bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prioritized imputed sequence variants from multi-population GWAS improve prediction accuracy for sea lice count in Atlantic salmon (Salmo salar)
Authors: Garcia Baltasar F. , Cáceres Pablo A. , Marín-Nahuelpi Rodrigo , Lopez Paulina , Cichero Daniela , Ødegård Jorgen , Moen Thomas , Yáñez José M. 
Published: July 2023

AbstractSea lice infestation is one of the major fish health problems during the grow-out phase in Atlantic salmon (Salmo salar) aquaculture. In this study, we integrated different genomic approaches, including whole-genome sequencing (WGS), genotype imputation and meta-analysis of genome-wide association studies (GWAS), to identify single-nucleotide polymorphisms (SNPs) associated with sea lice count in Atlantic salmon. Different sets of trait-associated SNPs were prioritized and compared against randomly chosen markers, based on the accuracy of genomic predictions for the trait. Lice count phenotypes and dense genotypes of five breeding populations challenged against sea lice were used. Genotype imputation was applied to increase SNP density of challenged animals to WGS level. The summary statistics from GWAS of each population were then combined in a meta-analysis to increase the sample size and improve the statistical power of associations. Eight different genotyping scenarios were considered for genomic prediction: 70K_array: 70K standard genotyping panel; 70K_priori: 70K SNPs with the highest p-values identified in the meta-analysis; 30K_priori: 30K SNPs with the highest p-values identified in the meta-analysis; WGS: SNPs imputed to whole-genome sequencing level; and the remaining four scenarios were the same SNP sets with a linkage disequilibrium (LD) pruning filter: 70K_array_LD; 70K_priori_LD; 30K_priori_LD and WGS_LD, respectively. Genomic prediction accuracy was evaluated using a five-fold cross-validation scheme in two different populations excluding them from the meta-analysis to remove possible validation-reference bias. Results showed significant genetic variation for sea lice counting in Atlantic salmon across populations, with heritabilities ranging from 0.06 to 0.24. The meta-analysis identified several SNPs associated with sea lice resistance, mainly inSsa03andSsa09chromosomes. Genomic prediction using the GWAS-based prioritized SNPs showed higher accuracy compared to using the standard SNP array in most of scenarios, achieving up to 57% increase in accuracy. Accuracy of prioritized scenarios was higher for the 70K_priori in comparison to 30K_priori. The use of WGS data in genomic prediction presented marginal or negative accuracy gain compared to the standard SNP array. The LD-pruning filter presented no benefits, reducing accuracy in most of scenarios. Overall, our study demonstrated the potential of prioritized of imputed sequence variants from multi-population GWAS meta-analysis to improve prediction accuracy for sea lice count in Atlantic salmon. The findings suggest that incorporating WGS data and prioritized SNPs from GWAS meta-analysis can accelerate the genetic progress of selection for polygenic traits in salmon aquaculture.
Evolution from mixed to fixed handedness in mirror-image flowers: insights from adaptive dynamics
Authors: Saltini Marco , Barrett Spencer C.H. , Deinum Eva E. 
Published: July 2023

AbstractMirror-image flowers (enantiostyly) involve a form of sexual asymmetry in which a flower’s style is deflected either to the left or right side, with a pollinating anther orientated in the opposite direction. This curious floral polymorphism, which was known but not studied by Charles Darwin, occurs in at least 11 unrelated angiosperm families and represents a striking example of adaptive convergence in form and function associated with cross-pollination by insects. In several lineages, dimorphic enantiostyly (one stylar orientation per plant, both forms occurring within populations) has evolved from monomorphic enantiostyly, in which all plants can produce both style orientations. We use a modelling approach to investigate the emergence of dimorphic enantiostyly from monomorphic enantiostyly under gradual evolution. We show using adaptive dynamics that depending on the balance between inbreeding depression following geitonogamy, pollination efficiency and plant density, dimorphism can evolve from an ancestral monomorphic population. In general, the newly emergent dimorphic population is stable against invasion of a monomorphic mutant. However, our model predicts that under certain ecological conditions, e.g., a decline of pollinators, dimorphic enantiostyly may revert to a monomorphic state. We demonstrate using population genetics simulations that the observed evolutionary transitions are possible assuming a plausible genetic architecture.
DNA Recognition and Induced Genome Modification by a Hydroxymethyl-γ Tail-Clamp Peptide Nucleic Acid
Authors: Oyaghire Stanley N. , Quijano Elias , Perera J. Dinithi. R. , Mandl Hanna K. , Saltzman W. Mark , Bahal Raman , Glazer Peter M. 
Published: July 2023

