bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Avian Adeno-Associated Virus for the Delivery of Transgenes to Pekin Duck Cells in vitro and in vivo
Authors: Robinson Carleigh R. , Fraley Gregory S. , Kopek Benjamin G. 
Published: March 2022

AbstractThe Pekin duck was domesticated between 4000 and 10,000 years ago from the Mallard duck and is the predominate meat type duck in the world (Cherry and Morris, 2008). The global production of waterfowl is a rapidly growing industry. Total meat duck production increased from 2.9 million tons in 2000 to nearly 4.4 million tons in 2013, a growth rate of 3.2% per year, and further increased to 7.2 million tons in 2018, and valued at $19B in 2019 (IndexBox, 2019). Pekin ducks (Anas platyrhynchus domesticus) are the fastest growing poultry species growing from hatch to 4.5 kg market weight in as little as 28 days (Blois et al., 2019; Campbell et al., 2015; Cherry and Morris, 2008). Thus, there is a need to study the growth and reproduction of this economically important species. While Pekin duck biology is being explored by many researchers, there are fewer molecular tools available for duck compared to other poultry species and many fewer compared to mammalian systems. For example, one molecular tool commonly used to interrogate other systems are adeno-associated virus (AAV) vectors. AAV vectors are being utilized by many researchers to deliver transgenes to target tissues or cells and for genetic manipulation. Recently, avian adeno-associated virus (A3V) has been used to deliver genes to the cells and neurons of the domestic chicken (Gallus gallus domesticus). Here, we show that A3V can be used to deliver genes to Pekin duck neurons and cells in culture. Together, these results suggest that A3V will be a useful molecular tool in Pekin duck research.Summary StatementHere we demonstrate the use of viral vectors to deliver transgenes to Pekin duck cells. These vectors can be used to advance understanding of reproduction in this economically important species.
Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads
Authors: David Julianne K. , Maden Sean K. , Wood Mary A. , Thompson Reid F. , Nellore Abhinav 
Published: March 2022

AbstractThere is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by overlapping genes and transcripts as well as the presence of unprocessed or partially processed RNAs. We compared introns detected by 5 tools using short RNA-seq reads with introns observed in long RNA-seq reads from the same biological specimens and found: (1) significant disagreement among tools (Fleiss’ κ = 0.231) such that 52.4% of all detected intron retentions were not called by more than one tool; (2) that no tool achieved greater than 20% precision or 35% recall under generous conditions; and (3) that retained intron detectability was adversely affected by greater intron length and overlap with annotated exons.
Integration of multi-omics data reveals interplay between brassinosteroid and TORC signaling in Arabidopsis
Authors: Montes Christian , Wang Ping , Liao Ching-Yi , Nolan Trevor M , Song Gaoyuan , Clark Natalie M , Elmore J. Mitch , Guo Hongqing , Bassham Diane C , Yin Yanhai , Walley Justin W 
Published: March 2022

AbstractBrassinosteroids (BR) and Target of Rapamycin Complex (TORC) are two major actors coordinating plant growth and stress responses. BRs function through a signaling pathway to extensively regulate gene expression and TORC is known to regulate translation and autophagy. Recent studies revealed that these two pathways crosstalk, but a system-wide view of their interplay is still missing. Thus, we quantified the level of 23,975 transcripts, 11,183 proteins, and 27,887 phosphorylation sites in wild-type Arabidopsis and in mutants with altered levels of either BRASSINOSTEROID INSENSITIVE 2 (BIN2) or REGULATORY ASSOCIATED PROTEIN OF TOR 1B (RAPTOR1B), two key players in BR and TORC signaling, respectively. We found that perturbation of BIN2 or RAPTOR1B levels affects a common set of gene-products involved in growth and stress responses. Furthermore, we used the multi-omic data to reconstruct an integrated signaling network. We screened 41 candidate genes identified from the reconstructed network and found that loss of function mutants of many of these proteins led to an altered BR response and/or modulated autophagy activity. Altogether, these results establish a predictive network that defines different layers of molecular interactions between BR-or TORC-regulated growth and autophagy.
Interstrand Crosslinks in Donor DNA Boost Gene Editing in Human Cells
Authors: Ghasemi Hannah I. , Bacal Julien , Yoon Amanda , Cruz Carmen , Vu Jonathan , Gardner Brooke , Richardson Chris D. 
Published: March 2022

