Influence of water availability and temperature on estimates of microbial extracellular enzyme activity
Soils are highly heterogeneous and support highly diverse microbial communities. Microbial extracellular enzymes breakdown complex polymers into small assimilable molecules representing the limiting step of soil organic matter mineralization. This process occurs on to soil particles although currently it is typically estimated in laboratory aqueous solutions. Herein, estimates of microbial extracellular enzyme activity were obtained over a broad range of temperatures and water availabilities frequently observed at soil upper layers. A Pseudomonas strain presented optimum extracellular enzyme activities at high water activity whereas a desiccation resistant bacterium (Deinococcus) and a soil thermophilic isolate (Parageobacillus) showed optimum extracellular enzyme activity under dried (i.e., water activities ranging 0.5–0.8) rather that wet conditions. Different unamended soils presented a distinctive response of extracellular enzyme activity as a function of temperature and water availability. This study presents a procedure to obtain realistic estimates of microbial extracellular enzyme activity under natural soil conditions of extreme water availability and temperature. Improving estimates of microbial extracellular enzyme activity contribute to better understand the role of microorganisms in soils.
Gomez et al. (2021) Influence of water availability and temperature on estimates of microbial extracellular enzyme activity. PeerJ 9:e10994 https://doi.org/10.7717/peerj.10994
Cranial ornamentation in the Late Cretaceous nodosaurid ankylosaur Hungarosaurus
Bony cranial ornamentation is developed by many groups of vertebrates, including ankylosaur dinosaurs. To date, the morphology and ontogenetic origin of ankylosaurian cranial ornamentation has primarily focused on a limited number of species from only one of the two major lineages, Ankylosauridae. For members of the sister group Nodosauridae, less is known. Here, we provide new details of the cranial anatomy of the nodosaurid Hungarosaurus from the Santonian of Europe. Based on a number of previously described and newly identified fragmentary skulls and skull elements, we recognize three different size classes of Hungarosaurus. We interpret these size classes as representing different stages of ontogeny. Cranial ornamentation is already well-developed in the earliest ontogenetic stage represented herein, suggesting that the presence of outgrowths may have played a role in intra- and interspecific recognition. We find no evidence that cranial ornamentation in Hungarosaurus involves the contribution of coossified osteoderms. Instead, available evidence indicates that cranial ornamentation forms as a result of the elaboration of individual elements. Although individual differences and sexual dimorphism cannot be excluded, the observed variation in Hungarosaurus cranial ornamentation appears to be associated with ontogeny.
Ősi et al. (2021) Cranial ornamentation in the Late Cretaceous nodosaurid ankylosaur Hungarosaurus. PeerJ 9:e11010 https://doi.org/10.7717/peerj.11010
Examining long-term natural vegetation dynamics in the Aral Sea Basin applying the linear spectral mixture model
Background Associated with the significant decrease in water resources, natural vegetation degradation has also led to many widespread environmental problems in the Aral Sea Basin. However, few studies have examined long-term vegetation dynamics in the Aral Sea Basin or distinguished between natural vegetation and cultivated land when calculating the fractional vegetation cover. Methods Based on the multi-temporal Moderate Resolution Imaging Spectroradiometer, this study examined the natural vegetation coverage by introducing the Linear Spectral Mixture Model to the Google Earth Engine platform, which greatly reduces the experimental time. Further, trend line analysis, Sen trend analysis, and Mann–Kendall trend test methods were employed to explore the characteristics of natural vegetation cover change in the Aral Sea Basin from 2000 to 2018. Results Analyses of the results suggest three major conclusions. First, the development of irrigated agriculture in the desert area is the main reason for the decrease in downstream water. Second, with the reduction of water, the natural vegetation coverage in the Aral Sea Basin showed an upward trend of 17.77% from 2000 to 2018. Finally, the main driving factor of vegetation cover changes in the Aral Sea Basin is the migration of cultivated land to the desert.