SUMMARYPeptide nucleic acids (PNA) can target and stimulate recombination reactions in genomic DNA. We have reported that gamma (γ)-PNA oligomers possessing the diethylene glycol γ-substituent show improved efficacy over unmodified PNAs in stimulating recombination-induced gene modification. However, this structural modification poses a challenge because of the inherent racemization risk inO-alkylation of the precursory serine side chain. To circumvent this risk and improve γPNA accessibility, we explore the utility of γPNA oligomers possessing the hydroxymethyl-γ moiety for gene editing applications. We demonstrate that a γPNA oligomer possessing the hydroxymethyl modification, despite weaker preorganization, retains the ability to form a hybrid with the double-stranded DNA target of comparable stability and with higher affinity to that of the diethylene glycol-γPNA. When formulated into poly(lactic-co-glycolic acid) nanoparticles, the hydroxymethyl-γPNA stimulates higher frequencies (≥ 1.5-fold) of gene modification than the diethylene glycol γPNA in mouse bone marrow cells.
Cholesterol-associated LocusEHBP1Protects against NASH Fibrosis
Authors: Ma Fanglin , Longo Miriam , Huang Xin , Meroni Marica , Prakash Satya , Paolini Erika , Bhattacharya Dipankar , Wang Shuang , Wang Xiaobo , Mughal Shama , Hussain Syed , Anand Sumit , Yurdagul Arif , Rom Oren , Dongiovanni Paola , Friedman Scott , Cai Bishuang 
Published: July 2023

SUMMARYHepatic free cholesterol contributes to fibrosis in nonalcoholic steatohepatitis (NASH), but how hepatic cholesterol metabolism becomes dysregulated in NASH is not completely understood. We show here that human fibrotic NASH livers have decreasedEHBP1, a novel GWAS locus associated with LDL-cholesterol, and that theEHBP1rs10496099 T>C variant in NASH patients is associated with decreased hepaticEHBP1expression and augmented NASH fibrosis. Congruent with the human data, EHBP1 loss- and gain-of-function increases and decreases NASH fibrosis in mice, respectively. Mechanistic studies reveal that EHBP1 promotes sortilin (SORT1)-mediated PCSK9 secretion, leading to LDLR degradation, decreased LDL uptake, and reduced TAZ, a fibrogenic effector. Moreover, we show that the TNFα/PPARα pathway suppresses EHBP1 in NASH. These data not only provide new mechanistic insight into the role of EHBP1 in cholesterol metabolism and NASH fibrosis by uncovering the interaction between EHBP1 and other cholesterol–related loci, includingSORT1,PCSK9, andLDLR, but also elucidate a novel interplay between inflammation and EHBP1-mediated cholesterol metabolism.HighlightsHepatic EHBP1 is reduced in human and mouse fibrotic NASHEHBP1rs10496099 T>C is associated with decreased hepatic EHBP1 and augmented NASHEHBP1 reduces LDLR, cholesterol uptake, and TAZ in hepatocytesEHBP1 promotes sortilin-mediated PCSK9 secretion in hepatocytesTNFα suppresses EHBP1 expression in hepatocytes
Diversity and modularity of tyrosine-accepting tRNA-like structures
Authors: Sherlock Madeline E. , Langeberg Conner J. , Kieft Jeffrey S. 
Published: July 2023

ABSTRACTCertain positive-sense single-stranded RNA viruses contain elements at their 3’ termini that structurally mimic tRNAs. These tRNA-like structures (TLSs) are classified based on which amino acid is covalently added to the 3’ end by host aminoacyl-tRNA synthetase. Recently, a cryoEM reconstruction of a representative tyrosine-accepting tRNA-like structure (TLSTyr) from brome mosaic virus (BMV) revealed a unique mode of recognition of the viral anticodon-mimicking domain by tyrosyl-tRNA synthetase. Some viruses in thehordeivirusgenus ofVirgaviridaeare also selectively aminoacylated with tyrosine, yet these TLS RNAs have a different architecture in the 5’ domain that comprises the atypical anticodon loop mimic. Herein, we present bioinformatic and biochemical data supporting a distinct secondary structure for the 5′ domain of thehordeivirusTLSTyrcompared to those inBromoviridae. Despite forming a different secondary structure, the 5′ domain is necessary to achieve robustin vitroaminoacylation. Furthermore, a chimeric RNA containing the 5′ domain from the BMV TLSTyrand the 3′ domain from ahordeivirusTLSTyrare aminoacylated, illustrating modularity in these structured RNA elements. We propose that the structurally distinct 5′ domain of thehordeivirusTLSTyrs performs the same role in mimicking the anticodon loop as its counterpart in the BMV TLSTyr. Finally, these structurally and phylogenetically divergent types of TLSTyrprovide insight into the evolutionary connections between all classes of viral tRNA-like structures.
The Lion’s Share: Implications of carnivore diet on endangered herbivores in Tsavo
Authors: King Eliza , Chakrabarti Stotra , Lala Fredrick , Nyagah Stephen , Waiguchu Grace , Chiyo Patrick I. , Kimaile Joseph , Moller Richard , Omondi Patrick , Morris Aaron , Bump Joseph K. 
Published: July 2023

