Computational analysis of propeptide-containing proteins and prediction of their post-cleavage conformation changes.

A propeptide is removed from a precursor protein to generate its active or mature form. Propeptides play essential roles in protein folding, transportation, and activation and are present in about 2.3% of reviewed proteins in the UniProt database. They are often found in secreted or membrane-bound proteins including proteolytic enzymes, hormones, and toxins. We identified a variety of globular and nonglobular Pfam domains in protein sequences designated as propeptides, some of which form intramolecular interactions with other domains in the mature proteins. Propeptide-containing enzymes mostly function as proteases, as they are depleted in other enzyme classes such as hydrolases acting on DNA and RNA, isomerases, and lyases. We applied AlphaFold to generate structural models for over 7000 proteins with propeptides having no less than 20 residues. Analysis of residue contacts in these models revealed conformational changes for over 300 proteins before and after the cleavage of the propeptide. Examples of conformation change occur in several classes of proteolytic enzymes in the families of subtilisins, trypsins, aspartyl proteases, and thermolysin-like metalloproteases. In most of the observed cases, cleavage of the propeptide releases the constraints imposed by the covalent bond between the propeptide and the mature protein, and cleavage enables stronger interactions between the propeptide and the mature protein. These findings suggest that post-cleavage propeptides could play critical roles in regulating the activity of mature proteins.

Design of Bionic Foot Inspired by the Anti-Slip Cushioning Mechanism of Yak Feet.

In recent years, legged robots have been more and more widely used on non-structured terrain, and their foot structure has an important impact on the robot's motion performance and stability. The structural characteristics of the yak foot sole with a high outer edge and low middle, which has excellent soil fixation ability and is an excellent bionic prototype, can improve the friction between the foot and the ground. At the same time, the foot hooves can effectively alleviate the larger impact load when contacting with the ground, which is an excellent anti-slip buffer mechanism. The bionic foot end design was carried out based on the morphology of the yak sole; the bionic foot design was carried out based on the biological anatomy observation of yak foot skeletal muscles. The virtual models of the bionic foot end and the bionic foot were established and simulated using Solidworks 2022 and Abaqus 2023, and the anti-slip performance on different ground surfaces and the influence of each parameter of the bionic foot on the cushioning effect were investigated. The results show that (1) the curved shape of the yak sole has a good anti-slip performance on both soil ground and rocky ground, and the anti-slip performance is better on soil ground; (2) the curved shape of the yak sole has a larger maximum static friction than the traditional foot, and the anti-slip performance is stronger under the same pressure conditions; (3) the finger pillow-hoof ball structure of the bionic foot has the greatest influence on the buffering effect, and the buffering effect of the bionic foot is best when the tip of the bionic foot touches the ground first.

Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands.

Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from 14 characterized Salmonella pathogenicity islands (SPIs). Among SPIs-related proteins, 90 proteins function in the secretion machinery. 41% domains of SPI proteins have no previous sequence annotation. By comparing clinical and environmental isolates, we identified 3682 proteins that are overrepresented in clinical group that we consider as potentially pathogenic. Among domains of potentially pathogenic proteins only 50% domains were annotated by sequence methods previously. Moreover, 36% (1330 out of 3682) of potentially pathogenic proteins cannot be classified into Evolutionary Classification of Protein Domains database (ECOD). Among classified domains of potentially pathogenic proteins the most populated homology groups include helix-turn-helix (HTH), Immunoglobulin-related, and P-loop domains-related. Functional analysis revealed overrepresentation of these protein in biological processes related to viral entry into host cell, antibiotic biosynthesis, DNA metabolism and conformation change, and underrepresentation in translational processes. Analysis of the potentially pathogenic proteins indicates that they form 119 clusters or novel potential pathogenicity islands (NPPIs) within the Salmonella genome, suggesting their potential contribution to the bacterium's virulence. One of the NPPIs revealed significant overrepresentation of potentially pathogenic proteins. Overall, our analysis revealed that identified potentially pathogenic proteins are poorly studied.

