Microenvironment-related gene TNFSF13B predicts poor prognosis in kidney renal clear cell carcinoma
Background Kidney renal clear cell carcinoma (KIRC) affects the genitourinary system. Although treatment of KIRC in early stages can be highly successful, this type of cancer is difficult to detect until later stages of disease that are less easily treatable. Previous studies have focused on tumor cells, but have ignored the contributions of the tumor microenvironment. Methods We analyzed KIRC gene expression data from The Cancer Genome Atlas with the ESTIMATE algorithm to identify differentially expressed genes. Through protein–protein interaction network analysis, we identified clusters and picked genes from the clusters for further analysis. Differential expression, Kaplan–Meier, and univariate Cox analyses were used to select prognostic biomarkers. Gene Set Enrichment Analysis (GSEA) and Tumor Immune Estimation Resource (TIMER) analysis were used to explore the immune characteristics of these genes as biomarkers. Results Through the ESTIMATE algorithm and other system biology tools, TNFSF13B was identified as a prognostic biomarker. TNFSF13B is highly expressed in tumors, and high expression of TNFSF13B leads to poor prognosis. Further GSEA and TIMER analysis revealed that the expression of TNFSF13B was related to the immune signaling pathway and lymphocyte infiltration. Our findings strongly suggest that TNFSF13B may be a potential biomarker or target related to the tumor microenvironment for KIRC.
Jiang et al. (2020) Microenvironment-related gene TNFSF13B predicts poor prognosis in kidney renal clear cell carcinoma. PeerJ 8:e9453 https://doi.org/10.7717/peerj.9453
Cranial osteology of the Early Cretaceous turtle Pleurosternon bullockii (Paracryptodira: Pleurosternidae)
Pleurosternon bullockii is a turtle from the Early Cretaceous of Europe known from numerous postcranial remains. Only one skull has so far been referred to the species. Pleurosternon bullockii belongs to a group of turtles called pleurosternids, which is thought to include several poorly known taxa from the Late Jurassic and Early Cretaceous of Europe and North America. Pleurosternids and baenids, a group of North American turtles that lived from the Late Cretaceous to the Eocene, define a clade called Paracryptodira. Additionally, Paracryptodira likely includes compsemydids, and, potentially, helochelydrids. Character support for Paracryptodira is relatively weak, and many global phylogenetic studies fail to support paracryptodiran monophyly altogether. Proposed paracryptodiran synapomorphies are largely cranial, despite the poor characterization of pleurosternid cranial material. In addition to their questionable monophyly, the global position of paracryptodires is debated. Early studies suggest crown-turtle affinities, but most phylogenies find them as stem-turtles, irrespective of their monophyly. Here, we document the cranial osteology of Pleurosternon bullockii with the use of three-dimensional models derived from segmenting high-resolution X-ray micro-computed tomography (CT) scans. Pleurosternon bullockii has a primitive basipterygoid region of the skull, but a cryptodire-like acustico-jugular region. A surprising number of similarities with pleurodires exist, particularly in the laterally expanded external process of the pterygoid and in the posterior orbital wall. Our observations constitute an important step toward a phylogenetic re-evaluation of Paracryptodira.
Evers et al. (2020) Cranial osteology of the Early Cretaceous turtle Pleurosternon bullockii (Paracryptodira: Pleurosternidae). PeerJ 8:e9454 https://doi.org/10.7717/peerj.9454
Investigation of microbial community interactions between Lake Washington methanotrophs using ­­­­­­­genome-scale metabolic modeling
Background The role of methane in global warming has become paramount to the environment and the human society, especially in the past few decades. Methane cycling microbial communities play an important role in the global methane cycle, which is why the characterization of these communities is critical to understand and manipulate their behavior. Methanotrophs are a major player in these communities and are able to oxidize methane as their primary carbon source. Results Lake Washington is a freshwater lake characterized by a methane-oxygen countergradient that contains a methane cycling microbial community. Methanotrophs are a major part of this community involved in assimilating methane from lake water. Two significant methanotrophic species in this community are Methylobacter and Methylomonas. In this work, these methanotrophs are computationally studied via developing highly curated genome-scale metabolic models. Each model was then integrated to form a community model with a multi-level optimization framework. The competitive and mutualistic metabolic interactions among Methylobacter and Methylomonas were also characterized. The community model was next tested under carbon, oxygen, and nitrogen limited conditions in addition to a nutrient-rich condition to observe the systematic shifts in the internal metabolic pathways and extracellular metabolite exchanges. Each condition showed variations in the methane oxidation pathway, pyruvate metabolism, and the TCA cycle as well as the excretion of formaldehyde and carbon di-oxide in the community. Finally, the community model was simulated under fixed ratios of these two members to reflect the opposing behavior in the two-member synthetic community and in sediment-incubated communities. The community simulations predicted a noticeable switch in intracellular carbon metabolism and formaldehyde transfer between community members in sediment-incubated vs. synthetic condition. Conclusion In this work, we attempted to predict the response of a simplified methane cycling microbial community from Lake Washington to varying environments and also provide an insight into the difference of dynamics in sediment-incubated microcosm community and synthetic co-cultures. Overall, this study lays the ground for in silico systems-level studies of freshwater lake ecosystems, which can drive future efforts of understanding, engineering, and modifying these communities for dealing with global warming issues.
