bluuebunny/crossref_metadata_2025_split huggingface dataset:
A scalable phenotyping approach for female floral organ development and senescence in the absence of pollination in wheat
Authors: Millan-Blanquez Marina , Hartley Matthew , Bird Nicholas , Manes Yann , Uauy Cristobal , Boden Scott 
Published: April 2022

AbstractIn the absence of pollination, female reproductive organs senesce leading to an irrevocable loss in the reproductive potential of the flower and directly affecting seed set. In self-pollinating crops like wheat (Triticum aestivum), the post-anthesis viability of the unpollinated carpel has been overlooked, despite its importance for hybrid seed production systems. To advance our knowledge of carpel development in the absence of pollination, we created a relatively high-throughput phenotyping approach to quantify stigma and ovary morphology. We demonstrate the suitability of the approach, which is based on light microscopy imaging and machine learning, for the detailed study of floral organ traits in field grown plants using both fresh and fixed samples. We show that the unpollinated carpel undergoes a well-defined initial growth phase, followed by a peak phase (in which stigma area reaches its maximum and the radial expansion of the ovary slows), and a final deterioration phase. These developmental dynamics were largely consistent across years and could be used to classify male sterile cultivars, however the absolute duration of each phase varied across years. This phenotyping approach provides a new tool for examining carpel morphology and development which we hope will help advance research into this field and increase our mechanistic understanding of female fertility in wheat.
Nonlethal effects of predation: Presence of insectivorous birds affects the behaviour and level of stress in insects
Authors: Kollross Jan , Jancuchova-Laskova Jitka , Kleckova Irena , Freiberga Inga , Kodrik Dalibor , Sam Katerina 
Published: April 2022

AbstractInsect exposure to their predators can affect individuals and community processes, through direct consumption or nonlethal (i.e., nonconsumptive) effects. However, the links between behavioural and physiological responses and stimuli needed for development of the fear are not clear. We therefore subjected the desert locusts (Schistocerca gregaria) to three nonlethal treatments, using the great tits (Parus major) as a potential predator. The treatments involved: (1) bird - presence of a live great tit and its calls, (2) call - great tit calls only, (3) control - without any treatment. In the first behavioural laboratory experiment, hungry locusts were kept in an experimental cage with a shelter and food on opposite sides of the cage. The duration of hiding and feeding were considered as an indicator of fear responses. In the second laboratory experiment with the same three treatments, levels of the adipokinetic hormone (AKH) were evaluated in the central nervous system (CNS) and haemolymph. In the third experiment in an outdoor aviary, birds were free to fly in larger distances from locusts, before hormone levels were measured as response to bird and control treatments. In the first behavioural experiment, the presence of tits and their call resulted in significantly longer hiding time and significantly shorter feeding time than in the call/control treatments. The proximity of birds and locusts in the laboratory experiment elicited a significant increase in the AKH levels in the CNS and haemolymph as compared to the call/control treatments. In the outdoor experiment, the AKH levels were significantly higher in the CNS of locusts exposed to the bird than to control; no difference was recorded in their haemolymph. We showed that predator exposure quickly affected behavioural responses and physiological processes of locusts. Playback of the avian calls was not an appropriate stimulus to induce stress responses in desert locusts.
Prediction of designer-recombinases for DNA editing with generative deep learning
Authors: Schmitt Lukas Theo , Paszkowski-Rogacz Maciej , Jug Florian , Buchholz Frank 
Published: April 2022

AbstractSite-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designer-recombinases has been achieved mostly through iterative cycles of directed molecular evolution. While effective, directed molecular evolution methods are laborious and time consuming. Here we present RecGen (Recombinase Generator), an algorithm for the intelligent generation of designer-recombinases. We gathered the sequence information of over two million Cre-like recombinase sequences evolved for 89 different target sites with which we trained Conditional Variational Autoencoders for recombinase generation. Experimental validation demonstrated that the algorithm can predict recombinase sequences with activity on novel target-sites, indicating that RecGen is useful to accelerate the development of future designer-recombinases.Abstract FigureTeaser Figure:Recombinase prediction generates active recombinases for a desired target site, while existing libraries with a similar target site need to go through directed evolution to achieve activity on the new site. While evolution takes weeks, prediction and synthesis of recombinases can be done in days.
Population estimation of a cryptic moss frog using acoustic spatially explicit capture recapture
Authors: Stark Debra , Turner Andrew , van Rensburg Berndt J. , Measey John 
Published: April 2022

