title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=821 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: In silico evaluation of molecular virus–virus interactions taking place between Cotton leaf curl Kokhran virus- Burewala strain and Tomato leaf curl New Delhi virus link: https://peerj.com/articles/12018 last-modified: 2021-10-19 description: BackgroundCotton leaf curl disease (CLCuD) is a disease of cotton caused by begomoviruses, leading to a drastic loss in the annual yield of the crop. Pakistan has suffered two epidemics of this disease leading to the loss of billions in annual exports. The speculation that a third epidemic of CLCuD may result as consequence of the frequent occurrence of Tomato leaf curl New Delhi virus (ToLCNDV) and Cotton leaf curl Kokhran Virus-Burewala Strain (CLCuKoV-Bu) in CLCuD infected samples, demand that the interactions taking between the two viruses be properly evaluated. This study is designed to assess virus-virus interactions at the molecular level and determine the type of co-infection taking place.MethodsBased on the amino acid sequences of the gene products of both CLCuKoV-Bu and ToLCNDV, protein structures were generated using different software, i.e., MODELLER, I-TASSER, QUARKS, LOMETS and RAPTORX. A consensus model for each protein was selected after model quality assessment using ERRAT, QMEANDisCo, PROCHECK Z-Score and Ramachandran plot analysis. The active and passive residues in the protein structures were identified using the CPORT server. Protein–Protein Docking was done using the HADDOCK webserver, and 169 Protein–Protein Interaction (PPIs) were performed between the proteins of the two viruses. The docked complexes were submitted to the PRODIGY server to identify the interacting residues between the complexes. The strongest interactions were determined based on the HADDOCK Score, Desolvation energy, Van der Waals Energy, Restraint Violation Energy, Electrostatic Energy, Buried Surface Area and Restraint Violation Energy, Binding Affinity and Dissociation constant (Kd). A total of 50 ns Molecular Dynamic simulations were performed on complexes that exhibited the strongest affinity in order to validate the stability of the complexes, and to remove any steric hindrances that may exist within the structures.ResultsOur results indicate significant interactions taking place between the proteins of the two viruses. Out of all the interactions, the strongest were observed between the Replication Initiation protein (Rep) of CLCuKoV-Bu with the Movement protein (MP), Nuclear Shuttle Protein (NSP) of ToLCNDV (DNA-B), while the weakest were seen between the Replication Enhancer protein (REn) of CLCuKoV-Bu with the REn protein of ToLCNDV. The residues identified to be taking a part in interaction belonged to domains having a pivotal role in the viral life cycle and pathogenicity. It maybe deduced that the two viruses exhibit antagonistic behavior towards each other, and the type of infection may be categorised as a type of Super Infection Exclusion (SIE) or homologous interference. However, further experimentation, in the form of transient expression analysis, is needed to confirm the nature of these interactions and increase our understanding of the direct interactions taking place between two viruses. creator: Nida Fatima Ali creator: Rehan Zafar Paracha creator: Muhammad Tahir uri: https://doi.org/10.7717/peerj.12018 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ali et al. title: New phiocricetomyine rodents (Hystricognathi) from the Jebel Qatrani Formation, Fayum Depression, Egypt link: https://peerj.com/articles/12074 last-modified: 2021-10-19 description: BackgroundThe rich rodent assemblages from the Eocene–Oligocene deposits of the Jebel Qatrani Formation (Fayum Depression, Egypt) have important implications for our understanding of the origin and paleobiogeography of Hystricognathi, a diverse clade that is now represented by the Afro-Asiatic Hystricidae, New World Caviomorpha, and African Phiomorpha.MethodsHere we present previously undescribed material of the enigmatic hystricognath clade Phiocricetomyinae, from two stratigraphic levels in the lower sequence of the Jebel Qatrani Formation—a new genus and species (Qatranimys safroutus) from the latest Eocene Locality 41 (~34 Ma, the oldest and most productive quarry in the formation) and additional material of Talahphiomys lavocati from that species’ type locality, early Oligocene Quarry E (~31–33.2 Ma).ResultsThe multiple specimens of Qatranimys safroutus from L-41 document almost the entire lower and upper dentition, as well as mandibular fragments and the first cranial remains known for a derived phiocricetomyine. Specimens from Quarry E allow us to expand comparisons with specimens from Libya (late Eocene of Dur at-Talah and early Oligocene of Zallah Oasis) that have been placed in T. lavocati, and we show that the Dur at-Talah and Zallah specimens do not pertain to this species. These observations leave the Fayum Quarry E as the only locality where T. lavocati occurs. creator: Shorouq F. Al-Ashqar creator: Erik R. Seiffert creator: Dorien de Vries creator: Sanaa El-Sayed creator: Mohamed S. Antar creator: Hesham M. Sallam