Explore the vast range of titles available.

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.

Background: Objective assessment of shoulder joint active range of motion (AROM) is critical to monitor patient progress after conservative or surgical intervention. Advancements in miniature devices have led researchers to validate inertial sensors to capture human movement. This study investigated the construct validity as well as intra- and inter-rater reliability of active shoulder mobility measurements using a coupled system of inertial sensors and the Microsoft Kinect (HumanTrak). Methods: 50 healthy participants with no history of shoulder pathology were tested bilaterally for fixed and free ROM: (1) shoulder flexion, and (2) abduction using HumanTrak and goniometry. The repeat testing of the standardised protocol was completed after seven days by two physiotherapists. Results: All HumanTrak shoulder movements demonstrated adequate reliability (intra-class correlation (ICC) ≥ 0.70). HumanTrak demonstrated higher intra-rater reliability (ICCs: 0.93 and 0.85) than goniometry (ICCs: 0.75 and 0.53) for measuring free shoulder flexion and abduction AROM, respectively. Similarly, HumanTrak demonstrated higher intra-rater reliability (ICCs: 0.81 and 0.94) than goniometry (ICCs: 0.70 and 0.93) for fixed flexion and abduction AROM, respectively. Construct validity between HumanTrak and goniometry was adequate except for free abduction. The differences between raters were predominately acceptable and below ±10°. Conclusions: These results indicated that the HumanTrak system is an objective, valid and reliable way to assess and track shoulder ROM.

Long-read sequencing facilitates assembly of complex genomic regions. In plants, loci containing nucleotide-binding, leucine-rich repeat (NLR) disease resistance genes are an important example of such regions. NLR genes constitute one of the largest gene families in plants and are often clustered, evolving via duplication, contraction, and transposition. We recently mapped the Xo1 locus for resistance to bacterial blight and bacterial leaf streak, found in the American heirloom rice variety Carolina Gold Select, to a region that in the Nipponbare reference genome is NLR gene-rich. Here, toward identification of the Xo1 gene, we combined Nanopore and Illumina reads and generated a high-quality Carolina Gold Select genome assembly. We identified 529 complete or partial NLR genes and discovered, relative to Nipponbare, an expansion of NLR genes at the Xo1 locus. One of these has high sequence similarity to the cloned, functionally similar Xa1 gene. Both harbor an integrated zfBED domain, and the repeats within each protein are nearly perfect. Across diverse Oryzeae, we identified two sub-clades of NLR genes with these features, varying in the presence of the zfBED domain and the number of repeats. The Carolina Gold Select genome assembly also uncovered at the Xo1 locus a rice blast resistance gene and a gene encoding a polyphenol oxidase (PPO). PPO activity has been used as a marker for blast resistance at the locus in some varieties; however, the Carolina Gold Select sequence revealed a loss-of-function mutation in the PPO gene that breaks this association. Our results demonstrate that whole genome sequencing combining Nanopore and Illumina reads effectively resolves NLR gene loci. Our identification of an Xo1 candidate is an important step toward mechanistic characterization, including the role(s) of the zfBED domain. Finally, the Carolina Gold Select genome assembly will facilitate identification of other useful traits in this historically important variety.

Lygus species of plant-feeding insects have emerged as economically important pests of cotton in the United States. These species are not controlled by commercial Bacillus thuringiensis (Bt) cotton varieties resulting in economic losses and increased application of insecticide. Previously, a Bt crystal protein (Cry51Aa2) was reported with insecticidal activity against Lygus spp. However, transgenic cotton plants expressing this protein did not exhibit effective protection from Lygus feeding damage. Here we employ various optimization strategies, informed in part by protein crystallography and modelling, to identify limited amino-acid substitutions in Cry51Aa2 that increase insecticidal activity towards Lygus spp. by >200-fold. Transgenic cotton expressing the variant protein, Cry51Aa2.834_16, reduce populations of Lygus spp. up to 30-fold in whole-plant caged field trials. One transgenic event, designated MON88702, has been selected for further development of cotton varieties that could potentially reduce or eliminate insecticide application for control of Lygus and the associated environmental impacts. Plant-feeding insects of the Lygus genus have emerged as a major pest effecting cotton crops in the USA. Here the authors optimize the insecticidal activity of a Bacillus thuringiensis crystal protein and produce transgenic plants that are resistant to feeding damage by Lygus species.

