Near-gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research.

Complete, gapless telomere-to-telomere chromosome assemblies are a prerequisite for comprehensively investigating the architecture of complex regions, like centromeres or telomeres and removing uncertainties in the order, spacing, and orientation of genes. Using complementary genomics technologies and assembly algorithms, we developed highly contiguous, nearly gapless, genome assemblies for two economically important soybean [Glycine max (L.) Merr] cultivars (Williams 82 and Lee). The centromeres were distinctly annotated on all the chromosomes of both assemblies. We further found that the canonical telomeric repeats were present at the telomeres of all chromosomes of both Williams 82 and Lee genomes. A total of 10 chromosomes in Williams 82 and eight in Lee were entirely reconstructed in single contigs without any gap. Using the combination of ab initio prediction, protein homology, and transcriptome evidence, we identified 58,287 and 56,725 protein-coding genes in Williams 82 and Lee, respectively. The genome assemblies and annotations will serve as a valuable resource for studying soybean genomics and genetics and accelerating soybean improvement.

Direct long-acting antibodies: updating the language of RSV prevention to reflect the evolution of mAbs.

Introduction: The language of medicine is constantly evolving, typically to better describe a new understanding of disease, adjust to changing social sensibilities, or simply to reflect a new drug class or category. We address the need for an updated language around monoclonal antibodies, or "mAbs" - a widely used medical term, but one which is now too general to accurately reflect the range of mAb pharmaceuticals, their effects, and the intended patients. Methods: The question of "what should we call a monoclonal antibody immunisation against respiratory syncytial virus (RSV) to ensure accurate understanding of the product?" was the basis for a virtual advisory panel in May 2022. The panel was convened by Sanofi with the intention of reviewing appropriate language in terminology in the context of mAb-based prophylaxis for RSV. The panel comprised several global experts on RSV and vaccination, a trained linguist specialising in doctor-patient interactions and medical language, and several experts in marketing and communications. Results: We suggest the term "Direct Long-acting Antibody" (DLA) for a specific sub-class of mAbs for use in prevention of RSV disease in infants. This terminology should differentiate from other mAbs, which are generally not used as therapies in infants. Discussion and Conclusions: This change will more accurately convey the specific mode of action of a mAb in infants, and how it could impact the prevention of communicable diseases: this class of mAbs is not an active treatment, but rather will offer direct and rapid protection lasting at least 5 months.

Efficient gene targeting in soybean using Ochrobactrum haywardense-mediated delivery of a marker-free donor template.

Gene targeting (GT) for precise gene insertion or swap into pre-defined genomic location has been a bottleneck for expedited soybean precision breeding. We report a robust selectable marker-free GT system in soybean, one of the most economically important crops. An efficient Oh H1-8 (Ochrobactrum haywardense H1-8)-mediated embryonic axis transformation method was used for the delivery of CRISPR-Cas9 components and donor template to regenerate T0 plants 6-8 weeks after transformation. This approach generated up to 3.4% targeted insertion of the donor sequence into the target locus in T0 plants, with ∼ 90% mutation rate observed at the genomic target site. The GT was demonstrated in two genomic sites using two different donor DNA templates without the need for a selectable marker within the template. High-resolution Southern-by-Sequencing analysis identified T1 plants with precise targeted insertion and without unintended plasmid DNA. Unlike previous low-frequency GT reports in soybean that involved particle bombardment-mediated delivery and extensive selection, the method described here is fast, efficient, reproducible, does not require a selectable marker within the donor DNA, and generates nonchimeric plants with heritable GT.

The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize.

Southern corn rust (SCR), caused by the fungal pathogen Puccinia polysora, is a major threat to maize production worldwide. Efficient breeding and deployment of resistant hybrids are key to achieving durable control of SCR. Here, we report the molecular cloning and characterization of RppC, which encodes an NLR-type immune receptor and is responsible for a major SCR resistance quantitative trait locus. Furthermore, we identified the corresponding avirulence effector, AvrRppC, which is secreted by P. polysora and triggers RppC-mediated resistance. Allelic variation of AvrRppC directly determines the effectiveness of RppC-mediated resistance, indicating that monitoring of AvrRppC variants in the field can guide the rational deployment of RppC-containing hybrids in maize production. Currently, RppC is the most frequently deployed SCR resistance gene in China, and a better understanding of its mode of action is critical for extending its durability.

Application of quality improvement techniques to reduce parenteral nutrition wastage in a national intestinal failure unit.