Essential and virulence-related protein interactions of pathogens revealed through deep learning.

Identification of bacterial protein-protein interactions and predicting the structures of the complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here, we developed a deep learning-based pipeline that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.

Experimental Study on the Adhesion of Abalone to Surfaces with Different Morphologies.

To date, research on abalone adhesion has primarily analyzed the organism's adhesion to smooth surfaces, with few studies on adhesion to non-smooth surfaces. The present study examined the surface morphology of the abalone's abdominal foot, followed by measuring the adhesive force of the abalone on a smooth force measuring plate and five force measuring plates with different surface morphologies. Next, the adhesion mechanism of the abdominal foot was analyzed. The findings indicated that the abdominal foot of the abalone features numerous stripe-shaped folds on its surface. The adhesion of the abalone to a fine frosted glass plate, a coarse frosted glass plate, and a quadrangular conical glass plate was not significantly different from that on a smooth glass plate. However, the organism's adhesion to a small lattice pit glass plate and block pattern glass plate was significantly different. The abalone could effectively adhere to the surface of the block pattern glass plate using the elasticity of its abdominal foot during adhesion but experienced difficulty in completely adhering to the surface of the quadrangular conical glass plate. The abdominal foot used its elasticity to form an independent sucker system with each small lattice pit, significantly improving adhesion to the small lattice pit glass plate. The elasticity of the abalone's abdominal foot created difficulty in handling slight morphological size changes in roughness, resulting in no significant differences in its adhesion to the smooth glass plate.

What one genus of showy moths can say about migration, adaptation, and wing pattern.

The Ornate Moth, Utetheisa ornatrix, has served as a model species in chemical ecology studies for decades. Like in the widely publicized stories of the Monarch and other milkweed butterflies, the Ornate Moth and its relatives are tropical insects colonizing whole continents assisted by their chemical defenses. With the recent advances in genomic techniques and evo-devo research, it is becoming a model for studies in other areas, from wing pattern development to phylogeography, from toxicology to epigenetics. We used a genomic approach to learn about Utetheisa's evolution, detoxification, dispersal abilities, and wing pattern diversity. We present an evolutionary genomic analysis of the worldwide genus Utetheisa, then focusing on U. ornatrix. Our reference genome of U. ornatrix reveals gene duplications in the regions possibly associated with detoxification abilities, which allows them to feed on toxic food plants. Finally, comparative genomic analysis of over 100 U. ornatrix specimens from the museum with apparent differences in wing patterns suggest the potential roles of cortex and lim3 genes in wing pattern formation of Lepidoptera and the utility of museum-preserved collection specimens for wing pattern research.

Hedgehog Signaling Controls Chondrogenesis and Ectopic Bone Formation via the Yap-Ihh Axis.

Fibrodysplasia ossificans progressiva (FOP) is a rare congenital disorder characterized by abnormal bone formation due to ACVR1 gene mutations. The identification of the molecular mechanisms underlying the ectopic bone formation and expansion in FOP is critical for the effective treatment or prevention of HO. Here we find that Hh signaling activation is required for the aberrant ectopic bone formation in FOP. We show that the expression of Indian hedgehog (Ihh), a Hh ligand, as well as downstream Hh signaling, was increased in ectopic bone lesions in Acvr1R206H; ScxCre mice. Pharmacological treatment with an Ihh-neutralizing monoclonal antibody dramatically reduced chondrogenesis and ectopic bone formation. Moreover, we find that the activation of Yap in the FOP mouse model and the genetic deletion of Yap halted ectopic bone formation and decreased Ihh expression. Our mechanistic studies showed that Yap and Smad1 directly bind to the Ihh promoter and coordinate to induce chondrogenesis by promoting Ihh expression. Therefore, the Yap activation in FOP lesions promoted ectopic bone formation and expansion in both cell-autonomous and non-cell-autonomous manners. These results uncovered the crucial role of the Yap-Ihh axis in FOP pathogenesis, suggesting the inhibition of Ihh or Yap as a potential therapeutic strategy to prevent and reduce HO.

ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2.

Protein structure prediction has now been deployed widely across several different large protein sets. Large-scale domain annotation of these predictions can aid in the development of biological insights. Using our Evolutionary Classification of Protein Domains (ECOD) from experimental structures as a basis for classification, we describe the detection and cataloging of domains from 48 whole proteomes deposited in the AlphaFold Database. On average, we can provide positive classification (either of domains or other identifiable non-domain regions) for 90% of residues in all proteomes. We classified 746,349 domains from 536,808 proteins comprised of over 226,424,000 amino acid residues. We examine the varying populations of homologous groups in both eukaryotes and bacteria. In addition to containing a higher fraction of disordered regions and unassigned domains, eukaryotes show a higher proportion of repeated proteins, both globular and small repeats. We enumerate those highly populated domains that are shared in both eukaryotes and bacteria, such as the Rossmann domains, TIM barrels, and P-loop domains. Additionally, we compare the sampling of homologous groups from this whole proteome set against our stable ECOD reference and discuss groups that have been enriched by structure predictions. Finally, we discuss the implication of these results for protein target selection for future classification strategies for very large protein sets.

A Mesostructure Multivariant-Assembly Reinforced Ultratough Biomimicking Superglue.

The imitation of mussels and oysters to create high-performance adhesives is a cutting-edge field. The introduction of inorganic fillers is shown to significantly alter the adhesive's properties, yet the potential of mesoporous materials as fillers in adhesives is overlooked. In this study, the first report on the utilization of mesoporous materials in a biomimetic adhesive system is presented. Incorporating mesoporous silica nanoparticles (MSN) profoundly enhances the adhesion of pyrogallol (PG)-polyethylene imine (PEI) adhesive. As the MSN concentration increases, the adhesion strength to glass substrates undergoes an impressive fivefold improvement, reaching an outstanding 2.5 mPa. The adhesive forms an exceptionally strong bond, to the extent that the glass substrate fractures before joint failure. The comprehensive tests involving various polyphenols, polymers, and fillers reveal an intriguing phenomenon-the molecular structure of polyphenols significantly influences adhesive strength. Steric hindrance emerges as a crucial factor, regulating the balance between π-cation and charge interactions, which significantly impacts the multicomponent assembly of polyphenol-PEI-MSN and, consequently, adhesive strength. This groundbreaking research opens new avenues for the development of novel biomimetic materials.

Computational analysis of protein-protein interactions of cancer drivers in renal cell carcinoma.

Renal cell carcinoma (RCC) is the most common type of kidney cancer with rising cases in recent years. Extensive research has identified various cancer driver proteins associated with different subtypes of RCC. Most RCC drivers are encoded by tumor suppressor genes and exhibit enrichment in functional categories such as protein degradation, chromatin remodeling, and transcription. To further our understanding of RCC, we utilized powerful deep-learning methods based on AlphaFold to predict protein-protein interactions (PPIs) involving RCC drivers. We predicted high-confidence complexes formed by various RCC drivers, including TCEB1, KMT2C/D and KDM6A of the COMPASS-related complexes, TSC1 of the MTOR pathway, and TRRAP. These predictions provide valuable structural insights into the interaction interfaces, some of which are promising targets for cancer drug design, such as the NRF2-MAFK interface. Cancer somatic missense mutations from large datasets of genome sequencing of RCCs were mapped to the interfaces of predicted and experimental structures of PPIs involving RCC drivers, and their effects on the binding affinity were evaluated. We observed more than 100 cancer somatic mutations affecting the binding affinity of complexes formed by key RCC drivers such as VHL and TCEB1. These findings emphasize the importance of these mutations in RCC pathogenesis and potentially offer new avenues for targeted therapies.

Phylogeography of Two Enigmatic Sulphur Butterflies, Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897 (Lepidoptera, Pieridae), with Relations to Wolbachia Infection.