AbstractPredation by mammalian carnivores can have cascading, regulatory effects across ecological communities. An understanding of predator diet can therefore provide crucial information regarding their ecology and conservation, as well as their impacts on prey populations. Using scats collected between 2019 and 2023, coupled with estimates of prey abundance from aerial surveys, we characterized lion prey-consumption and preference in Tsavo, Kenya. A lion-specific biomass model applied to prey frequencies in scats revealed that more than 85% of lion diet consisted of large ungulates weighing over 150 kg. While large ungulates were also preferred prey items in terms of their availability, we found a disproportionately high consumption and preference of lions for the endangered hirola and Grevy’s zebra— species that were introduced in Tsavo as part of ex-situ conservation programs. Hirola and Grevy’s zebra populations have historically remained small in Tsavo despite strong recovery efforts, and our results likely indicate a disproportionate impact of lion predation on these small but crucial populations. Preferential predation, coupled with high availability of alternative prey, may trap hirola and Grevy’s zebra within apredator-pit. Our findings have strong implications for understanding lion diet, optimal foraging, and the potential effects predators have on endangered prey species in a landscape of critical conservation importance.
Synovial 1 Sarcoma X Breakpoint Protein Uses a Cryptic Groove to Selectively Recognize H2AK119Ub Nucleosomes
Authors: Tong Zebin , Ai Huasong , Xu Ziyu , He Kezhang , Chu Guo-Chao , Shi Qiang , Deng Zhiheng , Xue Qiaomei , Sun Maoshen , Du Yunxiang , Liang Lujun , Li Jia-Bin , Pan Man , Liu Lei 
Published: July 2023

AbstractThe cancer-specific fusion oncoprotein SS18-SSX1 disturbs chromatin accessibility by hijacking the BAF complex from the promoters and enhancers to the polycomb-repressed chromatin regions. This process relies on the selective recognition of H2AK119Ub nucleosomes by SSX1. However, the mechanism by which SSX1 selective recognition of H2AK119Ub nucleosomes in the absence of ubiquitin (Ub)-binding capacity remains unknown. Here we report the cryo-EM structure of SSX1 bound to H2AK119Ub nucleosomes at 3.1 Å resolution. Combinedin vitrobiochemical and cellular assays revealed that the Ub recognition by SSX1 is unique and depends on a cryptic basic groove formed by H3 and the Ub motif on the H2AK119 site. Moreover, this unorthodox binding mode of SSX1 induces DNA unwrapping at the entry/exit sites. Together, our results describe a unique mode of site-specific ubiquitinated nucleosome recognition that underlies the specific hijacking of the BAF complex to polycomb regions by SS18-SSX1 in synovial sarcoma.
Label-free ghost cytometry for manufacturing of cell therapy products
Authors: Teranishi Kazuki , Wagatsuma Keisuke , Toda Keisuke , Nomaru Hiroko , Yanagihashi Yuichi , Ochiai Hiroshi , Akai Satoru , Mochizuki Emi , Onda Yuuki , Nakagawa Keiji , Sugimoto Keiki , Takahashi Shinya , Yamaguchi Hideto , Ota Sadao 
Published: July 2023