OBJECTIVES: Parenteral nutrition (PN) costs approximately £80 per day per bag. Unpredictable changes in patients' clinical condition, venous access loss or reasons related to the processes involved in administering PN can lead to PN wastage. Cost efficiencies are imperative to optimise limited resource utilisation in all current healthcare economies. We undertook a quality improvement (QI) project to reduce PN wastage in an adult acute hospital setting. The project SMART's (specific, measurable, achievable, realistic, time-based) objective was reducing in-patient PN wastage by 10% in 9 months using QI methodology on a national intestinal failure unit (IFU). METHOD: Wastage reasons were evaluated through pareto charts to target waste reduction using 'Plan, Do, Study, Act' (PDSA) cycles. Variation was mapped using c-charts. RESULTS: 12-week baseline wastage data predicted 1000 bags wasted per annum (p.a.). PDSA cycles actioned included: regular enhanced clinical team awareness of wastage; unused PN bags redistributed within expiry date; stock bag rotation; critical path analysis of PN bag journey; enhanced discharge planning/coordination; reorganisation of fridge PN storage according to weekday; changing ordering frequency and bag type (from tailored to standard) to increase flexibility around discharge date and PN weaning. Implementation of PDSA cycles led to a 34% reduction in PN wastage in 9 months. CONCLUSION: In a high-use IFU, PN wastage is common and costly. Using a QI approach with concurrent PDSA cycles and a motivated multidisciplinary team, high levels of wastage reduction are possible with associated significant cost savings and from this study a predicted cost saving of approximately £30 000 p.a.

Pilot study of methods for assessing unmet secondary health care need in New Zealand.

AIMS: In this pilot study, the primary aim was to compare four potential methods for undertaking a national survey of unmet secondary healthcare need in New Zealand (one collecting data from GPs, and three from community surveys). The secondary aim was to obtain an estimate of the prevalence of unmet secondary healthcare need, to inform sample size calculations for a national survey. METHODS: An electronic system was set up for GPs in Christchurch (Pegasus PHO) and Auckland (Auckland PHO) to record cases of unmet need as encountered in clinics. For the community surveys, a questionnaire developed by the authors was administered to people from the same electoral wards as the GP clinics. Three modes of questionnaire administration were trialled: online, telephone and face-to-face interview. Random population sampling from the Maori and General Electoral Rolls was used to identify eligible survey participants until there were approximately 200 respondents for each method in each city. Data collection took place from November 2015 to February 2016. RESULTS: GP reports: Pegasus PHO: 8/78 eligible practices recorded 28 cases of unmet secondary healthcare need in 10 weeks. Auckland PHO: 3/26 practices participated and recorded no cases in three weeks. Surveys: 1,277 interviews were completed (online 428, telephone 447, face-to-face 402). For primary healthcare, 211/1,277 (16.5%) had missed a GP visit because of cost (online 25.0%, telephone 11.6%, face-to-face 12.9%). For secondary healthcare, 119/1,277 (9.3%) reported unmet healthcare need that had been identified by a health professional (online 11.2%; telephone 9.2%; face-to-face 7.5%). Of these, 75/119 (63.0%) required a consultation, and 47/119 (39.5%) required a procedure. Completed interview rates as a percentage of names on the Electoral Roll were low (online 8.8%, telephone 15.4%, face-to-face 13.9%), affected by changed addresses and lack of listed telephone numbers. The response rate for those with valid phone numbers was 47.6%, and for those with valid addresses was 31.5%. CONCLUSIONS: Using the Electoral Rolls to identify respondents is problematic. For a national survey, random population sampling by address, similar to the method employed for the New Zealand Health Survey, but giving respondents a choice between face-to-face and phone interviews, is proposed. Asking GPs to record data on unmet need for secondary care was not successful. Our pilot study suggests there is sufficient unmet secondary healthcare need in New Zealand to merit a national survey.

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize.

Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.

Phage display identification of functional binding peptides against 4-acetamidophenol (Paracetamol): an exemplified approach to target low molecular weight organic molecules.

Peptide-phage display has been widely used to explore protein-protein interactions, however, despite the potential range of applications the use of this technology to identify peptides that bind low molecular weight organic molecules has not been explored. In this current study, we identified a phage clone (PARA-061) displaying the cyclic 7-mer peptide sequence N' AC-NPNNLSH-CGGGS C' that binds the low molecular weight organic molecule 4-acetamidophenol (4-AAP; paracetamol). To avoid occupancy of key functional groups on the target 4-AAP molecule our panning strategy was directed against insoluble complexes of 4-AAP rather than against the target linked to a stationary support or bearing an affinity tag. To augment the panning procedure we deleted phage that also bound the 4-AAP isomers, 2-AAP and 3-AAP. The identified PARA-061 peptide-phage clone displayed functional binding properties against 4-AAP in solution, able in a peptide sequence-dependant manner to prevent the in vitro hepatotoxicity of 4-AAP and reduce ( approximately 20%) the permeability of 4-AAP across a semi-permeable membrane. Molecular dynamic simulations generated a stable binding conformation between the PARA-061 peptide sequence and 4-AAP. In conclusion, we show that a phage display library can be used to identify peptide sequence-specific clones able to modulate the functional binding of a low molecular weight organic molecule. Such peptides may be expected to find utility in the next generation of hybrid polymer-based biosensing devices.

