Morphological Identification of Actinobacteria

Actinobacteria is a phylum of gram-positive bacteria with high G+C content. Among gram-positive bacteria, actinobacteria exhibit the richest morphological differentiation, which is based on a filamentous degree of organization like filamentous fungi. The actinobacteria morphological characteristics are basic foundation and information of phylogenetic systematics. Classic actinomycetes have well-developed radial mycelium, which can be divided into substrate mycelium and aerial mycelium according to morphology and function. Some actinobacteria can form complicated structures, such as spore, spore chain, sporangia, and sporangiospore. The structure of hyphae and ultrastructure of spore or sporangia can be observed with microscopy. Actinobacteria have different cultural characteristics in various kinds of culture media, which are important in the classification identification, general with spores, aerial hyphae, with or without color and the soluble pigment, different growth condition on various media as the main characteristics. The morphological differentiation of actinobacteria, especially streptomycetes, is controlled by relevant genes. Both morphogenesis and antibiotic production in the streptomycetes are initiated in response to starvation, and these events are coupled

Isolation and Cultivation Methods of Actinobacteria

Actinobacteria (actinomycetes) have been received much attention, as these bacteria produce a variety of natural drugs and other bioactive metabolites. The distribution of actinomycetes in various natural habitats, including soil, ocean, extreme environments, plant, lichens and animals, is described. The collection and pretreatment of test samples from different sources, design principle of selective isolation media, selection of inhibitors, selective isolation procedures of special actinomycetes, and cultivation methods are introduced and discussed

Cultural, Physiological, and Biochemical Identification of Actinobacteria

The traditional phenotypic tests are commonly used in actinobacterial identification. They constitute the basis for the formal description of taxa, from species and subspecies up to genus and family. The classical phenotypic characteristics of actinobacteria comprise morphological, physiological, and biochemical features. The morphology of actinobacteria includes both cellular and colonial characters. The physiological and biochemical features include data on growth at different temperatures, pH values, salt concentrations, or atmospheric conditions, and data on growth in the presence of various substances such as antimicrobial agents, the presence or activity of various enzymes, and with respect to metabolization of compounds. The phenotype is the observable expression of the genotype. Gene expression is directly related to the environmental conditions. Actinobacterial phenotype cannot be based on the simple observation of the organism. Strains of the most closely related taxa should be compared in their phenotypic analysis using identical methods. The comparisons must include the type strain of the type species of the appropriate genera. Furthermore, with the development of technology, microbial physiological and biochemical identification technology is becoming fast, simple, and automated

Molecular Phylogenetic Identification of Actinobacteria

Molecular phylogenetics plays an important role in prokaryote taxonomy and identification. The content of this chapter is to introduce the common application of genetic criteria including 16S rRNA gene sequence nucleotide similarity and phylogeny, DNA G+C content, and DNA–DNA hybridization. However, the genomics era might put forward some new criteria. This chapter emphasizes the methods and basic principles of molecular identification and taxonomy of actinobacteria

Genomic Scaffold Filling Revisited

The genomic scaffold filling problem has attracted a lot of attention recently. The problem is on filling an incomplete sequence (scaffold) I into I\u27, with respect to a complete reference genome G, such that the number of adjacencies between G and I\u27 is maximized. The problem is NP-complete and APX-hard, and admits a 1.2-approximation. However, the sequence input I is not quite practical and does not fit most of the real datasets (where a scaffold is more often given as a list of contigs). In this paper, we revisit the genomic scaffold filling problem by considering this important case when, (1) a scaffold S is given, the missing genes X = c(G) - c(S) can only be inserted in between the contigs, and the objective is to maximize the number of adjacencies between G and the filled S\u27 and (2) a scaffold S is given, a subset of the missing genes X\u27 subset X = c(G) - c(S) can only be inserted in between the contigs, and the objective is still to maximize the number of adjacencies between G and the filled S\u27\u27. For problem (1), we present a simple NP-completeness proof, we then present a factor-2 greedy approximation algorithm, and finally we show that the problem is FPT when each gene appears at most d times in G. For problem (2), we prove that the problem is W[1]-hard and then we present a factor-2 FPT-approximation for the case when each gene appears at most d times in G

Research on borehole transient electromagnetic positioning method of azimuthal coil scanning detection

