Species-specific Features Research Articles

Spore morphology of Selaginella borealis, S. sanguinolenta and S. helvetica (Selaginellaceae, Lycopodiophyta)

For the first time we have conducted a study of three species of the genus Selaginella P. Beauv. from Russia: S. sanguinolenta (L.) Spring, S. helvetica (L.) Link and S. borealis (Kaulf.) Rupr. using the method of scanning electron microscopy (SEM). In a comparative analysis of the morphology of micro- and megaspores of S. sanguinolenta, S. helvetica and S. borealis, we first compiled an information on representatives of Selaginella from the territories of China and Russia. A distinctive feature of S. borealis and S. sanguinolenta based on the megaspore morphology is the different nature of the exosporium surface: S. borealis has the exosporium with rounded-polygonal tubercles, and S. sanguinolenta has the exosporium with roller-like folds rising above the sporoderma. S. sanguinolenta is characterized by following species-specific features of microspores: the presence of radially arranged convolutions on the proximal surface of the spore, outside the laesura, and convoluted folds on the distal surface of the microspores. S. helvetica is characterized by the following microspore morphology: the hemispherical distal side is in the equatorial position, and flat proximal side; the surface of the exosporium is granular, completely covered with rounded-polygonal tubercles. In the research we confirmed the presence of S. borealis in China (Yunnan). It has been established that the morphology of S. sanguinolenta microspores from the Khabarovsk Territory, the Republics of Buryatia, Tuva and the Irkutsk Region is identical to the microspores of representatives of S. sanguinolenta from China (Yunnan); and the morphology of S. helvetica microspores from the territory of the Chita Region, Trans-Baikal and Primorye Territories is identical to the morphology of the species samples from Liaoning Province (China).

In Situ Structures of Polar and Lateral Flagella Revealed by Cryo-Electron Tomography.

The bacterial flagellum is a sophisticated self-assembling nanomachine responsible for motility in many bacterial pathogens, including Pseudomonas aeruginosa, Vibrio spp., and Salmonella enterica The bacterial flagellum has been studied extensively in the model systems Escherichia coli and Salmonella enterica serovar Typhimurium, yet the range of variation in flagellar structure and assembly remains incompletely understood. Here, we used cryo-electron tomography and subtomogram averaging to determine in situ structures of polar flagella in P. aeruginosa and peritrichous flagella in S Typhimurium, revealing notable differences between these two flagellar systems. Furthermore, we observed flagellar outer membrane complexes as well as many incomplete flagellar subassemblies, which provide additional insight into mechanisms underlying flagellar assembly and loss in both P. aeruginosa and S Typhimurium.IMPORTANCE The bacterial flagellum has evolved as one of the most sophisticated self-assembled molecular machines, which confers locomotion and is often associated with virulence of bacterial pathogens. Variation in species-specific features of the flagellum, as well as in flagellar number and placement, results in structurally distinct flagella that appear to be adapted to the specific environments that bacteria encounter. Here, we used cutting-edge imaging techniques to determine high-resolution in situ structures of polar flagella in Pseudomonas aeruginosa and peritrichous flagella in Salmonella enterica serovar Typhimurium, demonstrating substantial variation between flagella in these organisms. Importantly, we observed novel flagellar subassemblies and provided additional insight into the structural basis of flagellar assembly and loss in both P. aeruginosa and S Typhimurium.

Comparative morphofunctional and species-specific vascularization features of of the knee capsule of some mammals

