title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=993 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2 link: https://peerj.com/articles/10666 last-modified: 2021-01-04 description: SARS-CoV-2 genome encodes four structural proteins that include the spike glycoprotein, membrane protein, envelope protein and nucleocapsid phosphoprotein (N-protein). The N-protein interacts with viral genomic RNA and helps in packaging. As SARS-CoV-2 spread to almost all countries worldwide within 2–3 months, it also acquired mutations in its RNA genome. Therefore, this study was conducted with an aim to identify the variations present in N-protein of SARS-CoV-2. Here, we analysed 4,163 reported sequence of N-protein from United States of America (USA) and compared them with the first reported sequence from Wuhan, China. Our study identified 107 mutations that reside all over the N-protein. Further, we show the high rate of mutations in intrinsically disordered regions (IDRs) of N-protein. Our study show 45% residues of IDR2 harbour mutations. The RNA-binding domain (RBD) and dimerization domain of N-protein also have mutations at key residues. We further measured the effect of these mutations on N-protein stability and dynamicity and our data reveals that multiple mutations can cause considerable alterations. Altogether, our data strongly suggests that N-protein is one of the mutational hotspot proteins of SARS-CoV-2 that is changing rapidly and these mutations can potentially interferes with various aspects of N-protein functions including its interaction with RNA, oligomerization and signalling events. creator: Gajendra Kumar Azad uri: https://doi.org/10.7717/peerj.10666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Azad title: DHA content in milk and biohydrogenation pathway in rumen: a review link: https://peerj.com/articles/10230 last-modified: 2020-12-22 description: Docosahexaenoic acid (DHA) is an essential human nutrient that may promote neural health and development. DHA occurs naturally in milk in concentrations that are influenced by many factors, including the dietary intake of the cow and the rumen microbiome. We reviewed the literature of milk DHA content and the biohydrogenation pathway in rumen of dairy cows aim to enhance the DHA content. DHA in milk is mainly derived from two sources: α-linolenic acid (ALA) occurring in the liver and consumed as part of the diet, and overall dietary intake. Rumen biohydrogenation, the lymphatic system, and blood circulation influence the movement of dietary intake of DHA into the milk supply. Rumen biohydrogenation reduces DHA in ruminal environmental and limits DHA incorporation into milk. The fat-1 gene may increase DHA uptake into the body but this lacks experimental confirmation. Additional studies are needed to define the mechanisms by which different dietary sources of DHA are associated with variations of DHA in milk, the pathway of DHA biohydrogenation in the rumen, and the function of the fat-1 gene on DHA supply in dairy cows. creator: Guoxin Huang creator: Yangdong Zhang creator: Qingbiao Xu creator: Nan Zheng creator: Shengguo Zhao creator: Kaizhen Liu creator: Xueyin Qu creator: Jing Yu creator: Jiaqi Wang uri: https://doi.org/10.7717/peerj.10230 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Lack of guilt, shame, and remorse following weight stigma expression: a real-time assessment pilot study link: https://peerj.com/articles/10294 last-modified: 2020-12-22 description: ObjectiveWeight stigma is pervasive and is associated with negative health and psychological outcomes. Few studies have examined weight stigma perpetration or the emotions individuals experience after perpetrating weight stigma. This study used experience sampling to explore the nature and frequency of weight stigma behaviors and cognitions and moral emotions (shame, guilt, remorse, pride) in the perpetrator following weight stigma perpetration.MethodsParticipants were college students (N = 31, 77.1% female). Participants completed baseline measures of anti-fat attitudes and one week of experience sampling phone prompts assessing: (1) weight stigma behaviors and cognitions and (2) moral emotions. Generalized estimating equation analyses were used to model trajectories of moral emotions after weight stigma events.ResultsThirty-one participants reported 1,008 weight stigma events over 7.5 days. Feelings of guilt, shame, and remorse decreased after weight stigma perpetration. Individuals also reported feeling less proud after engaging in weight stigma.ConclusionsWeight stigma occurs frequently as reported by perpetrators. A lack of remorse, guilt, and shame is evident in undergraduates after they express weight stigma; however, individuals in this study also reported feeling less pride after perpetration. This study highlights the need for future studies to explore the expression of weight stigma from the perspective of perpetrators instead of targets. Results highlight the pervasiveness and normative nature