AbstractCo-introduction of targeted nucleases and DNA/RNA templates encoding new genomic sequence is the basis for rapid, effective, and iterable gene editing workflows for therapeutic, agricultural, and basic science applications. Extensive optimization of reagent delivery and nuclease activity have improved genome editing workflows, but comparatively few efforts have been made to alter the gene editing activity of template molecules. Here, we report template DNA modified with interstrand crosslinks (ICLs) – xHDRTs - increases editing frequencies in Cas9-directed gene editing workflows by up to five-fold. xHDRTs increase gene editing frequencies independent of DNA template topology, amount of sequence added, or cell type. Gene editing using xHDRTs requires the DNA repair kinase, ATR, and partially requires Fanconi Anemia proteins, including FANCA, but is independent of other ICL-repair pathways. Covalent modification of donor DNA thus presents a compelling opportunity to improve nonviral gene editing workflows.
Species-specific chromatin landscape determines how transposable elements shape genome evolution
Authors: Huang Yuheng , Shukla Harsh , Lee Yuh Chwen G. 
Published: March 2022

AbstractTransposable elements (TEs) are selfish genomic parasites that increase their copy number at the expense of host fitness. The “success,” or genome-wide abundance, of TEs differs widely between species. Deciphering the causes for this large variety in TE abundance has remained a central question in evolutionary genomics. We previously proposed that species-specific TE abundance could be driven by the inadvertent consequences of host-direct epigenetic silencing of TEs—the spreading of repressive epigenetic marks from silenced TEs into adjacent sequences. Here, we compared this TE-mediated “epigenetic effect” in six species in the Drosophila melanogaster subgroup to dissect step-by-step the role of such effect in determining genomic TE abundance.We found that TE-mediated spreading of repressive marks is prevalent and substantially varies across and even within species. While this TE-mediated effect alters the epigenetic states of adjacent genes, we surprisingly discovered that the transcription of neighboring genes could reciprocally impact this spreading. Importantly, our multi- species analysis provides the power and appropriate phylogenetic resolution to connect species-specific host chromatin regulation, TE-mediated epigenetic effects, the strength of natural selection against TEs, and genomic TE abundance unique to individual species. Our findings point towards the importance of host chromatin landscapes in shaping genome evolution through the epigenetic effects of a selfish genetic parasite.
Evolutionary Principles of Bacterial Signaling Capacity and Complexity
Authors: Mo Ran , Liu Yugeng , Chen Yuanyuan , Mao Yingjin , Gao Beile 
Published: March 2022

AbstractMicrobes rely on signal transduction systems to sense and respond to environmental changes for survival and reproduction. It is generally known that niche adaptation plays an important role in shaping the signaling repertoire. However, the evolution of bacterial signaling capacity lacks systematic studies with a temporal direction. Particularly, it is unclear how complexity evolved from simplicity or vice versa for signaling networks. Here we examine the evolutionary processes of major signal transduction systems in Campylobacterota (formerly Epsilonproteobacteria), a phylum with sufficient evolutionary depth and ecological diversity. Evolution of signaling systems within Campylobacterota shows two opposite trends. During niche expansion, signaling complexity increases with gene expansions through horizontal gene transfer (HGT), gene duplication, fusion and fission, which create opportunities for genetic innovation and pathway integration. In contrast, as the lineages adapt to a specialized niche, complexity decreases with massive gene losses that lead to the decline or disappearance of pathways mediated by multiple transmitters. Overall, signaling capacity and complexity arise and drop together in Campylobacterota, determined by sensory demand, genetic resources and co-evolution within the genomic context. These findings reflects plausible evolutionary principles for other cellular networks and genome evolution of the Bacteria domain.
Visualization of mRNA Expression in Pseudomonas aeruginosa Aggregates Reveals Spatial Patterns of Fermentative and Denitrifying Metabolism
Authors: Livingston Jadzia , Spero Melanie A. , Lonergan Zachery R. , Newman Dianne K. 
Published: March 2022

