title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=742 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean link: https://peerj.com/articles/13118 last-modified: 2022-03-18 description: BackgroundSoybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes.MethodsThree soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of −1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed.ResultsWater deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water deficit, greater efficiency was observed in the L13241 genotype through adjustments in morphological, physiological, genetic and metabolic characteristics that are combined in the same plant. This study contributes to the advancement in the knowledge about the resistance to drought in cultivated plants and provides bases for the genetic improvement of the soybean culture. creator: Adinan Alves da Silva creator: Cíntia Oliveira Silva creator: Vanessa do Rosario Rosa creator: Michel Filiphy Silva Santos creator: Kacilda Naomi Kuki creator: Maximiller Dal-Bianco creator: Rafael Delmond Bueno creator: Juraci Alves de Oliveira creator: Danielle Santos Brito creator: Alan Carlos Costa creator: Cleberson Ribeiro uri: https://doi.org/10.7717/peerj.13118 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Alves da Silva et al. title: High-performance pipeline for MutMap and QTL-seq link: https://peerj.com/articles/13170 last-modified: 2022-03-18 description: SummaryBulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5–8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies.AvailabilityThe new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq). creator: Yu Sugihara creator: Lester Young creator: Hiroki Yaegashi creator: Satoshi Natsume creator: Daniel J. Shea creator: Hiroki Takagi creator: Helen Booker creator: Hideki Innan creator: Ryohei Terauchi creator: Akira Abe uri: https://doi.org/10.7717/peerj.13170 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sugihara et al. title: Sensitivity of soil hydrogen uptake to natural and managed moisture dynamics in a semiarid urban ecosystem link: https://peerj.com/articles/12966 last-modified: 2022-03-17 description: The North American Monsoon season (June–September) in the Sonoran Desert brings thunderstorms and heavy rainfall. These rains bring cooler temperature and account for roughly half of the annual precipitation making them important for biogeochemical processes. The intensity of the monsoon rains also increase flooding in urban areas and rely on green infrastructure (GI) stormwater management techniques such as water harvesting and urban rain gardens to capture runoff. The combination of increased water availability during the monsoon and water management provide a broad moisture regime for testing responses in microbial metabolism to natural and managed soil moisture pulses in drylands. Soil microbes rely on atmospheric hydrogen (H2) as an important energy source in arid and semiarid landscapes with low soil moisture and carbon availability. Unlike mesic ecosystems, transient water availability in arid and semiarid ecosystems has been identified as a key limiting driver of microbe-mediated H2 uptake. We measured soil H2 uptake in rain gardens exposed to three commonly used water harvesting practices during the monsoon season in Tucson AZ, USA. In situ static chamber measurements were used to calculate H2 uptake in each of the three water harvesting treatments passive (stormwater runoff), active (stored rooftop runoff), and greywater (used laundry water) compared to an unaltered control treatment to assess the effects of water management practices on soil microbial activity. In addition, soils were collected from each treatment and brought to the lab for an incubation experiment manipulating the soil moisture to three levels capturing the range observed from field samples. H2 fluxes from all treatments ranged between −0.72 nmol m−2 s−1 and −3.98 nmol m−2 s−1 over the monsoon season. Soil H2 uptake in the greywater treatment was on average 53% greater than the other treatments during pre-monsoon, suggesting that the increased frequency and availability of water in the greywater treatment resulted in higher H2 uptake during the dry season. H2 uptake was significantly correlated with soil moisture (r = −0.393, p = 0.001, df = 62) and temperature (r = 0.345, p = 0.005, df = 62). Our findings suggest that GI managed residential soils can maintain low levels of H2 uptake during dry periods, unlike unmanaged systems. The more continuous H2 uptake associated with GI may help reduce the impacts of drought on H2 cycling in semiarid urban ecosystems. creator: Vanessa Buzzard creator: Dana Thorne creator: Juliana