iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC
Sumoylation is the post-translational modification that is involved in the adaption of the cells and the functional properties of a large number of proteins. Sumoylation has key importance in subcellular concentration, transcriptional synchronization, chromatin remodeling, response to stress, and regulation of mitosis. Sumoylation is associated with developmental defects in many human diseases such as cancer, Huntington’s, Alzheimer’s, Parkinson’s, Spin cerebellar ataxia 1, and amyotrophic lateral sclerosis. The covalent bonding of Sumoylation is essential to inheriting part of the operative characteristics of some other proteins. For that reason, the prediction of the Sumoylation site has significance in the scientific community. A novel and efficient technique is proposed to predict the Sumoylation sites in proteins by incorporating Chou’s Pseudo Amino Acid Composition (PseAAC) with statistical moments-based features. The outcomes from the proposed system using 10 fold cross-validation testing are 94.51%, 94.24%, 94.79% and 0.8903% accuracy, sensitivity, specificity and MCC, respectively. The performance of the proposed system is so far the best in comparison to the other state-of-the-art methods. The codes for the current study are available on the GitHub repository using the link: https://github.com/csbioinfopk/iSumoK-PseAAC.
Khan et al. (2021) iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC. PeerJ 9:e11581 https://doi.org/10.7717/peerj.11581
Effects of delivery via pressure-adjustable pneumatic gas-powered dart gun of three antimicrobial drugs (ceftiofur crystalline free acid, tildopirosin, and tulathromycin) on drug disposition and meat quality in cattle
Background Although Beef Quality Assurance guidelines do not recommend use of darting methods to deliver drugs, cattle in the US may be raised on farms and ranches without restraint facilities, and reports from the field suggest that dart guns are being used to deliver antimicrobial drugs. Few studies report whether this route of administration results in altered drug disposition or carcass quality. Methods Forty steers were blocked by sire and then randomly assigned to treatment with saline, ceftiofur crystalline free acid, tildipirosin, or tulathromycin delivered via dart gun. To assess drug disposition, eight ceftiofur, six tulathromycin, and six tildipirosin-treated calves were selected to measure plasma concentrations of drugs up to 10 days after drug administration. Steers were then fed a balanced ration for approximately 6.5 months and slaughtered. To evaluate carcass quality, tenderness of steaks from darted-side and non-darted sides was evaluated via Warner–Bratzler shear force testing. Due to the prohibition of extralabel routes of administration for ceftiofur in the U.S., animals treated with this drug did not enter the food supply. Results Ceftiofur disposition differed from published reports with lower mean Cmax but similar mean apparent elimination half-life. Tildipirosin disposition differed from published reports with lower Cmax and shorter apparent elimination half-life. Tulathromycin was similar to previous published reports but Cmax and apparent elimination half-life was highly variable. All steaks (from darted and non-darted sides) from cattle treated with ceftiofur and saline were more tender than from cattle treated with tulathromycin or tildipirosin (P = 0.003). There was a trend toward more tenderness in steaks from the non-darted compared to the darted side. Steaks from the darted side for one treatment, tildipirosin, were less tender than the non-darted side. Conclusions Pharmacokinetic parameters of ceftiofur crystalline free acid, tildipirosin, and tulathromycin to cattle using pressure-adjustable pneumatic gas-powered dart gun were estimated in this study. Delivery of tildipirosin and tulathromycin to cattle with dart gun may also result in detectable decreases in tenderness of harvested steaks.
Hairgrove et al. (2021) Effects of delivery via pressure-adjustable pneumatic gas-powered dart gun of three antimicrobial drugs (ceftiofur crystalline free acid, tildopirosin, and tulathromycin) on drug disposition and meat quality in cattle. PeerJ 9:e11822 https://doi.org/10.7717/peerj.11822
Optimization of change in epicardial fat thickness for obese patients who lost weight via the bariatric surgery method using central composite and Box-Behnken experimental designs
Background The aim of this study was to detect the optimal values for Age, Body Mass Index (BMI) and HOMA-IR of obese patients prior to surgery that results in a maximal decrease of visceral fat mass 6 months after bariatric surgery. Method In this study, 33 experimental set-ups were designed. This study was approved by Baskent University Medical and Health Sciences Research Board (Approval number: KA16/281). The study data consisted of 40 obese patients who lost weight through the bariatric surgery between February 2015 and December 2016. The values of BMI, Age and HOMA for the obese patients who lost weight through the bariatric surgery were evaluated in three categories and at three levels; the response variable was determined as the Change in Epicardial Fat Thickness (ΔEFT). Results As a result of CCD analysis, the optimum ΔEFT = 2.571 was determined when Age = 30.52, BMI = 45.30, and HOMA = 34.62. As a result of the BBD analysis, the optimum ΔEFT = 3.756 was determined, when Age = 38.36, BMI = 63.18, and HOMA = 14.95. The optimum ΔEFT was modeled with Contour and Response Surface plots. Conclusion Based on the two surface response models used in our study, the maximal decrease of visceral fat mass as assessed by measuring echography images of epicardial fat thickness can be obtained by bariatric surgery of persons who are between 31 and 38 year old, have a BMI between 45 and 63 kg/m2 and have a HOMA-IR 34 between 15 and 35. Central Composite Design and a Box-Behnken Design of suitable patient data predicted 35 optimal settings of independent variables for the maximal clinical response of an intervention.