The metabolic, reparative and plastic properties, as well as the functional activity of the multiorgan synovial environment of the knee joint, are organically and functionally related to their morphology and blood supply. The aim of our research was to determine the general biological and specific features of the structural organization and vascularization of the knee joint capsule in animals with different supports, locomotion and body weight. A complex of morphological research methods is used in this work: anatomical, histological, neurohistological. Used neurohistological method of impregnation in its own algorithm. The structural organization of synovial and fibrous capsule, histotopography of intraorganic vessels was studied on 43 objects of various groups of animals. The selection of animals was carried out according to the type of limb specialization to the substrate. Animals were taking into account the ecology, types of support, the nature of locomotion and the speed of movement – phalanoid animals – a domestic horse, a domestic bull and a finger animal – a domestic dog and a domestic cat. As a result of the complex comparative-morphological study the general patterns of the structural organization of the articular capsule, the general-biological and species-specific features of the angioarchitectonics and angiotopography were established. The zones of the most intense intraorganic vascularization and the topography of the vascular fields and glomeruli of the articular capsule are shown. The zones of intensive vascularization are localized: in the domestic bull – in the medial, dorsal, lateral parts, vascular glomeruli – in the lateral; in the domestic horse – in all parts of the capsule, vascular glomeruli – in the plantar area; in the domestic dog – in the medial, dorsal, plantar parts, vascular glomeruli – in the plantar area; in a domestic cat, the same type of angioarchitectonics is observed, the vascular fields and glomeruli are absent. The more intense angioarhitectonics in the capsule of the knee joint in phalanoid animals (horse, cattle) than in the finger (dog, cat) possibly due to the different nature of the support and type of locomotion, is determined. Key words: vascular fields, vascular glomeruli, angioarchitectonics, knee joint, joint capsule, domestic horse, domestic bull, domestic dog, domestic cat.

STUDIES OF THE BAT FAUNA (MAMMALIA, CHIROPTERA) IN THE GREEN BELT OF FENNOSCANDIA

The article deals with the least-studied taxonomic group of mammals in the Green Belt of Fennoscandia (GBF) and Karelia as a whole – bats (Chiroptera, Vespertilionidae). The aim was to determine the status of species in the process of their inventory us-ing traditional and modern research methods. For the first time, an integrated assess-ment of the species composition, relative abundance (%) and relative numbers (ind./km of the route) of bats during the hibernation period and summer activity is given for GBF. Underground hibernacula (mines and former military concrete bunkers) were mon-itored in 2009–2018 years. Up to 25 bats of 5 species overwinter in the largest hibernac-ulum described for Karelia (Ruskeala) – the northern bat Eptesicus nilssonii Keyserling, Blasius, 1839, Brandt’s bat Myotis brandtii Eversmann, 1845, whiskered bat M. mystac-inus Kuhl, 1817, Daubenton’s bat M. daubentonii Kuhl, 1817, and brown long-eared bat Plecotus auritusLinnaeus, 1758. The northern bat dominated, with a relative abundance of 65.8 %. The history of bats hibernating in the Ruskeala Mining Park in connection with the reconstruction of the gallery was traced. Changes in the habitat conditions for bats and their consequences for the diversity, species numbers and hibernation ecology are shown. In summer, in addition to the species recorded at hibernacula, car transect and control point surveys using the Song Meter SM2 Bat+ (USA) static ultrasound detec-tor and Kaleidoscope Pro software (ver. 3.1.1) detected common noctule Nyctalus noct-ula Schreber, 1774, parti-coloured bat Vespertilio murinusLinnaeus, 1758, Natterer’s bat M. nattereri Kuhl, 1817, and pond bat M. Dasycneme Boie, 1825. The summer censuses reached up to 66°23ʹN, and the northern bat also dominated the records, with 52.4 % rel-ative abundance, and 0.238 ind./km route relative numbers. The high prevalence of bats at waterbodies in GBF (69.2 %) and its species-specific features at waterbodies of var-ious categories are shown. The first inventory of bats in protected areas within GBF has significantly expanded the list of bat species known in these territories. In general, studies have shown the northern bat predominated in the bat communities both at hibernacula and during the summer period. The northernmost records of species, including migrants, have been updated, modifying the previous ideas about their distribution in the region.

