Phylogenetic Levels Research Articles

Changes in the Gut and Oral Microbiome in Children with Phenylketonuria in the Context of Dietary Restrictions-A Preliminary Study.

Phenylketonuria (PKU) is a metabolic disorder that necessitates dietary restrictions, potentially impacting the composition of gut and oral microbiota. This study aimed to compare the microbiota composition between children with PKU and healthy controls. Using 16S rRNA gene sequencing, we analysed microbial communities at six phylogenetic levels. Our findings revealed significant differences in the gut microbiota: Euryarchaeota was more abundant in controls (p = 0.01), while Bacilli and Lactobacillales were higher in PKU children (p = 0.019). Methanobacteriales were significantly elevated in controls (p = 0.01). At the genus and species levels, PKU children had higher Streptococcus and Eubacterium dolichum (p = 0.019, p = 0.015), whereas controls had more Barnesiella, Coprococcus, and Faecalibacterium prausnitzii (p = 0.014, p = 0.019, p = 0.014). In the oral microbiota, control children exhibited significantly higher Bacteroidetes (p = 0.032), while PKU children had increased Bacilli and Betaproteobacteria (p = 0.0079, p = 0.016). Streptococcus and Neisseria were more prevalent in PKU (p = 0.0079, p = 0.016). These results suggest that PKU and its dietary management significantly alter the gut and oral microbiota composition. Understanding these microbial shifts could have implications for managing PKU and improving patient outcomes.

The Complex of Steroid Hormones in Invertebrate Hydrobionts

The presence of a complex of biologically active steroid compounds (BASC) – hydrocortisone, corticosterone, progesterone, testosterone and estrogens (vertebrate hormones) in invertebrate hydrobionts of different phylogenetic levels was revealed in the experiments. The features of the quantitative content of BASC in different organs/tissues of hydrobionts and their changes at different stages of development are shown. The level of BASC in organisms or their organs is largely due to their own steroidogenesis, but at the same time, organisms can accumulate exogenous steroid compounds. The adaptive role of ALS in some invertebrates in changing conditions of the aquatic environment has been found. The similarity of the concentration of steroid compounds in different groups of bionts leads to the idea of a certain “physiological constant” of this complex of compounds in all organisms.

The bioenergetic cost of building a metazoan

All life forms depend on the conversion of energy into biomass used in growth and reproduction. For unicellular heterotrophs, the energetic cost associated with building a cell scales slightly sublinearly with cell weight. However, observations on multiple Daphnia species and numerous other metazoans suggest that although a similar size-specific scaling is retained in multicellular heterotrophs, there is a quantum leap in the energy required to build a replacement soma, presumably owing to the added investment in nonproductive features such as cell adhesion, support tissue, and intercellular communication and transport. Thus, any context-dependent ecological advantages that accompany the evolution of multicellularity come at a high baseline bioenergetic cost. At the phylogenetic level, for both unicellular and multicellular eukaryotes, the energetic expense per unit biomass produced declines with increasing adult size of a species, but there is a countergradient scaling within the developmental trajectories of individual metazoan species, with the cost of biomass production increasing with size. Translation of the results into the universal currency of adenosine triphosphate (ATP) hydrolyses provides insight into the demands on the electron-transport/ATP-synthase machinery per organism and on the minimum doubling times for biomass production imposed by the costs of duplicating the energy-producing infrastructure.

Methylisothiazolinone modulates community assembly and improves syntrophic cooperation via adaptive evolution during sludge anaerobic digestion

Various antimicrobials could pose multifaced threats to anaerobic digestion (AD) of waste-activated sludge (WAS), yet it is still unclear how antimicrobials would affect the metabolic activity and assembly process of anaerobic microbiome. In this study, a typical antimicrobial, methylisothiazolinone (MIT), was introduced in AD and induced an initial lag effect on methane production that was eventually recovered. Although MIT disintegrated WAS to promote the release of bioavailable substrates from extracellular polymeric substances (EPS), it also caused adverse stress to the microbiome. The initial microbial metabolic activities and syntrophic relationships associated with methane generation were distinctly inhibited. Because the self-adaptive systems of two-component systems (e.g., ddpF, and ddpD) and quorum sensing (e.g., cheR, and cydB) were activated to restore the syntrophic interaction among functional anaerobes, metabolic activities were gradually recovered for methane generation. Ultimately, the methane-generation species (e.g., Methanobacterium, and Methanomassiliicoccus) were driven as core species by deterministic processes, while non-functional species (e.g., Nitrospirota) were marginalized by stochastic processes under MIT stress. Overall, this finding indicated the intrinsic drive of evolutionary adaptation, unraveled the community assembly process at phylogenetic level under antimicrobial stress, and gave direction on the assessment and mitigation of external contaminant-related ecological risks in WAS treatment.