of weight stigma perpetration in everyday life and the need to better understand the emotional response following weight stigma perpetration as a potential mechanism of its perpetuation. creator: Paige J. Trojanowski creator: Lauren Breithaupt creator: Sonakshi Negi creator: Joseph Wonderlich creator: Sarah Fischer uri: https://doi.org/10.7717/peerj.10294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Trojanowski et al. title: The relationship between anti-Müllerian hormone (AMH) levels and pregnancy outcomes in patients undergoing assisted reproductive techniques (ART) link: https://peerj.com/articles/10390 last-modified: 2020-12-22 description: A variety of predictors are available for ovarian stimulation cycles in assisted reproductive technology (ART) forecasting ovarian response and reproductive outcome in women including biomarkers such as anti- Müllerian hormone (AMH). The aim of our present study was to compare the relationship between AMH levels and pregnancy outcomes in patients undergoing intra-cytoplasmic sperm injection (ICSI). Overall, fifty patients (n = 50), aged 20–45 years were recruited for the present prospective study. Three AMH levels were presented with high often poly cystic ovarian syndrome (PCOS) amongst 52.4% patients, 40.5% in normal and 7.1% in low to normal, correspondingly. There was statistically significant relationship between AMH and day of embryo transfer (p < 0.05). The Pearson analysis between AMH, age, E2 and FSH displayed no statistically significant relationship between E2 and AMH (p < 0.05) and negative correlation between FSH and age (p > 0.05). The area under the receiver operating characteristic curve for E2 was 0.725 and for AMH levels as predictors of CPR was 0.497 indicating E2 as better predictor than AMH. The number of oocytes, mature oocytes and fertilized oocytes all presented a weak positive relationship to AMH. Our results confirm the clinical significance of AMH to accurately predict ovarian reserve as a marker and its limitations to use as predictor for a positive pregnancy outcome. Additional prospective studies should be conducted to validate the predictive capability of AMH levels for the outcome of clinical pregnancy. creator: Shalini Umarsingh creator: Jamila Khatoon Adam creator: Suresh Babu Naidu Krishna uri: https://doi.org/10.7717/peerj.10390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Umarsingh et al. title: Supraspecific units in correlative niche modeling improves the prediction of geographic potential of biological invasions link: https://peerj.com/articles/10454 last-modified: 2020-12-22 description: BackgroundBiological invasions rank among the most significant threats to biodiversity and ecosystems. Correlative ecological niche modeling is among the most frequently used tools with which to estimate potential distributions of invasive species. However, when areas accessible to the species across its native distribution do not represent the full spectrum of environmental conditions that the species can tolerate, correlative studies often underestimate fundamental niches.MethodsHere, we explore the utility of supraspecific modeling units to improve the predictive ability of models focused on biological invasions. Taking into account phylogenetic relationships in correlative ecological niche models, we studied the invasion patterns of three species (Aedes aegypti, Pterois volitans and Oreochromis mossambicus).ResultsUse of supraspecific modeling units improved the predictive ability of correlative niche models in anticipating potential distributions of three invasive species. We demonstrated that integrating data on closely related species allowed a more complete characterization of fundamental niches. This approach could be used to model species with invasive potential but that have not yet invaded new regions. creator: Sandra Castaño-Quintero creator: Jazmín Escobar-Luján creator: Luis Osorio-Olvera creator: A Townsend Peterson creator: Xavier Chiappa-Carrara creator: Enrique Martínez-Meyer creator: Carlos Yañez-Arenas uri: https://doi.org/10.7717/peerj.10454 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Castaño-Quintero et al. title: BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis link: https://peerj.com/articles/10469 last-modified: 2020-12-22 description: BackgroundRNA sequencing is an indispensable research tool used in a broad range of transcriptome analysis studies. The most common application of RNA Sequencing is differential expression analysis and it is used to determine genetic loci with distinct expression across different conditions. An emerging field called single-cell RNA sequencing is used for transcriptome profiling at the individual cell level. The standard protocols for both of these approaches include the processing of sequencing libraries and result in the generation of count matrices. An obstacle to these analyses and the acquisition of meaningful results is that they require programing expertise. Although some effort has