ABSTRACTCryptic amphibians pose a problem for conservation managers as they are difficult to find to assess initial populations, and monitor changes during potentially threatening processes. The rough moss frog,Arthroleptella rugosa, is small and occurs in seepages on a single unprotected mountain in South Africa’s fire prone, biodiverse fynbos biome. The area is heavily impacted by invasive plants, which dry seepages and increase the frequency and intensity of fires, leading to the assessment of this species as Critically Endangered. We aimed to test the efficacy of acoustic spatially explicit capture recapture (aSCR) to estimate the entire population of calling adultA. rugosa, and assess the impacts by invasive plants. Using aSCR, our estimates suggest that the population ofA. rugosais more than five times that previously estimated using aural calling surveys on the mountain, at ∼2000 individuals. This despite an intense fire over the entire area three years earlier that reduced the calling population to a few tens of individuals. Our vegetation surveys suggest that the ongoing removal of invasive plants from the mountain is successful in areas occupied byA. rugosa, but that adjacent areas invaded by pines and hakea have a negative impact on calling density. The private public conservancy partnership on Klein Swartberg Mountain, is conserving this frog but will require ongoing management and monitoring to ensure conservation in the future.
Combined drought resistance strategies and the hydraulic limit in co-existing Mediterranean woody species
Authors: Alon Asaf , Cohen Shabtai , Burlett Regis , Hochberg Uri , Lukyanov Victor , Rog Ido , Klein Tamir , Cochard Herve , Delzon Sylvain , David-Schwartz Rakefet 
Published: April 2022

SummaryWoody species employ various strategies to cope with drought stress. We investigated similarities and differences in response to chronic drought to understand resistance strategies in co-occurring Mediterranean species.We studied five predominant Mediterranean species;Quercus calliprinos, Pistacia palaestina, Pistacia lentiscus, Rhamnus lycioides, andPhillyrea latifoliaover two summers at three sites with different aridities. We measured key hydraulic and osmotic traits related to drought resistance, including resistance to embolism (Ψ50), carbon isotope signature (δ13C), pre-dawn (ΨPD) and mid-day (ΨMD) water potentials, and native (Ψs) and full turgor (П0) osmotic potentials.Significant differences among species appeared in resistance to embolism. The species also showed differences in the water potential plastic response over the dry season. This interspecific variation increased at the end of the dry season and resulted in very narrow hydraulic safety margins (HSM). Consequently, predicted loss of hydraulic conductivity revealed species with significant native embolism. Two of the species also had seasonal changes in osmotic adjustment.Our detailed analysis indicates that co-existing Mediterranean woody species combine various drought resistance strategies to minimize mortality risk. However, all of them risk mortality as they approach their hydraulic limit near the dry margin of their distribution.
Single-cell profiling of lncRNAs in human germ cells and molecular analysis reveals transcriptional regulation of LNC1845 on LHX8
Authors: Wang Nan , He Jing , Feng Xiaoyu , Liao Shengyou , Zhao Yi , Tang Fuchou , Kee Kehkooi 
Published: April 2022