uri: https://doi.org/10.7717/peerj.12074 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Al-Ashqar et al. title: Visual assessment of dynamic knee joint alignment in patients with patellofemoral pain: an agreement study link: https://peerj.com/articles/12203 last-modified: 2021-10-19 description: BackgroundAssessment of knee kinematics plays an important role in the clinical examination of patients with patellofemoral pain (PFP). There is evidence that visual assessments are reliable in healthy subjects, but there is a lack of evidence in injured populations. The purpose of this study was to examine the intra- and interrater agreement in the visual assessment of dynamic knee joint alignment in patients with PFP.MethodsThe study was a cross-sectional agreement study. Sixty participants (42 females) were included. We assessed the intra- and interrater agreement of two functional tests: The single leg squat (SLS) and the forward lunge (FL). One investigator scored the movement according to preset criteria while video recording the movement for retest. Moreover, the performance was scored by another investigator using the video recording. Agreement was assessed using weighted kappa statistics.ResultsThe intrarater agreement ranged from moderate to good (Kappa 0.58 (FL) to 0.70 (SLS)) whereas the interrater agreement ranged from fair to moderate (Kappa 0.22 (SLS) to 0.50 (FL)).ConclusionThe agreement within raters was better than between raters, which suggests that assessments should preferably be performed by the same tester in research and in a clinical setting, e.g., to evaluate any treatment effect. We promote FL as a reliable clinical tool for evaluating dynamic knee alignment, since it shows equally good intra- and interrater agreement, and it is an inexpensive and easy method to use. creator: Rudi Hansen creator: Mathilde Lundgaard-Nielsen creator: Marius Henriksen uri: https://doi.org/10.7717/peerj.12203 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hansen et al. title: Upright walking has driven unique vascular specialization of the hominin ilium link: https://peerj.com/articles/12240 last-modified: 2021-10-19 description: BackgroundA novel physis in hominins modulates broadening and shortening of the ilium. We report analysis of a vascular canal system whose origin may be associated with this physis and which appears to be also unique to hominins. Its presence is potentially identifiable in the fossil record by its association with a highly enlarged foramen that is consistently present in modern humans and hominin fossils.MethodsWe measured the diameter of this foramen in humans, fossil hominins, and African great apes and corrected for body size.ResultsThe mean relative human foramen diameter is significantly greater than those of either Pan or Gorilla. Moreover, eight of the nine values of the Cohen’s d for these differences in ratios are highly significant and support the ordering of magnitudes: Pan < Gorilla < Homo. The relative foramen diameter of A.L. 288-1 is above the 75th percentile of all other hominoids and at the high end of humans. The foramen is also present in ARA-VP-6/500.ConclusionsWe posit that the presence and significant enlargement of this foramen in fossils can reasonably serve as an indicator that its anterior inferior iliac spine emerged via the unique hominin physis. The foramen can therefore serve as an indicator of hominin iliac ontogenetic specialization for bipedality in fossil taxa. creator: Dexter Zirkle creator: Richard S. Meindl creator: C. Owen Lovejoy uri: https://doi.org/10.7717/peerj.12240 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zirkle et al. title: Marine amphipods (Parhyale hawaiensis) as an alternative feed for the lined seahorse (Hippocampus erectus, Perri 1810): nutritional value and feeding trial link: https://peerj.com/articles/12288 last-modified: 2021-10-19 description: Finding new alternatives to traditional live preys such as Artemia and rotifers, which do not always promote optimal fish growth and survival, is required for the successful aquaculture of highly specialized predatory species, including seahorses. The present study assessed the nutritional value of an interesting marine amphipod (Parhyale hawaiensis), and evaluates through a feeding trial its potential use as a natural prey for 10-months lined seahorse, Hippocampus erectus. P. hawaiensis showed high levels of valuable lipids (20.4–26.7% on dry matter basis) and polyunsaturated fatty acids (PUFAs) ( 26.4–41% of total FAs), including the long-chain PUFAs (LC-PUFAs) arachidonic acid (ARA) (2.9–7.7%), eicosapentaenoic acid (EPA) (4.3–6.5%) and docosahexaenoic acid (DHA) (2.1–6.2%). A comparison between wild-captured and cultured amphipods revealed a significant improvement of the amphipod FA profile in terms of DHA%, total omega-3 (n3) FAs and n3/n6 ratio when employing both a conventional amphipod culture based on a commercial shrimp diet, and, to a lesser extent, a large (3,500 L) biofloc system. Seahorses fed with frozen/wild amphipods, either singly or in combination with Artemia enriched with Super Selco® (INVE Aquaculture, Belgium) for 57 days, substantially improved seahorse growth and FA profiles