xCAPT5: protein-protein interaction prediction using deep and wide multi-kernel pooling convolutional neural networks with protein language model.

BACKGROUND: Predicting protein-protein interactions (PPIs) from sequence data is a key challenge in computational biology. While various computational methods have been proposed, the utilization of sequence embeddings from protein language models, which contain diverse information, including structural, evolutionary, and functional aspects, has not been fully exploited. Additionally, there is a significant need for a comprehensive neural network capable of efficiently extracting these multifaceted representations. RESULTS: Addressing this gap, we propose xCAPT5, a novel hybrid classifier that uniquely leverages the T5-XL-UniRef50 protein large language model for generating rich amino acid embeddings from protein sequences. The core of xCAPT5 is a multi-kernel deep convolutional siamese neural network, which effectively captures intricate interaction features at both micro and macro levels, integrated with the XGBoost algorithm, enhancing PPIs classification performance. By concatenating max and average pooling features in a depth-wise manner, xCAPT5 effectively learns crucial features with low computational cost. CONCLUSION: This study represents one of the initial efforts to extract informative amino acid embeddings from a large protein language model using a deep and wide convolutional network. Experimental results show that xCAPT5 outperforms recent state-of-the-art methods in binary PPI prediction, excelling in cross-validation on several benchmark datasets and demonstrating robust generalization across intra-species, cross-species, inter-species, and stringent similarity contexts.

Prime editing: Mechanism insight and recent applications in plants.

Prime editing (PE) technology utilizes an extended prime editing guide RNA (pegRNA) to direct a fusion peptide consisting of nCas9 (H840) and reverse transcriptase (RT) to a specific location in the genome. This enables the installation of base changes at the targeted site using the extended portion of the pegRNA through RT activity. The resulting product of the RT reaction forms a 3' flap, which can be incorporated into the genomic site through a series of biochemical steps involving DNA repair and synthesis pathways. PE has demonstrated its effectiveness in achieving almost all forms of precise gene editing, such as base conversions (all types), DNA sequence insertions and deletions, chromosomal translocation and inversion and long DNA sequence insertion at safe harbour sites within the genome. In plant science, PE could serve as a groundbreaking tool for precise gene editing, allowing the creation of desired alleles to improve crop varieties. Nevertheless, its application has encountered limitations due to efficiency constraints, particularly in dicotyledonous plants. In this review, we discuss the step-by-step mechanism of PE, shedding light on the critical aspects of each step while suggesting possible solutions to enhance its efficiency. Additionally, we present an overview of recent advancements and future perspectives in PE research specifically focused on plants, examining the key technical considerations of its applications.

Generation of parthenocarpic tomato plants in multiple elite cultivars using the CRISPR/Cas9 system.

Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit production. Advances in cutting-edge techniques have enabled the development of numerous critical traits related to the quality and quantity of tomatoes. Genetic engineering techniques, such as gene transformation and gene editing, have emerged as powerful tools for generating new plant varieties with superior traits. In this study, we induced parthenocarpic traits in a population of elite tomato (ET) lines. At first, the adaptability of ET lines to genetic transformation was evaluated to identify the best-performing lines by transforming the SlANT1 gene overexpression cassette and then later used to produce the SlIAA9 knockout lines using the CRISPR/Cas9 system. ET5 and ET8 emerged as excellent materials for these techniques and showed higher efficiency. Typical phenotypes of knockout sliaa9 were clearly visible in G0 and G1 plants, in which simple leaves and parthenocarpic fruits were observed. The high efficiency of the CRISPR/Cas9 system in developing new tomato varieties with desired traits in a short period was demonstrated by generating T-DNA-free homozygous sliaa9 knockout plants in the G1 generation. Additionally, a simple artificial fertilization method was successfully applied to recover seed production from parthenocarpic plants, securing the use of these varieties as breeding materials. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01452-1.

Genome editing and beyond: what does it mean for the future of plant breeding?