Spatial and Geographic Information Science
Su et al. (2021) Examining long-term natural vegetation dynamics in the Aral Sea Basin applying the linear spectral mixture model. PeerJ 9:e10747 https://doi.org/10.7717/peerj.10747
Comparative transcriptome analyses of maize seedling root responses to salt stress
Salt stress affects crop yield by limiting growth and delaying development. In this study, we constructed 16 transcriptome libraries from maize seedling roots using two maize lines, with contrasting salt tolerance, that were exposed to salt stress for 0, 6, 18 and 36 h. In total, 6,584 differential expression genes (DEGs; 3,669 upregulated, 2,915 downregulated) were induced in the salt-sensitive line and 6,419 DEGs (3,876 upregulated, 2,543 downregulated) were induced in the salt-tolerant line. Several DEGs common to both lines were enriched in the ABA signaling pathway, which was presumed to coordinate the process of maize salt response. A total of 459 DEGs were specifically induced in the salt-tolerant line and represented candidate genes responsible for high salt-tolerance. Expression pattern analysis for these DEGs indicated that the period between 0 and 6 h was a crucial period for the rapid response of the tolerant genes under salt stress. Among these DEGs, several genes, Aux/IAA, SAUR, and CBL-interacting kinase have been reported to regulate salt tolerance. In addition, the transcription factors WRKY, bZIP and MYB acted as regulators in the salt-responsive regulatory network of maize roots. Our findings will contribute to understanding of the mechanism on salt response and provide references for functional gene revelation in plants.
Zhang et al. (2021) Comparative transcriptome analyses of maize seedling root responses to salt stress. PeerJ 9:e10765 https://doi.org/10.7717/peerj.10765
Comparison of circulating tumor cell (CTC) detection rates with epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) antibodies in different solid tumors: a retrospective study
Purpose Status of epithelial-mesenchymal transition (EMT) varies from tumors to tumors. Epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) are the most common used targets for isolating epithelial and mesenchymal CTCs, respectively. This study aimed to identify a suitable CTC capturing antibody for CTC enrichment in each solid tumor by comparing CTC detection rates with EpCAM and CSV antibodies in different solid tumors. Methods Treatment-naive patients with confirmed cancer diagnosis and healthy people who have performed CTC detection between April 2017 and May 2018 were included in this study. CTC detection was performed with CytoSorter® CTC system using either EpCAM or CSV antibody. In total, 853 CTC results from 690 cancer patients and 72 healthy people were collected for analysis. The performance of CTC capturing antibody was determined by the CTC detection rate. Results EpCAM has the highest CTC detection rate of 84.09% in CRC, followed by BCa (78.32%). CTC detection rates with EpCAM antibody are less than 40% in HCC (25%), PDAC (32.5%) and OC (33.33%). CSV has the highest CTC detection rate of 90% in sarcoma, followed by BC (85.71%), UC (84.62%), OC (83.33%) and BCa (81.82%). CTC detection rates with CSV antibody are over 60% in all 14 solid tumors. Except for CRC, CSV has better performances than EpCAM in most solid tumors regarding the CTC detection rates. Conclusion EpCAM can be used as a target to isolate CTCs in CRC, LC, GC, BCa, EC, HNSCC, CC and PCa, especially in CRC, while CSV can be used in most solid tumors for isolating CTCs.