Gil-Loaiza creator: Alejandro Cueva creator: Laura K. Meredith uri: https://doi.org/10.7717/peerj.12966 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Buzzard et al. title: A comparative study of the capability of MSCs isolated from different human tissue sources to differentiate into neuronal stem cells and dopaminergic-like cells link: https://peerj.com/articles/13003 last-modified: 2022-03-17 description: BackgroundNeurodegenerative diseases are characterized by progressive neuronal loss and degeneration. The regeneration of neurons is minimal and neurogenesis is limited only to specific parts of the brain. Several clinical trials have been conducted using Mesenchymal Stem Cells (MSCs) from different sources to establish their safety and efficacy for the treatment of several neurological disorders such as Parkinson’s disease, multiple sclerosis and amyotrophic lateral sclerosis.AimThe aim of this study was to provide a comparative view of the capabilities of MSCs, isolated from different human tissue sources to differentiate into neuronal stem cell-like cells (NSCs) and possibly into dopaminergic neural- like cells.MethodsMesenchymal stem cells were isolated from human bone marrow, adipose, and Wharton’s jelly (WJ) tissue samples. Cells were characterized by flow cytometry for their ability to express the most common MSC markers. The differentiation potential was also assessed by differentiating them into osteogenic and adipogenic cell lineages. To evaluate the capacity of these cells to differentiate towards the neural stem cell-like lineage, cells were cultured in media containing small molecules. Cells were utilized for gene expression and immunofluorescence analysis at different time points.ResultsOur results indicate that we have successfully isolated MSCs from bone marrow, adipose tissue, and Wharton’s jelly. WJ-MSCs showed a slightly higher proliferation rate after 72 hours compared to BM and AT derived MSCs. Gene expression of early neural stem cell markers revealed that WJ-MSCs had higher expression of Nestin and PAX6 compared to BM and AT-MSCs, in addition to LMX expression as an early dopaminergic neural marker. Immunofluorescence analysis also revealed that these cells successfully expressed SOX1, SOX2, Nestin, TUJ1, FOXA2 and TH.ConclusionThese results indicate that the protocol utilized has successfully differentiated BM, AT and WJ-MSCs into NSC-like cells. WJ-MSCs possess a higher potential to transdifferentiate into NSC and dopaminergic-like cells. Thus, it might indicate that this protocol can be used to induce MSC into neuronal lineage, which provides an additional or alternative source of cells to be used in the neurological cell-based therapies. creator: Nidaa A. Ababneh creator: Ban Al-Kurdi creator: Fatima Jamali creator: Abdalla Awidi uri: https://doi.org/10.7717/peerj.13003 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ababneh et al. title: An ODE model of yaws elimination in Lihir Island, Papua New Guinea link: https://peerj.com/articles/13018 last-modified: 2022-03-17 description: Yaws is a chronic infection that affects mainly the skin, bone and cartilage and spreads mostly between children. The new approval of a medication as treatment in 2012 has revived eradication efforts and now only few known localized foci of infection remain. The World Health Organization strategy mandates an initial round of total community treatment (TCT) with single-dose azithromycin followed either by further TCT or by total targeted treatment (TTT), an active case-finding and treatment of cases and their contacts. We develop the compartmental ODE model of yaws transmission and treatment for these scenarios. We solve for disease-free and endemic equilibria and also perform the stability analysis. We calibrate the model and validate its predictions on the data from Lihir Island in Papua New Guinea. We demonstrate that TTT strategy is efficient in preventing outbreaks but, due to the presence of asymptomatic latent cases, TTT will not eliminate yaws within a reasonable time frame. To achieve the 2030 eradication target, TCT should be applied instead. creator: Presley Kimball creator: Jacob Levenson creator: Amy Moore creator: Jan Rychtar creator: Dewey Taylor uri: https://doi.org/10.7717/peerj.13018 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kimball et al. title: International football players with cerebral palsy maintained their physical fitness after a self-training program during the COVID-19 lockdown link: https://peerj.com/articles/13059 last-modified: 2022-03-17 description: BackgroundThe COVID-19 global pandemic caused a complete stop in sport participation which meant a detraining period for