PhosVarDeep: deep-learning based prediction of phospho-variants using sequence information
Human DNA sequencing has revealed numerous single nucleotide variants associated with complex diseases. Researchers have shown that these variants have potential effects on protein function, one of which is to disrupt protein phosphorylation. Based on conventional machine learning algorithms, several computational methods for predicting phospho-variants have been developed, but their performance still leaves considerable room for improvement. In recent years, deep learning has been successfully applied in biological sequence analysis with its efficient sequence pattern learning ability, which provides a powerful tool for improving phospho-variant prediction based on protein sequence information. In the study, we present PhosVarDeep, a novel unified deep-learning framework for phospho-variant prediction. PhosVarDeep takes reference and variant sequences as inputs and adopts a Siamese-like CNN architecture containing two identical subnetworks and a prediction module. In each subnetwork, general phosphorylation sequence features are extracted by a pre-trained sequence feature encoding network and then fed into a CNN module for capturing variant-aware phosphorylation sequence features. After that, a prediction module is introduced to integrate the outputs of the two subnetworks and generate the prediction results of phospho-variants. Comprehensive experimental results on phospho-variant data demonstrates that our method significantly improves the prediction performance of phospho-variants and compares favorably with existing conventional machine learning methods.
Liu et al. (2022) PhosVarDeep: deep-learning based prediction of phospho-variants using sequence information. PeerJ 10:e12847 https://doi.org/10.7717/peerj.12847
Textural quality, growth parameters and oxidative responses in Nile tilapia (Oreochromis niloticus) fed faba bean water extract diet
Texture is one of the key quality attributes used in the fresh and processed fish industry to assess product quality and consumer acceptability. To improve the textural quality of tilapia, we formulated the expanded pellet diet (EPD) and pellet diet (PD), both containing faba bean (Vicia faba, FB) water extract, a previously reported potential aquafeed additive to increase flesh texture. The common diet was used as a control. After Nile tilapia (Oreochromis niloticus) were fed three kinds of experimental diet for 120 days, muscle textural quality, growth parameters, oxidative response and immune parameters were analyzed. The results showed that there was no significant difference in the growth parameters between the three groups (P > 0.05). The highest measure of textural quality (hardness and chewiness) was found for the PD group, followed by the EPD and the control (P < 0.05). Less oxidative damage to the hepatopancreas and intestine was found in the EPD compared with the PD group, as demonstrated by the decreased levels of reactive oxygen species and increased levels of nicotinamide adenine dinucleotide and intestinal digestive enzyme activity (amylase and lipase). Taken together, this study highlights the potential usefulness in commercial settings of FB water extract for improving the textural quality of tilapia, and EPD containing faba bean water extract could be more advanced substitute for faba bean in tilapia culture in term of both effectiveness in textural quality improvement and health status enhancement compared with PD.
Li et al. (2022) Textural quality, growth parameters and oxidative responses in Nile tilapia (Oreochromis niloticus) fed faba bean water extract diet. PeerJ 10:e13048 https://doi.org/10.7717/peerj.13048
Full vaccination coverage and associated factors among children aged 12 to 23 months in remote rural area of Demba Gofa District, Southern Ethiopia
Background Full vaccination refers to the administration of vaccines/antigens recommended for children in the first year of life. However, little is known about full vaccination in remote, rural Ethiopia. This study aimed to measure full vaccination coverage and associated factors among children aged 12 to 23 months in Demba Gofa District, Southern Ethiopia. Methods A community-based cross-sectional study was conducted in April and May 2019 using a multistage sampling technique to select 677 mothers with children 12–23 months of age. Data was collected using a pre-tested structured questionnaire, and data were edited, coded, entered, and cleaned using Epi Info v3.1 and analyzed using SPSS v20. Bivariate and multivariable logistic regression was used to understand associations between dependent and independent variables. Results Three-hundred and nine children (47.0%) were fully vaccinated, 274 (41.7%) were partially vaccinated, and 74 (11.3%) were not vaccinated at all. Children were more likely to be vaccinated if decisions were made jointly with husbands (AOR = 1.88, 95% CI [1.06–3.34]), were made by mothers (AOR = 4.03, 95% CI [1.66–9.78]), followed postnatal care (AOR = 5.02, 95% CI [2.28–11.05]), if the child’s age for completing vaccination was known (AOR = 2.54, 95% CI [1.04–6.23]), and if vaccinations did not make the child sick (AOR = 0.32, 95% CI [0.16–0.64]). Conclusion Full vaccination coverage was less than average in the study district and far below the governmental target (90%) necessary for sustained control of vaccine-preventable diseases. Interventions targeted towards maternal healthcare decision-making, postnatal care, knowledge on vaccination timing, and importance should be prioritized to improve full vaccination coverage. A continuous supply of vaccination cards needs to be ensured to improve vaccination conditions.
