Ciliates are highly divergent unicellular eukaryotic organisms with nuclear dualism and a highly specialized ciliary pattern. They inhabit all biotopes and play crucial roles in regulating microbial ...food webs as they prey on bacteria, protists and even on microscopic animals. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. In the present review, an attempt has been made to elaborate the various approaches used by modern day ciliate taxonomists for species identification. The different approaches involved in taxonomic characterization of ciliates such as classical (using live-cell observations, staining techniques, etc.), molecular (involving various marker genes) and statistical (delimitation of cryptic species) methods have been reviewed. Ecological and behavioural aspects in species identification have also been discussed. In present-day taxonomy, it is important to use a 'total evidence' approach in identifying ciliates, relying on both classical and molecular information whenever possible. This integrative approach will help in the mergence of classical methods with modern-day tools for comprehensive species description in future.
Enteric pathogens can be present in drinking water catchments due to several point and non-point sources of faecal contamination. Pathogen and contaminant signatures will decay due to environmental ...stresses, such as temperature, Ultra Violet (UV) radiation, salinity, and predation. In this study, we determined the decay of the culturable faecal indicator bacterium (FIB) Escherichia coli (E. coli), two sewage-associated marker genes (Bacteroides HF183 and crAssphage CPQ_056), and enteric pathogens (Campylobacter spp., human adenovirus 40/41, and Cryptosporidium parvum) in two freshwater laboratory microcosms using culture-based, quantitative PCR (qPCR) and vital dye (determine the fraction of viable Cryptosporidium oocysts) assays. Freshwater samples from the Lake Wappa and Lake Wivenhoe (Australia) were seeded with untreated sewage and C. parvum oocysts, and their declining concentrations were measured over a 28-day period. Moreover, 16S rRNA amplicon sequencing was also undertaken to determine the change/shift in sewage-associated bacterial communities using SourceTracker. Overall, culturable E. coli and the HF183 marker gene decayed significantly (p < 0.05) faster than did the qPCR measured enteric pathogens suggesting that the absence of culturable FIB or qPCR HF183 in water samples may not indicate the absence of pathogens. The decay of crAssphage was similar to that of HAdV 40/41 and other pathogens tested, suggesting crAssphage may be a better surrogate for enteric viruses in sub-tropical catchment waters. The decay rates were greater at 25 °C compared to 15 °C, suggesting that FIB and pathogens persist longer in the winter season compared to summer. Overall decay rates of the tested microorganisms in this microcosm study suggest that sub-tropical conditions, especially temperature, have a negative impact on the persistence of tested microorganisms. Sewage-associated bacterial communities also showed similar patterns. Based on the results, which showed differences in simulated summer and winter temperatures for pathogen decay, corresponding management options and treatment need to be adjusted accordingly to minimize human health risks effectively.
Display omitted
•The HF183 marker gene decayed significantly (p < 0.05) faster than pathogens.•The decay of crAssphage was similar to that of HAdV 40/41.•The decay rates of tested organisms were greater at 25 °C compared to 15 °C.•The persistence of microorganisms is affected by temperature.
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. ...Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.
The reproductive life span of the organism mainly depends on follicular development that maintains the primordial follicle pool in the cohort of follicles within the ovary. The total count of ...primordial follicles decreases with age due to ovulation and follicular atresia. Follicular atresia, a process of ovarian follicles degradation, mainly occurs via apoptosis, but recent studies also favor autophagy existence. Autophagy is a cellular and energy homeostatic response that helps to maintain the number of healthy primordial follicles, germ cell survival, and removal of corpus luteum remnants. But the excessive autophagic cell death changes both the quality and quantity of oocytes that ultimately affect female reproductive health. Autophagy regulation occurs by various autophagy‐regulated genes like BECN1 and LC3‐II (autophagy marker genes). Their abnormal regulation or mutation highly influences follicular development by alteration of primordial follicles formation, the decline in oocytes count, and germ cell loss. Various classical signaling pathways such as PI3K/AKT/mTOR, MAPK/ERK1/2, AMPK, and IRE1 are involved in granulosa and oocytes autophagy, while mTOR signaling is the primary mechanism. Along with basal level autophagy, chemical/hormone/stress‐mediated autophagy also affects follicular development and female reproduction. In this review, we have primarily focused on granulosa cell and oocytes' autophagy, mechanism, and the role of autophagy determining marker genes in follicular development.
