Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus
Background Type 2 diabetes mellitus (T2DM) is a metabolic disease affecting a huge population worldwide. Teucrium polium L. has been used as a folk medicine for the treatment of T2DM in Anatolia, Turkey. The antihyperglycemic effect of the plant was reported previously. However, there was no detailed study on the underlying molecular mechanisms. In this study, we generated a research plan to clarify the active constituents of the extract and uncover the molecular mechanisms using network pharmacology analysis. Methods For this purpose, we composed a dataset of 126 compounds for the phytochemical profile of the aerial parts of T. polium. Drug-likeness of the compounds was evaluated, and 52 compounds were selected for further investigation. A total of 252 T2DM related targets hit by selected compounds were subjected to DAVID database. Results The KEGG pathway analysis showed enrichment for the TNF signaling pathway, insulin resistance, the HIF-1 signaling pathway, apoptosis, the PI3K-AKT signaling pathway, the FOXO signaling pathway, the insulin signaling pathway, and type 2 diabetes mellitus which are related to T2DM . AKT1, IL6, STAT3, TP53, INS, and VEGFA were found to be key targets in protein-protein interaction. Besides these key targets, with this study the role of GSK3β, GLUT4, and PDX1 were also discussed through literature and considered as important targets in the antidiabetic effect of T. polium. Various compounds of T. polium were shown to interact with the key targets activating PI3K-AKT and insulin signaling pathways. Conclusions According to these findings, mainly phenolic compounds were identified as the active components and IRS1/PI3K/AKT signaling and insulin resistance were identified as the main pathways regulated by T. polium. This study reveals the relationship of the compounds in T. polium with the targets of T2DM in human. Our findings suggested the use of T. polium as an effective herbal drug in the treatment of T2DM and provides new insights for further research on the antidiabetic effect of T. polium.
Kutluay et al. (2020) Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus. PeerJ 8:e10111 https://doi.org/10.7717/peerj.10111
Pseudodiaptomus marinus Sato, 1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance
Calanoid copepod Peudodiaptomus marinus Sato, 1913 was first recorded in Sevastopol Bay in the northern Black Sea in September 2016. We performed regular observations of this new invasive species between October 2016 and December 2018. We conducted bi-weekly plankton sampling at three stations located within or adjacent to Sevastopol Bay. This is the first paper to combine (i) a detailed morphological study, (ii) molecular genetic analysis, and (iii) an investigation of P. marinus seasonal dynamics and interannual abundance variability in the coastal Black Sea. Our morphological research showed similarities between Pseudodiaptomus specimens and existing P. marinus illustrations and descriptions. Our morphological analysis results were confirmed using molecular genetic studies. Based on the genetic variability of ITS2 and cytb, we found that all investigated specimens from Sevastopol Bay belonged to P. marinus. Investigations of P. marinus seasonal and interannual abundance variability showed the same seasonal patterns throughout the studied period, with a higher seasonal abundance from October to November and one pronounced density peak in autumn. The highest abundances (2,000 ind m–3 at the mouth of the bay and more than 5,000 ind m–3at its centre) were recorded in November 2018. In the samples, we found adults of both sexes, including ovigerous females, copepodites I–V, and nauplii, suggesting that the species reproduce in Sevastopol Bay. Our research indicated that P. marinus is a new non-indigenous species (NIS) in the Black Sea, and we will discuss a possible vector of its introduction into this basin.