Darebo et al. (2022) Full vaccination coverage and associated factors among children aged 12 to 23 months in remote rural area of Demba Gofa District, Southern Ethiopia. PeerJ 10:e13081 https://doi.org/10.7717/peerj.13081
3,4-dihydroxyphenylethyl alcohol glycoside reduces acetaminophen-induced acute liver failure in mice by inhibiting hepatocyte ferroptosis and pyroptosis
APAP is one of the most commonly used antipyretic and pain medications, but excessive use can cause liver toxicity and damage. 3,4-dihydroxyphenylethyl alcohol glycoside (DAG) is a component isolated from Sargentodoxa cuneata known to have anti-apoptotic, anti-oxidation and anti-inflammatory effects. However, the effects of DAG on acute liver failure (ALF) are largely unknown. The purpose of this study is to study the protective effects and mechanism of DAG on APAP-induced ALF in mice. We established an ALF model in adult male pathogen-free C57BL/6 mice treated with APAP (300 mg/kg) by intraperitoneal injection and resolved by 24 h. Hematoxylin and eosin (HE) staining was used to evaluate the pathological changes in mouse liver tissue. The infiltration of neutrophils in liver tissue and reactive oxygen species (ROS) in AML12 cells were analyzed by flow cytometry. The levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), glutathione (GSH), malondialdehyde (MDA), catalase (CAT), and superoxide dismutase (SOD) were analyzed using relevant kits. Our results show that DAG reduced APAP-induced serum ALT and AST levels, histopathological changes, liver neutrophil infiltration and proinflammatory cytokines production, also attenuated the accumulation of MDA and the exhaustion of GSH, CAT and SOD. In vitro experiment indicated that DAG dose-dependently inhibited APAP-induced the levels of pro-inflammatory factors (IL-1β and IL18), and reactive oxygen species (ROS) and preventing GSH depletion in mouse AML12 hepatocytes. More interestingly, DAG inhibited the expression of ERK, HO-1, NLRP3, Caspase1 (p20) and Gasdermin-D and upregulated the expression of GPX4 in liver tissues and AML12hepatocytes. Therefore, our results indicate that DAG may act as a potential agent to treat ALF induced by APAP by inhibiting hepatocyte ferroptosis and pyroptosis.
Liu et al. (2022) 3,4-dihydroxyphenylethyl alcohol glycoside reduces acetaminophen-induced acute liver failure in mice by inhibiting hepatocyte ferroptosis and pyroptosis. PeerJ 10:e13082 https://doi.org/10.7717/peerj.13082
The application of sudoscan for screening microvascular complications in patients with type 2 diabetes
The aim of the study was to evaluate the performance of sudoscan in screening diabetic microvascular complications in patients with type 2 diabete mellitus (T2DM). 515 patients with T2DM aged from 23 to 89 years were included for analysis in our study. The mean age was 60.00 ± 11.37 years and the mean duration of T2DM was 8.44 ± 7.56 years. Electrochemical skin conductance (ESC) in hands and feet was evaluated by SUDOCAN. Diabetic peripheral neuropathy (DPN) was diagnosed in 378 patients (44.3%), diabetic kidney disease (DKD) in 161 patients (31.26%), diabetic retinopathy (DR) in 148 patients (28.74%). Hands and feet ESC was significantly and independently associated with the presence of DPN, DKD and DR. Patients with a lower ESC (<60 µS) had 5.63-fold increased likelihood of having DPN, 4.90-fold increased likelihood of having DKD, 1.01-fold increased likelihood of having DR, than those with a higher ESC. Age, duration of T2DM, smoking, renal function and vibration perception thresholds were negatively correlated with ESC. Sudoscan parameters were correlated with diabetic microvascular complications, especially with DPN. Sudoscan could be an effective screening tool in primary health care for early screening microvascular complications.