Root-soil-water hydrological interaction and its impact on slope stability

ABSTRACTVegetation is known to provide mechanical reinforcement and hydrological influences on soils, thus affecting the soil shear strength and the stability of rooted soil slopes. Professor Tien H. Wu pioneered the research on the root mechanical reinforcement effect. This study focuses on hydrological influences of vegetation. Factors including species-specific genetic features and soil conditions that control the transpiration process are often varying, leading to significant uncertainty in the transpiration process. The primary objective of this paper is to investigate the influence of the uncertainty of the maximum transpiration rate Etp on the pore-water pressure distributions in and the stability of a vegetated slope. Random field theory is applied to model the spatial variation of Etp, which maintains constant along the vertical direction by its definition but varies along the slope surface. A modified Richards equation governing water flow in unsaturated media is employed to incorporate a sink term that models the root-water uptake. Three idealised types of root geometry, i.e. uniform, triangular and parabolic types, are considered, along with the spatial variation of Etp. The uniform root geometry shows the most significant impact on enhancing the slope factor of safety through transpiration, compared with the triangular and parabolic geometry types.

Seasonal Formation of Tree Rings in Siberian Larch and Scots Pine in the Southern Taiga of Central Siberia

A comparative analysis of the seasonal formation of tree rings has been performed in Siberian larch (Larix sibirica Ledeb.) and Scots pine (Pinus sylvestris L.), growing in the southern taiga of Central Siberia in two sites on the altitudinal transect (200 and 536 m a.s.l.). Core samples were taken from April to September in 2012. The results have shown that the onset and duration of different phases of tree ring formation in larch and pine are determined by the geographic location of the sites and the related temperature gradient. It should be noted that species-specific features of tree growth have an effect on the formation of xylem cells during the growing period and, as a consequence, on the dimensional anatomical parameters of tracheids.

Prevalence of feline lungworm Aelurostrongylus abstrusus in England.

Infection of cats with lungworm Aelurostrongylus abstrusus has recently been documented in the UK. Here, we aimed to study the prevalence of A. abstrusus in fecal samples from cats across England. A total of 950 fecal samples were collected from cats together with information on their age, breed, gender, geographic region, lifestyle, and treatment history. A total of 17 (1.7%) cats were positive for A. abstrusus based on species-specific morphological features of the larvae isolated by Baermann's technique. There was no statistically significant difference in the proportion of positive samples between females (506; 53.2%) and males (444; 46.7%). Multiple regression analysis showed that prevalence of feline lungworm was significantly different across geographic regions: in comparison with East Midlands, some regions had shown significantly increased odds of A. abstrusus-positive samples (South East [odds ratio [OR] = 7.68; 95% confidence interval [CI] = 1.70 to 32.76; p = .01]; West Midlands [OR = 6.20; 95% CI = 1.21 to 26.84; p = .02]), while other regions had also increased odds although not statistically significant (Greater London [OR = 9.63; 95% CI = 0.43 to 84.05; p = .07]; North West [OR = 4.25; 95% CI = 0.59 to 20.89; p = .09]; South West [OR = 2.48; 95% CI = 0.12 to 17.64; p = .43]; and North East [OR = 1.88; 95% CI = 0.10 to 12.24; p = .57]). Keeping cats inside was protective against the risk of infection compared with those having outdoor access (OR = 0.09; 95% CI = 0.01 to 0.48; p = .02). On the other hand, age, breed, gender and deworming history did not have any significant effect on the likelihood of infection. Our data indicate that A. abstrusus is a parasite of potential significance in cats, in particular those from certain geographic regions in England. To reduce the spread of this parasite, an integrated feline lungworm control program needs to be implemented.

Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei.

According to the synthesis of 30 years of multidisciplinary studies, parthenogenetic species of rock lizards of genus Darevskia were formed as a result of different combination patterns of interspecific hybridization of the four bisexual parental species: Darevskia raddei, D. mixta, D. valentini, and D. portschinskii. In particular, D. portschinskii and D. raddei are considered as the parental species for the parthenogenetic species D. rostombekowi. Here for the first time, we present the result of comparative immunocytochemical study of primary spermatocyte nuclei spreads from the leptotene to diplotene stages of meiotic prophase I in two species: D. portschinskii and D. raddei. We observed similar chromosome lengths for both synaptonemal complex (SC) karyotypes as well as a similar number of crossing over sites. However, unexpected differences in the number and distribution of anti-centromere antibody (ACA) foci were detected in the SC structure of bivalents of the two species. In all examined D. portschinskii spermatocyte nuclei, one immunostained centromere focus was detected per SC bivalent. In contrast, in almost every studied D. raddei nuclei we identified three to nine SCs with additional immunostained ACA foci per SC bivalent. Thus, the obtained results allow us to identify species-specific karyotype features, previously not been detected using conventional mitotic chromosome analysis. Presumably the additional centromere foci are result of epigenetic chromatin modifications. We assume that this characteristic of the D. raddei karyotype could represent useful marker for the future studies of parthenogenetic species hybrid karyotypes related to D. raddei.

