Identifying multiple collagen gene family members as potential gastric cancer biomarkers using integrated bioinformatics analysis
Background Gastric cancer is one of the most common malignant cancers worldwide. Despite substantial developments in therapeutic strategies, the five-year survival rate remains low. Therefore, novel biomarkers and therapeutic targets involved in the progression of gastric tumors need to be identified. Methods We obtained the mRNA microarray datasets GSE65801, GSE54129 and GSE79973 from the Gene Expression Omnibus database to acquire differentially expressed genes (DEGs). We used the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to analyze DEG pathways and functions, and the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape to obtain the protein–protein interaction (PPI) network. Next, we validated the hub gene expression levels using the Oncomine database and Gene Expression Profiling Interactive Analysis (GEPIA), and conducted stage expression and survival analysis. Results From the three microarray datasets, we identified nine major hub genes: COL1A1, COL1A2, COL3A1, COL5A2, COL4A1, FN1, COL5A1, COL4A2, and COL6A3. Conclusion Our study identified COL1A1 and COL1A2 as potential gastric cancer prognostic biomarkers.
Li et al. (2020) Identifying multiple collagen gene family members as potential gastric cancer biomarkers using integrated bioinformatics analysis. PeerJ 8:e9123 https://doi.org/10.7717/peerj.9123
Herbicide applications increase greenhouse gas emissions of alfalfa pasture in the inland arid region of northwest China
Herbicides are used to control weeds in agricultural crops such as alfalfa (Medicago sativa L.), which is a forage crop. It is unclear what, if any, effect herbicides have on greenhouse gas (GHG) emissions when used on alfalfa. Our study was conducted in 2017 and 2018 to investigate the effects of two herbicides (Quizalofop-p-ethyl, QE and Bentazone, BT) on methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) emissions from soil planted with alfalfa. QE is used to control grasses and BT is used for broadleaf weed control. Soil CO2 emissions and soil uptake of CH4 increased significantly in both years following the QE and BT treatments, although CO2 emissions differed significantly between the trial years. N2O emissions decreased relative to the control and showed no significant differences between the trial years. The application of QE and BT on alfalfa resulted in a significant increase in CO2 emissions which contributed to a significant increase in GHG emissions. The application of QE influenced GHG emissions more than BT. We demonstrated the potential effect that herbicide applications have on GHG fluxes, which are important when considering the effect of agricultural practices on GHG emissions and the potential for global warming over the next 100 years.
Shi et al. (2020) Herbicide applications increase greenhouse gas emissions of alfalfa pasture in the inland arid region of northwest China. PeerJ 8:e9231 https://doi.org/10.7717/peerj.9231
Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods
Background Research has shown that Poly-ADP-ribose polymerases 1 (PARP-1) is a potential therapeutic target in the clinical treatment of breast cancer. An increasing number of studies have focused on the development of highly selective inhibitors that target PARP-1 over PARP-2, its closest isoform, to mitigate potential side effects. However, due to the highly conserved and similar binding sites of PARP-1 and PARP-2, there is a huge challenge for the discovery and design of PARP-1 inhibitors. Recently, it was reported that a potent PARP-1 inhibitor named NMS-P118 exhibited greater selectivity to PARP-1 over PARP-2 compared with a previously reported drug (Niraparib). However, the mechanisms underlying the effect of this inhibitor remains unclear. Methods In the present study, classical molecular dynamics (MD) simulations and accelerated molecular dynamics (aMD) simulations combined with structural and energetic analysis were used to investigate the structural dynamics and selective mechanisms of PARP-1 and PARP-2 that are bound to NMS-P118 and Niraparib with distinct selectivity. Results The results from classical MD simulations indicated that the selectivity of inhibitors may be controlled by electrostatic interactions, which were mainly due to the residues of Gln-322, Ser-328, Glu-335, and Tyr-455 in helix αF. The energetic differences were corroborated by the results from aMD simulations. Conclusion This study provides new insights about how inhibitors specifically bind to PARP-1 over PARP-2, which may help facilitate the design of highly selective PARP-1 inhibitors in the future.