Background Extracorporeal cardiopulmonary resuscitation (ECPR) is an established rescue therapy for both out-of-hospital cardiac arrest (OHCA) and in-hospital cardiac arrest (IHCA). However, there remains significant heterogeneity in populations and outcomes across different studies. The primary aim of this study was to compare commonly used selection criteria and their effect on survival and utilisation in an Australian ECPR cohort. Methods We performed a retrospective, observational study of three established ECPR centres in Australia, including cases from 1 January 2013 to 31 December 2020 to establish the baseline cohort. We applied five commonly used ECPR selection criteria, ranging from restrictive to liberal. Results The baseline cohort included 199 ECPR cases: 95 OHCA and 104 IHCA patients. Survival to hospital discharge was 20% for OHCA and 41.4% for IHCA. For OHCA patients, strictly applying the most restrictive criteria would have resulted in the highest survival rate 7/16 (43.8%) compared to the most liberal criteria 16/73 (21.9%). However, only 16/95 (16.8%) in our cohort strictly met the most restrictive criteria versus 73/95 (76.8%) with the most liberal criteria. Similarly, in IHCA, the most restrictive criteria would have resulted in a higher survival rate in eligible patients 10/15 (66.7%) compared to 27/59 (45.8%) with the most liberal criteria. With all criteria a large portion of survivors in IHCA would not have been eligible for ECMO if strictly applying criteria, 33/43 (77%) with restrictive and 16/43 (37%) with the most liberal criteria. Conclusions Adherence to different selection criteria impacts both the ECPR survival rate and the total number of survivors. Commonly used selection criteria may be unsuitable to select IHCA ECPR patients.

Background Fusarium Head Blight (FHB) is a destructive fungal disease affecting wheat and barley, leading to significant yield losses and reduced grain quality. Susceptibility to FHB is influenced by genetic factors, environmental conditions, and genotype-by-environment interactions (GxE), making it challenging to predict disease resistance across diverse environments. This study investigates GxE in a long-term spring wheat multi-environment uniform nursery trial focusing on the evaluation of resistant lines in northern US breeding programs. Results Traditionally, GxE has been analyzed as a reaction norm over an environment index. Here, we computed the environment index as a linear combination of environmental covariables specific to each environment, and we derived an environment relationship matrix. Three methods were compared, all aimed at predicting untested genotypes in untested environments: the widely used Finlay-Wilkinson regression (FW), the joint-genomic regression analysis (JGRA) method, and mixed models incorporating an environmental covariates matrix. These were benchmarked against a baseline genomic selection model (GS) without environmental covariates. Predictive abilities were assessed within and across environments. The results revealed that the JGRA marker effect method was more accurate than GS in within- and across-environment predictions, although the differences were small. The predictive ability slightly decreased when the target environment was less related to the training environments. Mixed models performed similarly to JGRA within-environment, but JGRA outperformed the other methods for across-environment predictions. Additionally, JGRA identified significant genetic markers associated with baseline FHB resistance and environmental sensitivity. Furthermore, location-specific genomic estimated breeding values were predicted, providing insights into genotype stability across varying locations. Conclusion These findings highlight the value of incorporating environmental covariates to increase predictive ability and improve the selection of resistant genotypes for diverse, untested environments. By leveraging this approach, breeders can effectively exploit GxE interactions to improve disease management at no additional cost.