A Fluorogenic Assay To Monitor Rho-Dependent Termination of Transcription.

Transcription termination mediated by the ring-shaped, ATP-dependent Rho motor is a multipurpose regulatory mechanism specific to bacteria and constitutes an interesting target for the development of new antibiotics. Although Rho-dependent termination can punctuate gene expression or contribute to the protection of the genome at hundreds of sites within a given bacterium, its exact perimeter and site- or species-specific features remain insufficiently characterized. New advanced approaches are required to explore thoroughly the diversity of Rho-dependent terminators and the complexity of associated mechanisms. Current in vitro analyses of Rho-dependent termination rely on radiolabeling, gel electrophoresis, and phosphorimaging of transcription reaction products and are thus hazardous, inconvenient, and low-throughput. To address these limitations, we have developed the first in vitro assay using a fluorescence detection modality to study Rho-dependent transcription termination. This powerful experimental tool accurately estimates terminator strengths in a matter of minutes and is optimized for a microplate reader format allowing multiplexed characterization of putative terminator sequences and mechanisms or high-throughput screening of new drugs targeting Rho-dependent termination.

Comparative morphological analysis during larval development of three syntopic newt species (Urodela: Salamandridae)

We provide comparative and updated staging tables for the larvae of three syntopic newt species – Triturus carnifex, Lissotriton italicus and Ichthyosaura alpestris inexpectatus –living in Calabria. A detailed description, stage by stage, of the full larval period until completion of metamorphosis is furnished, accompanied by photographic tables of the most important stages. The appearance of the most prominent and easily identifiable morphological features (i.e. development of gills, balancers and limbs; and body pigmentation), and length, have been used as staging criteria. Ontogenic development in the three considered species is compared with that of other Caudata species. For the three newt species, we also performed a comparative analysis of the developmental larval phases, emphasising the shared and species-specific features. The present descriptive study adds comparative information on distinctive morphological traits that may be useful for the recognition of newts during larval ontogeny and, in some cases, when sampling in the field.

The concentration of 17β-estradiol in tissue of diploid and triploid Carassius gibelio (Bloch, 1782) females during the reproduction season

The concentration of 17β-estradiol in tissue of diploid and triploid Carassius gibelio (Bloch, 1782) females during the reproduction season

Species-Specific Features of Intraorganic Vascularization of the Tarsal Joint Capsule in Cattle and Canines

Abstract The comparative studies of the tarsal joint capsule of cattle (Bos taurus) and canines (Canis lupus) have clarified general patterns of the structural organization of a joint capsule and the species-specific features of its angioarchitectonics. The differences in the formation of the fibroelastic layer and the location of vascular fields in the cases of animals with different stances were established. The zones of intensive intraorganic vascularization of the joint capsule were revealed; that being—the plantar and dorsal surface in the case of cattle, the lateral and medial surfaces—in case of the canine.

Postjuvenile Moult in the Common Crossbill (Loxia curvirostra curvirostra): Photoperiodic Regulation and Its Role in Synchronization of the Annual Cycle