been directed toward the development of user-friendly RNA-Seq analysis analysis tools, few have the flexibility to explore both Bulk and single-cell RNA sequencing.ImplementationBingleSeq was developed as an intuitive application that provides a user-friendly solution for the analysis of count matrices produced by both Bulk and Single-cell RNA-Seq experiments. This was achieved by building an interactive dashboard-like user interface which incorporates three state-of-the-art software packages for each type of the aforementioned analyses. Furthermore, BingleSeq includes additional features such as visualization techniques, extensive functional annotation analysis and rank-based consensus for differential gene analysis results. As a result, BingleSeq puts some of the best reviewed and most widely used packages and tools for RNA-Seq analyses at the fingertips of biologists with no programing experience.AvailabilityBingleSeq is as an easy-to-install R package available on GitHub at https://github.com/dbdimitrov/BingleSeq/. creator: Daniel Dimitrov creator: Quan Gu uri: https://doi.org/10.7717/peerj.10469 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dimitrov and Gu title: Expression of the neurotrophic tyrosine kinase receptors, ntrk1 and ntrk2a, precedes expression of other ntrk genes in embryonic zebrafish link: https://peerj.com/articles/10479 last-modified: 2020-12-22 description: BackgroundThe neurotrophic tyrosine kinase receptor (Ntrk) gene family plays a critical role in the survival of somatosensory neurons. Most vertebrates have three Ntrk genes each of which encode a Trk receptor: TrkA, TrkB, or TrkC. The function of the Trk receptors is modulated by the p75 neurotrophin receptors (NTRs). Five ntrk genes and one p75 NTR gene (ngfrb) have been discovered in zebrafish. To date, the expression of these genes in the initial stages of neuron specification have not been investigated.PurposeThe present work used whole mount in situ hybridization to analyze expression of the five ntrk genes and ngfrb in zebrafish at a timepoint when the first sensory neurons of the zebrafish body are being established (16.5 hpf). Because expression of multiple genes were not found at this time point, we also checked expression at 24 hpf to ensure the functionality of our six probes.ResultsAt 16.5 hpf, we found tissue specific expression of ntrk1 in cranial ganglia, and tissue specific expression of ntrk2a in cranial ganglia and in the spinal cord. Other genes analyzed at 16.5 hpf were either diffuse or not detected. At 24 hpf, we found expression of both ntrk1 and ntrk2a in the spinal cord as well as in multiple cranial ganglia, and we identified ngfrb expression in cranial ganglia at 24 hpf. ntrk2b, ntrk3a and ntrk3b were detected in the developing brain at 24 hpf.ConclusionThese data are the first to demonstrate that ntrk1 and ntrk2a are the initial neurotrophic tyrosine kinase receptors expressed in sensory neurons during the development of the zebrafish body, and the first to establish expression patterns of ngfrb during early zebrafish development. Our data indicate co-expression of ntrk1, ntrk2a and ngfrb, and we speculate that these overlapping patterns indicate relatedness of function. creator: Katie Hahn creator: Paul Manuel creator: Cortney Bouldin uri: https://doi.org/10.7717/peerj.10479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hahn et al. title: The ecomorphology of the shell of extant turtles and its applications for fossil turtles link: https://peerj.com/articles/10490 last-modified: 2020-12-22 description: Turtles are a successful clade of reptiles that originated in the Late Triassic. The group adapted during its evolution to different types of environments, ranging from dry land to ponds, rivers, and the open ocean, and survived all Mesozoic and Cenozoic extinction events. The body of turtles is characterized by a shell, which has been hypothesized to have several biological roles, like protection, thermal and pH regulation, but also to be adapted in its shape to the ecology of the animal. However, only few studies have investigated the relationships between shell shape and ecology in a global context or clarified if shape can be used to diagnose habitat preferences in fossil representatives. Here, we assembled a three-dimensional dataset of 69 extant turtles and three fossils, in particular, the Late Triassic Proganochelys quenstedtii and Proterochersis robusta and the Late Jurassic Plesiochelys bigleri to test explicitly for a relationship between shell shape and ecology. 