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

Antimicrobial peptide temporin derivatives inhibit biofilm formation and virulence factor expression of Streptococcus mutans

IntroductionTemporin-GHa obtained from the frog Hylarana guentheri showed bactericidal efficacy against Streptococcus mutans. To enhance its antibacterial activity, the derived peptides GHaR and GHa11R were designed, and their antibacterial performance, antibiofilm efficacy and potential in the inhibition of dental caries were evaluated.MethodsBacterial survival assay, fluorescent staining assay and transmission electron microscopy observation were applied to explore how the peptides inhibited and killed S. mutans. The antibiofilm efficacy was assayed by examining exopolysaccharide (EPS) and lactic acid production, bacterial adhesion and cell surface hydrophobicity. The gene expression level of virulence factors of S. mutans was detected by qRT-PCR. Finally, the impact of the peptides on the caries induced ability of S. mutans was measured using a rat caries model.ResultsIt has been shown that the peptides inhibited biofilm rapid accumulation by weakening the initial adhesion of S. mutans and reducing the production of EPS. Meanwhile, they also decreased bacterial acidogenicity and aciduricity, and ultimately prevented caries development in vivo.ConclusionGHaR and GHa11R might be promising candidates for controlling S. mutans infections

Additional file 3: of The structure of a prophenoloxidase (PPO) from Anopheles gambiae provides new insights into the mechanism of PPO activation

The six Cu-coordinating His residues are stabilized by three Phe residues at the active site of AgPPO8 via hydrophobic interactions. The six His and three Phe residues are shown as magenta and red sticks, respectively. The shortest carbon-carbon distances (Å) are indicated as black (F99), yellow (F248), and green (F415) dashes, respectively. CuA and CuB are shown as brown spheres. (TIF 3116 kb

The Review of the Studies on the Spatial Structure of Japanese Medieval Cities (Special Issue : HISTORICAL RESEARCH TODAY, 2006)

Studies of Japanese medieval cities have been interdisciplinary, including the fields of history, archaeology, architectural history, and geography. The central issue of the studies has been how to reconstruct and explain the "space" of the cities, but the strict meaning of the key concept "spatial structure" has never been explored. However, current studies have arrived at the point of reassessing their perspectives and methods of spatial analysis from their own academic points of view. This paper aims to review the studies of Japanese medieval cities by examining the meaning of the spatial structure and perspectives on spatial analysis. Prior to the 1970s, historians had displayed a strong interest in the late-medieval castle towns, which were seen as immature feudal cities on the verge of developing into the consummate feudal cities of early-modern times. They determined the locations of the castle, residences of the warriors, and markets in each city, and they used this data as a standard to estimate the level of development as a feudal city. They understood the "spatial structure" as the relative connection of the locations of these three elements. In the late 1970s, influential papers were published by the historian Amino Yoshihiko, who defined the space where people engaged in various economic activities free from the intervention of a feudal lord as an "urban location" During the same period, archaeological surveys produced many remarkable results, especially on some early medieval cities. The conceptual term urban location was reconstructed in actual spatial form by a group of historians and archaeologists working together who used the many actual excavations of early-medieval sites. Because this method of reconstruction was used to make up for the lack of space where archaeological surveys had not been conducted, the abstract model of the center and periphery was applied to the entire urban space. This method caused confusion between abstract and concrete spatial structures when using the term urban location. On the other hand, other historians and archaeologists joined to initiate the study of the changes in castle towns from late medieval to early modern times, but in manner divorced from the older theories about feudal cities. They found the medieval castle towns had two different varieties of space. One type of space was under the control of powerful lords, and the other type was space that was free to a certain extent from the power of the lords. They claimed such multivalent space was unified by the powerful lords in early modern times. Their dynamic but linear view of the development of the history of castle towns had a great influence on many researchers. Furthermore, their method of reconstructing space that clarified the concrete morphology and function of urban elements of the city as a whole was also widely accepted. The space reconstructed by this method was recognized as the spatial structure of the city. In the 1990s, an architectural historian presented a remarkable model to explain the history of the space of the Japanese cities from ancient through modern times. That model, composed of two symbolic factors, was exceedingly abstract. It succeeded in explaining the multiple and complex space of medieval cities in their totality. In other words, this meant that the spatial structure of the city was a model that was symbolic and highly abstract. As is demonstrated in this paper, studies of Japanese medieval cities have not shared a common understanding of the most important concept of spatial structure, so researchers have employed perspectives appropriate to their own themes in analyzing space. Due to the confusion borne of a lack of recognition of the concepts of space and spatial structure, researchers have faced problems in exchanging results of studies with each other. The fundamental cause of this problem lies in the attitudes of most researchers who have not paid serious attention to space itself. What then would be an effective solution to this problem? This paper proposes that one solution is to distinguish the space planned by the lords from the actual space of the cities, while recognizing the diversity of space itself and carefully referring to the basic concepts of space used in geography. Applying this perspective toward the studies of castle towns, this paper constructs a new history of these spaces from late medieval to early modern times and demonstrates the validity of the method. From the last quarter of the 15th century to the first quarter of the 16th century, lords who were linked to the political center possessed city plans that consisted of a rectangular format and grid road pattern. But their plans were not always realized in actual space as planned because local societies did not always accept them in total. The actual spatial structure was formed by the lords and local societies modifying the city plans to fit local contexts. In the second and third quarters of the 16th century, lords who had developed into representatives of local societies did not have any clear city plans. Actual spatial structure was influenced not only by the actions of the lords, but also by that of other local representatives and other types of spatial structures in local cities. As a result, there was a variety of actual spatial structure of castle towns. In the last quarter of the 16th century, powerful lords unified the diversity of regional society in Japan and started to establish a nation state. These powerful lords had rigid city plans and forced their vassals and bureaucracy to realize them in their own territories as a proof of submission to the lords during the process of unification. Many castle towns were built, and then rebuilt, in a common format all over Japan. The city plans of lords had great influence on the actual spatial structure of local castle towns, nevertheless, the plans were accepted and modified to some extent depending on the local context. As this exploration of castle towns suggests, the studies of medieval cities contain latent possibilities for constructing a new history of space by modifying the way the space of cities is seen