Ecological shifts underlie parallels between ontogenetic and evolutionary allometries in parrotfishes.

During ontogeny, animals often undergo significant shape and size changes, coinciding with ecological shifts. This is evident in parrotfishes (Eupercaria: Labridae), which experience notable ecological shifts during development, transitioning from carnivorous diets as larvae and juveniles to herbivorous and omnivorous diets as adults, using robust beaks and skulls for feeding on coral skeletons and other hard substrates. These ontogenetic shifts mirror their evolutionary history, as parrotfishes are known to have evolved from carnivorous wrasse ancestors. Parallel shifts at ontogenetic and phylogenetic levels may have resulted in similar evolutionary and ontogenetic allometric trajectories within parrotfishes. To test this hypothesis, using micro-computed tomography (μCT) scanning and three-dimensional geometric morphometrics, we analyse the effects of size on the skull shape of the striped parrotfish Scarus iseri and compare its ontogenetic allometry to the evolutionary allometries of 57 parrotfishes and 162 non-parrotfish wrasses. The young S. iseri have skull shapes resembling non-parrotfish wrasses and grow towards typical adult parrotfish forms as they mature. There was a significant relationship between size and skull shapes and strong evidence for parallel ontogenetic and evolutionary slopes in parrotfishes. Our findings suggest that morphological changes associated with the ecological shift characterizing interspecific parrotfish evolution are conserved in their intraspecific ontogenies.

Plant phylogenetic diversity along the urban–rural gradient and its association with urbanization degree in Shanghai, China

ContextThe spatial distribution of plant diversity in urban areas is fundamental to understanding the relationship between urbanization and biodiversity. Previous research has primarily focused on taxonomic levels to assess species richness. In contrast, investigations into the spatial patterns of phylogenetic diversity in urban plants remain limited.ObjectivesThis study aims to investigate the spatial patterns of plant phylogenetic diversity along an urban–rural gradient and quantify how phylogenetic diversity and the degree of urbanization are related.MethodsA survey of vascular plants was conducted at 134 randomly selected sample plots along four urban–rural transects in Shanghai, China. Three phylogenetic diversity metrics were calculated: Faith’s phylogenetic diversity (PD), net relatedness index (NRI), and net nearest taxon index (NTI), along with the urbanization degree index (UDI). Regression analysis was employed to quantify the spatial patterns of plant phylogenetic diversity across different taxa along the urban–rural gradients and their relationships with UDI.ResultsThe study observed seven distinct patterns of plant phylogenetic diversity along the urban–rural gradients in different taxa, which support the previous hypotheses that biological distribution patterns at the species level also hold true at the phylogenetic level. Faith’s phylogenetic diversity (PD) showed a linear increase with increasing UDI for total, woody, perennial, and cultivated plant assemblages. The UDI explained 3–36% of the variation in PD for these taxa. In contrast, PD for annual and spontaneous plants exhibited a linear decrease with increasing UDI, which explained 25% and 3% variation in PD for annual and spontaneous plants, respectively. The net relatedness index (NRI) for woody, perennial, and cultivated plants, as well as the net nearest taxon index (NTI) for perennial and cultivated plants, linearly increases with UDI, whereas the NRI for total, annual, and spontaneous plants, as well as NTI for total, woody, annual, and spontaneous plants linearly decrease with UDI. However, some of these trends were only marginally significant.ConclusionsThe spatial patterns of plant phylogenetic diversity varied along the urban-to-rural gradients, indicating that urban environmental filtering has an impact on plant phylogenetic diversity. Urbanization increased the phylogenetic richness of different plant taxa in Shanghai but resulted in more clustering and relatedness of species within plant assemblages. Phylogenetic richness exhibited a linear increase with UDI, while the phylogenetic divergence decreased with UDI. The UDI is a useful predictor for examining variations in plant phylogeny due to urbanization. Our findings provide insights into how urbanization impacts plant phylogenetic diversity, helping urban plant diversity conservation.