Islam et al. (2020) Investigation of microbial community interactions between Lake Washington methanotrophs using ­­­­­­­genome-scale metabolic modeling. PeerJ 8:e9464 https://doi.org/10.7717/peerj.9464
Bite force data suggests relationship between acrodont tooth implantation and strong bite force
Extant and extinct reptiles exhibit numerous combinations of tooth implantation and attachment. Tooth implantation ranges from those possessing roots and lying within a socket (thecodonty), to teeth lying against the lingual wall of the jawbone (pleurodonty), to teeth without roots or sockets that are attached to the apex of the marginal jawbones (acrodonty). Attachment may be ligamentous (gomphosis) or via fusion (ankylosis). Generally speaking, adaptative reasonings are proposed as an underlying driver for evolutionary changes in some forms of tooth implantation and attachment. However, a substantiated adaptive hypothesis is lacking for the state of acrodont ankylosis that is seen in several lineages of Lepidosauria, a clade that is plesiomorphically pleurodont. The convergent evolution of acrodont ankylosis in several clades of lepidosaurs suggests a selective pressure shaped the evolution of the trait. We hypothesize that acrodont ankylosis as seen in Acrodonta and Sphenodon punctatus, is an adaptation either resulting from or allowing for a stronger bite force. We analyzed bite force data gathered from the literature to show that those taxa possessing acrodont dentition possess a stronger bite force on average than those taxa with pleurodont dentition. Dietary specialists with pleurodont dentition may also possess relatively high bite forces, though body size may also play a role in their ability to bite hard. Furthermore, our results have implications for the evolution of acrodont ankylosis and potential behaviors related to strong bite force that influenced the evolution of acrodonty within Acrodonta and Rhynchocephalia.
Jenkins et al. (2020) Bite force data suggests relationship between acrodont tooth implantation and strong bite force. PeerJ 8:e9468 https://doi.org/10.7717/peerj.9468
Comparative metabolomic analyses of Dendrobium officinale Kimura et Migo responding to UV-B radiation reveal variations in the metabolisms associated with its bioactive ingredients
Background Dendrobium officinale Kimura et Migo, a member of the genus Dendrobium, is a traditional Chinese medicine with high commercial value. The positive roles of UV-B radiation on active ingredient metabolism in various medicinal plants have been studied. However, the metabolic responses of D. officinale stems to UV-B treatment is largely unknown. Methods An untargeted metabolomics method was used to investigate the metabolic variations in D. officinale stems between the control and UV-B treatments. Results In total, 3,655 annotated metabolites, including 640 up- and 783 down-regulated metabolites, were identified and grouped into various primary metabolic categories. Then, a number of metabolites involved in the polysaccharide, alkaloid and flavonoid biosynthesis pathways were identified. For polysaccharide biosynthesis, several intermediate products, such as pyruvate, secologanate, tryptophan and secologanin, were significantly up-regulated by the UV-B treatment. For polysaccharide biosynthesis, many key fundamental building blocks, from the glycolysis, starch and sucrose metabolism, and fructose and mannose metabolism pathways, were induced by the UV-B treatment. For flavonoid metabolism, accumulations of several intermediate products of chalcone synthase, chalcone isomerase and flavanone 3-hydroxylase were affected by the UV-B treatment, indicating an involvement of UV-B in flavonoid biosynthesis. The UV-B induced accumulation of polysaccharides, alkaloids and flavonoids was confirmed by HPLC analysis. Our study will help to understand the effects of UV-B on the accumulation of active ingredients in D. officinale.
