Effect of Starch Types on the Textural and Rehydration Properties of Extruded Peanut Protein Pore Gel Particles.

In this study, the effect of different starches from corn, potato and pea containing varying amylose/amylopectin ratios on the textural and rehydration properties of extruded peanut protein gel particles were investigated. Results showed that textural and rehydration properties of peanut protein extruded with corn starch, potato starch and amylopectin are slightly inferior to those of peanut protein with pea starch extrudates. The addition of pea starch led to an increase in the pore structure of the peanut protein extrudates and improved their water absorption index, simultaneously reducing the hardness and density. Pea starch, as a natural water-absorbing expansion material, helped peanut protein to form cross-linked gel polymers that bind more water molecules, in addition to further polymerization with peanut protein, which made the protein secondary structure became disordered. These changes directly affected the textural properties of the extrudates. In addition, the blended system of starches and peanut protein tended to form more elastic solids, which affected the expansion of the extrudates. These findings indicate that starch can effectively improve the poor expansion of proteins, making it suitable for use in the production of plant protein-based foods.

ALK inhibitors increase ALK expression and sensitize neuroblastoma cells to ALK.CAR-T cells.

Selection of the best tumor antigen is critical for the therapeutic success of chimeric antigen receptor (CAR) T cells in hematologic malignancies and solid tumors. The anaplastic lymphoma kinase (ALK) receptor is expressed by most neuroblastomas while virtually absent in most normal tissues. ALK is an oncogenic driver in neuroblastoma and ALK inhibitors show promising clinical activity. Here, we describe the development of ALK.CAR-T cells that show potent efficacy in monotherapy against neuroblastoma with high ALK expression without toxicity. For neuroblastoma with low ALK expression, combination with ALK inhibitors specifically potentiates ALK.CAR-T cells but not GD2.CAR-T cells. Mechanistically, ALK inhibitors impair tumor growth and upregulate the expression of ALK, thereby facilitating the activity of ALK.CAR-T cells against neuroblastoma. Thus, while neither ALK inhibitors nor ALK.CAR-T cells will likely be sufficient as monotherapy in neuroblastoma with low ALK density, their combination specifically enhances therapeutic efficacy.

Preparation of Whole-Cut Plant-Based Pork Meat and Its Quality Evaluation with Animal Meat.

Low-moisture (20~40%) and high-moisture (40~80%) textured vegetable proteins (TVPs) can be used as important components of plant-based lean meat, while plant-based fat can be characterized by the formation of gels from polysaccharides, proteins, etc. In this study, three kinds of whole-cut plant-based pork (PBP) were prepared based on the mixed gel system, which were from low-moisture TVP, high-moisture TVP, and their mixtures. The comparisons of these products with commercially available plant-based pork (C-PBP1 and C-PBP2) and animal pork meat (APM) were studied in terms of appearance, taste, and nutritional qualities. Results showed the color changes of PBPs after frying were similar to that of APM. The addition of high-moisture TVP would significantly improve hardness (3751.96~7297.21 g), springiness (0.84~0.89%), and chewiness (3162.44~6466.94 g) while also reducing the viscosity (3.89~10.56 g) of products. It was found that the use of high-moisture TVP led to a significant increase in water-holding capacity (WHC) from 150.25% to 161.01% compared with low-moisture TVP; however, oil-holding capacity (OHC) was reduced from 166.34% to 164.79%. Moreover, essential amino acids (EAAs), the essential amino acids index (EAAI), and biological value (BV) were significantly increased from 272.68 mg/g, 105.52, and 103.32 to 362.65 mg/g, 141.34, and 142.36, respectively, though in vitro protein digestibility (IVPD) reduced from 51.67% to 43.68% due to the high-moisture TVP. Thus, the high-moisture TVP could help to improve the appearance, textural properties, WHC, and nutritional qualities of PBPs compared to animal meat, which was also better than low-moisture TVP. These findings should be useful for the application of TVP and gels in plant-based pork products to improve the taste and nutritional qualities.

Massively parallel base editing to map variant effects in human hematopoiesis.