athletes. High-level athletes had to train at home guided by their coaches and conditioning trainers in an effort to maintain their physical fitness. The aim of maintaining the training adaptations and physical fitness during the COVID-19 mandatory lockdown was especially important for CP athletes, in which the detraining period was expected to cause early declines in motor function, poor coordination and muscle weakness due to their disability.MethodsThe present study assessed the effect of a guided self-training program on international CP football players’ physical fitness during the COVID-19 mandatory lockdown. Fifteen CP football players from the Spanish National Team participated in the study. An experimental design with a pre- (T1) and a post-intervention (T2) assessment was carried out, with a 12-week period of players’ self-training (divided in two periods of 6 weeks) which combined strength and endurance training. Physical performance assessment consisted in the free countermovement jump (CMJ), 5, 10 and 20-m sprint, the modified agility T-test (MAT) and a dribbling test. The Kruskal–Wallis test was used for between-group comparisons, while the Student’s paired t test or the Fisher Pitman permutation test, based on the normality of the data, were used for within-group comparisons.ResultsThe results showed no differences between sport classes (FT1, FT2 and FT3) in physical fitness change after the training program (Chi2 = 0.16 to 1.73; p = 0.42 to 0.92). Within-group comparisons showed an increase of jump height in the CMJ (4.19 cm [2.46, 5.93]; p < 0.001) and a maintenance of the 5, 10 and 20-m sprint, MAT and dribbling ability (<0.01 to 0.09 s; p = 0.19 to 0.97).DiscussionTo the authors’ knowledge, this is the first study that examined the physical fitness adaptations to a training program with CP football players. The results show that a 12-week guided self-training program without football-specific stimulus may be effective to maintain or even improve the specific physical performance of international CP football players during a non-competitive period (as the COVID-19 lockdown). This study reveals that CP football players are able to show adaptations to the strength and endurance training and this could be the basis for future research regarding training adaptations in CP football players. creator: Iván Peña-González creator: José Manuel Sarabia creator: Agustín Manresa-Rocamora creator: Manuel Moya-Ramón uri: https://doi.org/10.7717/peerj.13059 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Peña-González et al. title: Geometric morphometrics as a tool to understand biogeographical and evolutionary patterns in crane fly genus Ischnotoma Skuse (Diptera, Tipulidae) link: https://peerj.com/articles/13123 last-modified: 2022-03-17 description: BackgroundThe geometric morphometric analysis is applied for the first time for the family Tipulidae to distinguish evolutionary and biogeographical patterns on Ischnotoma species from Neotropical and Australian regions. We included 45 recognized species of the genus, representing its three subgenera I. (Icriomastax), I. (Ischnotoma), and I. (Neotipula). This paper aims to test if the three subgenera are recoverable using this set of morphometric data.MethodsTwenty-two landmarks were selected on the wing, mostly located on the radial and medial veins. A Regression Analysis, Principal Components Analysis (PCA), a Shape Coordinates PCA and a Canonical Variate Analysis (CVA) were used to test the variations among individuals, wing shape and groups.ResultsFor all analyses, the species of Ischnotoma (Neotipula) has a strong dissociation from the remaining species and the CVA shows a complete separation of the three subgenera. This study represents the first insight for a new assessment of Ischnotoma and the first step to giving a possible new status for I. (Neotipula). creator: Jéssica Gouvêa creator: Leonardo H. Gil-Azevedo uri: https://doi.org/10.7717/peerj.13123 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Gouvêa and Gil-Azevedo title: Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease link: https://peerj.com/articles/13128 last-modified: 2022-03-17 description: BackgroundThe disease caused by Barley yellow mosaic virus (BaYMV) infection is a serious threat to autumn-sown barley (Hordeum vulgare L.) production in Europe, East Asia and Iran. Due to the rapid diversification of BaYMV strains, it is urgent to discover novel germplasm and genes to assist breeding new varieties with resistance to different BaYMV strains, thus minimizing the effect of BaYMV disease on barley cropping.MethodsA natural population consisting of 181 barley accessions with different levels