Chen et al. (2020) Comparative metabolomic analyses of Dendrobium officinale Kimura et Migo responding to UV-B radiation reveal variations in the metabolisms associated with its bioactive ingredients. PeerJ 8:e9107 https://doi.org/10.7717/peerj.9107
The genome of the butternut canker pathogen, Ophiognomonia clavigignenti-juglandacearum shows an elevated number of genes associated with secondary metabolism and protection from host resistance responses
Ophiognomonia clavigignenti-juglandacearum (Oc-j) is a plant pathogenic fungus that causes canker and branch dieback diseases in the hardwood tree butternut, Juglans cinerea. Oc-j is a member of the order of Diaporthales, which includes many other plant pathogenic species, several of which also infect hardwood tree species. In this study, we sequenced the genome of Oc-j and achieved a high-quality assembly and delineated its phylogeny within the Diaporthales order using a genome-wide multi-gene approach. We also further examined multiple gene families that might be involved in plant pathogenicity and degradation of complex biomass, which are relevant to a pathogenic life-style in a tree host. We found that the Oc-j genome contains a greater number of genes in these gene families compared to other species in the Diaporthales. These gene families include secreted CAZymes, kinases, cytochrome P450, efflux pumps, and secondary metabolism gene clusters. The large numbers of these genes provide Oc-j with an arsenal to cope with the specific ecological niche as a pathogen of the butternut tree.
Wu et al. (2020) The genome of the butternut canker pathogen, Ophiognomonia clavigignenti-juglandacearum shows an elevated number of genes associated with secondary metabolism and protection from host resistance responses. PeerJ 8:e9265 https://doi.org/10.7717/peerj.9265
A new species of freshwater crab genus Fredius Pretzmann, 1967 (Crustacea: Brachyura: Pseudothelphusidae) from a naturally isolated orographic forest enclave within the semiarid Caatinga in Ceará, northeastern Brazil
A new species of freshwater crab, Fredius ibiapaba, is described and illustrated from a mid-altitude forested patch in Ipú (Ibiapaba plateau, Ceará, northeastern Brazil), between 635 to 782 m. The new species can be separated from its congeners by the morphology of its first gonopod: proximal half remarkably swollen, sloping abruptly downwards distally to a nearly right-angular shoulder; mesial lobe much smaller than cephalic spine; cephalic lobe moderately developed; auxiliary lobe lip, delimiting field of apical spines, protruded all the way to distal margin of auxiliary lobe. Comparative 16S rDNA sequencing used to infer the phylogenetic placement of Fredius ibiapaba n. sp. revealed that it is the sister taxon of F. reflexifrons, a species which occurs allopatrically in the Amazon and Atlantic basin’s lowlands (<100 m). Fredius ibiapaba n. sp. and F. reflexifrons are highly dependent upon humidity and most probably were once part of an ancestral population living in a wide humid territory. Shrinking humid forests during several dry periods of the Tertiary and Quaternary likely have resulted in the fragmentation of the ancestral humid area and hence of the ancestral crab population. Fredius reflexifrons evolved and spread in a lowland, humid river basin (Amazon and Atlantic basins), whilst F. ibiapaba n. sp. evolved isolated on the top of a humid plateau. The two species are now separated by a vast intervening area occupied by the semiarid Caatinga
Santos et al. (2020) A new species of freshwater crab genus Fredius Pretzmann, 1967 (Crustacea: Brachyura: Pseudothelphusidae) from a naturally isolated orographic forest enclave within the semiarid Caatinga in Ceará, northeastern Brazil. PeerJ 8:e9370 https://doi.org/10.7717/peerj.9370
Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies
Background The Shannon diversity index has been widely used in population genetics studies. Recently, it was proposed as a unifying measure of diversity at different levels—from genes and populations to whole species and ecosystems. The index, however, was proven to be negatively biased at small sample sizes. Modifications to the original Shannon’s formula have been proposed to obtain an unbiased estimator. Methods In this study, the performance of four different estimators of Shannon index—the original Shannon’s formula and those of Zahl, Chao and Shen and Chao et al.—was tested on simulated microsatellite data. Both the simulation and analysis of the results were performed in the R language environment. A new R function was created for the calculation of all four indices from the genind data format. Results Sample size dependence was detected in all the estimators analysed; however, the deviation from parametric values was substantially smaller in the derived measures than in the original Shannon’s formula. Error rate was negatively associated with population heterozygosity. Comparisons among loci showed that fast-mutating loci were less affected by the error, except for the original Shannon’s estimator which, in the smallest sample, was more strongly affected by loci with a higher number of alleles. The Zahl and Chao et al. estimators performed notably better than the original Shannon’s formula. Conclusion The results of this study show that the original Shannon index should no longer be used as a measure of genetic diversity and should be replaced by Zahl’s unbiased estimator.