The genus Colias Fabricius, 1807 includes numerous taxa and forms with uncertain status and taxonomic position. Among such taxa are Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897, interpreted in the literature either as conspecific forms, as subspecies of different but morphologically somewhat similar Colias species or as distinct species-level taxa. Based on mitochondrial and nuclear DNA markers, we reconstructed a phylogeographic pattern of the taxa in question. We recover and include in our analysis DNA barcodes of the century-old type specimens, the lectotype of C. tamerlana deposited in the Natural History Museum (Museum für Naturkunde), Berlin, Germany (ZMHU) and the paralectotype of C. tamerlana and the lectotype of C. mongola deposited in the Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia (ZISP). Our analysis grouped all specimens within four (HP_I-HP_IV) deeply divergent but geographically poorly structured clades which did not support nonconspecifity of C. mongola-C. tamerlana. We also show that all studied females of the widely distributed haplogroup HP_II were infected with a single Wolbachia strain belonging to the supergroup B, while the males of this haplogroup, as well as all other investigated specimens of both sexes, were not infected. Our data highlight the relevance of large-scale sampling dataset analysis and the need for testing for Wolbachia infection to avoid erroneous phylogenetic reconstructions and species misidentification.

Insights into virulence: structure classification of the Vibrio parahaemolyticus RIMD mobilome.

IMPORTANCE: The pandemic Vpar strain RIMD causes seafood-borne illness worldwide. Previous comparative genomic studies have revealed pathogenicity islands in RIMD that contribute to the success of the strain in infection. However, not all virulence determinants have been identified, and many of the proteins encoded in known pathogenicity islands are of unknown function. Based on the EOCD database, we used evolution-based classification of structure models for the RIMD proteome to improve our functional understanding of virulence determinants acquired by the pandemic strain. We further identify and classify previously unknown mobile protein domains as well as fast evolving residue positions in structure models that contribute to virulence and adaptation with respect to a pre-pandemic strain. Our work highlights key contributions of phage in mediating seafood born illness, suggesting this strain balances its avoidance of phage predators with its successful colonization of human hosts.

Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle.

Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute a disproportionately large fraction of microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow as epibionts on host Actinobacteria. Due to a lack of suitable tools, the genetic basis of this lifestyle and other unique features of Patescibacteira remain unexplored. Here, we show that Saccharibacteria exhibit natural competence, and we exploit this property for their genetic manipulation. Imaging of fluorescent protein-labeled Saccharibacteria provides high spatiotemporal resolution of phenomena accompanying epibiotic growth, and a transposon-insertion sequencing (Tn-seq) genome-wide screen reveals the contribution of enigmatic Saccharibacterial genes to growth on their hosts. Finally, we leverage metagenomic data to provide cutting-edge protein structure-based bioinformatic resources that support the strain Southlakia epibionticum and its corresponding host, Actinomyces israelii, as a model system for unlocking the molecular underpinnings of the epibiotic lifestyle.

Computational analysis of regulatory regions in human protein kinases.

Eukaryotic proteins often feature modular domain structures comprising globular domains that are connected by linker regions and intrinsically disordered regions that may contain important functional motifs. The intramolecular interactions of globular domains and nonglobular regions can play critical roles in different aspects of protein function. However, studying these interactions and their regulatory roles can be challenging due to the flexibility of nonglobular regions, the long insertions separating interacting modules, and the transient nature of some interactions. Obtaining the experimental structures of multiple domains and functional regions is more difficult than determining the structures of individual globular domains. High-quality structural models generated by AlphaFold offer a unique opportunity to study intramolecular interactions in eukaryotic proteins. In this study, we systematically explored intramolecular interactions between human protein kinase domains (KDs) and potential regulatory regions, including globular domains, N- and C-terminal tails, long insertions, and distal nonglobular regions. Our analysis identified intramolecular interactions between human KDs and 35 different types of globular domains, exhibiting a variety of interaction modes that could contribute to orthosteric or allosteric regulation of kinase activity. We also identified prevalent interactions between human KDs and their flanking regions (N- and C-terminal tails). These interactions exhibit group-specific characteristics and can vary within each specific kinase group. Although long-range interactions between KDs and nonglobular regions are relatively rare, structural details of these interactions offer new insights into the regulation mechanisms of several kinases, such as HASPIN, MAPK7, MAPK15, and SIK1B.