AbstractGaining insight into the behavior of bacteria at the single cell level is important given that heterogeneous microenvironments strongly influence microbial physiology. The hybridization chain reaction (HCR) is a technique that provides in situ molecular signal amplification, enabling simultaneous mapping of multiple target RNAs at small spatial scales. To refine this method for biofilm applications, we designed and validated new probes to visualize expression of key catabolic genes in Pseudomonas aeruginosa aggregates. In addition to using existing probes for the dissimilatory nitrate reductase (narG), we developed probes for a terminal oxidase (ccoN1), nitrite reductase (nirS), nitrous oxide reductase (nosZ), and acetate kinase (ackA). These probes can be used to determine gene expression levels both in liquid culture and in biofilms. Using these probes, we quantified gene expression across oxygen gradients in aggregate populations grown using the agar block biofilm assay (ABBA). We observed distinct patterns of catabolic gene expression, with upregulation occurring in particular ABBA regions both within individual aggregates and over the aggregate population. Aerobic respiration (ccoN1) showed peak expression under oxic conditions, whereas fermentation (ackA) showed peak expression in the anoxic cores of high metabolic activity aggregates near the air-agar interface. Denitrification genes narG, nirS, and nosZ showed peak expression in hypoxic and anoxic regions, although nirS expression was much stronger in anoxic environments compared to other denitrification genes. These results reveal that the microenvironment correlates with catabolic gene expression in aggregates, and demonstrate the utility of HCR in unveiling cellular activities at the microscale in heterogeneous populations.ImportanceTo understand bacteria in diverse contexts we must understand the variations in behaviors and metabolisms they express spatiotemporally. Populations of bacteria are known to be heterogeneous, but the ways this variation manifests can be challenging to characterize due to technical limitations. By focusing on energy conservation, we demonstrate that HCR v3.0 can visualize nuances in gene expression, allowing us to understand how metabolism in Pseudomonas aeruginosa biofilms responds to microenvironmental variation at high spatial resolution. We validated probes for four catabolic genes: a constitutively expressed oxidase, acetate kinase, nitrite reductase, and nitrous oxide reductase. We showed that the genes for different modes of metabolism are expressed in overlapping but distinct subpopulations according to oxygen concentrations in a predictable fashion. The spatial transcriptomic technique described here has the potential to be used to map microbial activities across diverse environments.
The Speech Envelope Following Response in Normal and Hearing Impaired Listeners
Authors: Wartenberg Tijmen , Garrett Markus , Verhulst Sarah 
Published: March 2022

AbstractThe aim of this work was to investigate the perceptual relevance of the frequency following response to the syllable /da/ for speech intelligibility in noise based on age and hearing deficits. Recordings of the auditory evoked potential from young normal hearing (NH) and older individuals with both normal hearing and high-frequency (HF) hearing loss were analyzed. EFR metrics obtained in quiet and noise condition were calculated and correlated with speech reception. The envelope following responses were analyzed in terms of amplitude, latency and noise robustness. The response was first simulated to form predictions on the effect of cochlear synaptopathy and outer hair cell loss on the EFR. The experimental findings were in line with the computational predictions in the found observation that the EFR was reduced as a consequence of ageing and HF hearing loss. Both the audiogram and the speech EFR magnitude fell short in the individual prediction of SRT in stationary noise, but they accounted well for group performance. We also obtained within-group EFR latency with a cross covariance matrix. Validation of the method confirmed that speech EFR latency was predictive of click ABR Wave V peak latency. Moreover, statistical analysis not only showed that the robustness of the EFR obtained in the noise condition was dependent on the degree of high-frequency hearing loss in the older NH adults, but also dependent on the EFR magnitude in the NH younger adults. These findings provide evidence towards the important role of the EFR in speech-in-noise perception.
Non-histone protein methylation inTrypanosoma cruziepimastigotes
Authors: de Almeida Rafael Fogaça , Rodrigues Lucena Aline Castro , Batista Michel , Marchini Fabricio Klerynton , de Godoy Lyris Martins Franco 
Published: March 2022