Konopiński (2020) Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies. PeerJ 8:e9391 https://doi.org/10.7717/peerj.9391
Using Bumble Bee Watch to investigate the accuracy and perception of bumble bee (Bombus spp.) identification by community scientists
Community science programs provide an opportunity to gather scientific data to inform conservation policy and management. This study examines the accuracy of community science identifications submitted to the North American Bumble Bee Watch program on a per species level and as compared to each species’ conservation status, as well as users (members of the public) and experts (those with expertise in the field of bumble bee biology) perceived ease of species identification. Photos of bumble bees (Hymenoptera: Apidae: Bombus) are submitted to the program by users and verified (species name corrected or assigned as necessary) by an expert. Over 22,000 records from over 4,900 users were used in the analyses. Accuracy was measured in two ways: percent agreement (percent of all records submitted correctly by users) and veracity (percent of all verified records submitted correctly by the users). Users generally perceived it harder to identify species than experts. User perceptions were not significantly different from the observed percent agreement or veracity, while expert perceptions were significantly different (overly optimistic) from the observed percent agreement but not the veracity. We compared user submitted names to final expert verified names and found that, for all species combined, the average percent agreement was 53.20% while the average veracity was 55.86%. There was a wide range in percent agreement values per species, although sample size and the role of chance did affect some species agreements. As the conservation status of species increased to higher levels of extinction risk, species were increasingly more likely to have a lower percent agreement but higher levels of veracity than species of least concern. For each species name submitted, the number of different species verified by experts varied from 1 to 32. Future research may investigate which factors relate to success in user identification through community science. These findings could play a role in informing the design of community science programs in the future, including for use in long-term and national-level monitoring of wild pollinators.
MacPhail et al. (2020) Using Bumble Bee Watch to investigate the accuracy and perception of bumble bee (Bombus spp.) identification by community scientists. PeerJ 8:e9412 https://doi.org/10.7717/peerj.9412
A preoperative nomogram for sepsis in percutaneous nephrolithotomy treating solitary, unilateral and proximal ureteral stones
Background Postoperative sepsis is a lethal complication for percutaneous nephrolithotomy (PCNL). An early predictive model combined local and systemic conditions is urgently needed to predict infectious events. We aim to determine the preoperative predictors of sepsis after PCNL in patients with unilateral, solitary, and proximal ureteral stones. Methods A total of 745 patients who underwent PCNL between January 2012 and December 2018 were retrospectively enrolled. Sepsis was defined based on the International Sepsis Definitions in 2001, and the preoperative factors were compared between the non-sepsis and sepsis groups. Univariable analysis and multivariable logistic regression analysis were conducted to determine the predictors for sepsis after PCNL. A nomogram was generated using the predictors. Results In this study, 35 patients (4.7%) developed sepsis after PCNL. Univariate analysis showed that post-PCNL sepsis was associated with the female, lower albumin, higher globulin, lower albumin globulin ratio (AGR < 1.5), preoperative fever, leukocytosis (WBC ≥ 10,000 cells/μL), positive urine culture, leukocyturia (≥50 cells/μL) and positive urine nitrite. Multivariate logistic regression analysis suggested that AGR < 1.5 (odds ratio [OR] = 5.068, 95% confidence interval [CI] [1.135–22.624], P = 0.033), positive urine culture (OR = 3.243, 95% CI [1.162–9.047], P = 0.025), leukocytosis (OR = 3.706, 95% CI [1.444–9.512], P = 0.006) and female (OR = 2.529, 95% CI [1.127–5.672], P = 0.024) were independent risk factors for sepsis. A nomogram was generated and displayed favorable fitting (Hosmer–Lemeshow test P = 0.797), discrimination (area under receiver operating characteristic curve was 0.807), and clinical usefulness by decision curve analysis. Conclusions Patients with certain preoperative characteristics, such as female, lower AGR, positive urine culture, and leukocytosis, who undergo PCNL may have a higher risk of developing sepsis. A cautious preoperative evaluation and optimized treatment strategy should be considered in these patients to minimize infectious complications.
Xun et al. (2020) A preoperative nomogram for sepsis in percutaneous nephrolithotomy treating solitary, unilateral and proximal ureteral stones. PeerJ 8:e9435 https://doi.org/10.7717/peerj.9435