Captures of Common Crossbills on the southeastern shore of Lake Ladoga and in the St. Petersburg suburbs (1482 individuals from 1968 to 2015) show that the postjuvenile moult is preceded by migration and the overwhelming majority of migrating young birds have plumage that consists solely of juvenile feathers. The postjuvenile moult is recorded from the end of the first ten days of August to the middle of November, the timing of the onset of moult varies within one and a half months with different individuals being observed to have significant distinctions in the number of replaced feathers. The experiments with photoperiodic regulation of the postjuvenile moult were made on 48 individuals captured in nature in the second half of summer and six young birds from one pair of Crossbills, which bred in captivity. The experimental groups were kept in the conditions of a natural decrease in the day (60° N), decrease in the daylength after the transfer from a long day to a short daylength, increasing daylength, constant long daylength, and constant short daylength. The results of the experiments show that the species-specific features of moult in the Common Crossbill are its start being regulated in a wide age range (from 50 to 180 days) and a rather narrow photoperiodic interval of moult with short daylengths (14.5–9 h of daylight). As long as there is more than 14.5 h of daylight, moult begins under the influence of the endogenous rhythm, but not earlier than the age of 4–6 months. The individuals that moult within the photoperiodic interval replace plumage at high rates. After the daylength gets below the lower threshold of the photoperiodic interval, an inhibiting role of the photoperiodic response is activated, terminating moult in the birds that started moult too late, and their plumage mainly retains juvenile generation feathers. Due to the regulation of moult, intrapopulation differences in the timing of annual cycles that are more than seven months at the time of birth of young Common Crossbills decrease almost five times by its start and become even smaller as it ends. It is assumed that this not only makes it possible to implement moult under optimal conditions but also makes first-year birds ready to start breeding in a timely manner if they find themselves in an area with abundantly fruiting spruce trees.

Ecological and genetic features of the Ukrainian Antoninsko- Zozulinetsky species of scaly carp (Cyprinus carpio L.) population

The main ecological and genetic features of growing in the internal reservoirs of Ukraine of promising populations of the Antonino-Zozulentskyi sparse carp are presented. A morphometric evaluation of the breeding material was conducted. The studied herd is homogeneous, the coefficients of variability are stable and correspond to the normative indexes of Ukrainian flint breed. According to the results of the analysis, the pedigrees were divided into classes, elite groups were isolated, from which the material material was formed for performing carp reproduction. Species-specific features of the genetic structure were revealed by distribution of allelic frequencies by albumin loci, esterase, transferrin. The analysis of the genetic structure showed the specificity of the distribution of allelic frequencies and genotypic composition of the protein loci. An analysis of the variety of genotypes of the studied populations in the context of the farms gave an opportunity to detect specific genotypes according to the transferrin locus, and the lack of some theoretically expected ones, namely TF АВ, ВВ snd DD. Specific in Medzhybizh fishpond, the genotypes of TF С1С1 were genotypes for scapular carps, the specifics of the TF С1С2 genotype, Antoninus — AC1 and AC2, were specific for carps from the Staraya Sinyava fishpond. The differences in terms of average heterozygosity are obtained, which makes it possible to control the level of variability in the genetic structure of the studied populations. A statistically significant excess of heterozygotes was found in most loci except TF and EST in the study group. The highest level of heterozygosity in the studied groups of carp is marked by loci ALB (78.8–82.8%) snd ME (72.7–82.8 %). The obtained data indicate that the optimal level of genetic heterogeneity (60–71%) in the carps of the «Medzhybizh» and «Antonina» sites is observed in comparison with the «Stara Synyava» section, where it is the lowest (57%). Data were obtained for the use of individual genetic-biochemical systems for differentiation and the conduct of permanent genetic monitoring of the populations of scaly carp. Promising and ecological safety of carp growing in Ukraine is proved.

Neutrophil progenitor populations of rhesus macaques.

Captive-bred rhesus macaques of Indian origin represent one of the most important large animal models for infectious disease, solid organ transplantation, and stem cell research. There is a dearth of information defining hematopoietic development, including neutrophil leukocyte differentiation in this species using multicolor flow cytometry. In the current study, we sought to identify cell surface markers that delineate neutrophil progenitor populations with characteristic immunophenotypes. We defined four different postmitotic populations based on their CD11b and CD87 expression pattern, and further refined their immunophenotypes using CD32, CD64, lactoferrin, and myeloperoxidase as antigenic markers. The four subsets contained myelocyte, metamyelocyte, band, and segmented neutrophil populations. We compared our flow cytometry-based classification with the classical nuclear morphology-based classification. We found overlap of immunological phenotype between populations of different nuclear morphology and identified phenotypically different subsets within populations of similar nuclear morphology. We assessed the responsiveness of these populations to stimulatory signals, such as LPS, fMLP, or PMA, and demonstrated significant differences between human and rhesus macaque neutrophil progenitors. In this study, we provided evidence for species-specific features of granulopoiesis that ultimately manifested in the divergent immunophenotypes of the fully differentiated segmented neutrophils of humans and rhesus macaques. Additionally, we found functional markers that can be used to accurately quantify neutrophil progenitors by flow cytometry. Although these markers do not coincide with the classical nuclear-morphology-based grading, they enable us to perform functional studies monitoring immunophenotypic markers.