'Dual role of autophagy and associated factors in ovarian follicular development ATG‐autophagy regulated gene; LC3‐microtubules‐associated protein 1A/1B light chain‐3; BECN1‐ Beclin‐1'
Bisphenol S (BPS) has been increasingly used as a substitute for bisphenol A (BPA), a known endocrine disruptor. Early-life exposure to BPA affects fetal development and the risk of obesity in ...adolescence and adulthood. However, the effects of fetal exposure BPS in later life are unknown. This study aimed to investigate the effects of prenatal BPS exposure on adiposity in adult F1 mice. Pregnant C57BL/6 N mice were exposed to BPS (0, 0.05, 0.5, 5, and 50 mg/kg/d) via drinking water from gestation day 9 until delivery. Thereafter, two groups of offspring (6 weeks old) were either administered a standard diet (STD) or a high-fat diet (HFD) for 4 weeks until euthanasia. The body weight and gonadal white adipose tissue (gWAT) mass were determined, and the energy expenditure for the adiposity phenotype was computed especially for male mice, followed by histological analysis of the gWAT. Thereafter, the expression levels of adipogenic marker genes (Pparg, Cebpa, Fabp4, Lpl, and Adipoq) were analyzed in the gWAT via reverse-transcription PCR analysis. BPS-exposed male mice displayed apparent gWAT hypertrophy, consistent with the significant increase in adipocyte size in the gWAT and upregulation of Pparg and its direct target genes among HFD mice in comparison with the control mice. These results suggest that prenatal BPS exposure potentially increases the susceptibility to HFD-induced adipogenesis in male adult mice.
Display omitted
•BPS has been used increasingly with insufficient evidence of toxicity.•Prenatal BPS exposure caused gonadal adipocyte hypertrophy in high-fat-fed mice.•Adipogenic genes were upregulated in the enlarged gonadal adipose tissues.•In utero BPS exposure affects the adipogenic susceptibility in male mice.
Incorporating bioactive molecules into synthetic ceramic scaffolds is challenging. In this study, to enhance bone regeneration, a magnesium phosphate (MgP) ceramic scaffold was incorporated with a ...novel indene compound, KR-34893. KR-34893 induced the deposition of minerals and expression of osteoblast marker genes in primary human bone marrow mesenchymal stem cells (BMSCs) and a mouse osteoblastic MC3T3-E1 cell line. Analysis of the mode of action showed that KR-34893 induced the phosphorylation of MAPK/extracellular signal-regulated kinase and extracellular signal-regulated kinase, and subsequently the expression of bone morphogenetic protein 7, accompanied by SMAD1/5/8 phosphorylation. Accordingly, KR-34893 was incorporated into an MgP scaffold prepared by 3D printing at room temperature, followed by cement reaction. KR-34893-incorporated MgP (KR-MgP) induced the expression of osteoblast differentiation marker genes in vitro. In a rat calvaria defect model, KR-MgP scaffolds enhanced bone regeneration and increased bone volume compared with MgP scaffolds, as assessed by micro-computed tomography and histological analyses. In conclusion, we developed a method for producing osteoinductive MgP scaffolds incorporating a bioactive organic compound, without high temperature sintering. The KR-MgP scaffolds enhanced osteoblast activation in vitro and bone regeneration in vivo.
There is a growing move towards using the quantitative polymerase chain (qPCR)-based sewage-associated marker genes to assess surface water quality. However, a lack of understanding about the ...persistence of many sewage-associated markers creates uncertainty for those tasked with investigating microbial water quality. In this study, we investigated the decay of two qPCR FIB E. coli (EC), and Enterococcus spp. (ENT) 23S rRNA genes and four sewage-associated microbial source tracking (MST) marker genes human Bacteroides HF183 16S rRNA, adenovirus (HAdV), and polyomavirus (HPyV), and crAssphage, a recently described bacteriophage in feces, in outdoor mesocosms containing fresh and marine waters and their corresponding sediments. Decay rates of EC 23S rRNA, ENT 23S rRNA, and HF183 16S rRNA were significantly (p < 0.05) faster than the HAdV, HPyV and crAssphage markers in water samples from all mesocosms. In general, decay rates of bacterial targets were similar in the water columns of the studied mesocosms. Similarly, decay rates of viral targets were also alike in mesocosm water columns in relation to each other. The decay rates of FIB and sewage-associated markers were significantly faster in water samples compared to sediments in all three mesocosms. In the event of resuspension, FIB and marker genes from sediments can potentially recontaminate overlying waters. Thus, care should be taken when interpreting the occurrence of FIB and sewage-associated MST markers in water, which may have originated from sediments. The differential decay of these targets may also influence health outcomes and need to be considered in risk assessment models.