of resistance to BaYMV disease was selected for field resistance identification in two separate locations (Yangzhou and Yancheng, Jiangsu Province, China). Additive main effects and multiplicative interaction (AMMI) analysis was used to identify accessions with stable resistance. Genome-wide association study (GWAS) of BaYMV disease resistance was broadly performed by combining both single nucleotide polymorphisms (SNPs) and specific molecular markers associated with the reported BaYMV disease resistance genes. Furthermore, the viral protein genome linked (VPg) sequences of the virus were amplified and analyzed to assess the differences between the BaYMV strains sourced from the different experimental sites.ResultsSeven barley accessions with lower standardized Area Under the Disease Progress Steps (sAUDPS) index in every environment were identified and shown to have stable resistance to BaYMV disease in each assessed location. Apart from the reported BaYMV disease resistance genes rym4 and rym5, one novel resistance locus explaining 24.21% of the phenotypic variation was identified at the Yangzhou testing site, while two other novel resistance loci that contributed 19.23% and 19.79% of the phenotypic variation were identified at the Yancheng testing site, respectively. Further analysis regarding the difference in the VPg sequence of the predominant strain of BaYMV collected from these two testing sites may explain the difference of resistance loci differentially identified under geographically distinct regions. Our research provides novel genetic resources and resistance loci for breeding barley varieties for BaMYV disease resistance. creator: Yuhan Pan creator: Juan Zhu creator: Yi Hong creator: Mengna Zhang creator: Chao Lv creator: Baojian Guo creator: Huiquan Shen creator: Xiao Xu creator: Rugen Xu uri: https://doi.org/10.7717/peerj.13128 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pan et al. title: Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny link: https://peerj.com/articles/13130 last-modified: 2022-03-17 description: BackgroundBats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat (Lasiurus cinereus) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor.MethodsTo better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML.ResultsOf 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch (P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov–Smirnov test (P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1-like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well. creator: Robert S. Cornman creator: Paul M. Cryan uri: https://doi.org/10.7717/peerj.13130 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cornman and Cryan title: Inhibition of Connexin 43 reverses ox-LDL-mediated inhibition of autophagy in VSMC by inhibiting the PI3K/Akt/mTOR signaling pathway link: https://peerj.com/articles/12969 last-modified: 2022-03-16 description: BackgroundOxidized low-density lipoproteins (ox-LDL) may induce foam cell formation from the vascular smooth muscle cell (VSMC) by inhibiting VSMC autophagy. This process accelerates the formation of atherosclerosis (AS). Connexin 43 (Cx43), which is the most widely distributed connexin in VSMC is associated with autophagy. However, the mechanism of action and the involvement of Cx43 in ox-LDL-inhibited VSMC autophagy remain unclear.MethodsThe primary VSMC were obtained and identified, before primary VSMC were pretreated with an inhibitor (Cx43-specific inhibitor Gap26 and PI3K inhibitor LY294002) and stimulated with ox-LDL.ResultsOx-LDL not only inhibited autophagy in VSMC via downregulation of autophagy-related proteins (such as Beclin 1, LC3B, p62), but also increased Cx43 protein levels. Then we added Gap26 to VSMC in the ox-LDL+Gap26 group, in which autophagy-related proteins were increased and the accumulation of lipid droplets was reduced. These result suggested that an enhanced level of autophagy and an alleviation of lipid accumulation might be caused by inhibiting Cx43 in VSMC. The phosphorylation levels of PI3K, AKT, mTOR were increased by ox-LDL, thus down-regulating autophagy-related proteins. However, this situation was partially reversed by the Gap26. Moreover, Cx43 expression were decreased by LY294002 in ox-LDL-induced VSMCs.ConclusionInhibiting Cx43 may activate VSMC autophagy to inhibit foam cell formation by inhibiting the PI3K/AKT/mTOR signaling pathway. creator: Xuqing Qin creator: Wenjun He creator: Rui Yang creator: Luqian Liu creator: Yingying Zhang creator: Li Li creator: Junqiang Si creator: Xinzhi Li creator: Ketao Ma uri: https://doi.org/10.7717/peerj.12969 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Qin et al.