Elmalı et al. (2021) Optimization of change in epicardial fat thickness for obese patients who lost weight via the bariatric surgery method using central composite and Box-Behnken experimental designs. PeerJ 9:e11831 https://doi.org/10.7717/peerj.11831
Genetic diversity and structure of the noble crayfish populations in the Balkan Peninsula revealed by mitochondrial and microsatellite DNA markers
Background The noble crayfish (Astacus astacus) is a native European species in decline, with a contracting range and diminishing populations and abundance. Previous studies revealed this species significant genetic diversity in the south-eastern Europe, with populations from the western and the southern part of the Balkan Peninsula being the most divergent. However, sampling of populations from the western part of the Balkans was limited and insufficient for investigating genetic diversity and population divergence for the purpose of conservation planning and management. Thus, the major aim of this study was to fill in this knowledge gap by studying mitochondrial and microsatellite DNA diversity, using 413 noble crayfish from 18 populations from waterbodies in the western part of the Balkan Peninsula. Methods Phylogenetic analysis of studied populations and their mitochondrial diversity were studied using COI and 16S sequences and population genetic structure was described using 15 microsatellite loci. Results Phylogeographic analysis revealed new divergent mitochondrial haplotypes for the populations in the westernmost part of the Balkan Peninsula in the tributaries of the Sava and Drava rivers. Microsatellite data indicated that these populations harbour an important component of genetic diversity within A. astacus. The results suggest that the western part of the Balkans played an important role as microrefugia during the Pleistocene climate fluctuations, allowing the long term persistence of A. astacus populations in this region. These results will also be important to supporting conservation decision making and planning.
Gross et al. (2021) Genetic diversity and structure of the noble crayfish populations in the Balkan Peninsula revealed by mitochondrial and microsatellite DNA markers. PeerJ 9:e11838 https://doi.org/10.7717/peerj.11838
Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach
Background Glucosinolates (GSLs) are plant secondary metabolites that contain nitrogen-containing compounds. They are important in the plant defense system and known to provide protection against cancer in humans. Currently, increasing the amount of data generated from various omics technologies serves as a hotspot for new gene discovery. However, sometimes sequence similarity searching approach is not sufficiently effective to find these genes; hence, we adapted a network clustering approach to search for potential GSLs genes from the Arabidopsis thaliana co-expression dataset. Methods We used known GSL genes to construct a comprehensive GSL co-expression network. This network was analyzed with the DPClusOST algorithm using a density of 0.5. 0.6. 0.7, 0.8, and 0.9. Generating clusters were evaluated using Fisher’s exact test to identify GSL gene co-expression clusters. A significance score (SScore) was calculated for each gene based on the generated p-value of Fisher’s exact test. SScore was used to perform a receiver operating characteristic (ROC) study to classify possible GSL genes using the ROCR package. ROCR was used in determining the AUC that measured the suitable density value of the cluster for further analysis. Finally, pathway enrichment analysis was conducted using ClueGO to identify significant pathways associated with the GSL clusters. Results The density value of 0.8 showed the highest area under the curve (AUC) leading to the selection of thirteen potential GSL genes from the top six significant clusters that include IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1, and At3g14220. A total of Four potential genes (MTO1, SIR, SAL1, and IMDH3) were identified from the pathway enrichment analysis on the significant clusters. These genes are directly related to GSL-associated pathways such as sulfur metabolism and valine, leucine, and isoleucine biosynthesis. This approach demonstrates the ability of the network clustering approach in identifying potential GSL genes which cannot be found from the standard similarity search.