AbstractPost-translational methylation of proteins, which occurs in arginines and lysines, modulates several biological processes at different levels of cell signaling. Recently, methylation has been demonstrated in the regulation beyond histones, for example, in the dynamics of protein-protein and protein-nucleic acid interactions. However, the presence and role of non-histone methylation inTrypanosoma cruzi, the etiologic agent of Chagas disease, has not yet been elucidated. Here, we applied mass spectrometry-based-proteomics (LC-MS/MS) to describe the methylproteome ofT. cruziepimastigotes. A total of 1253 methyl sites in 824 methylated proteins were identified, of these, 712 (86.4%) proteins were identified in two or more biological replicates. Our results of functional enrichment analysis, protein-protein interaction, and co-occurrence with other PTMs, show that protein methylation impacts different levels of biological processes, such translation, RNA and DNA binding, amino acid and carbohydrate metabolism. In addition, 171 methylated proteins were previously reported with phosphorylation sites inT. cruzi, including flagellar proteins and RNA binding proteins, indicating that there may be an interplay between these different modifications in non-histone proteins. Our results show that a broad spectrum of functions are affected by methylation indicating its potential to impact important processes in the biology of the parasite and other trypanosomes.Statement of the significanceTrypanosoma cruziis a protozoan parasite that causes Chagas’ disease in humans and faces different environmental changes throughout its life cycle. Protein methylation is an important post-translational modification by which cells respond and adapt to the environment. We applied mass spectrometry-based proteomics and reported the first proteomic analysis of arginine and lysine methylation inT. cruzi. Our data demonstrate that protein methylation is broad and impacts different cellular processes inT. cruzi. This study represents a significant advance in the investigation of the importance of protein methylation in trypanosomes.
Dynamics of endogenous PARP1 and PARP2 during DNA damage revealed by live-cell single-molecule imaging
Authors: Mahadevan Jyothi , Jha Asmita , Rudolph Johannes , Bowerman Samuel , Narducci Domenic , Hansen Anders S , Luger Karolin 
Published: March 2022

Summary/AbstractPARP1 contributes to genome architecture and DNA damage repair through its dynamic association with chromatin. PARP1 and PARP2 (PARP1/2) recognize damaged DNA and recruit the DNA repair machinery. Using single molecule microscopy in live cells, we monitored the movement of PARP1/2 on undamaged and damaged chromatin. We identify two classes of freely diffusing PARP1/2 and two classes of bound PARP1/2. The majority (> 60%) of PARP1/2 diffuse freely in both undamaged and damaged nuclei and in the presence of inhibitors of PARP1/2 used for cancer therapy (PARPi). Laser induced DNA damage results in a small fraction of slowly diffusing PARP1 and PARP2 to become transiently bound. Treatment of cells with PARPi in the presence of DNA damage causes subtle changes in the dynamics of bound PARP1/2, in contrast to bulk studies that suggest PARP trapping. Our results imply that next-generation PARPi could specifically target the small fraction of DNA-bound PARP1/2.
Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search
Authors: Bryant Patrick , Pozzati Gabriele , Zhu Wensi , Shenoy Aditi , Kundrotas Petras , Elofsson Arne 
Published: March 2022

AbstractAlphaFold can predict the structure of single- and multiple-chain proteins with very high accuracy. However, the accuracy decreases with the number of chains, and the available GPU memory limits the size of protein complexes which can be predicted. Here we show that one can predict the structure of large complexes starting from predictions of subcomponents. We assemble 91 out of 175 complexes with 10-30 chains from predicted subcomponents using Monte Carlo tree search, with a median TM-score of 0.51. There are 30 highly accurate complexes (TM-score ≥0.8, 33% of complete assemblies). We create a scoring function, mpDockQ, that can distinguish if assemblies are complete and predict their accuracy. We find that complexes containing symmetry are accurately assembled, while asymmetrical complexes remain challenging. The method is freely available and accesible as a Colab notebook https://colab.research.google.com/github/patrickbryant1/MoLPC/blob/master/MoLPC.ipynb.
Piezo2 expressing nociceptors mediate mechanical sensitization in experimental osteoarthritis
Authors: Obeidat Alia M. , Wood Matthew J. , Ishihara Shingo , Li Jun , Wang Lai , Ren Dongjun , Bennett David A. , Miller Richard J. , Malfait Anne-Marie , Miller Rachel E. 
Published: March 2022