Delivered into plant cells by type III secretion from pathogenic species, TAL (transcription activator-like) effectors are nuclear-localized, DNA-binding proteins that directly activate specific host genes. Targets include genes important for disease, genes that confer resistance, and genes inconsequential to the host-pathogen interaction. TAL effector specificity is encoded by polymorphic repeats of 33-35 amino acids that interact one-to-one with nucleotides in the recognition site. Activity depends also on N-terminal sequences important for DNA binding and C-terminal nuclear localization signals (NLS) and an acidic activation domain (AD). Coding sequences missing much of the N- and C-terminal regions due to conserved, in-frame deletions are present and annotated as pseudogenes in sequenced strains of pv. oryzicola (Xoc) and pv. oryzae (Xoo), which cause bacterial leaf streak and bacterial blight of rice, respectively. Here we provide evidence that these sequences encode proteins we call \"truncTALEs,\" for \"truncated TAL effectors.\" We show that truncTALE Tal2h of Xoc strain BLS256, and by correlation truncTALEs in other strains, specifically suppress resistance mediated by the locus recently described in the heirloom rice variety Carolina Gold. -mediated resistance is triggered by different TAL effectors from diverse strains, irrespective of their DNA binding specificity, and does not require the AD. This implies a direct protein-protein rather than protein-DNA interaction. Similarly, truncTALEs exhibit diverse predicted DNA recognition specificities. And, , Tal2h did not bind any of several potential recognition sites. Further, a single candidate NLS sequence in Tal2h was dispensable for resistance suppression. Many truncTALEs have one 28 aa repeat, a length not observed previously. Tested in an engineered TAL effector, this repeat required a single base pair deletion in the DNA, suggesting that it or a neighbor disengages. The presence of the 28 aa repeat, however, was not required for resistance suppression. TruncTALEs expand the paradigm for TAL effector-mediated effects on plants. We propose that Tal2h and other truncTALEs act as dominant negative ligands for an immune receptor encoded by the locus, likely a nucleotide binding, leucine-rich repeat protein. Understanding truncTALE function and distribution will inform strategies for disease control.

Fusarium head blight (FHB) is a fungal disease posing a major threat to wheat production. Plant breeding that leverages genotyping is an effective method to improve the genetic resistance of cultivars. Started in 1995, the uniform regional scab nursery (URSN) consists of germplasm from several public breeding programs in the Northern US region. Its main objective is to showcase new sources of resistance and enable germplasm exchange among the cooperators; however, the data from the URSN have not been studied. Phenotypic and genotypic data from this nursery were gathered, as well as from two current breeding programs in the US Midwest. Genomic prediction on eight traits related to FHB and agronomic traits was applied, and the effects of statistical method, marker density, training set size, genetic structure, and genetic architecture of the trait were studied. Using the URSN population, reproducing kernel Hilbert space was the best method in various prediction settings, with an average accuracy of 0.63, marker density could be as low as 500 without decreasing the prediction accuracy, and training set optimization was useful for two traits. Furthermore, genotypic values were predicted in breeding programs using the URSN population as a training set with various prediction scenarios. Predicting unrelated populations led to a significant decrease in accuracy but with encouraging values for some traits and populations. Ultimately, when progressively decreasing the number of lines from breeding populations in the training set, the advantage of adding the URSN population was more pronounced, with an increase in accuracy up to 0.19. Core Ideas Genomic predictive ability ranged from 0.49 to 0.72 for predicting Fusarium head blight (FHB) and agronomical traits in wheat. Training set size had more impact on accuracy than marker density, which could be reduced to between 500 and 1000 markers. Training set optimization with a sparse selection index increased the accuracy of genomic prediction for two traits. Adding an unrelated population in the training set allows a reduction in phenotyping effort. Plain Language Summary Genomic prediction was used as a tool to improve the genetic resistance of spring wheat to Fusarium head blight, using data from a historical nursery and from two current breeding programs. Parameters related to genomic predictive ability were thoroughly studied. Predictive ability within the historical nursery was medium to high for all the eight traits studied and all methods gave similar results. Marker density did not affect predictive ability compared to training set size. Training set optimization had mixed results depending on the trait. We tested several prediction scenarios useful in a breeding context by harnessing the historical dataset in the training set for predicting breeding lines. While the lack of genetic relatedness decreased the accuracy of genomic prediction, we showed that breeding programs could benefit from these historical data by incorporating their information into training models, thus reducing the phenotyping effort.

Prime editing is an adaptation of the CRISPR-Cas system that uses a Cas9(H840A)-reverse transcriptase fusion and a guide RNA amended with template and primer binding site sequences to achieve RNA-templated conversion of the target DNA, allowing specified substitutions, insertions, and deletions. In the first report of prime editing in plants, a variety of edits in rice and wheat were described, including insertions up to 15 bp. Several studies in rice quickly followed, but none reported a larger insertion. Here, we report easy-to-use vectors for prime editing in dicots as well as monocots, their validation in Nicotiana benthamiana , rice, and Arabidopsis, and an insertion of 66 bp that enabled split-GFP fluorescent tagging.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.An amendment to this paper has been published and can be accessed via a link at the top of the paper.