Display omitted
•Decay rates of bacterial gene markers were significantly faster than the viruses.•Markers decay rates were significantly faster in water samples compared to sediments.•Decay rates of marker genes were similar for both fresh and marine waters.•Markers decay positively correlated with water temperature, TOC, and turbidity.
Abstract
In molecular biology, just as in many other fields of science, data often come in the form of matrices or contingency tables with many observations (rows) for a set of variables (columns). ...While projection methods like principal component analysis or correspondence analysis (CA) can be applied for obtaining an overview of such data, in cases where the matrix is very large the associated loss of information upon projection into two or three dimensions may be dramatic. However, when the set of variables can be grouped into clusters, this opens up a new angle on the data. We focus on the question of which observations are associated to a cluster and distinguish it from other clusters. CA employs a geometry geared towards answering this question. We exploit this feature in order to introduce Association Plots for visualizing cluster-specific observations in complex data. Regardless of the data matrix dimensionality Association Plots are two-dimensional and depict the observations associated to a cluster of variables. We demonstrate our method on two small data sets and then use it to study a challenging genomic data set comprising >10,000 samples. We show that Association Plots can clearly highlight those observations which characterise a cluster of variables.
18FFluorodeoxyglucose-PET/CT (18F-FDG-PET/CT) imaging has been invaluable for visualizing metabolically active adipose tissues in humans with potential anti-diabetic and anti-obesity effects. To ...explore whether mice display human-like fat depots in anatomically comparable regions, we mapped fat depots using glucose or fatty acid imaging tracers, such as 18F-FDG through PET/CT or 123/125I-β-methyl-p-iodophenyl-pentadecanoic acid with SPECT/CT imaging, to analogous depots in mice. Using this type of image analysis with both probes, we define a large number of additional areas of high metabolic activity corresponding to novel fat pads. Histological and gene expression analyses validate these regions as bona fide fat pads. Our findings indicate that fat depots of rodents show a high degree of topological similarity to those of humans. Studies involving both glucose and lipid tracers indicate differential preferences for these substrates in different depots and also suggest that fatty acid-based visualized approaches may reveal additional brown adipose tissue and beige depots in humans.
Display omitted
•Rodents and humans share topological similarity of thermogenic fat depots•PET/CT and SPECT/CT differentially highlight newly identified fat pads in mice•Histological and gene expression analyses confirm the regions as bona fide fat pads•SPECT/CT with lipid tracers may reveal additional BAT and beige depots in humans
18F-FDG-PET/CT imaging in humans has been invaluable for visualizing metabolically active adipose tissues. Using PET/CT and SPECT/CT for imaging glucose and lipid metabolism, respectively, in mice, Zhang et al. define an atlas of fat depots, topologically analogous to those observed in humans.
Pancreatic islets of Langerhans contain several specialized endocrine cell types, which are commonly identified by the expression of single marker genes. However, the established marker genes cannot ...capture the complete spectrum of cellular heterogeneity in human pancreatic islets, and existing bulk transcriptome datasets provide averages across several cell populations. To dissect the cellular composition of the human pancreatic islet and to establish transcriptomes for all major cell types, we performed single‐cell RNA sequencing on 70 cells sorted from human primary tissue. We used this dataset to validate previously described marker genes at the single‐cell level and to identify specifically expressed transcription factors for all islet cell subtypes. All data are available for browsing and download, thus establishing a useful resource of single‐cell expression profiles for endocrine cells in human pancreatic islets.
Synopsis
We provide a resource of single‐cell transcriptomes from primary human pancreatic islets and describe the detection of specific marker genes, cellular heterogeneity, and mouse–human species differences.
We performed single‐cell RNA‐seq on 70 cells sorted from primary human pancreatic islets.
Bioinformatic analysis of single‐cell transcriptomes rediscovered all the major pancreatic cell types including new cell type‐specific marker genes.
All the data are provided as an online resource for browsing and download.
This study provides a resource of single‐cell transcriptomes from primary human pancreatic islets and describes the detection of specific marker genes, cellular heterogeneity and mouse–human species differences.
PDF