The borehole transient electromagnetic method is used to detect the long-range water-bearing bodies around the borehole wall by using the advanced water exploration borehole in the heading roadway, which avoids the “one’s opinion in one hole” because the normal logging methods can only detect the rock layer of the borehole wall. At present, because of the whole space effect, the current borehole transient electromagnetic method cannot distinguish the orientation of abnormal bodies by the received single-component response, and it can approximate the orientation of abnormal bodies by multi-component response, but it is difficult to precisely locate and interpret the profiles by the visual and effective means such as imaging. Based on the theory of borehole transient electromagnetic method and azimuthal electromagnetic logging, this paper proposes a borehole transient electromagnetic positioning method with azimuthal coil scanning detection. The azimuth coil is used as the detection device to reduce the mutual inductance of the coil and enhance the detection effect of the borehole transient electromagnetic method. At the same time, by changing the rotation angle of the coil, the borehole wall is scanned by 360° to form a radial all-round detection of the borehole, aiming at a precise localization and profile interpretation of low-resistance abnormal bodies in the rock mass at the periphery of the borehole wall. Firstly, the authors derive an analytical expression for the mutual inductance of an azimuth coil, discuss the effect of azimuth angle on azimuth coil mutual inductance, and determine the optimum azimuth angle by numerical calculation. Secondly, a full-space 3D geological-geophysical model of the borehole with homogeneous medium and low-resistance abnormal bodies are established respectively and the numerical simulation of transient electromagnetic field is carried out. The multi-component response characteristics of the azimuthal coil scanning detection transient electromagnetic response are analyzed, and the law of transient electromagnetic response of azimuthal coil scanning detection is summarized, and the borehole transient electromagnetic positioning method with azimuthal coil scanning detection is determined. Namely, through the transient electromagnetic response characteristics of the axial and radial directions of the borehole, the position of the low-resistance abnormal bodies in the rock body at the periphery of the borehole wall is determined. Finally, by establishing the geological-geophysical model with two low-resistance bodies and using azimuth coils set to the best azimuth angle for numerical experiments, it is verified that the method can intuitively and effectively determine the orientation of low resistance abnormal bodies. The study shows that the azimuth coil scanning detection results of the borehole transient electromagnetic method can better reflect the transient electromagnetic field anomaly caused by the low-resistance abnormal bodies in the rock body at the periphery of the borehole wall, and the resolution of the full-space apparent resistivity imaging results is high. Based on the transient electromagnetic response characteristics of the axial and radial directions of the borehole, the borehole transient electromagnetic positioning method with azimuthal coil scanning detection has a high resolution and localization accuracy for the low-resistance abnormal bodies in the rock body at the periphery of the borehole wall. The research results provide a theoretical basis for the practical application of the borehole transient electromagnetic positioning method with azimuthal coil scanning detection

AiluRus: A Scalable ViT Framework for Dense Prediction

Vision transformers (ViTs) have emerged as a prevalent architecture for vision tasks owing to their impressive performance. However, when it comes to handling long token sequences, especially in dense prediction tasks that require high-resolution input, the complexity of ViTs increases significantly. Notably, dense prediction tasks, such as semantic segmentation or object detection, emphasize more on the contours or shapes of objects, while the texture inside objects is less informative. Motivated by this observation, we propose to apply adaptive resolution for different regions in the image according to their importance. Specifically, at the intermediate layer of the ViT, we utilize a spatial-aware density-based clustering algorithm to select representative tokens from the token sequence. Once the representative tokens are determined, we proceed to merge other tokens into their closest representative token. Consequently, semantic similar tokens are merged together to form low-resolution regions, while semantic irrelevant tokens are preserved independently as high-resolution regions. This strategy effectively reduces the number of tokens, allowing subsequent layers to handle a reduced token sequence and achieve acceleration. We evaluate our proposed method on three different datasets and observe promising performance. For example, the "Segmenter ViT-L" model can be accelerated by 48% FPS without fine-tuning, while maintaining the performance. Additionally, our method can be applied to accelerate fine-tuning as well. Experimental results demonstrate that we can save 52% training time while accelerating 2.46 times FPS with only a 0.09% performance drop. The code is available at https://github.com/caddyless/ailurus/tree/main.Comment: Accepted by NeurIPS 202