Hu et al. (2020) Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods. PeerJ 8:e9241 https://doi.org/10.7717/peerj.9241
Agreement between the GAITRite® System and the Wearable Sensor BTS G-Walk® for measurement of gait parameters in healthy adults and Parkinson’s disease patients
Background Nowadays, the most widely used types of wearable sensors in gait analysis are inertial sensors. The aim of the study was to assess the agreement between two different systems for measuring gait parameters (inertial sensor vs. electronic walkway) on healthy control subjects (HC) and patients with Parkinson’s disease (PD). Methods Forty healthy volunteers (26 men, 14 women, mean age 58.7 ± 7.7 years) participated in the study and 24 PD patients (19 men, five women, mean age 62.7 ± 9.8 years). Each participant walked across an electronic walkway, GAITRite, with embedded pressure sensors at their preferred walking speed. Concurrently a G-Walk sensor was attached with a semi-elastic belt to the L5 spinal segment of the subject. Walking speed, cadence, stride duration, stride length, stance, swing, single support and double support phase values were compared between both systems. Results The Passing-Bablock regression slope line manifested the values closest to 1.00 for cadence and stride duration (0.99 ≤ 1.00) in both groups. The slope of other parameters varied between 0.26 (double support duration in PD) and 1.74 (duration of single support for HC). The mean square error confirmed the best fit of the regression line for speed, stride duration and stride length. The y-intercepts showed higher systematic error in PD than HC for speed, stance, swing, and single support phases. Conclusions The final results of this study indicate that the G-Walk system can be used for evaluating the gait characteristics of the healthy subjects as well as the PD patients. However, the duration of the gait cycle phases should be used with caution due to the presence of a systematic error.
Vítečková et al. (2020) Agreement between the GAITRite® System and the Wearable Sensor BTS G-Walk® for measurement of gait parameters in healthy adults and Parkinson’s disease patients. PeerJ 8:e8835 https://doi.org/10.7717/peerj.8835
Maternal trauma and fear history predict BDNF methylation and gene expression in newborns
Trauma and related fear exert significant influence on mental and physical health throughout the lifespan and are associated with intergenerational patterns of development, health, and behavior. DNA methylation and gene expression are involved in our developmental adaptations to our experiences and can be influenced by social interventions. Patterns of DNA methylation and expression of a gene involved in neurodevelopment and psychiatric risk (BDNF) have been linked with childhood trauma. Given the intergenerational patterns of health and behavior, and previous links between childhood trauma and BDNF methylation and expression, this study investigated the potential for maternal history of traumatic experiences to influence development in her newborn, via changes in her newborn’s BDNF methylation and expression. We found that mothers’ trauma history was associated with epigenetic regulation of BDNF in their newborns. Moreover, the association between maternal trauma and BDNF methylation and expression patterns were moderated by newborn sex. Male newborns showed increased BDNF expression with maternal exposure to child abuse (p = .001), and increased BDNF methylation with greater maternal fear (p = .001). Female newborns showed reduced BDNF expression with greater maternal fear (p = .004). Practitioners strive to identify prevention and intervention avenues that will reduce the harmful effects of trauma. Future research should consider the potential for maternal historical trauma experiences to influence offspring DNA methylation and gene expression in a manner that could alter development and inform novel prevention strategies.
Pilkay et al. (2020) Maternal trauma and fear history predict BDNF methylation and gene expression in newborns. PeerJ 8:e8858 https://doi.org/10.7717/peerj.8858
A new insect trackway from the Upper Jurassic—Lower Cretaceous eolian sandstones of São Paulo State, Brazil: implications for reconstructing desert paleoecology
The new ichnospecies Paleohelcura araraquarensis isp. nov. is described from the Upper Jurassic-Lower Cretaceous Botucatu Formation of Brazil. This formation records a gigantic eolian sand sea (erg), formed under an arid climate in the south-central part of Gondwana. This trackway is composed of two track rows, whose internal width is less than one-quarter of the external width, with alternating to staggered series, consisting of three elliptical tracks that can vary from slightly elongated to tapered or circular. The trackways were found in yellowish/reddish sandstone in a quarry in the Araraquara municipality, São Paulo State. Comparisons with neoichnological studies and morphological inferences indicate that the producer of Paleohelcura araraquarensis isp. nov. was most likely a pterygote insect, and so could have fulfilled one of the ecological roles that different species of this group are capable of performing in dune deserts. The producer could have had a herbivorous or carnivorous diet or been part of the fauna of omnivores, being able to adopt herbivorous, carnivorous, and saprophagous diets when necessary. In modern dune deserts, some species of pterygote insects are detritivores (like Tenebrionidae), relying on organic matter that accumulated among the sand grains of the dunes during dry periods with no plant growth. The presence of additional burrows suggests that the Botucatu paleodesert would have had a detritivorous fauna like this. Based on the interpretation of the ichnofossil producers, it was possible to reconstruct the food web of this paleodesert. All the omnivorous and herbivorous invertebrates and the herbivorous ornithopod dinosaurs made up the primary consumers. These animals were, in turn, the food source for bigger carnivorous or omnivorous animals unable to feed on detritus, like arachnids, possible predatory insects, mammaliaforms, and theropod dinosaurs. The highest trophic level was occupied by larger theropod dinosaurs and mammaliaforms, which, because of their size, could prey upon a wide range of animals. The producer of Paleohelcura araraquarensis isp. nov. could have been a primary consumer if it were an omnivorous detritivore or a herbivore, or a secondary consumer if it were produced by a predatory insect or an omnivore relying on animal biomass. The description of this new trackway expands the knowledge on the faunal composition of the Botucatu paleodesert and provides insights into the ecological relationships in ancient deserts. The presence of these arthropod trackways in Mesozoic eolian deposits helps to trace a continuity between Paleozoic and post-Paleozoic desert ichnofaunas, further reinforcing a single Octopodichnus—Entradichnus Ichnofacies for eolian deposits.