Research Progress of Superhydrophobic Materials in the Field of Anti-/De-Icing and Their Preparation: A Review.

Accumulated ice has brought much damage to engineering and people's lives. The accumulation of ice can affect the flight safety of aircraft and lead to the failure of cables and power generation blades; it can even cause damage to human life. Traditional anti-icing and de-icing strategies have many disadvantages such as high energy consumption, low efficiency, or pollution of the environment. Therefore, inspired by animal communities, researchers have developed new passive anti-icing materials such as superhydrophobic material. In this paper, the solid surface wetting phenomenon and superhydrophobic anti-icing and de-icing mechanism were introduced. The methods of fabrication of superhydrophobic surfaces were summarized. The research progress of wear-resistant superhydrophobic coatings, self-healing/self-repairing superhydrophobic coatings, photothermal superhydrophobic coatings, and electrothermal superhydrophobic coatings in the field of anti-icing and de-icing was reviewed. The current problems and challenges were analyzed, and the development trend of superhydrophobic materials was also prospected in the field of anti-icing and de-icing. The practicality of current superhydrophobic materials should continue to be explored in depth.

Taxonomic notes on Neotropical Hesperiidae (Lepidoptera).

Genomic sequencing (or morphology when indicated) and analysis of Hesperiidae that includes a number of primary type specimens reveals inconsistencies between the phylogenetic trees and the current classification that are resolved here. The following taxonomic changes are proposed. Oeonus Godman, 1900, stat. nov. is a subgenus of Oxynthes Godman, 1900. Decinea lydora (Plötz, 1882), stat. rev. is a valid species, not a synonym of Lindra neroides (Herrich-Schäffer, 1869), comb. nov. The following are: species-level taxa, not subspecies: Cabirus junta Evans, 1952, stat. nov. and Cabirus purda Evans, 1952, stat. nov. (not Cabirus procas (Cramer, 1777)), Orthos hyalinus (E. Bell, 1930), stat. rest. and Orthos minka Evans, 1955, stat. nov. (not Orthos orthos (Godman, 1900)), Eprius obrepta (Kivirikko, 1936), stat. rest. (not Eprius veleda (Godman, 1901)), Corra catargyra (C. Felder & R. Felder, 1867), stat. rest. and Corra conka (Evans, 1955), stat. nov. (not Corra coryna (Hewitson, 1866)), Cymaenes macintyrei Hayward, 1939, stat. rest. (not Cymaenes tripunctata (Latreille, [1824])), Duroca lenta (Evans, 1955), stat. rest. (not Duroca duroca Plötz, 1882), Oarisma (Copaeodes) favor (Evans, 1955), stat. nov. (not Oarisma (Copaeodes) jean (Evans, 1955)), Panoquina eugeon (Godman & Salvin, 1896), stat. rest., Panoquina calna Evans, 1955, stat. nov. and Panoquina albistriga O. Mielke, 1980, stat. nov. (not Panoquina panoquinoides (Skinner, 1891)); subspecies-level taxa, not species: Carystus elvira rufoventris Austin & O. Mielke, 2007, stat. nov.; junior subjective synonyms: Bungalotis gagarini O. Mielke, 