Systematic evaluation of the impact of genetic variants is critical for the study and treatment of human physiology and disease. While specific mutations can be introduced by genome engineering, we still lack scalable approaches that are applicable to the important setting of primary cells, such as blood and immune cells. Here, we describe the development of massively parallel base-editing screens in human hematopoietic stem and progenitor cells. Such approaches enable functional screens for variant effects across any hematopoietic differentiation state. Moreover, they allow for rich phenotyping through single-cell RNA sequencing readouts and separately for characterization of editing outcomes through pooled single-cell genotyping. We efficiently design improved leukemia immunotherapy approaches, comprehensively identify non-coding variants modulating fetal hemoglobin expression, define mechanisms regulating hematopoietic differentiation, and probe the pathogenicity of uncharacterized disease-associated variants. These strategies will advance effective and high-throughput variant-to-function mapping in human hematopoiesis to identify the causes of diverse diseases.

Application of transglutaminase modifications for improving protein fibrous structures from different sources by high-moisture extruding.

Plant proteins can be extruded under high moisture content (above 40 %) to form meat-like fibrous structures, which is the basis for meat-like substitute products. However, the proteins' extrudability from various sources remain challenging in terms of generating fibrous structures under combinations of high-moisture extrusion with transglutaminase (TGase) modifications. In this study, proteins from soy (soy protein isolate, SPI, and soy protein concentrate, SPC), pea (pea protein isolate, PPI), peanut (peanut protein powder, PPP), wheat (wheat gluten, WG), and rice (rice protein isolate, RPI) were texturized using high-moisture extrusion combined with transglutaminase (TGase) modifications to enact changes in protein structure and extrusion capabilities. The results showed that soy proteins (SPI or SPC) responsed to torque, die pressure and temperature during extrusion, and this phenomenon was more pronounced at a higher protein content (SPI). In contrast, rice protein exhibited poor extrudability, leading to large losses of thermomechanical energy. TGase significantly affects the orientation of protein fibrous structures along the extrusion direction by impacting the rate of protein gelation during the high-moisture extrusion process, with the impact mainly occurring in the cooling die. Globulins (mainly 11S) played a major role in forming fibrous structures and the aggregation of globulins or reduction of gliadins under TGase modification impacted the orientation of the fibrous structure along the extrusion direction. Some thermomechanical treatment during high-moisture extrusion results in protein conversion from compact structure into more extended or stretched state, and the increase of random coil structures for proteins derived from wheat and rice would lead to these looser structures in the extrudates. Thus, TGase can be combined with high-moisture extrusion to regulate the formation of plant protein fibrous structures, dependent on the specific protein source and content.

RAMIHM generates fully human monoclonal antibodies by rapid mRNA immunization of humanized mice and BCR-seq.

As a clinical vaccine, lipid nanoparticle (LNP) mRNA has demonstrated potent and broad antibody responses, leading to speculation about its potential for antibody discovery. Here, we developed RAMIHM, a highly efficient strategy for developing fully human monoclonal antibodies that employs rapid mRNA immunization of humanized mice followed by single B cell sequencing (scBCR-seq). We immunized humanized transgenic mice with RAMIHM and generated 15 top-ranked clones from peripheral blood, plasma B, and memory B cell populations, demonstrating a high rate of antigen-specificity (93.3%). Two Omicron-specific neutralizing antibodies with high potency and one broad-spectrum neutralizing antibody were discovered. Furthermore, we extended the application of RAMIHM to cancer immunotherapy targets, including a single transmembrane protein CD22 and a multi-transmembrane G protein-coupled receptor target, GPRC5D, which is difficult for traditional protein immunization methods. RAMIHM-scBCR-seq is a broadly applicable platform for the rapid and efficient development of fully human monoclonal antibodies against an assortment of targets.

Microscopic insight into the interactions between pea protein and fatty acids during high-moisture extrusion processing.

To provide a theoretical basis for the quality improvement of plant protein-based meat substitutes with lipids, the interactions between pea protein and fatty acids (stearic, oleic and linoleic acids) and the effect on protein conformational changes during high-moisture extrusion (HME) processing were investigated using a dead-stop operation. The surface hydrophobicity analysis and Fourier transform infrared spectroscopy results revealed that the fatty acids induced the exposure of hydrophobic groups in the pea proteins, weakened hydrogen bonds, affected the aggregation of legumin subunits and promoted the conversion of α-helix and ß-sheet structures to ß-turn and random coil during HME processing. In the die, unsaturated fatty acids limited the refolding of protein chains and covalent interactions between proteins. Micromorphology analysis indicated that the coalescence of oleic and linoleic acids in the cooling zone hindered the formation of anisotropic structures while stearic acid promoted the formation of fibrous structures by enhanced disulfide bonds.