Peixoto et al. (2020) A new insect trackway from the Upper Jurassic—Lower Cretaceous eolian sandstones of São Paulo State, Brazil: implications for reconstructing desert paleoecology. PeerJ 8:e8880 https://doi.org/10.7717/peerj.8880
Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review
The animal’s blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular markers are in progress. The standard and modern biochemical tests are commonly used for general screening and, finally, complete diagnosis of animal health. Interpretation of major biochemical parameters is similar across animal species, but there are a few peculiarities in each case, especially well-known for cattle. The following directions are discussed here: hematological indicators; “total protein” and its fractions; some enzymes; major low-molecular metabolites (glucose, lipids, bilirubin, etc.); cations and anions. As example, the numerous correlations between DT data and biochemical parameters of cattle serum have been obtained and discussed. Changes in the cell-free nucleic acids (cfDNA) circulating in the blood have been studied and analyzed in a variety of conditions; for example, pregnancy, infectious and chronic diseases, and cancer. CfDNA can easily be detected using standard molecular biological techniques like DNA amplification and next-generation sequencing. The application of digital PCR even allows exact quantification of copy number variations which are for example important in prenatal diagnosis of chromosomal aberrations.
Zaitsev et al. (2020) Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review. PeerJ 8:e8997 https://doi.org/10.7717/peerj.8997
Plant-derived angiogenin fusion protein’s cytoprotective effect on trabecular meshwork damage induced by Benzalkonium chloride in mice
Background Benzalkonium chloride (BAK), commonly used in glaucoma treatment, is an eye drop preservative with dose-dependent toxicity. Previous studies have observed the multi-functional benefits of angiogenin (ANG) against glaucoma. In our study, we evaluated ANG’s cytoprotective effect on the trabecular meshwork (TM) damage induced by BAK. Additionally, we developed a plant-derived ANG fusion protein and evaluated its effect on TM structure and function. Methods We synthesized plant-derived ANG (ANG-FcK) by fuzing immunoglobulin G’s Fc region and KDEL to conventional recombinant human ANG (Rh-ANG) purified from transgenic tobacco plants. We established a mouse model using BAK to look for degenerative changes in the TM, and to evaluate the protective effects of ANG-FcK and Rh-ANG. Intraocular pressure (IOP) was measured for 4 weeks and ultrastructural changes, deposition of fluorescent microbeads, type I and IV collagen, fibronectin, laminin and α-SMA expression were analyzed after the mice were euthanized. Results TM structural and functional degeneration were induced by 0.1% BAK instillation in mice. ANG co-treatment preserved TM outflow function, which we measured using IOP and a microbead tracer. ANG prevented phenotypic and ultrastructure changes, and that protective effect might be related to the anti-fibrosis mechanism. We observed a similar cytoprotective effect in the BAK-induced degenerative TM mouse model, suggesting that plant-derived ANG-FcK could be a promising glaucoma treatment.
Jeong et al. (2020) Plant-derived angiogenin fusion protein’s cytoprotective effect on trabecular meshwork damage induced by Benzalkonium chloride in mice. PeerJ 8:e9084 https://doi.org/10.7717/peerj.9084
Oldest co-occurrence of Varanus and Python from Africa—first record of squamates from the early Miocene of Moghra Formation, Western Desert, Egypt
Lizard and snake remains from the early Miocene (Burdigalian) of the Moghra Formation, Egypt, are described herein. This material comprises the first fossil remains of squamates recovered from the otherwise rich and well known vertebrate assemblage of Moghra. The material pertains to two different genera, the varanid lizard Varanus and the pythonid snake Python and adds to the so far rather poorly known squamate fossil record from Africa. On the basis of the new remains, Moghra marks the oldest so far described co-occurrence of Varanus and Python in the African continent. The close sympatry of these two genera in the African fossil record is thoroughly analyzed and discussed, a co-existence, which is still widespread in the extant herpetofauna of the continent. Situated rather close to the so called “Levantine Corridor” and dated at the Burdigalian, practically when Afro-Arabia collided with Eurasia, the Moghra squamate assemblage offers the potential of important insights in the biogeography and dispersal events of vertebrate groups during the early Miocene.
Georgalis et al. (2020) Oldest co-occurrence of Varanus and Python from Africa—first record of squamates from the early Miocene of Moghra Formation, Western Desert, Egypt. PeerJ 8:e9092 https://doi.org/10.7717/peerj.9092
Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment
The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.
He et al. (2020) Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment. PeerJ 8:e9132 https://doi.org/10.7717/peerj.9132