Challenges in using DNA barcodes for authentication of Sida species

The Indian system of medicine’s “Ayurvedic pharmacopeia of India (API)” recommends the use of Sida cordifolia Linn (root), Sida cordata (Burm.f.) Borss.Waalk. (aerial part), Sida rhombifolia Linn. (root) and Abutilon indicum (Linn.) Sw. (root) in drug preparations of Bala, Nagabala, Mahabala and Atibala respectively. Moreover many Sida sp. are being used in China, South East Asia, Africa and South America in their traditional healthcare systems. It is a taxonomically complex genus often difficult to authenticate from dried/chopped herbal market samples. Many Sida sequences from the NCBI database, including published reports, were highly suspect and were redesignated into species groups during phylogenetic clustering. Among the four loci studied, ITS2 region was identified as the best for the Sida species identification followed by trnH-psbA. The trnH-psbA phylogeny however fails to differentiate between (1) S. beddomei and S. cordata, (2) S. alnifolia and S. scabrida, (3) S. cordifolia and S. fryxellii that formed monophyletic clusters. The average evolutionary divergence over Sequence Pairs within each species group for ITS2 locus ranged from 0.000 to 0.009 (Average=0.0021), while average Interspecific distance between species was 0.1175 making them ideal for authentication of Sida species. The matK and rbcL is recommended as a back-up loci for identifying intergeneric adulterants in case, the ITS2 or trnH-psbA amplification fails. The present study identified two market samples as adulterant species; (1) S. alnifolia and (2) a mixture of S. acuta and S. alnifolia/S.scabrida. The study provides a roadmap for Ayurvedic/herbal industry to utilize DNA barcoding for authentication of Sida species. At the same time the presence of “Unknown Sida group” highlights the need for further research to accurately classify and identify all Sida species at the phylogenetic level, utilizing the DNA barcode sequences to thoroughly understand the diversity and evolution of the Sida genus.

Phylogenetic and spatial patterns of herbal medicine compounds: Which medicinal plants are phytochemically characterized?

ObjectiveThe study of phytometabolites of medicinal plants and their phylogenetic distribution is an important content of pharmacophylogeny. The objectives of this study were to provide an updated estimate of the extent to which the medicinal plants were investigated phytochemically and relate this to the species-level phylogeny and their geographical pattern. MethodsHere, we further characterized 1 648 phytometabolites, including terpenoids, steroids, flavonoids, phenylpropanoids, phenolics, alkaloids, etc., reported in journals Chinese Traditional and Herbal Drugs (Zhong Cao Yao) and Chinese Herbal Medicines (CHM) from the phylogenetic and spatial perspectives. According to the structural characteristics, terpenoids, flavonoids, alkaloids and phenylpropanoids were subdivided into subclasses, and the research effort of phytometabolites was for the first time delineated at both subclass and phylogenetic levels. ResultsThe phytometabolites of 90 families were reported on two journals in three years. It is noted that terpenoids with diverse bioactivities still constitute the primary object of phytochemical research, followed by flavonoids, phenolics, phenylpropanoids and alkaloids. Among the reported species, the family Asteraceae had the most, followed by Lamiaceae, Fabaceae, and Ranunculaceae. In the phylogenetic distribution of the reported phytometabolites, the net relatedness index (NRI) results revealed a clustered structure for triterpene, iridoid, flavone, flavonol, coumarin, indole alkaloid and terpenoid alkaloid, while the nearest taxon index (NTI) metric identified the clustered structure for triterpene, sesquiterpene, indole alkaloid and terpenoid alkaloid. Especially in Ranunculaceae, there were more reports on triterpene and terpenoid alkaloid subclasses. The overdispersion pattern of diterpene and phenolic was suggested by NRI and NTI respectively, albeit more reported diterpenes and phenolics were in Lamiaceae. The geographical distribution hotspots of reported species and compounds thereof highlighted the enormous progress of herbal medicine research and industry, which play a positive role in the future drug discovery and development. ConclusionThese results provide new dimensions and perspectives in the context of pharmacophylogeny for perceiving and evaluating research trends and flashpoints in medicinal phytochemistry.