1967, syn. nov. of Bungalotis corentinus (Plötz, 1882), Salantoia dinka (Evans, 1952), syn. nov. of Adina adrastor (Mabille and Boullet, 1912), Lindra brasus ackeryi O. Mielke, 1978, stat. nov. of Lindra neroides neroides (Herrich-Schäffer, 1869) (but Lindra brasus (O. Mielke, 1968) is still a valid species), Vidius felus O. Mielke, 1968, syn. nov. of Vidius dagon (Evans, 1955), comb. nov., and Cobalopsis dorpa de Jong, 1983, syn. nov. of Vidius catocala (Herrich-Schäffer, 1869), comb. nov.; new genus-species combinations: Oxynthes (Oxynthes) egma (Evans, 1955), comb. nov. (not Oeonus Godman, 1900), Lindra neroides (Herrich-Schäffer, 1869), comb. nov. (not Decinea Evans, 1955), Mucia rusta (Evans, 1955), comb. nov. (not Psoralis Mabille, 1904), Rhomba mirnae (Siewert, Nakamura & O. Mielke, 2014), comb. nov. (not Alychna Grishin, 2019), Eprius planus (Weeks, 1901), comb. nov. and Eprius penna (Evans, 1955), comb. nov. (changed based on morphology) (not Mnasicles Godman, 1901), Lattus minor (O. Mielke, 1967), comb. nov. (not Eutocus Godman, 1901), Panca fiedleri (Carneiro, O. Mielke & Casagrande, 2015), comb. nov., Eutocus rogan (Evans, 1955), comb. nov. (changed based on morphology and cytochrome c oxidase subunit I (COI) DNA barcode) and Eutocus brasilia (Carneiro, O. Mielke & Casagrande, 2015), comb. nov. (not Ginungagapus Carneiro, O. Mielke & Casagrande, 2015), Eutocus fosca (Evans, 1955), comb. nov. (not Artines Godman, 1901), Rectava cascatona (O. Mielke, 1992), comb. nov. (not Papias Godman, 1900), Lurida zama (Hayward, 1939), comb. nov. and Vehilius campestris (O. Mielke, 1980), comb. nov. (not Cymaenes Scudder, 1872), Corra xanthus (O. Mielke, 1989), comb. nov., Cymaenes catarinae (O. Mielke, 1989), comb. nov., Vehilius spitzi (O. Mielke, 1967), comb. nov., Vehilius tinta (Evans, 1955), comb. nov. (not Vidius Evans, 1955), Cymaenes incomptus (Hayward, 1934), comb. nov. and Vehilius tanta (Evans, 1955), comb. nov. (not Nastra Evans, 1955), Vidius catocala (Herrich-Schäffer, 1869), comb. nov. Vidius cocalus (Hayward, 1939), comb. nov., Vidius dagon (Evans, 1955), and Vidius obscurior (Hayward, 1934), comb. nov. (not Cobalopsis Godman, 1900), Duroca caraca (O. Mielke, 1992), comb. nov. (not Lerema Scudder, 1872), and Cantha eteocla (Plötz, 1882), comb. nov. and Cantha buriti (O. Mielke, 1968), comb. nov. (not Phlebodes Hübner, [1819]); and new species-subspecies combinations: Lindra neroides huxleyi O. Mielke, 1978, comb. nov. (not Lindra brasus (O. Mielke, 1968)), Corra conka argentus (H. Freeman, 1969), stat. nov. (not Corra coryna (Hewitson, 1866)), Panoquina eugeon minima de Jong, 1983, comb. nov. (not Panoquina panoquinoides (Skinner, 1891)). The following neotype and lectotypes are designated to ensure nomenclatural identity and stability: neotype of Cobalus neroides Herrich-Schäffer, 1869 and lectotypes of Cobalus catocala Herrich-Schäffer, 1869 and Lerema elgina Schaus, 1902.

Lessons from the genomic analysis of Hesperiidae (Lepidoptera) holotypes in the MIZA collection (Maracay, Venezuela).