Optimization of Porphyran Extraction from <i>Pyropia yezoensis</i> by Response Surface Methodology and Its Lipid-Lowering Effects

Macroalgae polysaccharides are phytochemicals that are beneficial to human health. In this study, response surface methodology was applied to optimize the extraction procedure of Pyropia yezoensis porphyran (PYP). The optimum extraction parameters were: 100 °C (temperature), 120 min (time), and 29.32 mL/g (liquid–solid ratio), and the maximum yield of PYP was 22.15 ± 0.55%. The physicochemical characteristics of PPYP, purified from PYP, were analyzed, along with its lipid-lowering effect, using HepG2 cells and Drosophila melanogaster larvae. PPYP was a β-type sulfated hetero-rhamno-galactan-pyranose with a molecular weight of 151.6 kDa and a rhamnose-to-galactose molar ratio of 1:5.3. The results demonstrated that PPYP significantly reduced the triglyceride content in palmitic acid (PA)-induced HepG2 cells and high-sucrose-fed D. melanogaster larvae by regulating the expression of lipid metabolism-related genes, reducing lipogenesis and increasing fatty acid β-oxidation. To summarize, PPYP can lower lipid levels in HepG2 cells and larval fat body (the functional homolog tissue of the human liver), suggesting that PPYP may be administered as a potential marine lipid-lowering drug

Don’t Waste Your Bits! Squeeze Activations and Gradients for Deep Neural Networks via TinyScript

Recent years have witnessed intensive research interests on training deep neural networks (DNNs) more efficiently by quantization-based compression methods, which facilitate DNNs training in two ways: (1) activations are quantized to shrink the memory consumption, and (2) gradients are quantized to decrease the communication cost. However, existing methods mostly use a uniform mechanism that quantizes the values evenly. Such a scheme may cause a large quantization variance and slow down the convergence in practice. In this work, we introduce TinyScript, which applies a non-uniform quantization algorithm to both activations and gradients. TinyScript models the original values by a family of Weibull distributions and searches for ”quantization knobs” that minimize quantization variance. We also discuss the convergence of the non-uniform quantization algorithm on DNNs with varying depths, shedding light on the number of bits required for convergence. Experiments show that TinyScript always obtains lower quantization variance, and achieves comparable model qualities against full precision training using 1-2 bits less than the uniform-based counterpart.ISSN:2640-349

Preparation and Property of Bio-Polyimide/Halloysite Nanocomposite Based on 2,5-Furandicarboxylic Acid

Bio-based polyimide (PI)/halloysite nanotube (HNT) nanocomposites based on 2,5-furandicarboxylic acid were prepared by in situ polymerization. The pristine HNTs were modified by tetraethoxysilane (TEOS) and 4,4&prime;-oxybisbenzenamine (ODA). The bio-based PI/HNT nanocomposite film exhibited lower moisture absorption than pure bio-based polyimide, showing that the water resistance of the bio-based polyimide film was improved. The thermal stability and glass transition temperature (Tg) of PI/HNTs nanocomposites were improved with the addition of modified HNTs. Both the tensile strength and Young&rsquo;s modulus of bio-based PI/HNTs nanocomposite films were enhanced. A 37.7% increase in tensile strength and a 75.1% increase in Young&rsquo;s modulus of bio-based PI/HNTs nanocomposite films, with 1 wt% of the modified HNTs, were achieved. The result confirmed that 2,5-furandicarboxylic acid could replace the oil-based material effectively, thus reducing pollution and protecting the environment. Finally, a preparation mechanism to prepare bio-based PI/HNTs nanocomposite is proposed