Lin et al. (2022) The application of sudoscan for screening microvascular complications in patients with type 2 diabetes. PeerJ 10:e13089 https://doi.org/10.7717/peerj.13089
Integration of the metabolome and transcriptome reveals indigo biosynthesis in Phaius flavus flowers under freezing treatment
Background Indigo-containing plant tissues change blue after a freezing treatment, which is accompanied by changes in indigo and its related compounds. Phaius flavus is one of the few monocot plants containing indigo. The change to blue after freezing was described to explore the biosynthesis of indigo in P. flavus. Methods In this study, we surveyed the dynamic change of P. flavus flower metabolomics and transcriptomics. Results The non-targeted metabolomics and targeted metabolomics results revealed a total of 98 different metabolites, the contents of indole, indican, indigo, and indirubin were significantly different after the change to blue from the freezing treatment. A transcriptome analysis screened ten different genes related to indigo upstream biosynthesis, including three anthranilate synthase genes, two phosphoribosyl-anthranilate isomerase genes, one indole-3-glycerolphosphate synthase gene, five tryptophan synthase genes. In addition, we further candidate 37 cytochrome P450 enzyme genes, one uridine diphosphate glucosyltransferase gene, and 24 β-D-glucosidase genes were screened that may have participated in the downstream biosynthesis of indigo. This study explained the changes of indigo-related compounds at the metabolic level and gene expression level during the process of P. flavus under freezing and provided new insights for increasing the production of indigo-related compounds in P. flavus. In addition, transcriptome sequencing provides the basis for functional verification of the indigo biosynthesis key genes in P. flavus.
Zhang et al. (2022) Integration of the metabolome and transcriptome reveals indigo biosynthesis in Phaius flavus flowers under freezing treatment. PeerJ 10:e13106 https://doi.org/10.7717/peerj.13106
A review of the opportunities to support pollinator populations in South African cities
Globally insects are declining, but some guilds of pollinators are finding refuge in urban landscapes. The body of knowledge on urban pollinators is relatively mature, which means it is now possible to begin to make generalization. Unfortunately, studies do not represent climatic regions evenly and there is a gap in research from the African continent. This study aimed to address some of the gaps on urban pollination knowledge in South Africa and to identify opportunities to improve urban habitats for pollinators. We reviewed the international literature on urban pollinators and the South African literature on pollinators with a landscape ecology focus, drawing on literature with an emphasis on agricultural and ecosystem services. The findings show that some taxa (e.g. large-bodied, cavity nesting bees) will exploit urban environments increasing in abundance with urban intensity. Moderately sensitive taxa (such as small-bodied, ground-nesting bees) take advantage of urban environments only if local habitats are supportive of their needs for resource provision and habitat connectivity. The South African urban poor rely on pollination services for subsistence agriculture and the reproduction of wild-foraged medicines and food. Potential interventions to improve habitat quality include strategic mowing practices, conversion of turf-grass to floral rich habitats, scientific confirmation of lists of highly attractive flowers, and inclusion of small-scale flower patches throughout the urban matrix. Further research is needed to fill the Africa gap for both specialized and generalized pollinators (Diptera, Halictids, Lepidoptera and Hopliini) in urban areas where ornamental and indigenous flowering plants are valued.
Brom et al. (2022) A review of the opportunities to support pollinator populations in South African cities. PeerJ 10:e12788 https://doi.org/10.7717/peerj.12788
Evolution analysis of FRIZZY PANICLE (FZP) orthologs explored the mutations in DNA coding sequences in the grass family (Poaceae)
FRIZZY PANICLE (FZP), an essential gene that controls spikelet differentiation and development in the grass family (Poaceae), prevents the formation of axillary bud meristems and is closely associated with crop yields. It is unclear whether the FZP gene or its orthologs were selected during the evolutionary process of grass species, which possess diverse spike morphologies. In the present study, we adopted bioinformatics methods for the evolutionary analysis of FZP orthologs in species of the grass family. Thirty-five orthologs with protein sequences identical to that of the FZP gene were identified from 29 grass species. Analysis of conserved domains revealed that the AP2/ERF domains were highly conserved with almost no amino acid mutations. However, species of the tribe Triticeae, genus Oryza, and C4 plants exhibited more significant amino acid mutations in the acidic C-terminus region. Results of the phylogenetic analysis showed that the 29 grass species could be classified into three groups, namely, Triticeae, Oryza, and C4 plants. Within the Triticeae group, the FZP genes originating from the same genome were classified into the same sub-group. When selection pressure analysis was performed, significant positive selection sites were detected in species of the Triticeae and Oryza groups. Our results show that the FZP gene was selected during the grass family’s evolutionary process, and functional divergence may have already occurred among the various species. Therefore, researchers investigating the FZP gene’s functions should take note of the possible presence of various roles in other grass species.