3D models were obtained using surface scanning and photogrammetry. The general shape of the shells was captured using geometric morphometrics. The habitat ecology of extant turtles was classified using the webbing of their forelimbs as a proxy. Principal component analysis (PCA) highlights much overlap between habitat groups. Discriminant analyses suggests significant differences between extant terrestrial turtles, extant fully aquatic (i.e., marine and riverine) turtles, and an unspecialized assemblage that includes extant turtles from all habitats, mostly freshwater aquatic forms. The paleoecology of the three fossil species cannot be determined with confidence, as all three fall within the unspecialized category, even if Plesiochelys bigleri plots closer to fully aquatic turtles, while the two Triassic species group closer to extant terrestrial forms. Although the shape of the shell of turtles indeed contains an ecological signal, it is overall too weak to uncover using shell shape in paleoecological studies, at least with the methods we selected. creator: Ilya Dziomber creator: Walter G. Joyce creator: Christian Foth uri: https://doi.org/10.7717/peerj.10490 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dziomber et al. title: SKP1-like protein, CrSKP1-e, interacts with pollen-specific F-box proteins and assembles into SCF-type E3 complex in ‘Wuzishatangju’ (Citrus reticulata Blanco) pollen link: https://peerj.com/articles/10578 last-modified: 2020-12-22 description: S-ribonuclease (S-RNase)-based self-incompatibility (SI) mechanisms have been extensively studied in Solanaceae, Rosaceae and Plantaginaceae. S-RNase-based SI is controlled by two closely related genes, S-RNase and S-locus F-box (SLF), located at a polymorphic S-locus. In the SI system, the SCF-type (SKP1-CUL1-F-box-RBX1) complex functions as an E3 ubiquitin ligase complex for ubiquitination of non-self S-RNase. Pummelo (Citrus grandis) and several mandarin cultivars are suggested to utilize an S-RNase-based SI system. However, the molecular mechanism of the non-S-factors involved in the SI reaction is not straightforward in Citrus. To investigate the SCF-type E3 complex responsible for the SI reaction in mandarin, SLF, SKP1-like and CUL1 candidates potentially involved in the SI reaction of ‘Wuzishatangju’ (Citrus reticulata Blanco) were identified based on the genome-wide identification and expression analyses. Sixteen pollen-specific F-box genes (CrFBX1-CrFBX16), one pollen-specific SKP1-like gene (CrSKP1-e) and two CUL1 genes (CrCUL1A and CrCUL1B) were identified and cloned from ‘Wuzishatangju’. Yeast two-hybrid (Y2H) and in vitro binding assays showed that five CrFBX proteins could bind to CrSKP1-e, which is an ortholog of SSK1 (SLF-interacting-SKP1-like), a non-S-factor responsible for the SI reaction. Luciferase complementation imaging (LCI) and in vitro binding assays also showed that CrSKP1-e interacts with the N-terminal region of both CrCUL1A and CrCUL1B. These results indicate that CrSKP1-e may serve as a functional member of the SCF-type E3 ubiquitin ligase complex in ‘Wuzishatangju’. creator: Yi Ren creator: Qingzhu Hua creator: Jiayan Pan creator: Zhike Zhang creator: Jietang Zhao creator: Xinhua He creator: Yonghua Qin creator: Guibing Hu uri: https://doi.org/10.7717/peerj.10578 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ren et al. title: The effect of brewery spent grain application on biogas yields and kinetics in co-digestion with sewage sludge link: https://peerj.com/articles/10590 last-modified: 2020-12-22 description: The present study examines the effect of introducing dried brewery spent grain (BSG), known as the main solid by-product of the brewery industry on biogas yields and kinetics in co-digestion with sewage sludge (SS). The experiment was conducted in semi-continuous anaerobic reactors (supplied once a day) operating under mesophilic conditions (35°C) at different hydraulic retention times (HRT) of 18 and 20 d. In co-digestion runs, the BSG mass to the feed volume ratio was constant and maintained 1:10.The results indicated that the addition of BSG did not influence the biogas production, by comparison with SS mono-digestion (control run). At HRT of 18 d, in the co-digestion run, the average methane yield was 0.27 m3 kg/VSadded, while in the control run the higher value of 0.29 m3 kg/VSaddedwas observed. However, there was no difference in terms of statistical significance. At HRT of 20 d, the methane yield was 0.21 m3 kg/VSadded for both mono- and co-digestion runs. In the BSG presence, the decrease in kinetic constant values was observed. As compared to SS mono-digestion, reductions by 21 and 35% were found at HRT of 20 and 18 d, respectively. However, due to the supplementation of the feedstock with BSG rich in organic compounds, the significantly enhanced energy profits were achieved with the highest value of approx. 40% and related to the longer HRT of 20 d. Importantly, the mono- and co-digestion process proceeded in stable manner. Therefore, the anaerobic co-digestion of SS and BSG might be considered as a cost-effective solution that could contribute to the energy self-efficiency of wastewater treatment plants (WWTPs) and sustainable waste management for breweries. creator: Aleksandra Szaja creator: Agnieszka Montusiewicz creator: Magdalena Lebiocka creator: Marta Bis uri: https://doi.org/10.7717/peerj.10590 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Szaja et al.