SUMMARYNon-coding RNAs exert diverse functions in many cell types. In addition to transcription factors from coding genes, non-coding RNAs may also play essential roles in shaping and directing the fate of germ cells. Here, we report the presence of many long non-coding RNAs (lncRNAs) which were specifically expressed in the germ cells during human gonadal development by single-cell profiling of the reported datasets, and the functional characterization of one divergent lncRNA, LNC1845. Comprehensive bioinformatic analysis of these lncRNAs indicates that divergent lncRNAs occupied the majority of female and male germ cells. Integrating lncRNA expression into the bioinformatic analysis also enhances the cell-type classification of female germ cells. Functional dissection using in vitro differentiation of human pluripotent stem cells to germ cells revealed the regulatory role of LNC1845 on a transcription factor essential for ovarian follicle development, LHX8, by modulating the levels of histone modifications, H3K4me3 and H3K27Ac. Hence, this study provides a comprehensive analysis of lncRNAs in developing germ cells and elucidates how a lncRNA function as a cis regulator during human germ cell development.GRAPHICAL ABSTRACTHIGHLIGHTSlncRNAs are expressed at significantly higher levels in both male and female germ cells than in somatic cells during human gonadal development.Divergent lncRNAs are enriched in the female meiotically and male mitotically arrested germ cells.LNC1845 regulates the transcriptional expression of LHX8 by modulating H3K4me3 and H3K27Ac levels.
Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain
Authors: Wu Di , Li Xiaowei , Tanaka Ryokei , Wood Joshua C. , Tibbs-Cortes Laura E. , Magallanes-Lundback Maria , Bornowski Nolan , Hamilton John P. , Vaillancourt Brieanne , Diepenbrock Christine H. , Li Xianran , Deason Nicholas T. , Schoenbaum Gregory R. , Yu Jianming , Robin Buell C. , DellaPenna Dean , Gore Michael A. 
Published: April 2022

AbstractTocochromanols (tocopherols and tocotrienols, collectively vitamin E) are lipid-soluble antioxidants important for both plant fitness and human health. The main dietary sources of vitamin E are seed oils that often accumulate high levels of tocopherol isoforms with lower vitamin E activity. The tocochromanol biosynthetic pathway is conserved across plant species but an integrated view of the genes and mechanisms underlying natural variation of tocochromanol levels in seed of most cereal crops remains limited. To address this issue, we utilized the high mapping resolution of the maize Ames panel of ∼1,500 inbred lines scored with 12.2 million single-nucleotide polymorphisms to generate metabolomic (mature grain tocochromanols) and transcriptomic (developing grain) data sets for genetic mapping. By combining results from genome- and transcriptome-wide association studies, we identified a total of 13 candidate causal gene loci, including five that had not been previously associated with maize grain tocochromanols: four biosynthetic genes (arodeH2paralog,dxs1,vte5, andvte7) and a plastid S-adenosyl methionine transporter (samt1). Expression quantitative trait locus (eQTL) mapping of these 13 gene loci revealed that they are predominantly regulated bycis-eQTL. Through a joint statistical analysis, we implicatedcis-acting variants as responsible for co-localized eQTL and GWAS association signals. Our multi-omics approach provided increased statistical power and mapping resolution to enable a detailed characterization of the genetic and regulatory architecture underlying tocochromanol accumulation in maize grain and provided insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in maize and other cereals.
Farnesyltransferase inhibition overcomes the adaptive resistance to osimertinib in EGFR-mutant NSCLC
Authors: Figarol Sarah , Delahaye Célia , Gence Rémi , Asslan Raghda , Pagano Sandra , Tardy Claudine , Colinge Jacques , Villemin Jean-Philippe , Maraver Antonio , Ferrer Irene , Paz-Ares Luis , Lajoie-Mazenc Isabelle , Clermont Estelle , Casanova Anne , Pradines Anne , Mazières Julien , Calvayrac Olivier , Favre Gilles 
Published: April 2022