in terms of ARA, EPA and DHA%, including indices associated to marine sources, such as Σn3 and n3/n6, compared to a diet based solely on enriched Artemia. These results support the use of marine amphipods as an alternative food organism for juvenile H. erectus and suggest a potential use for general marine aquaculture. creator: Jorge Arturo Vargas-Abúndez creator: Gemma Leticia Martínez-Moreno creator: Nuno Simões creator: Elsa Noreña-Barroso creator: Maite Mascaró uri: https://doi.org/10.7717/peerj.12288 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Vargas-Abúndez et al. title: Identification and evaluation of the novel genes for transcript normalization during female gametophyte development in sugarcane link: https://peerj.com/articles/12298 last-modified: 2021-10-19 description: BackgroundSugarcane (Saccharum spontaneum L.), the major sugar and biofuel feedstock crop, is cultivated mainly by vegetative propagation worldwide due to the infertility of female reproductive organs resulting in the reduction of quality and output of sugar. Deciphering the gene expression profile during ovule development will improve our understanding of the complications underlying sexual reproduction in sugarcane. Optimal reference genes are essential for elucidating the expression pattern of a given gene by quantitative real-time PCR (qRT-PCR).MethodIn this study, based on transcriptome data obtained from sugarcane ovule, eighteen candidate reference genes were identified, cloned, and their expression levels were evaluated across five developmental stages ovule (AC, MMC, Meiosis, Mitosis, and Mature).ResultsOur results indicated that FAB2 and MOR1 were the most stably expressed genes during sugarcane female gametophyte development. Moreover, two genes, cell cycle-related genes REC8 and CDK, were selected, and their feasibility was validated. This study provides important insights into the female gametophyte development of sugarcane and reports novel reference genes for gene expression research on sugarcane sexual reproduction. creator: Maokai Yan creator: Xingyue Jin creator: Yanhui Liu creator: Huihuang Chen creator: Tao Ye creator: Zhimin Hou creator: Zhenxia Su creator: Yingzhi Chen creator: Mohammad Aslam creator: Yuan Qin creator: Xiaoping Niu uri: https://doi.org/10.7717/peerj.12298 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yan et al. title: Vocal communication in wild chimpanzees: a call rate study link: https://peerj.com/articles/12326 last-modified: 2021-10-19 description: BackgroundPatterns of vocal communication have implications for species conservation: a change in calling behaviour can, for instance, reflect a disturbed habitat. More importantly, call rate is a parameter that allows conservation planners to convert call density into animal density, when detecting calls with a passive acoustic monitoring system (PAM).MethodsWe investigated chimpanzee (Pan troglodytes schweinfurthii) call rate during the late dry season in the Issa Valley, western Tanzania by conducting focal follows. We examined the socio-ecological factors that influence call production rate of savanna woodland chimpanzees.ResultsWe found that sex, proportion of time spent in a vegetation type, proportion of time spent travelling, time of the day, party size and swollen parous female presence had a significant effect on the call rate. Call rate differed among the different demographic classes with subadult and adult males vocalising twice as often as the subadult and adult females and three times as often as the juveniles.ApplicationsThe use of PAM and recent statistical developments to estimate animal density is promising but relies on our knowing individual call rate, often not available for many species. With the improvement in automatic call detection, we anticipate that PAM will increasingly be broadly applied to primates but also across taxa, for conservation. creator: Anne-Sophie Crunchant creator: Fiona A. Stewart creator: Alex K. Piel uri: https://doi.org/10.7717/peerj.12326 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Crunchant et al. title: A noteworthy case of rewilding Chinese yew from a garden population in eastern China link: https://peerj.com/articles/12341 last-modified: 2021-10-19 description: Chinese yew (Taxus wallichiana var. mairei) is ranked as a rare and endangered plant of first-grade protection of China. It has been widely cultivated in 17 provinces of China over the past few decades. However, little is known about the dispersion, rewilding, and ecological influence of Chinese yew’s offspring during cultivation. Here, we report a noteworthy case of this species, via ex situ conservation, which has successfully spread into different secondary forests, thus forming a stable regenerating population in eastern China. The establishment of this yew population, which has > 900 individuals and 7 ha area, can be ascribed to two key ecological factors: (1) secondary forest near the parent yews that provided suitable microhabitats in which progeny yews could germinate and grow, and (2) seed-foraging and transportation by native birds. Thus, this case may offer a pathway for conserving endangered Chinese Taxus species, which can attract