Harun et al. (2021) Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach. PeerJ 9:e11876 https://doi.org/10.7717/peerj.11876
Towards an open and synergistic framework for mapping global land cover
Global land-cover datasets are key sources of information for understanding the complex inter-actions between human activities and global change. They are also among the most critical variables for climate change studies. Over time, the spatial resolution of land cover maps has increased from the kilometer scale to 10-m scale. Single-type historical land cover datasets, including for forests, water, and impervious surfaces, have also been developed in recent years. In this study, we present an open and synergy framework to produce a global land cover dataset that combines supervised land cover classification and aggregation of existing multiple thematic land cover maps with the Google Earth Engine (GEE) cloud computing platform. On the basis of this method of classification and mosaicking, we derived a global land cover dataset for 6 years over a time span of 25 years. The overall accuracies of the six maps were around 75% and the accuracy for change area detection was over 70%. Our product also showed good similarity with the FAO and existing land cover maps.
Spatial and Geographic Information Science
Zhao et al. (2021) Towards an open and synergistic framework for mapping global land cover. PeerJ 9:e11877 https://doi.org/10.7717/peerj.11877
Wheat litter and feed with aluminosilicates for improved growth and meat quality in broiler chickens
Background Natural minerals have many beneficial properties in poultry production, taking into account production as well as hygiene, health, safety, and quality of broiler meat. The aim of the study was to evaluate the effect of aluminosilicates in feed and litter on the growth performance and meat quality in chickens. Aluminosilicates, including halloysite and zeolite, could be a good alternative for synthetics, as a good solution for the environment in line with the current trends. Methods Five-hundred male Ross 308 chickens were managed in 5 groups (10 replicates/group): LITTER: 1, control; 2, 0.95 kg/m2 of halloysite; 3, 0.475 kg/m2 of halloysite and 0.475 zeolite; 4, 0.95 kg/m2 of zeolite; 5, 0.25 kg/m2of halloysite and 0.7 kg/m2 of zeolite. FEED: groups 2–5, halloysite and zeolite addition (25:75 ratio; 0.5–2%). Growth performance (body weight and feed indicators), carcass, and meat quality (pH, colour, water-holding capacity, chemical composition of muscles) were recorded. The experimental setup, where the aluminosilicate additives were applied simultaneously, was proposed and approved by experts after pilot testing and on the basis of extensive literature where feed or litter additives were tested. Results Body weight and its gain were higher in groups 3 and 4 than in 1, and feed intake was higher in 4. The weight of the carcass and some of its components, including muscles and skin with subcutaneous fat, were higher in 2–4. Water loss from leg muscles was lower in 4. The content of protein in muscles was significantly higher in 3. The addition of aluminosilicates in feed and litter had a positive effect on the growth performance and some traits of carcasses and meat quality, especially in group 3. Halloysite and zeolite can be used in feed and litter (especially 0.475 kg/m2 for each mineral in the wheat litter).
Banaszak et al. (2021) Wheat litter and feed with aluminosilicates for improved growth and meat quality in broiler chickens. PeerJ 9:e11918 https://doi.org/10.7717/peerj.11918
The effect of uncorrected ametropia on ocular torsion induced by changes in fixation
Background and Objective Ocular torsion, the eye movements to rotating around the line of sight, has not been well investigated regarding the influence of refractive errors. The purpose of this study was to investigate the effect of uncorrected ametropia on ocular torsion induced by fixation distances. Methods Seventy-two subjects were classified according to the type of their refractive error, and ocular torsion of the uncorrected eye was compared based on changes induced by different fixation distances. Ocular torsion was measured using a slit-lamp biomicroscope equipped with an ophthalmic camera and a half-silvered mirror. Results In all groups, excyclotorsion values increased as the fixation distance decreased, but the myopia and astigmatism groups had larger amounts of ocular torsion than the emmetropia group. In addition, as the amount of uncorrected myopia and astigmatism increased, the amount of ocular torsion increased. Conclusion Since the amount of ocular torsion caused by a change to a shorter fixation distance was larger when the refractive error was uncorrected, we suggest that ametropia should be fully corrected in patients frequently exposed to ocular torsion due to changes in fixation distance.