ABSTRACTDrug-tolerant “dormant” cells (DTC) have emerged as one of the major non-genetic mechanisms driving resistance to targeted therapy in lung cancer, although the sequence of events leading to entry and exit from dormancy remain poorly described. Here, we performed real-time monitoring of the cell cycle dynamics during the adaptive response to Epidermal Growth Factor Receptor tyrosine kinase inhibitors (EGFR-TKi) in a panel of EGFR-mutated lung cancer cell lines. We identified a rare population of S/G2 cycling cells (referred to as early escapers) that emerged in the first hours of treatment amongst stably arrested and progressively dying G1 cells. We determined that early escapers evolved from a non-proliferative differentiated alveolar type 1 (AT1) phenotype which was invariably associated with cytoskeletal remodeling through Rho/ROCK pathway activation. Using a panel of Rho-pathway inhibitors, we found that the farnesyltransferase inhibitor tipifarnib induced a complete clearance of EGFR-TKi-induced DTC thus fully preventing relapse in vitro. Using a xenograft model and a PDX model of EGFRL858R/T790M lung cancer, co-treatment with tipifarnib prevented relapse to osimertinib for up to 6 months with no evidence of toxicity. Among the farnesylated proteins regulated during osimertinib treatment, concomitant inhibition of RHOE and LaminB1 was sufficient to recapitulated FTIs’ effect. Osimertinib and tipifarnib co-treatment completely suppressed the emergence of AT1 phenotype, prevented mitosis of S/G2-treated cells and increased the apoptotic response through activation of ATF4-CHOP-dependent Integrated Stress Response (ISR) pathway. Our data strongly support the use of tipifarnib in combination with osimertinib in patients to effectively and durably prevent relapse.
Allele mining, evolutionary genetic analysis of TaHKT1;5 gene and evaluation of salinity stress in selected lines of wheat
Authors: Thiyagarajan Karthikeyan , Mathur Prem Narain , Vikram Prashant , Sehgal Deepmala , Valluru Ravi , Govindan Velu , Rahman Hifzur , Thapa Dhruba Bahadur , Pantha Sumitra , Galeffi Patrizia , Latini Arianna , Cantale Cristina , Porceddu Enrico , Joshi Arun Kumar 
Published: April 2022

ABSTRACTThis study reports the novel allelic diversity in HKT 1;5 gene (High Affinity Potassium Transporter) in bread wheat and its phylogenetic relationship among the paralogs/orthologs of in Triticum aestivum and its wild relatives. HKT 1;5 gene is a known and pivotal gene associated with the salinity tolerance in plants upon the discrimination of K+ over Na+ in leaves without change in Na+ concentration in root. This gene was sequenced in a diverse collection of bread wheat, durum wheat, wild relatives, and ditelosomic lines. Sequence analysis in bread wheat led to the identification of four alleles, which could be distinguished by number of SNPs. Sequence comparison between monocot bread wheat and dicot Arabidopsis thaliana revealed that the HKT1;5 gene is conserved at level of exonic regions; however, the presence of transposable elements especially in intronic regions is further intriguing towards evolutionary relatedness. Two paralogous or major alleles observed in Triticum monoccum and Aegilops tauschii were further categorized as sub-alleles based on their SNPs comparison. This gene was absent in T. urartu in accordance with existing evidence, while it was found in A. speltoides (an allelic variant) with a few base pairs insertion in the exon1 region causing a frameshift mutation with an altered amino acids and genomic database mining unveiled additional alleles in this species. Ditelosomic lines with 4DL and 4DS chromosomes revealed a higher similarity with bread and durum wheat respectively. Phylogenetic studies of HKT1;5 orthologs from different Poaceae species revealed the occurrence of five different ortholog groups with taxonomic consistency. Phenotyping based salinity stress experiment distinguished the unknown lines for salinity tolerance and sensitiveness in comparison with known reference lines and possible allelic comparison was made. The salinity stress analysis further revealed that some known drought/heat tolerance lines showed slightly better salinity tolerance with mean values and variability of traits than known saline tolerant wheat line at controlled ambient.
Antibodies to Coagulase ofStaphylococcus aureuscrossreact to Efb and reveal different binding of shared Fibrinogen binding repeats
Authors: Bertoglio Federico , Ko Ya-Ping , Thomas Sheila , Giordano Liliana , Scommegna Francesca Romana , Meier Doris , Polten Saskia Helmsig , Becker Marlies , Arora Srishtee , Hust Michael , Höök Magnus , Visai Livia 
Published: April 2022