Differential expression of immune receptors in two marine sponges upon exposure to microbial-associated molecular patterns

The innate immune system helps animals to navigate the microbial world. The response to microbes relies on the specific recognition of microbial-associated molecular patterns (MAMPs) by immune receptors. Sponges (phylum Porifera), as early-diverging animals, provide insights into conserved mechanisms for animal-microbe crosstalk. However, experimental data is limited. We adopted an experimental approach followed by RNA-Seq and differential gene expression analysis in order to characterise the sponge immune response. Two Mediterranean species, Aplysina aerophoba and Dysidea avara, were exposed to a “cocktail” of MAMPs (lipopolysaccharide and peptidoglycan) or to sterile artificial seawater (control) and sampled 1 h, 3 h, and 5 h post-treatment for RNA-Seq. The response involved, first and foremost, a higher number of differentially-expressed genes in A. aerophoba than D. avara. Secondly, while both species constitutively express a diverse repertoire of immune receptors, they differed in their expression profiles upon MAMP challenge. The response in D. avara was mediated by increased expression of two NLR genes, whereas the response in A. aerophoba involved SRCR and GPCR genes. From the set of annotated genes we infer that both species activated apoptosis in response to MAMPs while in A. aerophoba phagocytosis was additionally stimulated. Our study assessed for the first time the transcriptomic responses of sponges to MAMPs and revealed conserved and species-specific features of poriferan immunity as well as genes potentially relevant to animal-microbe interactions.

Foetal Development in Mammals

During the fetal period are carried out a series of necessary changes, which prepare the fetus for extrauterine life, culminating embryonic development, leading to this physiological maturation of tissues, organs and systems, along with a rapidly growing body. Well being bought, the species-specific features. Other events of interest are beginning the process of ossification of the bones (short and long), formation of the eyelids; integumentary and other elements besides the surfactant secretion from lungs. In this paper we will make a description of the main events that characterized this period, along with a comparison of them among some domestic mammals.

The Japan Monkey Centre Primates Brain Imaging Repository for comparative neuroscience: an archive of digital records including records for endangered species

Advances in magnetic resonance imaging (MRI) and computational analysis technology have enabled comparisons among various primate brains in a three-dimensional electronic format. Results from comparative studies provide information about common features across primates and species-specific features of neuroanatomy. Investigation of various species of non-human primates is important for understanding such features, but the majority of comparative MRI studies have been based on experimental primates, such as common marmoset, macaques, and chimpanzee. A major obstacle has been the lack of a database that includes non-experimental primates’ brain MRIs. To facilitate scientific discoveries in the field of comparative neuroanatomy and brain evolution, we launched a collaborative project to develop an open-resource repository of non-human primate brain images obtained using ex vivo MRI. As an initial open resource, here we release a collection of structural MRI and diffusion tensor images obtained from 12 species: pygmy marmoset, owl monkey, white-fronted capuchin, crab-eating macaque, Japanese macaque, bonnet macaque, toque macaque, Sykes’ monkey, red-tailed monkey, Schmidt’s guenon, de Brazza’s guenon, and lar gibbon. Sixteen postmortem brain samples from the 12 species, stored in the Japan Monkey Centre (JMC), were scanned using a 9.4-T MRI scanner and made available through the JMC collaborative research program (http://www.j-monkey.jp/BIR/index_e.html). The expected significant contributions of the JMC Primates Brain Imaging Repository include (1) resources for comparative neuroscience research, (2) preservation of various primate brains, including those of endangered species, in a permanent digital form, (3) resources with higher resolution for identifying neuroanatomical features, compared to previous MRI atlases, (4) resources for optimizing methods of scanning large fixed brains, and (5) references for veterinary neuroradiology. User-initiated research projects beyond these contributions are also anticipated.