Gao et al. (2021) Comparison of circulating tumor cell (CTC) detection rates with epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) antibodies in different solid tumors: a retrospective study. PeerJ 9:e10777 https://doi.org/10.7717/peerj.10777
Residual dynamics and dietary exposure risk of dimethoate and its metabolite in greenhouse celery
This study aimed to explore the residual dynamics and dietary risk of dimethoate and its metabolite omethoate in celery. Celery was sprayed with 40% dimethoate emulsifiable concentrate (EC) at either a low concentration of 600 g a.i./ha or a high concentration of 900 g a.i./ha. Plants in the seedling, transplanting, or middle growth stages were sprayed once, and the samples were collected 90 days after transplantation. Plants in the harvesting stage were sprayed two or three times. The samples were collected on days 3, 5, 7, 10, 14 and 21 after the last pesticide application. The dimethoate and omethoate compounds were extracted from the celery samples using acetonitrile, and their concentrations were detected using ultra-performance liquid chromatography-tandem mass spectrometry. Also, the dietary risk assessments of dimethoate and omethoate were conducted in various populations and on different foods in China. The metabolism led to the formation of omethoate from dimethoate in the celery. The degradation dynamics of dimethoate and total residues in greenhouse celery followed the first-order kinetic equation. The half-lives of the compounds were 2.42 days and 2.92 days, respectively. The celery which received one application during the harvesting stage had a final residue of dimethoate after 14 days, which was lower than the maximum residue limit (MRL) 0.5 mg kg−1 for Chinese celery. The final deposition of the metabolite omethoate after 28 days was less than the maximum residue limit of 0.02 mg kg−1 for Chinese celery. Furthermore, the risk quotients of dimethoate in celery were less than 1; therefore, the level of chronic risk was acceptable after day 21. Only children aged 2–7 years had an HQ of dimethoate more than 1 (an unacceptable level of acute risk), while the acute dietary risks to other populations were within acceptable levels. It was recommended that any dimethoate applications to celery in greenhouses should happen before the celery reached the harvesting stage, with a safety interval of 28 days.
Guo et al. (2021) Residual dynamics and dietary exposure risk of dimethoate and its metabolite in greenhouse celery. PeerJ 9:e10789 https://doi.org/10.7717/peerj.10789
The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study
Tumor-derived circulating tumor DNA (ctDNA) has demonstrated its excellent potential for cancer diagnosis by DNA methylome; therefore, this study aimed to identify the retinoblastoma (RB) specific methylated CpG loci as the RB diagnostic biomarkers and design a methylation specific assay to detect these biomarker from aqueous humor of RB patients. Through a genome-wide methylation profiling of tissue samples from patients with RB, normal retina and other retinal diseases, we shortlisted two CpG loci were only methylated in RB but not in normal retina or other retinal diseases. Both of these two CpG loci were located in the genome of TFAP2A. Through the screening, a primer and probe set for the two CpG loci were tested in fully methylated standards and RB tissues with a significant differentiation of RB. Our results of this assay tested in aqueous humor from RB revealed an accuracy of 92.7% for RB diagnosis. These results suggested our assay targeting the TFAP2A ctDNA methylation can be utilized for RB diagnosis and cancer monitoring.
Zeng et al. (2021) The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study. PeerJ 9:e10830 https://doi.org/10.7717/peerj.10830
The regulatory roles and mechanisms of the transcription factor FOXF2 in human diseases
Many studies have focused on the relationship between transcription factors and a variety of common pathological conditions, such as diabetes, stroke, and cancer. It has been found that abnormal transcription factor regulation can lead to aberrant expression of downstream genes, which contributes to the occurrence and development of many diseases. The forkhead box (FOX) transcription factor family is encoded by the FOX gene, which mediates gene transcription and follow-up functions during physiological and pathological processes. FOXF2, a member of the FOX transcription family, is expressed in various organs and tissues while maintaining their normal structural and functional development during the embryonic and adult stages. Multiple regulatory pathways that regulate FOXF2 may also be controlled by FOXF2. Abnormal FOXF2 expression induced by uncontrollable regulatory signals mediate the progression of human diseases by interfering with the cell cycle, proliferation, differentiation, invasion, and metastasis. FOXF2 manipulates downstream pathways and targets as both a pro-oncogenic and anti-oncogenic factor across different types of cancer, suggesting it may be a new potential clinical marker or therapeutic target for cancer. However, FOXF2’s biological functions and specific roles in cancer development remain unclear. In this study, we provide an overview of FOXF2’s structure, function, and regulatory mechanisms in the physiological and pathological conditions of human body. We also discussed the possible reasons why FOXF2 performs the opposite function in the same types of cancer.
