni , Learned Jennifer , Penniman Jay , Edwards Scott V. 
Published: November 2022

ABSTRACTPlastic pollution is a global threat and affects almost every marine ecosystem. The amount of plastic in the ocean has increased substantially over the past decade, posing a mounting threat to biodiversity. Seabirds, typically top predators in marine food chains, have been negatively affected by plastic pollution. Here we focused on documenting the sublethal effects of plastic in Wedge-tailed Shearwaters (Ardenna pacifica, WTSH) on the island of Maui, Hawai’i. Through analyses of blood chemistry, gene expression, morphometrics and stomach contents, we documented the effects of plastic ingestion on adult WTHS from 3 established colonies. We detected a negative relationship between body weight and the presence of plastic in regurgitated stomach contents. Genes associated with metabolic, biosynthetic pathways, inflammatory responses and ribosome function were upregulated in lighter birds. Birds that had ingested plastic tended to be lighter in weight, in comparison to birds that did not have plastic and tended to weight more. Furthermore, there were 43 genes differentiating males and females that did not have plastic compared to only 11 genes differentiating males and females that had ingested plastic. There was also a marginal negative relationship between lighter birds and blood urea nitrogen levels. We also hope that the morphometric measurements, blood parameters and gene expression data we collected contributes to a database that will be used for future studies on understanding anthropogenic effects on seabird body condition.
The endocytic recycling pathway is controlled by the ADP-ribosylated GTPase Rab14
Authors: Corteggio Annunziata , Lo Monte Matteo , Schembri Laura , Dathan Nina , Di Paola Simone , Grimaldi Giovanna , Corda Daniela 
Published: November 2022

AbstractThe GTPase Rab14 is localized at the trans-Golgi network and at the intermediate compartment associated to sorting/recycling endosomes-like structures of the transferrin-recycling pathway: as other Rab family members, it is involved in the regulation of intracellular vesicle trafficking, though its role and functional relationship with effector/endosomal proteins is still incomplete.We have analysed whether post-translational modifications could affect Rab14 activity: the results obtained define mono-ADP-ribosylation (MARylation) as the yet-unknown Rab14 modification, catalysed by the ADP-ribosyltransferase PARP12, which specifically modifies glutamic acid residues in position 159/162. This modification is essential for the Rab14-dependent endosome progression. Accordingly, recycling of the transferrin receptor is inhibited when MARylation of Rab14 is prevented by PARP12 knocking-down or inhibition, or by overexpression of Rab14 ADP-ribosylation-defective mutant. Under these conditions, Rab14 and transferrin receptors are withheld at the cell periphery at the level of the Rab4-RUFY1-positive sorting endosomes, indicating that the interaction of Rab14 with the dual effectors RUFY and then FIP1c (which specifically binds both Rab11 and Rab14) determines the progression between the Rab4-RUFY- and Rab11-FIP1c-specific vesicles. Therefore Rab14-MARylation determines the sequential binding of this GTPase to RUFY and FIP1c, thus controlling endosome progression (i.e., transferrin receptors recycling) through the Rab4-, Rab14- and Rab11-specific vesicles. This identifies a Rab14-specific compartment of the recycling pathway and a crucial enzymatic reaction amenable to pharmacological control.
A deep neural network provides an ultraprecise multi-tissue transcriptomic clock for the short-lived fishNothobranchius furzeriand identifies predicitive genes translatable to human aging
Authors: Ferrari Elisa , Reichwald Kathrin , Koch Philipp , Groth Marco , Baumgart Mario , Cellerino Alessandro 
Published: November 2022