Study of the possibility of modulating the composition of the gastrointestinal microbiome of rabbits fed fermented rapeseed meal

Abstract Understanding digestive functions and the role of microorganisms in the prevention of gastrointestinal and systemic diseases may be a strategy for preventing intestinal dysbiosis during critical periods of animal rearing, strengthening the immune system and reducing herd mortality. The aim of the study was to determine the effect of the addition of fermented rapeseed meal (FRSM) to the diet of rabbits on the composition of the bacterial microbiota of the caecal contents. The experiment was conducted using 40 35-day-old rabbits (Oryctolagus cuniculus) assigned to four groups of 10 animals each. Animals in the control group (group C) were fed a standard diet, while the experimental groups received 4% (group E1), 8% (group E2) or 12% (group E3) dried FRSM in place of the previously used soybean meal (SBM). After 120 days, six rabbits (three males and three females), of average size and intended for slaughter, were selected from each group. The contents of the caecum were collected from these animals for metagenomic analysis. The research showed that the microbiome of the caecum of rabbits shows low diversity at higher phylogenetic levels, but is highly diverse at lower levels. The study showed no directly proportional relationship between the various groups of microorganisms inhabiting the digestive tract and the share of fermented rapeseed meal used in the diet. To the best of our knowledge, this is the first study to characterize the microbiome of rabbits fed diets with the inclusion of fermented feed components.

Using machine learning to link climate, phylogeny and leaf area in eucalypts through a 50‐fold expansion of leaf trait datasets

Abstract Leaf area varies within and between species, and previous work has linked this variation to environment and evolutionary history. However, many previous studies fail to examine both these factors and often are data‐limited. To address this, our study developed a new workflow using machine learning to automate the extraction of leaf area from herbarium collections of Australian eucalypts (Eucalyptus, Angophora and Corymbia). This dataset included 136,599 measurements, expanding existing data on this taxon's leaf area by roughly 50‐fold. Our methods were validated using field standard metrics of accuracy, and comparisons to manual measurements both from the present study and existing datasets. With this dataset for the eucalypt clade, we observed positive relationships between leaf area and mean annual temperature and precipitation similar to those reported for the global flora. However, these relationships were not consistently observed within species, potentially due to gene flow suppressing local adaptation. When we examined these relationships at different phylogenetic levels, the slope of trait–climate associations within lineages converged towards the overall eucalypt slope at shallow phylogenetic scales (5–12 MY), suggesting that effects of gene flow relax just above the species level. The strengthening of trait–climate correlations at evolutionary scales just beyond the intraspecific level may represent a widespread phenomenon across various traits and taxa. Future studies can unveil these relationships with the larger sample sizes of new trait datasets generated through machine learning. Synthesis. Using machine learning, researchers are able to confirm current positive global relationships between leaf area and mean annual temperature and precipitation. Additionally, they were able to take this a step further and examine how it changes across time. Here they saw that at roughly 5–12 million years ago in the phylogenetic tree, the trait–climate slope begins to show significantly less variation. Overall, the study shows the potential of machine learning in ecology, with exciting new potential findings with its use.

Base-substitution rates of nuclear and mitochondrial genes for polyclad flatworms

The increase in the use of molecular methodologies in systematics has driven the necessity for a comprehensive understanding of the limitations of different genetic markers. Not every marker is optimal for all species, which has led to multiple approaches in the study of the taxonomy and phylogeny of polyclad flatworms. The present study evaluates base-substitution rates of nuclear ribosomal (18S rDNA and 28S rDNA), mitochondrial ribosomal (16S rDNA), and protein-codifying (cytb, cox1) markers for this taxonomic group, with the main objective of assessing the robustness of these different markers for phylogenetic studies. Mutation rates and Ti/Tv ratios of the other markers were assessed for the first time. We estimated substitution rates and found cytb to be the most variable, while 18S rDNA was the least variable among them. On the other hand, the transition to transversion (Ti/Tv) ratio of the different genes revealed differences between the markers, with a higher number of transitions in the nuclear gene 28S and a higher number of transversions in the mitochondrial genes. Lastly, we identified that the third codon position of the studied protein-codifying genes was highly variable and that this position was saturated in the cox1 marker but not in cytb. We conclude that it is important to assess the markers employed for different phylogenetic levels for future studies, particularly in the order Polycladida. We encourage the use of mitochondrial genes cytb and 16S for phylogenetic studies at suborder, superfamily, and family levels and species delimitation in polyclads, in addition to the well-known 28S and cox1.