Wu et al. (2021) The regulatory roles and mechanisms of the transcription factor FOXF2 in human diseases. PeerJ 9:e10845 https://doi.org/10.7717/peerj.10845
Undercarboxylated osteocalcin inhibits the early differentiation of osteoclast mediated by Gprc6a
Osteocalcin (OCN) was the most abundant noncollagen protein and considered as an endocrine factor. However, the functions of Undercarboxylated osteocalcin (ucOCN) on osteoclast and bone resorption are not well understood. In the present study, preosteoclast RAW264.7 cells and bone marrow mononuclear cells (BMMs) were treated with ucOCN purified from prokaryotic bacteria. Our results showed that ucOCN attenuated the proliferation of RAW264.7 cells with a concentration dependant manner by MTS assay. Scrape wounding assay revealed the decreased motility of RAW264.7 cells after ucOCN treatment. RT-qPCR results manifested the inhibitory effects of ucOCN on the expression of osteoclastic marker genes in RAW264.7 cells during inducing differentiation of RANKL. It was also observed that ucOCN inhibited the formation of multinucleated cells from RAW264.7 cells and BMMs detected by TRAP staining. The number and area of bone resorb pits were also decreased after treatment with ucOCN during their osteoclast induction by toluidine blue staining. The formation and integrity of the osteoclast actin ring were impaired by ucOCN by immunofluorescent staining. Time dependant treatment of ucOCN during osteoclastic induction demonstrated the inhibitory effects mainly occurred at the early stage of osteoclastogenesis. Signaling analysis of luciferase activity of the CRE or SRE reporter and ERK1/2 phosphorylation showed the selective inhibitor or siRNA of Gprc6a (a presumptive ucOCN receptor) could attenuate the promotion of ucOCN on CRE-luciferase activity. Taken together, we provided the first evidence that ucOCN had negative effects on the early differentiation and bone resorption of osteoclasts via Gprc6a.
Wang et al. (2021) Undercarboxylated osteocalcin inhibits the early differentiation of osteoclast mediated by Gprc6a. PeerJ 9:e10898 https://doi.org/10.7717/peerj.10898
Taxonomic revision of the Malagasy Aphaenogaster swammerdami group (Hymenoptera: Formicidae)
Background Madagascar is famous for its extremely rich biodiversity; the island harbors predominantly endemic and threatened communities meriting special attention from biodiversity scientists. Continuing ongoing efforts to inventory the Malagasy ant fauna, we revise the species currently placed in the myrmicine genus Aphaenogaster Mayr. One species described from Madagascar, Aphaenogaster friederichsi Forel, is synonymized with the Palearctic A. subterranea Latreille syn. nov. This species is considered neither native to Madagascar nor established in the region. This revision focuses on the balance of species in the A. swammerdami group which are all endemic to Madagascar. Methods The diversity of the Malagasy Aphaenogaster fauna was assessed via application of multiple lines of evidence involving quantitative morphometric, qualitative morphological, and DNA sequence data. (1) Morphometric investigation was based on hypothesis-free Nest Centroid clustering (NC-clustering) combined with PArtitioning based on Recursive Thresholding (PART) to estimate the number of morphological clusters and determine the most probable boundaries between them. This protocol provides a repeatable and testable approach to find patterns in continuous morphometric data. Species boundaries and the reliability of morphological clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA). (2) Qualitative, external morphological characteristics (e.g., shape, coloration patterns, setae number) were subjectively evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. (3) Species delimitation analyses based on mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were carried out to test the putative species previously delimited by morphological and morphometric analyses. Results Five species can be inferred based on the integrated evaluation of multiple lines of evidence; of these, three are new to science: Aphaenogaster bressleri sp. n., A. gonacantha (Emery, 1899), A. makay sp. n., A. sahafina sp. n., and A. swammerdami Forel, 1886. In addition, three new synonymies were found for A. swammerdami Forel, 1886 (A. swammerdami clara Santschi, 1915 syn. n., A. swammerdami curta Forel, 1891 syn. n. and A. swammerdami spinipes Santschi, 1911 syn. n.). Descriptions and redefinitions for each taxon and an identification key for their worker castes using qualitative traits and morphometric data are given. Geographic maps depicting species distributions and biological information regarding nesting habits for the species are also provided.
Csősz et al. (2021) Taxonomic revision of the Malagasy Aphaenogaster swammerdami group (Hymenoptera: Formicidae). PeerJ 9:e10900 https://doi.org/10.7717/peerj.10900