Discriminating five Polygonatum medical materials and monitoring their chemical changes associated with traditional process by FT-IR spectroscopy coupled with multivariate analysis

Several Polygonatum species are important medicinal materials as tonic to cure disorders in China. Because of their different medical effects, it is desired to distinguish them at species level. In addition, to ensure and control their medical quality, it is also important to monitor their chemical changes associated with traditional process. Taking the advantages of Fourier transform infrared spectroscopy (FT-IR) and multivariate analysis, we developed a convenient, fast and reliable approach to discriminate and quality control these materials. Despite similar absorption patterns, each species also presented spectral differences, especially on the FT-IR fingerprint range of 1800-600 cm−1. Second derivative method obviously enlarged those differences and then showed more species-specific features. These spectral differences could be used as powerful discriminating points to distinguish them. PCA results showed that each species separated clearly with their biological replicates grouped together, which indicated that the variance between species is greater than within species, therefore, these species could be distinguishable. Using this approach, the five herbal materials were discriminated successfully in their raw, processed and ethanol extracted formats. On the other hand, visual inspecting infrared spectra of samples from 1 to 9 process steps, absorbance near 1737, 1259, 817 and 780 cm-1 increased gradually but decreased gradually at 927 cm−1. Besides, spectral contour near 1050 cm−1 changed sharply with process treatment. These spectral changes indicated that hydrolyzing polysaccharides into oligo- and mono-saccharides, especially glucose and fructose, are the main chemical changes associated with traditional process. This is consistent with the traditional experience that the processed materials are dark as night and sweet as malt sugar. Meanwhile, our results also indicated that their chemical constituents changed profoundly after process, which might be the chemical basis for raw and processed materials have different medical effects. Based on absorbance at 817 and 780 cm−1 and the color, taste, smell of processed materials followed by energy efficacy, raw materials had to be processed more than 21 h to ensure their quality. This research shows the potential of FT-IR spectroscopy coupled with multivariate analysis to discriminate different herbs and to monitor chemical changes with process and then control their quality. This could be very helpful to ensure the quality, safety, and efficacy of herbs on clinical practices.

Genomic and metabolic features of the Bacillus amyloliquefaciens group– B. amyloliquefaciens, B. velezensis, and B. siamensis– revealed by pan-genome analysis

The genomic and metabolic features of the Bacillus amyloliquefaciens group comprising B. amyloliquefaciens, B. velezensis, and B. siamensis were investigated through a pan-genome analysis combined with an experimental verification of some of the functions identified. All B. amyloliquefaciens group genomes were retrieved from GenBank and their phylogenetic relatedness was subsequently investigated. Genome comparisons of B. amyloliquefaciens, B. siamensis, and B. velezensis showed that their genomic and metabolic features were similar; however species-specific features were also identified. Energy metabolism-related genes are more enriched in B. amyloliquefaciens, whereas secondary metabolite biosynthesis-related genes are enriched in B. velezensis. Compared to B. amyloliquefaciens and B. siamensis, B. velezensis harbors more genes in its core-genome which are involved in the biosynthesis of antimicrobial compounds, as well as genes involved in d-galacturonate and d-fructuronate metabolism. B. amyloliquefaciens, B. siamensis, and B. velezensis all harbor a xanthine oxidase gene cluster (xoABCDE) in their core-genomes that is involved in metabolizing xanthine and uric acid to glycine and oxalureate. A reconstruction of B. amyloliquefaciens group metabolic pathways using their individual pan-genomes revealed that the B. amyloliquefaciens group strains have the ability to metabolize diverse carbon sources aerobically, or anaerobically, and can produce various metabolites such as lactate, ethanol, acetate, CO2, xylitol, diacetyl, acetoin, and 2,3-butanediol. This study therefore provides insights into the genomic and metabolic features of the B. amyloliquefaciens group.