MAIN CONCLUSION: Genome editing offers revolutionized solutions for plant breeding to sustain food production to feed the world by 2050. Therefore, genome-edited products are increasingly recognized via more relaxed legislation and community adoption. The world population and food production are disproportionally growing in a manner that would have never matched each other under the current agricultural practices. The emerging crisis is more evident with the subtle changes in climate and the running-off of natural genetic resources that could be easily used in breeding in conventional ways. Under these circumstances, affordable CRISPR-Cas-based gene-editing technologies have brought hope and charged the old plant breeding machine with the most energetic and powerful fuel to address the challenges involved in feeding the world. What makes CRISPR-Cas the most powerful gene-editing technology? What are the differences between it and the other genetic engineering/breeding techniques? Would its products be labeled as "conventional" or "GMO"? There are so many questions to be answered, or that cannot be answered within the limitations of our current understanding. Therefore, we would like to discuss and answer some of the mentioned questions regarding recent progress in technology development. We hope this review will offer another view on the role of CRISPR-Cas technology in future of plant breeding for food production and beyond.

CRISPR/Cas-based precision genome editing via microhomology-mediated end joining.

Gene editing and/or allele introgression with absolute precision and control appear to be the ultimate goals of genetic engineering. Precision genome editing in plants has been developed through various approaches, including oligonucleotide-directed mutagenesis (ODM), base editing, prime editing and especially homologous recombination (HR)-based gene targeting. With the advent of CRISPR/Cas for the targeted generation of DNA breaks (single-stranded breaks (SSBs) or double-stranded breaks (DSBs)), a substantial advancement in HR-mediated precise editing frequencies has been achieved. Nonetheless, further research needs to be performed for commercially viable applications of precise genome editing; hence, an alternative innovative method for genome editing may be required. Within this scope, we summarize recent progress regarding precision genome editing mediated by microhomology-mediated end joining (MMEJ) and discuss their potential applications in crop improvement.

CRISPR/Cas9-based precise excision of SlHyPRP1 domain(s) to obtain salt stress-tolerant tomato.

KEY MESSAGE: CRISPR/Cas9-based multiplexed editing of SlHyPRP1 resulted in precise deletions of its functional motif(s), thereby resulting in salt stress-tolerant events in cultivated tomato. Crop genetic improvement to address environmental stresses for sustainable food production has been in high demand, especially given the current situation of global climate changes and reduction of the global food production rate/population rate. Recently, the emerging clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-based targeted mutagenesis has provided a revolutionary approach to crop improvement. The major application of CRISPR/Cas in plant genome editing has been the generation of indel mutations via error-prone nonhomologous end joining (NHEJ) repair of DNA DSBs. In this study, we examined the power of the CRISPR/Cas9-based novel approach in the precise manipulation of protein domains of tomato hybrid proline-rich protein 1 (HyPRP1), which is a negative regulator of salt stress responses. We revealed that the precise elimination of SlHyPRP1 negative-response domain(s) led to high salinity tolerance at the germination and vegetative stages in our experimental conditions. CRISPR/Cas9-based domain editing may be an efficient tool to engineer multidomain proteins of important food crops to cope with global climate changes for sustainable agriculture and future food security.

Plans for Nationwide Serosurveillance Network in Vietnam.

In recent years, serosurveillance has gained momentum as a way of determining disease transmission and immunity in populations, particularly with respect to vaccine-preventable diseases. At the end of 2017, the Oxford University Clinical Research Unit and the National Institute of Hygiene and Epidemiology held a meeting in Vietnam with national policy makers, researchers, and international experts to discuss current seroepidemiologic projects in Vietnam and future needs and plans for nationwide serosurveillance. This report summarizes the meeting and the plans that were discussed to set up nationwide serosurveillance in Vietnam.

Highly efficient homology-directed repair using CRISPR/Cpf1-geminiviral replicon in tomato.