Complete Mitogenome of Oreolalax Omeimontis Reveals Phylogenetic Status and Novel Gene Arrangement of Archaeobatrachia.

Species of the genus Oreolalax displayed crucial morphological characteristics of vertebrates transitioning from aquatic to terrestrial habitats; thus, they can be regarded as a representative vertebrate genus for this landing phenomenon. But the present phylogenetic status of Oreolalax omeimontis has been controversial with morphological and molecular approaches, and specific gene rearrangements were discovered in all six published Oreolalax mitogenomes, which are rarely observed in Archaeobatrachia. Therefore, this study determined the complete mitogenome of O. omeimontis with the aim of identifying its precise phylogenetic position and novel gene arrangement in Archaeobatrachia. Phylogenetic analysis with Bayesian inference and maximum likelihood indicates O. omeimontis is a sister group to O. lichuanensis, which is consistent with previous phylogenetic analysis based on morphological characteristics, but contrasts with other studies using multiple gene fragments. Moreover, although the duplication of trnM occurred in all seven Oreolalax species, the translocation of trnQ and trnM occurred differently in O. omeimontis to the other six, and this unique rearrangement would happen after the speciation of O. omeimontis. In general, this study sheds new light on the phylogenetic relationships and gene rearrangements of Archaeobatrachia.

Complete Mitogenomes of Polypedates Tree Frogs Unveil Gene Rearrangement and Concerted Evolution within Rhacophoridae.

New developments in sequencing technology and nucleotide analysis have allowed us to make great advances in reconstructing anuran phylogeny. As a clade of representative amphibians that have radiated from aquatic to arboreal habitats, our understanding of the systematic status and molecular biology of rhacophorid tree frogs is still limited. We determined two new mitogenomes for the genus Polypedates (Rhacophoridae): P. impresus and P. mutus. We conducted comparative and phylogenetic analyses using our data and seven other rhacophorid mitogenomes. The mitogenomes of the genera Polypedates, Buergeria, and Zhangixalus were almost identical, except that the ATP8 gene in Polypedates had become a non-coding region; Buergeria maintained the legacy "LTPF" tRNA gene cluster compared to the novel "TLPF" order in the other two genera; and B. buergeri and Z. dennysi had no control region (CR) duplication. The resulting phylogenetic relationship supporting the above gene rearrangement pathway suggested parallel evolution of ATP8 gene loss of function (LoF) in Polypedates and CR duplication with concerted evolution of paralogous CRs in rhacophorids. Finally, conflicting topologies in the phylograms of 185 species reflected the advantages of phylogenetic analyses using multiple loci.

Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617.

COVID-19 pathogen SARS-CoV-2 has infected hundreds of millions and caused over 5 million deaths to date. Although multiple vaccines are available, breakthrough infections occur especially by emerging variants. Effective therapeutic options such as monoclonal antibodies (mAbs) are still critical. Here, we report the development, cryo-EM structures, and functional analyses of mAbs that potently neutralize SARS-CoV-2 variants of concern. By high-throughput single cell sequencing of B cells from spike receptor binding domain (RBD) immunized animals, we identify two highly potent SARS-CoV-2 neutralizing mAb clones that have single-digit nanomolar affinity and low-picomolar avidity, and generate a bispecific antibody. Lead antibodies show strong inhibitory activity against historical SARS-CoV-2 and several emerging variants of concern. We solve several cryo-EM structures at ~3 Å resolution of these neutralizing antibodies in complex with prefusion spike trimer ectodomain, and reveal distinct epitopes, binding patterns, and conformations. The lead clones also show potent efficacy in vivo against authentic SARS-CoV-2 in both prophylactic and therapeutic settings. We also generate and characterize a humanized antibody to facilitate translation and drug development. The humanized clone also has strong potency against both the original virus and the B.1.617.2 Delta variant. These mAbs expand the repertoire of therapeutics against SARS-CoV-2 and emerging variants.

Structural basis for ligand reception by anaplastic lymphoma kinase.