Genomic sequencing and analysis of holotypes from the MIZA collection (Maracay, Venezuela) and their comparison with other species and their type specimens advances our understanding of their taxonomy. Jemadia demarmelsi Orellana, [2010] is confirmed as a species-level taxon and its female is genetically verified. The following are species-level taxa, not subspecies: Amenis pedro O. Mielke & Casagrande, 2022, stat. nov. (not Amenis pionia (Hewitson, 1857)) and Jemasonia sosia (Mabille, 1878), stat. rest. (not Jemasonia hewitsonii (Mabille, 1878)). Amenis ponina rogeri Orellana, [2010], stat. nov. and Jemasonia pater ortizi (Orellana, [2010]), stat. nov. are subspecies, not species. Jemadia pseudognetus imitator (Mabille, 1891), comb. nov. (not Jemadia hospita (Butler, 1877)) and Damas cervelina Orellana & Costa, 2019, comb. nov. (not Megaleas Godman, 1901) are new combinations.

Yap controls notochord formation and neural tube patterning by integrating mechanotransduction with FoxA2 and Shh expression.

Correct notochord and neural tube (NT) formation is crucial to the development of the central nervous system and midline structures. Integrated biochemical and biophysical signaling controls embryonic growth and patterning; however, the underlying mechanisms remain poorly understood. Here, we took the opportunities of marked morphological changes during notochord and NT formation and identified both necessary and sufficient roles of Yap, a key mechanosensor and mechanotransducer, in biochemical signaling activation during formation of notochord and floor plate, the ventral signaling centers that pattern the dorsal-ventral axis of NT and the surrounding tissues. We showed that Yap activation by a gradient of mechanical stress and tissue stiffness in the notochord and ventral NT induces FoxA2 and Shh expression. Hedgehog signaling activation rescued NT patterning defects caused by Yap deficiency, but not notochord formation. Therefore, mechanotransduction via Yap activation acts in feedforward mechanisms to induce FoxA2 expression for notochord formation and activate Shh expression for floor plate induction by synergistically interacting with FoxA2.

Abalone adhesion: The role of various adhesion forces and their proportion to total adhesion force.

Adhesion is the basic ability of many kinds of animals in nature, which ensures the survival and reproduction of animal populations. The aquatic abalone has a strong adhesion capacity. In this study, we observed the microscopic morphology of abalone abdominal foot surface, and found that the surface was covered with a large number of fibers. Then five types of force measuring plates were designed and processed for the adhesion test of abalone abdominal foot. According to the test results, the composition of abalone abdominal foot adhesion force was analyzed and the proportion of various adhesion force to the total adhesion force of abalone abdominal foot was calculated. Among them, the vacuum adhesion force accounts for more than half of the total adhesion force of abalone abdominal foot, and its proportion is more than 60%. Van der Waals force also plays an important role, and its proportion is more than 20%. The proportion of capillary force is very small, which is only about 1%. Its main role is to form a liquid film to prevent the gas from flowing into the sucker. The vacuum adhesion of abalone abdominal foot can be further divided into the whole adhesion of abdominal foot, the local adhesion of abdominal foot and the frictional equivalent vacuum adhesion. And the whole adhesion of abdominal foot is basically equivalent to the local adhesion of abdominal foot. This study quantifies the proportion of various adhesion forces to the total adhesion force of the abdominal foot, which provides a reference for the further study of other adhesive creatures and the design of bionic underwater adhesion devices.

Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter.

The study of bacteria has yielded fundamental insights into cellular biology and physiology, biotechnological advances and many therapeutics. Yet due to a lack of suitable tools, the significant portion of bacterial diversity held within the candidate phyla radiation (CPR) remains inaccessible to such pursuits. Here we show that CPR bacteria belonging to the phylum Saccharibacteria exhibit natural competence. We exploit this property to develop methods for their genetic manipulation, including the insertion of heterologous sequences and the construction of targeted gene deletions. Imaging of fluorescent protein-labeled Saccharibacteria provides high spatiotemporal resolution of phenomena accompanying epibiotic growth and a transposon insertion sequencing genome-wide screen reveals the contribution of enigmatic Saccharibacterial genes to growth on their Actinobacteria hosts. Finally, we leverage metagenomic data to provide cutting-edge protein structure-based bioinformatic resources that support the strain Southlakia epibionticum and its corresponding host, Actinomyces israelii , as a model system for unlocking the molecular underpinnings of the epibiotic lifestyle.