ABSTRACTAutomation and quality control (QC) are critical in manufacturing safe and effective cell and gene therapy products. However, current QC methods, reliant on molecular staining, pose difficulty in in-line testing and can increase manufacturing costs. Here we demonstrate the potential of using label-free ghost cytometry (LF-GC), a machine learning-driven, multidimensional, high-content, and high-throughput flow cytometry approach, in various stages of the cell therapy manufacturing processes. LF-GC accurately quantified cell count and viability of human peripheral blood mononuclear cells (PBMCs) and identified non-apoptotic live cells and early apoptotic/dead cells in PBMCs, T cells and non-T cells in white blood cells (WBCs), activated T cells and quiescent T cells in PBMCs, and particulate impurities in PBMCs. The data support that LF-GC is a non-destructive label-free cell analytical method that can be used to monitor cell numbers, assess viability, identify specific cell subsets or phenotypic states, and remove impurities during cell therapy manufacturing. Thus, LF-GC holds the potential to enable full automation in the manufacturing of cell therapy products with reduced cost and increased efficiency.
Coherent cortical representations develop after experience via feedforward-recurrent circuit alignment
Authors: Lempel Augusto Abel , Trägenap Sigrid , Tepohl Clara , Kaschube Matthias , Fitzpatrick David 
Published: July 2023

AbstractSensory cortical areas guide behavior by transforming stimulus-driven inputs into selective responses representing relevant features. A classic example is the representation of edge orientations in the visual cortex1–4, where layer 4 (L4) neurons co-activated by an orientation provide feedforward inputs to specific functional modules in layer 2/3 (L2/3) that share strong recurrent connections5–7. The aligned state of feedforward-recurrent interactions is critical for amplifying selective cortical responses8–12, but how it develops remains unclear. Using simultaneous electrophysiology and calcium imaging in visually naïve animals we find that coactivity of L4 neurons and L2/3 modular responses elicited by oriented gratings lacks the tight relationship to orientation preference found in experienced animals. One factor that could contribute to the lack of functionally specific coactivity is high variability in naïve L4 neuron responses that decreases significantly following experience. But a computational model of feedforward-recurrent interaction suggests that high variability alone is insufficient to explain the naïve state and provides a biological signature of feedforward-recurrent misalignment that we confirm with whole-cell recordings: dynamic changes in orientation tuning of L2/3 subthreshold responses shortly after stimulus onset. In conclusion, we provide diverse evidence for a realignment of feedforward-recurrent interactions following experience that is critical for building reliable sensory representations with interlaminar temporal coherence.
Real-Time Spatiotemporal Measurement of Extracellular Signaling Molecules Using an Aptamer Switch-Conjugated Hydrogel Matrix
Authors: Park Chan Ho , Thompson Ian A. P. , Newman Sharon S. , Hein Linus A. , Lian Xizhen , Fu Kaiyu , Pan Jing , Eisenstein Michael , Tom Soh H. 
Published: July 2023

AbstractCells rely on secreted signaling molecules to coordinate essential biological functions including development, metabolism, and immunity. Unfortunately, such signaling processes remain difficult to measure with sufficient chemical specificity and temporal resolution. To address this need, we have developed an aptamer-conjugated hydrogel matrix that enables continuous fluorescent measurement of specific secreted analytes – in two dimensions, in real-time. As a proof of concept, we performed real-time imaging ofDictyostelium discoideumcells, a well-studied amoeba model wherein inter-cellular communication is performed though cAMP signaling. We engineered a set of aptamer switches that generate a rapid and reversible change in fluorescence in response to cAMP signals. By combining multiple switches with different dynamic ranges, we can measure cAMP concentrations spanning three orders of magnitude in a single experiment. These sensors are embedded within a biocompatible hydrogel on which cells are cultured and their cAMP secretions can be imaged using fluorescent microscopy. Using this aptamer-hydrogel material system, we achieved the first direct measurements of oscillatory cAMP signaling that correlate closely with previous indirect measurements. Using different aptamer switches, this approach could be generalized for measuring other secreted molecules to directly visualize diverse extracellular signaling processes and the biological effects that they trigger in recipient cells.
Novel multifunctional glycan probes to elucidate specificities of diverse glycan recognition systems
Authors: Yu Jin , Decout Alexiane C. , Di Maio Antonio , Chai Wengang , Stehle Thilo , Turnbull W. Bruce , Feizi Ten , Liu Yan 
Published: July 2023