Gubanova et al. (2020) Pseudodiaptomus marinus Sato, 1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance. PeerJ 8:e10153 https://doi.org/10.7717/peerj.10153
Using ForeStereo and LIDAR data to assess fire and canopy structure-related risks in relict Abies pinsapo Boiss. forests
In this study we combine information from aerial LIDAR and hemispherical images taken in the field with ForeStereo—a forest inventory device—to assess the vulnerability and to design conservation strategies for endangered Mediterranean fir forests based on the mapping of fire risk and canopy structure spatial variability. We focused on the largest continuous remnant population of the endangered tree species Abies pinsapo Boiss. spanning 252 ha in Sierra de las Nieves National Park (South Andalusia, Spain). We established 49 sampling plots over the study area. Stand structure variables were derived from ForeStereo device, a proximal sensing technology for tree diameter, height and crown dimensions and stand crown cover and basal area retrieval from stereoscopic hemispherical images photogrammetry. With this information, we developed regression models with airborne LIDAR data (spatial resolution of 0.5 points∙m−2). Thereafter, six fuel models were fitted to the plots according to the UCO40 classification criteria, and then the entire area was classified using the Nearest Neighbor algorithm on Sentinel imagery (overall accuracy of 0.56 and a KIA-Kappa Coefficient of 0.46). FlamMap software was used for fire simulation scenarios based on fuel models, stand structure, and terrain data. Besides the fire simulation, we analyzed canopy structure to assess the status and vulnerability of this fir population. The assessment shows a secondary growth forest that has an increasing presence of fuel models with the potential for high fire spread rate fire and burn probability. Our methodological approach has the potential to be integrated as a support tool for the adaptive management and conservation of A. pinsapo across its whole distribution area (<4,000 ha), as well as for other endangered circum-Mediterranean fir forests, as A. numidica de Lannoy and A. pinsapo marocana Trab. in North Africa.
Cortés-Molino et al. (2020) Using ForeStereo and LIDAR data to assess fire and canopy structure-related risks in relict Abies pinsapo Boiss. forests. PeerJ 8:e10158 https://doi.org/10.7717/peerj.10158
Older adults at high risk of HIV infection in China: a systematic review and meta-analysis of observational studies
There is an increasing prevalence of human immunodeficiency virus (HIV) infection in older adults in China, but the findings across prevalence studies have been mixed. This is the first meta-analysis of the prevalence of HIV infection and its moderating factors in older adults in China. Two investigators systematically and independently searched both international (PubMed, PsycINFO, Web of Sciences and EMBASE) and Chinese (WanFang, CNKI, and CQVIP) databases. HIV infection rates in older adults were analyzed using the random-effects model. Altogether 46 studies were included in the analysis. The pooled prevalence of HIV infection in older adults was 2.1% (95% CI [1.9%–2.3%], I2 = 99.4%). Subgroup analyses revealed that men who have sex with men (MSM), hospital population samples, publications after 2014, studies conducted in the western region of China, and higher study quality were significantly associated with higher HIV infection rate. This meta-analysis found that the HIV infection prevalence in older adults is significantly higher than the general population in China. Attention should be given to this urgent public health issue, and effective HIV/AIDS preventive, screening and treatment measures are warranted in this population. PROSPERO: CRD42019124286.
Wang et al. (2020) Older adults at high risk of HIV infection in China: a systematic review and meta-analysis of observational studies. PeerJ 8:e9731 https://doi.org/10.7717/peerj.9731
De novo species identification using 16S rRNA gene nanopore sequencing
Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
Angell et al. (2020) De novo species identification using 16S rRNA gene nanopore sequencing. PeerJ 8:e10029 https://doi.org/10.7717/peerj.10029
Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef
Microbial communities distribute heterogeneously at small-scales (mm-cm) due to physical, chemical and biological processes. To understand microbial processes and functions it is necessary to appreciate microbes and matter at small scales, however, few studies have determined microbial, viral, and biogeochemical distribution over space and time at these scales. In this study, the small-scale spatial and temporal distribution of microbes (bacteria and chlorophyll a), viruses, dissolved inorganic nutrients and dissolved organic carbon were determined at five locations (spatial) along the Great Barrier Reef (Australia), and over 4 consecutive days (temporal) at a coastal location. Our results show that: (1) the parameters show high small-scale heterogeneity; (2) none of the parameters measured explained the bacterial abundance distributions at these scales spatially or temporally; (3) chemical (ammonium, nitrate/nitrite, phosphate, dissolved organic carbon, and total dissolved nitrogen) and biological (chl a, and bacterial and viral abundances) measurements did not reveal significant relationships at the small scale; and (4) statistically significant differences were found between sites/days for all parameter measured but without a clear pattern.
Carreira et al. (2020) Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef. PeerJ 8:e10049 https://doi.org/10.7717/peerj.10049
Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods
Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.