The proto-oncogene ALK encodes anaplastic lymphoma kinase, a receptor tyrosine kinase that is expressed primarily in the developing nervous system. After development, ALK activity is associated with learning and memory1 and controls energy expenditure, and inhibition of ALK can prevent diet-induced obesity2. Aberrant ALK signalling causes numerous cancers3. In particular, full-length ALK is an important driver in paediatric neuroblastoma4,5, in which it is either mutated6 or activated by ligand7. Here we report crystal structures of the extracellular glycine-rich domain (GRD) of ALK, which regulates receptor activity by binding to activating peptides8,9. Fusing the ALK GRD to its ligand enabled us to capture a dimeric receptor complex that reveals how ALK responds to its regulatory ligands. We show that repetitive glycines in the GRD form rigid helices that separate the major ligand-binding site from a distal polyglycine extension loop (PXL) that mediates ALK dimerization. The PXL of one receptor acts as a sensor for the complex by interacting with a ligand-bound second receptor. ALK activation can be abolished through PXL mutation or with PXL-targeting antibodies. Together, these results explain how ALK uses its atypical architecture for its regulation, and suggest new therapeutic opportunities for ALK-expressing cancers such as paediatric neuroblastoma.

Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617.

COVID-19 pathogen SARS-CoV-2 has infected hundreds of millions and caused over 5 million deaths to date. Although multiple vaccines are available, breakthrough infections occur especially by emerging variants. Effective therapeutic options such as monoclonal antibodies (mAbs) are still critical. Here, we report the development, cryo-EM structures, and functional analyses of mAbs that potently neutralize SARS-CoV-2 variants of concern. By high-throughput single cell sequencing of B cells from spike receptor binding domain (RBD) immunized animals, we identified two highly potent SARS-CoV-2 neutralizing mAb clones that have single-digit nanomolar affinity and low-picomolar avidity, and generated a bispecific antibody. Lead antibodies showed strong inhibitory activity against historical SARS-CoV-2 and several emerging variants of concern. We solved several cryo-EM structures at ∼3 Šresolution of these neutralizing antibodies in complex with prefusion spike trimer ectodomain, and revealed distinct epitopes, binding patterns, and conformations. The lead clones also showed potent efficacy in vivo against authentic SARS-CoV-2 in both prophylactic and therapeutic settings. We also generated and characterized a humanized antibody to facilitate translation and drug development. The humanized clone also has strong potency against both the original virus and the B.1.617.2 Delta variant. These mAbs expand the repertoire of therapeutics against SARS-CoV-2 and emerging variants.

Author Correction: H2A.Z facilitates licensing and activation of early replication origins.

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

H2A.Z facilitates licensing and activation of early replication origins.

DNA replication is a tightly regulated process that ensures the precise duplication of the genome during the cell cycle1. In eukaryotes, the licensing and activation of replication origins are regulated by both DNA sequence and chromatin features2. However, the chromatin-based regulatory mechanisms remain largely uncharacterized. Here we show that, in HeLa cells, nucleosomes containing the histone variant H2A.Z are enriched with histone H4 that is dimethylated on its lysine 20 residue (H4K20me2) and with bound origin-recognition complex (ORC). In vitro studies show that H2A.Z-containing nucleosomes bind directly to the histone lysine methyltransferase enzyme SUV420H1, promoting H4K20me2 deposition, which is in turn required for ORC1 binding. Genome-wide studies show that signals from H4K20me2, ORC1 and nascent DNA strands co-localize with H2A.Z, and that depletion of H2A.Z results in decreased H4K20me2, ORC1 and nascent-strand signals throughout the genome. H2A.Z-regulated replication origins have a higher firing efficiency and early replication timing compared with other origins. Our results suggest that the histone variant H2A.Z epigenetically regulates the licensing and activation of early replication origins and maintains replication timing through the SUV420H1-H4K20me2-ORC1 axis.

Discrete Element Method Simulations of the Inter-Particle Contact Parameters for the Mono-Sized Iron Ore Particles.