AbstractGlycan microarrays of sequence-defined glycans are the most widely used approach for high-throughput studies of interactions of glycans with glycan binding proteins. Currently nitrocellulose (NC) coated or N-hydroxysuccinimide (NHS) functionalized glass slides are the two most commonly used surfaces for immobilizing glycan probes as noncovalent and covalent arrays, respectively. The mode of glycan presentation can have an influence on the microarray readouts and is an important consideration in the glycan recognition knowledgebase. Here we present the development of glycan probes, tagged with a novel type of tri-functional Fmoc-amino-azido (FAA) linker, which can be readily converted into lipid-tagged or amino-terminating glycan probes for generating neoglycolipid (NGL)-based noncovalent arrays as well as covalent arrays. The azido functionality in the FAA glycan probes provides a means to ‘light up’ the glycans via biorthogonal ‘Click’ chemistry so that they become ‘scanner-readable’ on the covalent arrays, which represents an advance in array quality control. Here analyses were carried out with a diverse set of 36 glycan binding proteins (GBPs) to compare the performance of 44 glycans presented in a liposomal formulation as noncovalent arrays on NC coated slides and on two types of NHS slides as covalent arrays. With most of anti-glycan antibodies and plant lectins investigated, there were negligible or subtle differences in the binding detected in different arrays. However, there were some striking differences observed between the covalent and noncovalent arrays. These include binding ofLotus TetragonolobusLectin (LTL) on the covalent but not the noncovalent arrays, and a clear preference observed for glycans on the noncovalent array in the binding of adhesins (VP1 proteins) of two human polyomaviruses JCPyV and BKPyV, and the human immune lectins Siglecs 7 and 9. Subtle yet significant differences in the binding to low affinity glycan ligands were also observed with three bacterial toxins in different arrays. These results revealed interesting insights into the binding behaviour of different GBPs on the noncovalent and covalent arrays and highlight the importance to consider different array platforms in elucidating glycan mediated interactions. The FAA glycan probes can be readily rendered fluorescent via ‘Click’ chemistry in solution, enabling the detection of GBPs at the surface of cells.Abstract FigureA new trifunctional linker can present glycans on different array surfaces for analyses of soluble glycan binding proteins or as fluorescent probes for binding by proteins at the surface of cells.
Gene editing of putative cAMP and Ca2+-regulated proteins using an efficient cloning-free CRISPR/Cas9 system inTrypanosoma cruzi
Authors: Chiurillo Miguel A. , Ahmed Milad , González César , Raja Aqsa , Lander Noelia 
Published: July 2023

ABSTRACTTrypanosoma cruzi, the agent of Chagas disease, must adapt to a diversity of environmental conditions that it faces during its life cycle. The adaptation to these changes is mediated by signaling pathways that coordinate the cellular responses to the new environmental settings. Cyclic AMP (cAMP) and Calcium (Ca2+) signaling pathways regulate critical cellular processes in this parasite, such as differentiation, osmoregulation, host cell invasion and cell bioenergetics. Although the use of CRISPR/Cas9 technology prompted reverse genetics approaches for functional analysis inT. cruzi, it is still necessary to expand the toolbox for genome editing in this parasite, as for example to perform multigene analysis. Here we used an efficient T7RNAP/Cas9 strategy to tag and delete three genes predicted to be involved in cAMP and Ca2+signaling pathways: a putative Ca2+/calmodulin-dependent protein kinase (CAMK), Flagellar Member 6 (FLAM6) and Cyclic nucleotide-binding domain/C2 domain-containing protein (CC2CP). We endogenously tagged these three genes and determined the subcellular localization of the tagged proteins. Furthermore, the strategy used to knockout these genes allow us to presume thatTcCC2CPis an essential gene inT. cruziepimastigotes. Our results will open new venues for future research on the role of these proteins inT. cruzi.
Viruses in laboratoryDrosophilaand their impact on host gene expression
Authors: Kuyateh Oumie , Obbard Darren J 
Published: July 2023

AbstractDrosophila melanogasterhas one of the best characterized antiviral immune responses among invertebrates. However, relatively few easily-transmitted natural virus isolates are available, and so manyDrosophilaexperiments have been performed using artificial infection routes and artificial host-virus combinations. These may not reflect natural infections, especially for subtle phenotypes such as gene expression. Here, to explore the laboratory virus community and to better understand how natural virus infections induce changes in gene expression, we analyse seven publicly availableD. melanogastertranscriptomic sequencing libraries that were originally sequenced for projects unrelated to virus infection. We find ten known viruses—including five that have not been experimentally isolated—but no previously unknown viruses. Our analysis of host gene expression found numerous genes were differentially expressed in flies that were naturally infected with a virus. For example, flies infected with nora virus showed patterns of gene expression consistent with intestinal vacuolization and host attempted repair via the upd3 JAK/STAT pathway. We also found marked sex-differences in virus-induced differential gene expression. Our results show that natural virus infection in laboratoryDrosophiladoes indeed induce detectable changes in gene expression, suggesting that this may form an important background condition for experimental studies in the laboratory.