Reduction in Serum Concentrations of Uremic Toxins Driven by Bifidobacterium Longum Subsp. Longum BL21 is Associated with Gut Microbiota Changes in a Rat Model of Chronic Kidney Disease.

Gut microbiota dysbiosis and consequent impairment of gut barrier function, culminating in elevated levels of uremic toxins, are prevalent in chronic kidney disease (CKD) patients. These toxins, notably indoxyl sulphate (IS), indole-3-acetic acid (IAA), and trimethylamine oxide (TMAO), are implicated in a spectrum of CKD-related complications, including cardiovascular disease, bone and mineral disorders, and inflammation. The specific impacts of various probiotics on these CKD manifestations remain unexplored. This study delved into the potential of dietary probiotic interventions, particularly Bifidobacterium longum subsp. longum BL21, to modulate gut microbiota and mitigate metabolic disorders in a CKD rat model. Over a six-week period, we administered a dietary regimen of BL21 and conducted comprehensive analyses, including serum uremic toxin quantification and 16S rRNA gene sequencing, to systematically profile gut microbial alterations at the phylogenetic level. Our findings reveal that BL21 intervention significantly ameliorated CKD-induced disruptions in gut microbial populations, enhancing both microbial richness and the relative abundance of key taxa. Importantly, BL21 appeared to exert its beneficial effects by modulating the abundance of crucial species such as Barnesiella and Helicobacter. Functionally, the intervention markedly normalized serum levels of IS, IAA, and TMAO, while potentially attenuating p-cresol sulphate (PCS) and p-cresol glucuronide (PCG) concentrations. Consequently, BL21 demonstrated efficacy in regulating gut microbiota and curtailing the accumulation of uremic toxins. Our results advocate for the utilization of BL21 as a dietary intervention to diminish serum uremic toxins and re-establish gut microbiota equilibrium at the phylogenetic level, underscoring the promise of probiotic strategies in the management of CKD.

Molecular Identification of Endophytic Fungi Isolated from Bidara Root (Ziziphus mauritiana Lam.) Using Polymerase Chain Reaction (Pcr)

The roots of the bidara plant have the potential as antibacterial agents. The antibacterial compounds in the roots of the bidara plant originate from secondary metabolites produced by endophytic compounds known as endophytic fungi. The purpose of this research is to identify the types of endophytic fungi in bidara roots. The identification of microorganisms can be done through morphology or molecular methods. However, morphological identification alone is unable to depict the morphospecies to the phylogenetic level of a microorganism, thus molecular identification using the Polymerase Chain Reaction (PCR) method is required. This study utilized root isolates from the bidara plant with the sample code IFAZ-6, which, after sequencing, yielded a pair of base pairs measuring 558bp. The results of BLAST and phylogenetic analysis revealed that the IFAZ-6 isolate has a close relationship with the species Clonostachys rosea., which has been recorded in the database with a 100% identity level.

Genatically determined excitability of the nervous system: impact on brain function and behavior

The study of connections between the action of genes and the implementation of behavior involves analyzing their influence on the structure and functions of the nervous system at different levels of its organization, among which special importance is given to the basic properties of nervous processes, the excitatory process and the excitability of the nervous system. The review is devoted to a historical examination of studies devoted to elucidating the role of hereditarily determined excitability in determining the functional characteristics of the nervous system, its influence on the brain and behavior, and revealing the physiological and genetic mechanisms of their interaction using animal models of different phylogenetic levels.

Morphological variation, modularity and integration in the scapula and humerus of Lissotriton newts.