Aiming at predicting what happens in reality inside mills, the contact parameters of iron ore particles for discrete element method (DEM) simulations should be determined accurately. To allow the irregular shape to be accurately determined, the sphere clump method was employed in modelling the particle shape. The inter-particle contact parameters were systematically altered whilst the contact parameters between the particle and wall were arbitrarily assumed, in order to purely assess its impact on the angle of repose for the mono-sized iron ore particles. Results show that varying the restitution coefficient over the range considered does not lead to any obvious difference in the angle of repose, but the angle of repose has strong sensitivity to the rolling/static friction coefficient. The impacts of the rolling/static friction coefficient on the angle of repose are interrelated, and increasing the inter-particle rolling/static friction coefficient can evidently increase the angle of repose. However, the impact of the static friction coefficient is more profound than that of the rolling friction coefficient. Finally, a predictive equation is established and a very close agreement between the predicted and simulated angle of repose is attained. This predictive equation can enormously shorten the inter-particle contact parameters calibration time that can help in the implementation of DEM simulations.

Impact Load Behavior between Different Charge and Lifter in a Laboratory-Scale Mill.

The impact behavior between the charge and lifter has significant effect to address the mill processing, and is affected by various factors including mill speed, mill filling, lifter height and media shape. To investigate the multi-body impact load behavior, a series of experiments and Discrete Element Method (DEM) simulations were performed on a laboratory-scale mill, in order to improve the grinding efficiency and prolong the life of the lifter. DEM simulation hitherto has been extensively applied as a leading tool to describe diverse issues in granular processes. The research results shown as follows: The semi-empirical power draw of Bond model in this paper does not apply very satisfactorily for the ball mills, while the power draw determined by DEM simulation show a good approximation for the measured power draw. Besides, the impact force on the lifter was affected by mill speed, grinding media filling, lifter height and iron ore particle. The maximum percent of the impact force between 600 and 1400 N is at 70-80% of critical speed. The impact force can be only above 1400 N at the grinding media filling of 20%, and the maximum percent of impact force between 200 and 1400 N is obtained at the grinding media filling of 20%. The percent of impact force ranging from 0 to 200 N decreases with the increase of lifter height. However, this perfect will increase above 200 N. The impact force will decrease when the iron ore particles are added. Additionally, for the 80% of critical speed, the measured power draw has a maximum value. Increasing the grinding media filling increases the power draw and increasing the lifter height does not lead to any variation in power draw.

Novel Inhibitors of Toxin HipA Reduce Multidrug Tolerant Persisters.

Persisters are a small fraction of drug-tolerant bacteria without any genotype variations. Their existence in many life-threatening infectious diseases presents a major challenge to antibiotic therapy. Persistence is highly related to toxin-antitoxin modules. HipA (high persistence A) was the first toxin found to contribute to Escherichia coli persistence. In this study, we used structure-based virtual screening for HipA inhibitors discovery and identified several novel inhibitors of HipA that remarkably reduced E. coli persistence. The most potent one decreased the persister fraction by more than five-fold with an in vitro K D of 270 ± 90 nM and an ex vivo EC50 of 46 ± 2 and 28 ± 1 µM for ampicillin and kanamycin screening, respectively. These findings demonstrated that inhibition of toxin can reduce bacterial persistence independent of the antibiotics used and provided a framework for persistence treatment by interfering with the toxin-antitoxin modules.

Discovery of novel chemoeffectors and rational design of Escherichia coli chemoreceptor specificity.

Bacterial chemoreceptors mediate chemotactic responses to diverse stimuli. Here, by using an integrated in silico, in vitro, and in vivo approach, we screened a large compound library and found eight novel chemoeffectors for the Escherichia coli chemoreceptor Tar. Six of the eight new Tar binding compounds induce attractant responses, and two of them function as antagonists that can bind Tar without inducing downstream signaling. Comparison between the antagonist and attractant binding patterns suggests that the key interactions for chemotaxis signaling are mediated by the hydrogen bonds formed between a donor group in the attractant and the main-chain carbonyls (Y149 and/or Q152) on the α4 helix of Tar. This molecular insight for signaling is verified by converting an antagonist to an attractant when introducing an N-H group into the antagonist to restore the hydrogen bond. Similar signal triggering effect by an O-H group is also confirmed. Our study suggests that the Tar chemoeffector binding pocket may be separated into two functional regions: region I mainly contributes to binding and region II contributes to both binding and signaling. This scenario of binding and signaling suggests that Tar may be rationally designed to respond to a nonnative ligand by altering key residues in region I to strengthen binding with the novel ligand while maintaining the key interactions in region II for signaling. Following this strategy, we have successfully redesigned Tar to respond to l-arginine, a basic amino acid that does not have chemotactic effect for WT Tar, by two site-specific mutations (R69'E and R73'E).