frugivorous birds to disperse their seeds. In addition, it is necessary to monitor the growth performance of progeny population in the field. creator: Kaidi Li creator: Guangfu Zhang creator: Ying Zhang creator: M. Patrick Griffith uri: https://doi.org/10.7717/peerj.12341 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon link: https://peerj.com/articles/12343 last-modified: 2021-10-19 description: BackgroundWatermelon seeds are a powerhouse of value-added traits such as proteins, free amino acids, vitamins, and essential minerals, offering a paleo-friendly dietary option. Despite the availability of substantial genetic variation, there is no sufficient information on the natural variation in seed-bound amino acids or proteins across the watermelon germplasm. This study aimed to analyze the natural variation in watermelon seed amino acids and total protein and explore underpinning genetic loci by genome-wide association study (GWAS).MethodsThe study evaluated the distribution of seed-bound free amino acids and total protein in 211 watermelon accessions of Citrullus spp, including 154 of Citrullus lanatus, 54 of Citrullus mucosospermus (egusi) and three of Citrullus amarus. We used the GWAS approach to associate seed phenotypes with 11,456 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS).ResultsOur results demonstrate a significant natural variation in different free amino acids and total protein content across accessions and geographic regions. The accessions with high protein content and proportion of essential amino acids warrant its use for value-added benefits in the food and feed industries via biofortification. The GWAS analysis identified 188 SNPs coinciding with 167 candidate genes associated with watermelon seed-bound amino acids and total protein. Clustering of SNPs associated with individual amino acids found by principal component analysis was independent of the speciation or cultivar groups and was not selected during the domestication of sweet watermelon. The identified candidate genes were involved in metabolic pathways associated with amino acid metabolism, such as Argininosuccinate synthase, explaining 7% of the variation in arginine content, which validate their functional relevance and potential for marker-assisted analysis selection. This study provides a platform for exploring potential gene loci involved in seed-bound amino acids metabolism, useful in genetic analysis and development of watermelon varieties with superior seed nutritional values. creator: Vijay Joshi creator: Padma Nimmakayala creator: Qiushuo Song creator: Venkata Abburi creator: Purushothaman Natarajan creator: Amnon Levi creator: Kevin Crosby creator: Umesh K. Reddy uri: https://doi.org/10.7717/peerj.12343 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Joshi et al. title: Perception of footwear comfort and its relationship with the foot structure among youngest-old women and men link: https://peerj.com/articles/12385 last-modified: 2021-10-19 description: BackgroundAdequate footwear comfort and functionality are important regardless of age, but they become particularly important in the youngest-old women and men, mainly due to the fact that this age range is the initial period of old age with changes in shoe preferences. The aim of this study was to assess the perception of footwear comfort and its relationship with the feet structure in youngest-old women and men.MethodsThe cross-sectional study covered community dwellers living on their own aged 65–74 years (50 women; 50 men). The feet characteristics were measured using the CQ-ST podoscope (Electronic System, Ltd, EU), and the perception of footwear comfort was assessed with a visual analogue scale. The assessment took into account gender-specific footwear of a certain brand (Befado Dr orto).ResultsStatistically significant intergender differences were observed in the perception of footwear comfort with respect to the shoe heel width (p = 0.022), the arch height (p = 0.013), the overall comfort (p = 0.049) and the material properties of the footwear (p = 0.017). In women, there were statistically significant positive relationships among the heel angle (γ) and the perception of footwear comfort in terms of heel cushioning (p = 0.021), forefoot cushioning (p = 0.015), arch height (p = 0.029). In men, there was a statistically significant negative relationship of the left foot Clarke’s angle with the heel height (p = 0.043), and a positive relationship between the right foot width and the arch height (p = 0.044).ConclusionsYoungest-old women, compared to men of the same age range, have a higher perception of shoe comfort in terms of the shoe heel width, the arch height, the overall comfort of the footwear and the material properties of the footwear. The appropriate profile and construction of the shoe allows for an increase in the contact surface of the foot with the shoe, hence the improvement in the perception of footwear comfort in people with lowered arch or widened forefoot. creator: Ewa Puszczalowska-Lizis creator: Karolina Koziol creator: Jaroslaw Omorczyk uri: https://doi.org/10.7717/peerj.12385 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Puszczalowska-Lizis et al.