Genome editing via the homology-directed repair (HDR) pathway in somatic plant cells is very inefficient compared with error-prone repair by nonhomologous end joining (NHEJ). Here, we increased HDR-based genome editing efficiency approximately threefold compared with a Cas9-based single-replicon system via the use of de novo multi-replicon systems equipped with CRISPR/LbCpf1 in tomato and obtained replicon-free but stable HDR alleles. The efficiency of CRISPR/LbCpf1-based HDR was significantly modulated by physical culture conditions such as temperature and light. Ten days of incubation at 31 °C under a light/dark cycle after Agrobacterium-mediated transformation resulted in the best performance among the tested conditions. Furthermore, we developed our single-replicon system into a multi-replicon system that effectively increased HDR efficiency. Although this approach is still challenging, we showed the feasibility of HDR-based genome editing of a salt-tolerant SlHKT1;2 allele without genomic integration of antibiotic markers or any phenotypic selection. Self-pollinated offspring plants carrying the HKT1;2 HDR allele showed stable inheritance and germination tolerance in the presence of 100 mm NaCl. Our work may pave the way for transgene-free editing of alleles of interest in asexually and sexually reproducing plants.

Rapid and precise characterization of sub-µm surface defects using laser scatterometer devising a polygonal-shaped waveguide with double-slit aperture.

We present a method of various defects detection on a flat surface using a polygonal-shaped waveguide devised laser scatterometer capable of providing sub-µm precision. The optimized polygonal shape of the waveguide with double-slit aperture substantially improves the detection efficiency of scattered beam more than 10 times compared to that of the conventional circular-shaped waveguide. The scatterometer enables quantification of sub-µm lateral size and height of defects by counting the number of pixels and peak intensity, respectively. We validated the performance of the proposed inspection system by measuring a standard defective specimen and successfully apply to a pilot production line for inspection of 250×140 mm2 size glass panels providing 31,250 × 16,000 spatial resolution with the capability of a measuring time less than 10 s.

Development of a Quality Improvement Curriculum in a Pediatric Emergency Medicine Fellowship.

Quality improvement (QI) is a science of systematic analysis and improvement of health care delivery systems. Working knowledge of QI models is imperative to professional development of future pediatric emergency medicine practitioners. The Accreditation Council for Graduate Medical Education has established a list of QI and patient safety expectations for trainees. In order to address educational needs in this area, we have created a novel QI curriculum for pediatric emergency medicine fellows that include didactic sessions, active participation in QI projects, and mentorship by QI faculty. As a part of the curriculum, fellows are required to participate in variety of QI and patient safety activities, such as Morbidity and Mortality conferences, QI and Patient Case Review committees, and Clinical Care Guideline work groups. As a measure of success, fellows who have participated in this curriculum have shared their successful QI work at the local and national levels. This goal of this report is to share our experience in order to provide other institutions a framework for their own curriculum development.

Intracranial Complications of Pediatric Sinusitis.

"Headache and fever" is a common presentation to the urgent care and emergency department setting and can have many etiologies. We present a case of a 10-year-old girl who presented with headache and fever and was found to have intracranial extension of sinusitis despite lack of typical sinus or chronic upper respiratory tract infection symptoms. This case illustrates the need in the emergency department or urgent care to keep a broad differential diagnosis for pediatric headache, especially when initial interventions are unsuccessful. We also review the epidemiology of pediatric sinusitis, age at sinus development, and associated intracranial complications.

Bacterial bloodstream infections in a tertiary infectious diseases hospital in Northern Vietnam: aetiology, drug resistance, and treatment outcome.