Effect of posture change on tactile perception: impaired direction discrimination performance with interleaved fingers.

We report a series of experiments in which participants had to judge the direction in which a pair of vibrotactile stimuli presented to two adjacent digits of either the same or different hands were stimulated (left-to-right or vice versa in experiments 1 and 2; near-to-far or vice versa in experiment 3, at stimulus onset asynchronies varying between 100 and 600 ms). When the participant's hands were placed side-by-side (anatomical posture), with their fingers either pointing away from them or else pointing toward the midline, directional discrimination performance was generally accurate. By contrast, when the fingers of the two hands were interleaved in either of these postures, performance deteriorated significantly for certain specific combinations of digits, with a more pronounced impairment seen when the fingers pointed away from the participant than when they pointed toward the midline. This decline in tactile direction discrimination performance in the interleaved fingers posture appears to reflect a failure to represent the position of tactile stimuli correctly when the fingers of the two hands are interleaved.

Thrombotic thrombocytopenic purpura in the setting of systemic sclerosis.

OBJECTIVES: To describe the association between thrombotic thrombocytopenic purpura (TTP) and systemic sclerosis (SSc) and the methods to distinguish TTP from scleroderma renal crisis (SRC). METHODS: A case of TTP that developed in a patient with preexisting SSc is described. Medline/PubMed was searched for literature pertaining to an association between TTP and SSc, with special attention given to distinguishing TTP from SRC. In addition, the role of von Willebrand cleaving protease in the pathogenesis of TTP is reviewed. RESULTS: Including the present case, there have been 9 reports of TTP in association with SSc in the literature. In the majority of these cases TTP presented with features compatible with SRC such as renal dysfunction, thrombocytopenia, hypertension, and microangiopathic hemolytic anemia. Von Willebrand cleaving protease activity is depressed in patients with acute TTP. CONCLUSIONS: TTP in association with SSc has been reported rarely. The diagnosis of TTP, and the distinction from SRC, may be challenging, as these cases may resemble SRC. However, the correct diagnosis is critical because treatment differs substantially for each of these life-threatening conditions. Currently, the assessment of von Willebrand factor cleaving protease activity may assist in making this distinction.

The frequency of thrombotic thrombocytopenic purpura in patients with systemic lupus erythematosus undergoing kidney biopsy.

OBJECTIVE: To characterize the frequency of thrombotic thrombocytopenic purpura (TTP) among patients with systemic lupus erythematosus (SLE) undergoing kidney biopsy. METHODS: A retrospective review of all renal biopsies of patients with SLE at Rush-Presbyterian-St. Luke's Medical Center was performed for the years 1989 to 2001. RESULTS: Four cases of clinical and histopathological TTP were identified among the 257 patients with SLE who underwent renal biopsy during the 12 year study period. CONCLUSION: TTP appears to occur at higher than expected frequency among SLE patients undergoing biopsy for unexplained renal failure.

Architecture of the medial gastrocnemius in children with spastic diplegia.

Ultrasound images were obtained of the medial gastrocnemius at different ankle joint positions with the knee extended. Fascicle length and deep fascicle angle were measured in five normally developing adults (mean age 33 years, age range 24 to 36 years) and in five normally developing children (mean age 7.8 years, age range 7 to 11 years), and in seven children with spastic diplegia (mean age 10 years, age range 6 to 13 years). These architectural variables were similar in the groups of normally developing adults and children. Importantly, no statistical difference could be found between the normally developing children and those with diplegia for fascicle length. Deep fascicle angles were reduced significantly in the clinical group at a particular ankle joint angle but not at the resting angles. The difference in deep fascicle angles is explained as a function of resting muscle length and is not attributed any clinical importance. Our results do not explain the structural origin of muscle contracture explicitly. However, they do indicate that most of the fixed shortness in the medial gastrocnemii of ambulant children with spastic diplegia is not due to reduced muscle fibre length. We suggest that muscle contracture may be better explained in terms of shortness of the aponeuroses of pennate muscles, such as the medial gastrocnemius, through reduced muscle fibre diameter.

Drug-induced systemic lupus erythematosus associated with etanercept therapy.

Specific antagonists of tumour necrosis factor (TNF)-alpha have rapidly gained popularity for the treatment of rheumatoid arthritis. The monoclonal antibody against TNF-alpha, infliximab, has been associated with induction of systemic lupus erythematosus (SLE); however, there have been no published reports of drug-induced SLE associated with the soluble TNF-alpha receptor etanercept. We describe four female patients who developed signs and symptoms of SLE during treatment with etanercept; in two SLE was unambiguous. On diagnosis of SLE, etanercept was discontinued and the SLE-related symptoms promptly resolved. Etanercept should be considered in the list of agents associated with drug-induced SLE.