AbstractA key and unresolved question in aging research is how to quantify aging at the individual level that led to development of ”aging clocks”, machine learning algorhythms trained to predict individual age from high-dimensional molecular data under the the assumption that individual deviations of the predicted age from the chronological age contain information on the individual condition (often referred to as ”biological age”). A full validation of such clocks as biomarkers for clinical studies of ageing would require a comparison of their predictions with information on actual lifespan and long-term health. Such studies take decades in humans, but could be conducted in a much shorter time-frame in animal models. We developed a transcriptomic clock in the turquoise killifishNothobranchius furzeri. This species is the shortest-lived vertebrate that can be cultured in captivity and is an emerging model organism for genetic and experimental studies on aging. We developed a proprietary deep learning architecture that autonomously selects a customizable number of input genes to use for its predictions in order to reduce overfitting and increase interpretability, and adopts an adversarial learning framework to identify tissue-independent transcriptional patterns. We called this architecture the Selective Adversarial Deep Neural Network (SA-DNN) and trained it on a multi-tissue transcriptomic dataset ofN. furzeri. This SA-DNN predicted age of the test set with an accuracy of 1 day, i.e. less than 1% of the total species’ lifespan and detected genetic, pharmacological and environmental interventions that are known to influence lifespan in this species. Finally, a human transcriptomic multi-tissue clock that uses as input the orthologs of the genes selected by our SA-DNN inN. furzerireaches an average error of∼3 years rivalling epigenetic clocks. Our SA-DNN represents the prototype of a new class of aging clocks that provide biomarkers applicable to intervention studies in model organisms and humans.
CRISPR correction ofGBAmutation in hiPSCs restores normal function to Gaucher macrophages and increases their susceptibility toMycobacterium tuberculosis
Authors: Ramalingam Sivaprakash , Kumar Amit , Krug Stefanie , Mohan Harikrishnan , Rao Desirazu N , Bishai William R , Chandrasegaran Srinivasan 
Published: November 2022

AbstractGaucher disease (GD) is an autosomal recessive lysosomal storage disorder caused by mutations in the β-glucocerebrosidase (GCase)GBAgene, which result in macrophage dysfunction. To investigate whether correction ofGBAmutations restores normal function to Gaucher macrophages, we performed CRISPR editing of homozygous L444P (1448T→C)GBAmutation in Type 2 GD (GBA-/-) hiPSCs, which yielded both heterozygous (GBA+/-) and homozygous (GBA+/+) isogenic lines. Macrophages derived fromGBA-/-,GBA+/- andGBA+/+ hiPSCs, were compared for GCase enzymatic activity, motility, and phagocytosis, all of which showed thatGBAmutation correction restores normal macrophage functions. Furthermore, we investigated whether lysosomal disorders drive susceptibility toMycobacterium tuberculosis, by infectingGBA-/-,GBA+/- andGBA+/+ macrophages with the virulent H37Rv lab strain. The results showed that impaired mobility and phagocytic activity of Gaucher macrophages, correlated with reduced levels of TB engulfment and TB multiplication, supporting the hypothesis that GD may be protective against tuberculosis.
Kinetochore-fiber lengths are maintained locally but coordinated globally by poles in the mammalian spindle
Authors: Richter Manuela , Neahring Lila , Tao Jinghui , Sutanto Renaldo , Cho Nathan H. , Dumont Sophie 
Published: November 2022

AbstractAt each cell division, nanometer-scale components self-organize to build a micron-scale spindle. In mammalian spindles, microtubule bundles called kinetochore-fibers attach to chromosomes and focus into spindle poles. Despite evidence suggesting that poles can set spindle length, their role remains poorly understood. In fact, many species do not have spindle poles. Here, we probe the pole’s contribution to mammalian spindle length, dynamics, and function by inhibiting dynein to generate spindles whose kinetochore-fibers do not focus into poles, yet maintain a metaphase steady-state length. We find that unfocused kinetochore-fibers have a mean length indistinguishable from control, but a broader length distribution, and reduced length coordination between sisters and neighbors. Further, we show that unfocused kinetochore-fibers, like control, can grow back to their steady-state length if acutely shortened by drug treatment or laser ablation: they recover their length by tuning their end dynamics, albeit slower due to their reduced baseline dynamics. Thus, kinetochore-fiber dynamics are regulated by their length, not just pole-focusing forces. Finally, we show that spindles with unfocused kinetochore-fibers can segregate chromosomes but fail to correctly do so. We propose that mammalian spindle length emerges locally from individual k-fibers while spindle poles globally coordinate k-fibers across space and time.