Oh et al. (2021) The effect of uncorrected ametropia on ocular torsion induced by changes in fixation. PeerJ 9:e11932 https://doi.org/10.7717/peerj.11932
Transtibial limb loss does not increase metabolic cost in three-dimensional computer simulations of human walking
Loss of a lower limb below the knee, i.e., transtibial limb loss, and subsequently walking with a prosthesis, is generally thought to increase the metabolic cost of walking vs. able-bodied controls. However, high-functioning individuals with limb loss such as military service members often walk with the same metabolic cost as controls. Here we used a 3-D computer model and optimal control simulation approach to test the hypothesis that transtibial limb loss in and of itself causes an increase in metabolic cost of walking. We first generated N = 36 simulations of walking at 1.45 m/s using a “pre-limb loss” model, with two intact biological legs, that minimized deviations from able-bodied experimental walking mechanics with minimum muscular effort. We then repeated these simulations using a “post-limb loss” model, with the right leg’s ankle muscles and joints replaced with a simple model of a passive transtibial prosthesis. No other changes were made to the post-limb loss model’s remaining muscles or musculoskeletal parameters compared to the pre-limb loss case. Post-limb loss, the gait deviations on average increased by only 0.17 standard deviations from the experimental means, and metabolic cost did not increase (3.58 ± 0.10 J/m/kg pre-limb loss vs. 3.59 ± 0.12 J/m/kg post-limb loss, p = 0.65). The results suggest that transtibial limb loss does not directly lead to an increase in metabolic cost, even when deviations from able-bodied gait mechanics are minimized. High metabolic costs observed in individuals with transtibial limb loss may be due to secondary changes in strength or general fitness after limb loss, modifiable prosthesis issues, or to prioritization of factors that affect locomotor control other than gait deviations and muscular effort.
Miller et al. (2021) Transtibial limb loss does not increase metabolic cost in three-dimensional computer simulations of human walking. PeerJ 9:e11960 https://doi.org/10.7717/peerj.11960
Identification of key genes and crucial pathways for major depressive disorder using peripheral blood samples and chronic unpredictable mild stress rat models
Background Accurate diagnosis of major depressive disorder (MDD) remains difficult, and one of the key challenges in diagnosing MDD is the lack of reliable diagnostic biomarkers. The objective of this study was to explore gene networks and identify potential biomarkers for MDD. Methods In the present study, we performed a comprehensive analysis of the mRNA expression profiles using blood samples of four patients with MDD and four controls by RNA sequencing. Differentially expressed genes (DEGs) were screened, and functional and pathway enrichment analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. All DEGs were inputted to the STRING database to build a PPI network, and the top 10 hub genes were screened using the cytoHubba plugin of the Cytoscape software. The relative expression of 10 key genes was identified by quantitative real-time polymerase chain reaction (qRT-PCR) of blood samples from 50 MDD patients and 50 controls. Plasma levels of SQSTM1 and TNFα were measured using an enzyme-linked immunosorbent assay in blood samples of 44 MDD patients and 44 controls. A sucrose preference test was used to evaluate depression-like behavior in chronic unpredictable mild stress (CUMS) model rats. Immunofluorescence assay and western blotting were performed to study the expression of proteins in the brain samples of CUMS model rats Results We identified 247 DEGs that were closely associated with MDD. Gene ontology analyses suggested that the DEGs were mainly enriched in negative regulation of transcription by RNA polymerase II promoter, cytoplasm, and protein binding. Moreover, Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that the DEGs were significantly enriched in the MAPK signaling pathway. Ten hub genes were screened through the PPI network, and qRT-PCR assay revealed that one and six genes were downregulated and upregulated, respectively; however, SMARCA2, PPP3CB, and RAB5C were not detected. Pathway enrichment analysis for the 10 genes showed that the mTOR signaling pathway was also enriched. A strong positive correlation was observed between SQSTM1 and TNFα protein levels in patients with MDD. LC3 II and SQSTM1 protein levels were increased in the CUMS rat model; however, p-mTOR protein levels were decreased. The sucrose preference values decreased in the CUMS rat model. Conclusions We identified 247 DEGs and constructed an MDD-specific network; thereafter, 10 hub genes were selected for further analysis. Our results provide novel insights into the pathogenesis of MDD. Moreover, SQSTM1, which is related to autophagy and inflammatory reactions, may play a key role in MDD. SQSTM1 may be used as a promising therapeutic target in MDD; additionally, more molecular mechanisms have been suggested that should be focused on in future in vivo and in vitro studies.
He et al. (2021) Identification of key genes and crucial pathways for major depressive disorder using peripheral blood samples and chronic unpredictable mild stress rat models. PeerJ 9:e11694 https://doi.org/10.7717/peerj.11694