BACKGROUND: Bloodstream infections (BSIs) are associated with high morbidity and mortality worldwide. However their aetiology, antimicrobial susceptibilities and associated outcomes differ between developed and developing countries. Systematic data from Vietnam are scarce. Here we present aetiologic data on BSI in adults admitted to a large tertiary referral hospital for infectious diseases in Hanoi, Vietnam. METHODS: A retrospective study was conducted at the National Hospital for Tropical Diseases between January 2011 and December 2013. Cases of BSI were determined from records in the microbiology department. Case records were obtained where possible and clinical findings, treatment and outcome were recorded. BSI were classified as community acquired if the blood sample was drawn ≤48 h after hospitalization or hospital acquired if >48 h. RESULTS: A total of 738 patients with BSI were included for microbiological analysis. The predominant pathogens were: Klebsiella pneumoniae (17.5%), Escherichia coli (17.3%), Staphylococcus aureus (14.9%), Stenotrophomonas maltophilia (9.6%) and Streptococcus suis (7.6%). The overall proportion of extended spectrum beta-lactamase (ESBL) production among Enterobacteriaceae was 25.1% (67/267 isolates) and of methicillin-resistance in S. aureus (MRSA) 37% (40/108). Clinical data was retrieved for 477 (64.6%) patients; median age was 48 years (IQR 36-60) with 27.7% female. The overall case fatality rate was 28.9% and the highest case fatality was associated with Enterobacteriaceae BSI (34.7%) which accounted for 61.6% of all BSI fatalities. CONCLUSIONS: Enterobacteriaceae (predominantly K. pneumoniae and E. coli) are the most common cause of both community and hospital acquired bloodstream infections in a tertiary referral clinic in northern Vietnam.

High accumulation of anthocyanins via the ectopic expression of AtDFR confers significant salt stress tolerance in Brassica napus L.

KEY MESSAGE: The ectopic expression of AtDFR results in increased accumulation of anthocyanins leading to enhanced salinity and drought stress tolerance in B. napus plants. Flavonoids with antioxidant effects confer many additional benefits to plants. Evidence indicates that flavonoids, including anthocyanins, protect tissues against oxidative stress from various abiotic stressors. We determined whether increases in anthocyanins increased abiotic stress tolerance in Brassica napus, because the values of B. napus L. and its cultivation area are increasing worldwide. We overexpressed Arabidopsis dihydroflavonol-4-reductase (DFR) in B. napus. Increased DFR transcript levels for AtDFR-OX B. shoots correlated with higher anthocyanin accumulation. AtDFR-OX Brassica shoots exhibited lower reactive oxygen species (ROS) accumulation than wild-type (WT) shoots under high NaCl and mannitol concentrations. This was corroborated by 3,3-diaminobenzidine staining for ROS scavenging activity in 1,1-diphenyl-2-picryl-hydrazyl assays. Shoots of the AtDFR-OX B. napus lines grown in a high salt medium exhibited enhanced salt tolerance and higher chlorophyll content than similarly grown WT plants. Our observations suggested that the AtDFR gene can be effectively manipulated to modulate salinity and drought stress tolerance by directing to high accumulation of anthocyanins in oilseed plants.

Essentials of Pediatric Emergency Medicine Fellowship: Part 6: Program Administration.

This article is the sixth in a 7-part series that aims to comprehensively describe the current state and future directions of pediatric emergency medicine (PEM) fellowship training from the essential requirements to considerations for successfully administering and managing a program to the careers that may be anticipated upon program completion. This article provides a broad overview of administering and supervising a PEM fellowship program. It explores 3 topics: the principles of program administration, committee management, and recommendations for minimum time allocated for PEM fellowship program directors to administer their programs.

Lightweight Biobased Polyurethane Composites Derived from Liquefied Polyol Reinforced by Biomass Sources with High Mechanical Property and Enhanced Fire-Resistance Performance.

Lightweight biobased insulation polyurethane (BPU) composite foams with high fire-resistance efficiency are interested in building effective energy and low environmental impact today. This study focuses on manufacturing lightweight BPU from liquefied bamboo polyols and biomass resources, including rice husk and wood flour. Then, they are combined with three flame retardant (FR) additives, such as aluminum diethyl phosphinate, aluminum trihydroxide, and diammonium phosphate, to improve their fire resistance performance. The physicochemical properties, microstructure, thermal stability, mechanical properties, and flame-retardant properties of the BPU composites are characterized to optimize their compromise properties. The results showed that composites with optimized FRs achieved UL94 V-0 and those with nonoptimized FRs reached UL94 HB. The limiting oxygen index exhibited that the fire resistance of BPU composites could increase up to 21-37% within FR additives. In addition, the thermal stability of BPU composites was significantly improved in a temperature range of 300-700 °C and the compressive strength of the BPU composites was also enhanced with the presence of FRs. The scanning electron microscopy observation showed an influence of FRs on the morphology and cell size of the BPU composites. The bio-PU-derived samples in this study showed significantly low thermal conductivity values, demonstrating their remarkable thermal insulation effectiveness.

