Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing.

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.

Cloning of the Rice Xo1 Resistance Gene and Interaction of the Xo1 Protein with the Defense-Suppressing Xanthomonas Effector Tal2h.

The Xo1 locus in the heirloom rice variety Carolina Gold Select confers resistance to bacterial leaf streak and bacterial blight, caused by Xanthomonas oryzae pv. oryzicola and X. oryzae pv. oryzae, respectively. Resistance is triggered by pathogen-delivered transcription activator-like effectors (TALEs) independent of their ability to activate transcription and is suppressed by truncated variants called truncTALEs, common among Asian strains. By transformation of the susceptible variety Nipponbare, we show that one of 14 nucleotide-binding, leucine-rich repeat (NLR) protein genes at the locus, with a zinc finger BED domain, is the Xo1 gene. Analyses of published transcriptomes revealed that the Xo1-mediated response is more similar to those mediated by two other NLR resistance genes than it is to the response associated with TALE-specific transcriptional activation of the executor resistance gene Xa23 and that a truncTALE dampens or abolishes activation of defense-associated genes by Xo1. In Nicotiana benthamiana leaves, fluorescently tagged Xo1 protein, like TALEs and truncTALEs, localized to the nucleus. And endogenous Xo1 specifically coimmunoprecipitated from rice leaves with a pathogen-delivered, epitope-tagged truncTALE. These observations suggest that suppression of Xo1-function by truncTALEs occurs through direct or indirect physical interaction. They further suggest that effector coimmunoprecipitation may be effective for identifying or characterizing other resistance genes.

The Reliability and Validity of Wearable Inertial Sensors Coupled with the Microsoft Kinect to Measure Shoulder Range-of-Motion.

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.

The effect of restrictive versus liberal selection criteria on survival in ECPR: a retrospective analysis of a multi-regional dataset.

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.

The effect of a structured ECPR protocol aided by specific simulation training in a quaternary ECMO centre: A retrospective pre-post study.

Background: There is limited literature exploring the relationship between simulation training and extracorporeal cardiopulmonary resuscitation (ECPR) outcomes. We examined whether there was an association between the implementation of an in situ simulation training program and ECPR utilisation, time to extracorporeal membrane oxygenation (ECMO), and neurologically intact survival. Methods: In this retrospective pre-post study of in-hospital cardiac arrests (IHCA) and out-of-hospital cardiac arrests (OHCA), we analysed data for all patients recorded as receiving ECPR from September 2009 to December 2020 at our institution, relative to the implementation of an in situ ECPR simulation training program and a standardised procedure for high-quality ECPR. The primary outcome was Cerebral Performance Category (CPC) 1 or 2 at hospital discharge. Results: There were 27 patients in the pre-intervention period and 39 patients in the post-intervention period. The median ECPR rate per year was 2 pre-intervention and 7 post-intervention (p = 0.073). There was an association between the implementation of the program and decreased median time from OHCA to ECMO flow, from 87 (IQR 78-95) minutes pre-intervention to 70 (IQR 69-72) minutes post-intervention (p = 0.002). Median time from IHCA to ECMO flow was 40 (IQR 20-75) minutes pre-intervention and 28 (IQR 16-41) minutes post-intervention (p = 0.134). Survival with CPC 1 or 2 was 7/27 (25.9%) pre-intervention and 15/39 (38.5%) post-intervention (p = 0.288). Conclusion: We observed an association between the implementation of an ECPR-specific simulation program and decreased time from OHCA to ECMO flow. There was no association between the implementation of the program and neurologically intact survival at hospital discharge.

Spelling Changes and Fluorescent Tagging With Prime Editing Vectors for Plants.

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.

A Reference Genome Sequence for Giant Sequoia.

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.

Author Correction: A transgenic approach for controlling Lygus in cotton.

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

Does the form of venous thromboembolism prophylaxis following primary total knee arthroplasty alter the rate of early reoperation or revision surgery?

BACKGROUND: Currently there is significant variation in the management of venous thromboembolism prophylaxis following total knee arthroplasty (TKA). Excessive wound ooze and bleeding is thought to increase a patient's risk of haematoma formation and possible infection. We evaluated the rate of unexpected reoperation in the perioperative period in patients who received aspirin, rivaroxaban or enoxaparin following primary TKA. METHOD: A systematic literature search was conducted in MEDLINE, CENTRAL and Embase to identify patients who underwent primary TKA. Two researchers independently reviewed the references identified in the literature search. The final 11 studies included for review were published between 1996 and 2016. RESULTS: There was a higher rate of reoperation in patients treated with aspirin following TKA when compared to enoxaparin and rivaroxaban in the perioperative period. Of the 5141 patients treated with enoxaparin, 11 (0.21%) required reoperation; of the 2764 patients treated with rivaroxaban, 12 (0.43%) required reoperation; and of the 228 patients treated with aspirin, seven (3.07%) required reoperation. The average time to follow-up in the 11 studies was 55 days, ranging from 30 to 180 days post-operatively. CONCLUSION: There was a higher rate of reoperation in patients treated with aspirin following TKA when compared to enoxaparin and rivaroxaban in the perioperative period. While there is extensive data on the safety and efficacy of these medications following joint arthroplasty, improved reporting of surgically relevant outcomes are needed to assist both the surgeon and patient in clinical decision-making.

Suppression of Xo1-Mediated Disease Resistance in Rice by a Truncated, Non-DNA-Binding TAL Effector of Xanthomonas oryzae.

Delivered into plant cells by type III secretion from pathogenic Xanthomonas 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 Xanthomonas oryzae 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 Xo1 locus recently described in the heirloom rice variety Carolina Gold. Xo1-mediated resistance is triggered by different TAL effectors from diverse X. oryzae 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, in vitro, 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 Xo1 locus, likely a nucleotide binding, leucine-rich repeat protein. Understanding truncTALE function and distribution will inform strategies for disease control.

A transgenic approach for controlling Lygus in cotton.

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.