Li et al. (2022) Evolution analysis of FRIZZY PANICLE (FZP) orthologs explored the mutations in DNA coding sequences in the grass family (Poaceae). PeerJ 10:e12880 https://doi.org/10.7717/peerj.12880
Antimicrobial resistance and virulence profiles of Enterobacterales isolated from two-finger and three-finger sloths (Choloepus hoffmanni and Bradypus variegatus) of Costa Rica
Background Wildlife has been recently recognized as an environmental reservoir for antimicrobial resistance (AMR). However, less information on this topic is available in animals released back into the wild after rehabilitation in wildlife facilities, compared with studies performed exclusively in captive or free-ranging wildlife. This study aimed to evaluate the potential influence of captivity and/or treatment while in captivity of wild sloths on the AMR and virulence profiles of sloths’ Enterobacterales. Methods Oral and rectal swab samples were collected from 39 two-finger (Choloepus hoffmanni) and three-finger sloths (Bradypus variegatus) of Costa Rica (n = 78) and analyzed using conventional bacteriological techniques. A generalized linear mixed model was applied to estimate the isolates’ multiple antimicrobial resistance and virulence indices as a function of animal status. Results A considerable level of resistance was detected, especially for Citrobacter youngae and Escherichia coli, with 17.5% of isolates classified as multidrug-resistant. Virulence indices of isolates from rehabilitated sloths were significantly higher than the ones from sloths being hand-reared for shorter periods. Conclusions To our knowledge, this is the first description of sloths’ antimicrobial resistant Enterobacterales, suggesting that sloths’ rehabilitation and consequent exposure to humans, may promote the selection of bacteria with higher virulence. Ultimately, these bacteria may represent a threat to human and animal health due to their zoonotic potential and AMR and virulence profiles.
Fernandes et al. (2022) Antimicrobial resistance and virulence profiles of Enterobacterales isolated from two-finger and three-finger sloths (Choloepus hoffmanni and Bradypus variegatus) of Costa Rica. PeerJ 10:e12911 https://doi.org/10.7717/peerj.12911
The evolution of reproductive strategies in turtles
Optimal egg size theory assumes that changes in the egg and clutch are driven by selection, resulting in adjustments for the largest possible production of offspring with the highest fitness. Evidence supports the idea that large-bodied turtles tend to produce larger clutches with small and round eggs, while smaller species produce small clutches with large and elongated eggs. Our goals were to investigate whether egg and clutch size follow the predictions of egg size theory, if there are convergent reproductive strategies, and identify ecological factors that influence clutch and egg traits across all clades of living turtles. Using phylogenetic methods, we tested the covariance among reproductive traits, if they are convergent among different turtle lineages, and which ecological factors influence these traits. We found that both egg shape and size inversely correlate with clutch size, although with different evolutionary rates, following the predictions of the egg size theory. We also present compelling evidence for convergence among different turtle clades, over at least two reproductive strategies. Furthermore, climatic zone is the only ecological predictor to influence both egg size and fecundity, while diet only influences egg size. We conclude that egg and clutch traits in Testudines evolved independently several times across non-directly related clades that converged to similar reproductive strategies. Egg and clutch characteristics follow the trade-offs predicted by egg size theory and are influenced by ecological factors. Climatic zone and diet play an important role in the distribution of reproductive characteristics among turtles.
Jorgewich-Cohen et al. (2022) The evolution of reproductive strategies in turtles. PeerJ 10:e13014 https://doi.org/10.7717/peerj.13014