Antibacterial and Antifungal Fabrication of Natural Lining Leather Using Bio-Synthesized Silver Nanoparticles from Piper Betle L. Leaf Extract.

Leather is often used to make comfortable shoes due to its soft and breathable nature. However, its innate ability to retain moisture, oxygen and nutrients renders it a suitable medium for the adsorption, growth, and survival of potentially pathogenic microorganisms. Consequently, the intimate contact between the foot skin and the leather lining surface in shoes, which are subject to prolonged periods of sweating, may result in the transmission of pathogenic microorganisms and cause discomfort for the wearer. To address such issues, we modified pig leather with silver nanoparticles (AgPBL) that were bio-synthesized from Piper betle L. leaf extract as an antimicrobial agent via the padding method. The evidence of AgPBL embedded into the leather matrix, leather surface morphology and element profile of AgPBL-modified leather samples (pLeAg) was investigated using colorimetry, SEM, EDX, AAS and FTIR analyses. The colorimetric data confirmed that the pLeAg samples changed to a more brown color with higher wet pickup and AgPBL concentration, owing to the higher quantity of AgPBL uptake onto the leather surfaces. The antibacterial and antifungal activities of the pLeAg samples were both qualitatively and quantitatively evaluated using AATCC TM90, AATCC TM30 and ISO 16187:2013 test methods, approving a good synergistic antimicrobial efficiency of the modified leather against Escherichia coli and Staphylococcus aureus bacteria, a yeast Candida albicans and a mold Aspergillus niger. Additionally, the antimicrobial treatments of pig leather did not negatively impact its physico-mechanical properties, including tear strength, abrasion resistance, flex resistance, water vapour permeability and absorption, water absorption and desorption. These findings affirmed that the AgPBL-modified leather met all the requirements of upper lining according to the standard ISO 20882:2007 for making hygienic shoes.

CRISPR-Cas-mediated unfolded protein response control for enhancing plant stress resistance.

Plants consistently encounter environmental stresses that negatively affect their growth and development. To mitigate these challenges, plants have developed a range of adaptive strategies, including the unfolded protein response (UPR), which enables them to manage endoplasmic reticulum (ER) stress resulting from various adverse conditions. The CRISPR-Cas system has emerged as a powerful tool for plant biotechnology, with the potential to improve plant tolerance and resistance to biotic and abiotic stresses, as well as enhance crop productivity and quality by targeting specific genes, including those related to the UPR. This review highlights recent advancements in UPR signaling pathways and CRISPR-Cas technology, with a particular focus on the use of CRISPR-Cas in studying plant UPR. We also explore prospective applications of CRISPR-Cas in engineering UPR-related genes for crop improvement. The integration of CRISPR-Cas technology into plant biotechnology holds the promise to revolutionize agriculture by producing crops with enhanced resistance to environmental stresses, increased productivity, and improved quality traits.

Phylogenomic analyses reveal reticulate evolution between Neomicrocalamus and Temochloa (Poaceae: Bambusoideae).

Neomicrocalamus and Temochloa are closely related to bamboo genera. However, when considered with newly discovered and morphologically similar material from China and Vietnam, the phylogenetic relationship among these three groups was ambiguous in the analyses based on DNA regions. Here, as a means of investigating the relationships among the three bamboo groups and exploring potential sources of genomic conflicts, we present a phylogenomic examination based on the whole plastome, single-nucleotide polymorphism (SNP), and single-copy nuclear (SCN) gene datasets. Three different phylogenetic hypotheses were found. The inconsistency is attributed to the combination of incomplete lineage sorting and introgression. The origin of newly discovered bamboos is from introgressive hybridization between Temochloa liliana (which contributed 80.7% of the genome) and Neomicrocalamus prainii (19.3%), indicating that the newly discovered bamboos are closer to T. liliana in genetics. The more similar morphology and closer distribution elevation also imply a closer relationship between Temochloa and newly discovered bamboos.