AbstractOsteoarthritis is a very common painful joint disease, for which few treatment options exist. New non-opioid targets are needed for addressing osteoarthritis pain, which is mechanical in nature and associated with daily activities such as walking and climbing stairs. Piezo2 has been implicated in development of mechanical pain, but the mechanisms by which this occurs remain poorly understood. We observed that in two different murine models of osteoarthritis (destabilization of the medial meniscus and natural aging), nociceptor-specific Piezo2 conditional knock-out mice developed osteoarthritic joint damage, but were protected from associated mechanical sensitization. Since nerve growth factor (NGF) is known to mediate nociceptor sensitization, and antibodies that neutralize NGF are effective as a treatment for osteoarthritis pain, we explored the effects of intra-articularly injected NGF on the development of mechanical joint pain. Wild-type mice developed knee swelling and mechanical pain in response to intra-articular NGF, while nociceptor-specific Piezo2 conditional knock-out mice were protected from these effects. Single cell RNA sequencing and in situ hybridization of mouse and human lumbar dorsal root ganglia (DRG) revealed that a subset of nociceptors co-express Piezo2 and Ntrk1 (the gene that encodes the NGF receptor TrkA). These results indicate that Piezo2 plays a key role in nociceptor sensitization processes in the osteoarthritic joint, and targeting Piezo2 may represent a novel therapy for osteoarthritis pain control.One Sentence SummaryNociceptor sensitization to mechanical stimuli is dependent on Piezo2 in mouse models of osteoarthritis.
The NIN-LIKE PROTEIN 7 (NLP7) transcription factor modulates auxin pathways to regulate root cap development
Authors: Kumar Narender , Caldwell Chloe , Iyer-Pascuzzi Anjali S. 
Published: March 2022

AbstractThe root cap surrounds the root tip and promotes root growth by protecting the root apical meristem, influencing root branching, and sensing environmental signals like nitrate. The root cap maintains a constant size through the coordination of cell production in the root meristem with cell release at the tip of the root, a process that requires an auxin minima in the last layer of the root cap. To perform its functions, the root cap must maintain a constant size and synchronize external cues with development, but mechanisms underlying such coordination are not well understood. Mutations in the NIN LIKE PROTEIN 7 (NLP7) transcription factor, a master regulator of nitrate signaling, lead to defects in root cap cell release and cell production. Nitrate impacts root development through crosstalk with auxin. Therefore, we hypothesized that NLP7 regulates root cap cell release and cell production by modulating auxin pathways. Here we show that mutations in NLP7 abolish the auxin minima required for root cap cell release and alter root cap expression levels of the auxin carriers PIN-LIKES 3 (PILS3) and PIN-FORMED 7 (PIN7). We find that NLP7 is required for proper root cap cell production and differentiation and for expression of transcription factors that regulate these processes. Nitrate deficiency impacts auxin pathways in the last layer of the root cap, and this is mediated in part by NLP7. Together, our data suggest that NLP7 integrates nitrate signaling with auxin pathways to optimize root cap development in response to external nitrate cues.One sentence summaryThe nitrate master regulator NLP7 controls root cap development through auxin pathways.
Neural Activity in Afferent Projections to the Infralimbic Cortex is Associated with Individual Differences in the Recall of Fear Extinction
Authors: Russo Amanda S. , Parsons Ryan G. 
Published: March 2022

AbstractPost-traumatic stress disorder (PTSD) is characterized by an impaired ability to extinguish fear responses to trauma-associated cues. Studies in humans and non-human animals point to differences in the engagement of certain frontal cortical regions as key mediators determining whether or not fear extinction is successful, however the neural circuit interactions that dictate the differential involvement of these regions are not well understood. To better understand how individual differences in extinction recall are reflected in differences in neural circuit activity, we labeled projections to the infralimbic cortex (IL) in rats using a retrograde tracer and compared neural activity within, and outside, of IL-projecting neurons. We analyzed these data in groups separated on the basis of how well rats retained extinction memory. We found that within IL-projecting cells, neurons in the posterior paraventricular thalamus showed heightened activity in rats that showed good extinction recall. Outside of the IL-projecting cells, increased Fos activity was observed in good extinction rats in select regions of the claustrum and ventral hippocampus. Our results indicate that differences in extinction recall are associated with a specific pattern of neural activity both within and outside of projections to the IL.