The modular organization of tetrapod paired limbs and girdles, influenced by the expression of Hox genes is one of the primary driving forces of the evolution of animal locomotion. The increased morphological diversification of the paired limbs is correlated with reduced between-limb covariation, while correlation within the elements is usually higher than between the elements. The tailed amphibians, such as Lissotriton newts, have a biphasic lifestyle with aquatic and terrestrial environments imposing different constraints on limb skeleton. By employing the methods of computerized microtomography and 3D geometric morphometrics, we explored the pattern of morphological variation, disparity, modularity and morphological integration in the proximal parts of the anterior limbs of six species of Eurasian small bodied newts. Although the species significantly differ in limb shape, there is a great overlap in morphology of scapula and humerus, and there are no differences in morphological disparity. For the scapula, the shape differences related to the duration of the aquatic period are in length, depth and curvature. The shape of the humerus is not affected by the length of aquatic period, and shape differences between the species are related to robustness of the body. The length of aquatic period has statistically supported phylogenetic signal. The scapula and humerus are structures of varying modularity. For the humerus, the strongest support on the phylogenetic level was for the capitulum/shaft hypothesis, which can also be interpreted as functional modularity. For the scapula, the greatest support was for the antero-posterior hypothesis of modularity in case of Lissotriton vulgaris, which can be explained by different functional roles and muscle insertion patterns, while there was no phylogenetic modularity. The modularity patterns seem to correspond with the general tetrapod pattern, with modularity being more pronounced in the distal structure. The future research should include more salamandrid taxa with different habitat preferences and both adult and larval stages, in order to explore how size, phylogeny and ecology affect the morphology and covariation patterns of limbs.

The hierarchical radiation of phyllostomid bats as revealed by adaptive molar morphology

Adaptive radiations are bursts in biodiversity that generate new evolutionary lineages and phenotypes. However, because they typically occur over millions of years, it is unclear how their macroevolutionary dynamics vary through time and among groups of organisms. Phyllostomid bats radiated extensively for diverse diets-from insects to vertebrates, fruit, nectar, and blood-and we use their molars as a model system to examine the dynamics of adaptive radiations. Three-dimensional shape analyses of lower molars of Noctilionoidea (Phyllostomidae and close relatives) indicate that different diet groups exhibit distinct morphotypes. Comparative analyses further reveal that phyllostomids are a striking example of a hierarchical radiation; phyllostomids' initial, higher-level diversification involved an "early burst" in molar morphological disparity as lineages invaded new diet-affiliated adaptive zones, followed by subsequent lower-level diversifications within adaptive zones involving less dramatic morphological changes. We posit that strong selective pressures related to initial shifts to derived diets may have freed molars from morpho-functional constraints associated with the ancestral molar morphotype. Then, lineages with derived diets (frugivores and nectarivores) diversified within broad adaptive zones, likely reflecting finer-scale niche partitioning. Importantly, the observed early burst pattern is only evident when examining molar traits that are strongly linked to diet, highlighting the value of ecomorphological traits in comparative studies. Our results support the hypothesis that adaptive radiations are commonly hierarchical and involve different tempos and modes at different phylogenetic levels, with early bursts being more common at higher levels.

High pathogenicity avian influenza A (H5N1) clade 2.3.4.4b virus infection in a captive Tibetan black bear (Ursus thibetanus): investigations based on paraffin-embedded tissues, France, 2022.

Avian influenza viruses are able to cross the species barrier between birds and mammals because of their high genetic diversity and mutation rate. Using formalin-fixed paraffin-embedded tissues, we were able to investigate a Tibetan black bear's infection by a high pathogenicity H5N1 avian influenza virus at the molecular, phylogenetic, and histological levels. Our results highlight the importance of virological surveillance programs in mammals and the importance of raising awareness among veterinarians and zookeepers of the clinical presentations associated with H5Nx virus infection in mammals.

Associations of Single Versus Multiple Human Papillomavirus Infections With the Prevalence of Cervical Intraepithelial Neoplasia 2/3 and Squamous Cell Carcinoma Lesions: Human Papillomavirus Type–Specific Attribution