Pilus of Streptococcus pneumoniae: structure, function and vaccine potential

The pilus is an extracellular structural part that can be detected in some Streptococcus pneumoniae (S. pneumoniae) isolates (type I pili are found in approximately 30% of strains, while type II pili are found in approximately 20%). It is anchored to the cell wall by LPXTG-like motifs on the peptidoglycan. Two kinds of pili have been discovered, namely, pilus-1 and pilus-2. The former is encoded by pilus islet 1 (PI-1) and is a polymer formed by the protein subunits RrgA, RrgB and RrgC. The latter is encoded by pilus islet 2 (PI-2) and is a polymer composed mainly of the structural protein PitB. Although pili are not necessary for the survival of S. pneumoniae, they serve as the structural basis and as virulence factors that mediate the adhesion of bacteria to host cells and play a direct role in promoting the adhesion, colonization and pathogenesis of S. pneumoniae. In addition, as candidate antigens for protein vaccines, pili have promising potential for use in vaccines with combined immunization strategies. Given the current understanding of the pili of S. pneumoniae regarding the genes, proteins, structure, biological function and epidemiological relationship with serotypes, combined with the immunoprotective efficacy of pilins as protein candidates for vaccines, we here systematically describe the research status and prospects of S. pneumoniae pili and provide new ideas for subsequent vaccine research and development

Effects of S. cerevisiae strains on the sensory characteristics and flavor profile of kiwi wine based on E-tongue, GC-IMS and 1H-NMR

The fermentation of kiwifruit into kiwi wine (KW) can represent a strategy to reduce the economic losses linked to fruits imperfections, spoilage, over production and seasonality. In the study, Pujiang kiwifruit, a China National Geographical Indication Product, was used as raw material to produce KW fermented by four commercial S. cerevisiae strains, namely Drop Acid Yeast, DV10, SY and RW. The sensory characteristics and flavor profile of KW were assessed by means of sensory evaluation, E-tongue, GC-IMS and 1H-NMR. KW fermented by RW strain obtained the higher sensory evaluation score. E-tongue could clearly distinguish the taste differences of KW fermented by distinct S. cerevisiae strains. A total of 128 molecules were characterized by GC-IMS and 1H-NMR, indicating that the combinations of multiple technologies could provide a comprehensive flavor profile of KW. The main flavor compounds in KW pertained to the classes of esters and alcohols. Several pathways were found to be differently altered by the fermentation with the different yeast strains, namely butanoate metabolism, glycerolipid metabolism, alanine, aspartate and glutamate metabolism, arginine biosynthesis, arginine and proline metabolism. The present study will facilitate screening suitable S. cerevisiae strains for KW production and provide a theoretical basis for large-scale production of KW

Comprehensive comparison of flavor and metabolomic profiles in kiwi wine fermented by kiwifruit flesh with different colors

The objective of the study was to comprehensively assess flavor and metabolomic disparities in the aroma and taste profiles of kiwi wine (KW) derived from kiwifruits with green (Hayward), red (Donghong), and yellow (Jinshi) flesh. The findings revealed that Hayward wine exhibited the most “floral, fruity and pleasant” aromas, while Donghong wine demonstrated the most “sweet, fullness and balanced” tastes. In KW, a total of 106 compounds were characterized using a flavor-directed research strategy and metabolomics. PCA and PLS-DA effectively differentiated the three types of KW based on their aroma and taste characteristics. Ten volatile compounds (ethyl isovalerate, ethyl hexanoate, isoamyl acetate-D, acetone, hexyl acetate-M, hexyl acetate-D, ethyl isobutyrate, 2-butylfuran, 2-pentylfuran and 2-methylbutanal) and ten non-volatile compounds (malate, lactate, hydroxyacetone, pyroglutamate, succinate, 2-oxoglutarate, galactarate, acetoin, pyruvate and proline) were identified through multivariate analysis as key discriminators of flavor and metabolomic differences among the three types of KW. Furthermore, several metabolic pathways were investigated to distinguish the KW fermented with the three flesh-colored kiwifruits, mainly pertaining to glycerolipid, amino acid, sucrose, butanoate and pyruvate metabolism. This study could offer valuable insights into the effect of flesh colors on the flavor and metabolomic characteristics of KW