AbstractStaphylococcus aureuspathology is caused by a plethora of virulence factors able to combat multiple host defence mechanisms. Fibrinogen (Fg), a critical component in the host coagulation cascade, plays an important role in the pathogenesis of this bacterium, as it is the target of multiple staphylococcal virulence proteins. Amongst its secreted virulence factors, Coagulase (Coa) and Extracellular fibrinogen-binding protein (Efb) share common Fg binding motives and have been described to form a Fg shield around staphylococcal cells, thereby allowing efficient bacterial spreading, phagocytosis escape and evasion of host immune system responses. Targeting these proteins with monoclonal antibodies thus represents a new therapeutic option againstS. aureus. To this end, here we report the selection and characterization of fully human, sequence-defined, monoclonal antibodies selected against the C-terminus of Coagulase. Given the functional homology between Coa and Efb, we also investigated if the generated antibodies bound the two virulence factors. Thirteen unique antibodies were isolated from naïve antibodies gene libraries by antibody phage display. As anticipated, most of the selected antibodies showed cross-recognition of these two proteins and among them, four were able to block the interaction between Coa/Efb and Fg. Furthermore, our monoclonal antibodies could interact with the two main Fg binding repeats present at the C-terminus of Coa and distinguish them, suggesting the presence of two functionally different Fg-binding epitopes.ImportanceThe death toll related to methicillin-resistantS. aureuspiled to almost 1 million people in only one year (2019), ascribingS. aureusto the second leading cause of deaths associated with antimicrobial resistance. Therefore, new therapeutic strategies must be investigated. Blocking the adhesion step with the use of monoclonal antibodies is one promising alternative and Fg is a central plasma protein involved in staphylococcal infection. We present here a panel of monoclonal antibodies raised against Coa, cross-reacting to Efb and targeting the shared Fg binding repeats of Coa. In addition, we describe new epitope determinants in the repeated region of Coa, highlighted by differential binding of the newly selected antibodies.
Correlates of protection, viral load trajectories and symptoms in BA.1, BA.1.1 and BA.2 breakthrough infections in triple vaccinated healthcare workers
Authors: Marking Ulrika , Havervall Sebastian , Greilert Norin Nina , Bladh Oscar , Christ Wanda , Gordon Max , Ng Henry , Blom Kim , Phillipson Mia , Mangsbo Sara , Smed Sörensen Anna , Nilsson Peter , Hober Sophia , Åberg Mikael , Klingström Jonas , Thålin Charlotte 
Published: April 2022

AbstractBackgroundBooster vaccine doses offer protection against severe COVID-19 caused by omicron but are less effective against infection. Characteristics such as serological correlates of protection, viral abundance, and clearance of omicron infection in triple vaccinated individuals are scarce.MethodsWe conducted a 4-week twice-weekly SARS-CoV-2 qPCR screening shortly after an mRNA vaccine booster in 368 healthcare workers. Spike-specific IgG levels and neutralization titers were determined at study start. qPCR-positive participants were sampled repeatedly for two weeks and monitored for symptoms.ResultIn total 81 (cumulative incidence 22%) omicron infections were detected, divided between BA.1, BA.1.1 and BA.2. Increasing post-booster antibody titers were protective against infection (p<0.05), linked to reduced viral load (p<0.01) and time to viral clearance (p<0.05). Only 10% of infected participants remained asymptomatic through the course of their infection. Viral load peaked at day 3 and live virus could be detected for up to 9 days after first PCR-positive sample. Presence of symptoms correlated to elevated viral load (p<0.0001), but despite resolution of symptoms most participants showed Ct levels <30 at day 9. No significant differences were observed for viral load and time to viral clearance between BA.1, BA.1.1 and BA.2 infected individuals.ConclusionWe report a high incidence of omicron infection despite recent booster vaccination in triple vaccinated individuals. Increasing levels of vaccine-induced spike-specific WT antibodies entail increased protection against infection and reduce viral load if infected. High viral load and secretion of live virus for up to nine days may facilitate transmission in a triple vaccinated population.