The risk of developing cervical squamous lesions in women with multiple high-risk human papillomavirus (hrHPV) infections is uncertain. The aim of this retrospective study was to investigate the type-specific attribution and phylogenetic effects of single and multiple hrHPV subtypes in cervical squamous lesions. All cases with cervical histopathologic diagnosis and human papillomavirus (HPV) genotyping results in the 6 months preceding biopsy from October 2018 to December 2022 were studied and analyzed. Over the study period, 70,361 cases with histopathologic follow-up and prior HPV genotyping were identified. The hrHPV-positive rate was 55.6% (39,104/70,361), including single hrHPV detected in 27,182 (38.6%), 2 types of hrHPV detected in 8158 (11.6%), and 3 types of hrHPV detected in 2486 (3.5%). Among 16,457 cases with a histologically diagnosed squamous lesion (cervical intraepithelial neoplasia 1: 11411; cervical intraepithelial neoplasia 2/3: 4192; squamous cell carcinoma: 854 cases), the prevalence of single hrHPV infection increased, but the rate of multiple concomitant hrHPV infections showed negative association as the degree of squamous lesions increased. Among women with a single HPV16 infection, cervical intraepithelial neoplasia 2/3 and squamous cell carcinoma (CIN2+) diagnostic rate was 30.6%, and it increased to 47.6% when coinfected with HPV33 (P < .001) but significantly decreased when coinfected with all other hrHPV types (P < .05). By comparing CIN2+ diagnostic rates in 40 most common 2 types of hrHPV infections with related single hrHPV infection, CIN2+ rates were decreased in 12 combinations (30.0%), equivalent in 26 combinations (65.0%), and increased in 2 combinations (5.0%). The cases with 3 types of HPV infections reduced the risk for CIN2+ compared with related single HPV infections. HPV16+52+53, HPV16+52+68, HPV16+52+51, HPV16+39+52, and HPV16+58+53 significantly decreased the risk of CIN2+ compared with HPV16 single infection (P < .05). This study demonstrates that multiple hrHPV infections are not associated with cumulatively higher risk for CIN2+ development, suggesting that oncogenic progression of multiple hrHPV-associated cervical squamous lesions is neither synergistic nor a cumulative effect at the phylogenetic level, possibly a way of competitive interference.

RDNA and mtDNA analysis for the identification of genetic characters in the hybrid grouper derived from hybridization of Cromileptes altivelis (female) × Epinephelus lanceolatus (male)

BackgroundHybridization is a useful strategy to produce offspring with more desirable phenotypic characteristics than those of parents. The hybrid grouper derived from the cross of Cromileptes altivelis (♀, 2n = 48) with Epinephelus lanceolatus (♂, 2n = 48) exhibits improved growth compared with its female parent, which makes it valuable to aquaculture. However, the genetic traits of the hybrid grouper are poorly understood.ResultsThe observations showed that the hybrid grouper was diploid (2n = 48) and displayed intermediate morphology with the parent's measurable characteristics. The ribosomal DNA (rDNA) and mitochondria DNA (mtDNA) were characterized at molecular and phylogenetic level. High similarity and low genetic distance of 5S rDNA and mtDNA sequences between the hybrid grouper and C. altivelis showed that the hybrid grouper had a closer genetic relationship with female parents. The reconstructed phylogenetic tree based on COI gene and D-loop region of mtDNA recovered that mtDNA was maternally inherited in the hybrid grouper. Additionally, the DNA methylation level of 5S rDNA intergenic spacers (IGS) sequence was tested in here. The results showed that the DNA methylation status of the hybrid grouper was significantly lower than that of C. altivelis.ConclusionResults of this study provide important data on the genetic characteristics of the hybrid derived from the cross of C. altivelis and E. lanceolatus, and contribute the knowledge of both evolution and marine fish breeding.

Diversity and distribution of iron-oxidising bacteria belonging to Gallionellaceae in different sites of a hydroelectric power plant.

Iron (Fe) is the fourth most abundant element on the planet, and iron-oxidising bacteria (FeOB) play an important role in the biogeochemical cycle of this metal in nature. FeOB stands out as Fe oxidisers in microaerophilic environments, and new members of this group have been increasingly discussed in the literature, even though their isolation can still be challenging. Among these bacteria is the Gallionellaceae family, mainly composed of neutrophilic FeOB, highlighting Gallionella ferruginea, and nitrite-oxidiser genera. In the previous metagenomic study of the biofilm and sediments of the cooling system from the Irapé hydroelectric power plant (HPP-Irapé), 5% of the total bacteria sequences were related to Gallionellaceae, being 99% unclassified at genus level. Thus, in the present study, a phylogenetic tree based on this family was constructed, in order to search for shared and unique Gallionellaceae signatures in a deep phylogenetic level affiliation and correlated them with geomorphologic characteristics. The results revealed that Gallionella and Ferrigenium were ubiquitous reflecting their ability to adapt to various locations in the power plant. The cave was considered a hotspot for neutrophilic FeOB since it harboured most of the Gallionellaceae diversity. Microscopic biosignatures were detected only in the CS1 sample, which presented abundance of the stalk-forming Ferriphaselus and of the sheath-forming Crenothrix. Further studies are required to provide more detailed insights on Gallionellaceae distribution and diversity patterns in hydroelectric power plants, particularly its biotechnological potential in this industry.