Wang et al. (2020) Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods. PeerJ 8:e10060 https://doi.org/10.7717/peerj.10060
Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1
Over the past decades, Enterobacter spp. have been identified as challenging and important pathogens. The emergence of multidrug-resistant Enterobacteria especially those that produce Klebsiella pneumoniae carbapenemase has been a very worrying health crisis. Although efforts have been made to unravel the complex mechanisms that contribute to the pathogenicity of different Enterobacter spp., there is very little information associated with AHL-type QS mechanism in Enterobacter spp. Signaling via N-acyl homoserine lactone (AHL) is the most common quorum sensing (QS) mechanism utilized by Proteobacteria. A typical AHL-based QS system involves two key players: a luxI gene homolog to synthesize AHLs and a luxR gene homolog, an AHL-dependent transcriptional regulator. These signaling molecules enable inter-species and intra-species interaction in response to external stimuli according to population density. In our recent study, we reported the genome of AHL-producing bacterium, Enterobacter asburiae strain L1. Whole genome sequencing and in silico analysis revealed the presence of a pair of luxI/R genes responsible for AHL-type QS, designated as easI/R, in strain L1. In a QS system, a LuxR transcriptional protein detects and responds to the concentration of a specific AHL controlling gene expression. In E. asburiae strain L1, EasR protein binds to its cognate AHLs, N-butanoyl homoserine lactone (C4-HSL) and N–hexanoyl homoserine lactone (C6-HSL), modulating the expression of targeted genes. In this current work, we have cloned the 693 bp luxR homolog of strain L1 for further characterization. The functionality and specificity of EasR protein in response to different AHL signaling molecules to activate gene transcription were tested and validated with β-galactosidase assays. Higher β-galactosidase activities were detected for cells harboring EasR, indicating EasR is a functional transcriptional regulator. This is the first report documenting the cloning and characterization of transcriptional regulator, luxR homolog of E. asburiae.
Lau et al. (2020) Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1. PeerJ 8:e10068 https://doi.org/10.7717/peerj.10068
Morphological and molecular systematic review of Marphysa Quatrefages, 1865 (Annelida: Eunicidae) species from South Africa
A vast polychaete fauna is hidden behind complexes of cryptic and pseudo-cryptic species, which has greatly hindered our understanding of species diversity in several regions worldwide. Among the eunicids, Marphysa sanguinea Montagu, 1813 is a typical example, recorded in three oceans and with various species considered its junior synonyms. In South Africa, specimens previously misidentified as M. sanguinea are now known as Marphysa elityeni Lewis & Karageorgopoulos, 2008. Of the six Marphysa Quatrefages, 1865a species recorded from the same region, three have their distributions restricted to South Africa while the others are considered to have worldwide distributions. Here, we evaluated the taxonomic status of the indigenous M. elityeni and investigated the presence of the widespread species Marphysa macintoshi Crossland, 1903 and Marphysa depressa Schmarda, 1861 in South Africa using morphological and molecular data. Our results reveal that M. elityeni is a junior synonym of Marphysa haemasoma, a species previously described from South Africa which is herein reinstated as a valid species. Both M. macintoshi and M. depressa are not present in South Africa and their status as being distributed worldwide deserves further investigation. Marphysa durbanensis Day, 1934 and the new species described here, M. sherlockae n. sp., had been misidentified as M. macintoshi and M. depressa respectively. Thus, the number of Marphysa species with distributions restricted to South Africa increased from three to five. This study reiterates the importance of implementing an integrated taxonomic framework to unravel local biodiversity.
Kara et al. (2020) Morphological and molecular systematic review of Marphysa Quatrefages, 1865 (Annelida: Eunicidae) species from South Africa. PeerJ 8:e10076 https://doi.org/10.7717/peerj.10076
Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit
Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit regardless of vegetation density, showing a greater relative abundance of Hypocrea sp. Tailings deposit fungal communities were distinct from those found in boreal forest soils. Alder rhizosphere had greater relative abundances of Hypocrea sp. and Thelephora sp., while birch rhizosphere were more often associated with Mollisia sp. Our results indicate that, with increasing vegetation density on the mine site, the bacterial communities associated with the individual deciduous or coniferous species studied were increasingly similar to the bacterial communities found in the adjacent forest. In order to properly assess and restore disturbed sites, it is important to characterize and understand the plant-microbe associations that occur since they likely improve plant fitness in these harsh environments.
Environmental Contamination and Remediation
Gagnon et al. (2020) Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit. PeerJ 8:e10109 https://doi.org/10.7717/peerj.10109