title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=899
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Comparative analysis of fatty acid metabolism based on transcriptome sequencing of wild and cultivated Ophiocordyceps sinensis
link: https://peerj.com/articles/11681
last-modified: 2021-07-01
description: BackgroundOphiocordyceps sinensis is a species endemic to the alpine and high-altitude areas of the Qinghai-Tibet plateau. Although O. sinensis has been cultivated since the past few years, whether cultivated O. sinensis can completely replace wild O. sinensis remains to be determined.MethodsTo explore the differences of O. sinensis grown in varied environments, we conducted morphological and transcriptomic comparisons between wild and cultivated samples who with the same genetic background.ResultsThe results of morphological anatomy showed that there were significant differences between wild and cultivated O. sinensis, which were caused by different growth environments. Then, a total of 9,360 transcripts were identified using Illumina paired-end sequencing. Differential expression analysis revealed that 73.89% differentially expressed genes (DEGs) were upregulated in O. sinensis grown under natural conditions compared with that grown under artificial conditions. Functional enrichment analysis showed that some key DEGs related to fatty acid metabolism, including acyl-CoA dehydrogenase, enoyl-CoA hydratase, 3-ketoacyl-CoA thiolase, and acetyl-CoA acetyltransferase, were upregulated in wild O. sinensis. Furthermore, gas chromatography-mass spectrometry results confirmed that the fatty acid content of wild O. sinensis was significantly higher than that of cultivated O. sinensis and that unsaturated fatty acids accounted for a larger proportion.ConclusionThese results provide a theoretical insight to the molecular regulation mechanism that causes differences between wild and cultivated O. sinensis and improving artificial breeding.
creator: Han Zhang
creator: Pan Yue
creator: Xinxin Tong
creator: Tinghui Gao
creator: Ting Peng
creator: Jinlin Guo
uri: https://doi.org/10.7717/peerj.11681
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Zhang et al.

title: A synthetic defective interfering SARS-CoV-2
link: https://peerj.com/articles/11686
last-modified: 2021-07-01
description: Viruses thrive by exploiting the cells they infect, but in order to replicate and infect other cells they must produce viral proteins. As a result, viruses are also susceptible to exploitation by defective versions of themselves that do not produce such proteins. A defective viral genome with deletions in protein-coding genes could still replicate in cells coinfected with full-length viruses. Such a defective genome could even replicate faster due to its shorter size, interfering with the replication of the virus. We have created a synthetic defective interfering version of SARS-CoV-2, the virus causing the Covid-19 pandemic, assembling parts of the viral genome that do not code for any functional protein but enable the genome to be replicated and packaged. This synthetic defective genome replicates three times faster than SARS-CoV-2 in coinfected cells, and interferes with it, reducing the viral load of infected cells by half in 24 hours. The synthetic genome is transmitted as efficiently as the full-length genome, suggesting the location of the putative packaging signal of SARS-CoV-2. A version of such a synthetic construct could be used as a self-promoting antiviral therapy: by enabling replication of the synthetic genome, the virus would promote its own demise.
creator: Shun Yao
creator: Anoop Narayanan
creator: Sydney A. Majowicz
creator: Joyce Jose
creator: Marco Archetti
uri: https://doi.org/10.7717/peerj.11686
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Yao et al.

title: In silico-driven analysis of the Glossina morsitans morsitans antennae transcriptome in response to repellent or attractant compounds
link: https://peerj.com/articles/11691
last-modified: 2021-07-01
description: BackgroundHigh-throughput sequencing generates large volumes of biological data that must be interpreted to make meaningful inference on the biological function. Problems arise due to the large number of characteristics p (dimensions) that describe each record [n] in the database. Feature selection using a subset of variables extracted from the large datasets is one of the approaches towards solving this problem.MethodologyIn this study we analyzed the transcriptome of Glossina morsitans morsitans (Tsetsefly) antennae after exposure to either a repellant (δ-nonalactone) or an attractant (ε-nonalactone). We identified 308 genes that were upregulated or downregulated due to exposure to a repellant (δ-nonalactone) or an attractant (ε-nonalactone) respectively. Weighted gene coexpression network analysis was used to cluster the genes into 12 modules and filter unconnected genes. Discretized and association rule mining was used to find association between genes thereby predicting the putative function of unannotated genes.Results and discussionAmong the significantly expressed chemosensory genes (FDR < 0.05) in response to Ɛ-nonalactone were gustatory receptors (GrIA and Gr28b), ionotrophic receptors (Ir41a and Ir75a), odorant binding proteins (Obp99b, Obp99d, Obp59a and Obp28a) and the odorant receptor (Or67d). Several non-chemosensory genes with no assigned function in the NCBI database were co-expressed with the chemosensory genes. Exposure to a repellent (δ-nonalactone) did not show any significant change between the treatment and control samples. We generated a coexpression network with 276 edges and 130 nodes. Genes CAH3, Ahcy, Ir64a, Or67c, Ir8a and Or67a had node degree values above 11 and therefore could be regarded as the top hub genes in the network. Association rule mining showed a relation between various genes based on their appearance in the same itemsets as consequent and antecedent.
creator: Consolata Gakii
creator: Billiah Kemunto Bwana
creator: Grace Gathoni Mugambi
creator: Esther Mukoya
creator: Paul O. Mireji
creator: Richard Rimiru
uri: https://doi.org/10.7717/peerj.11691
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Gakii et al.

title: Taxonomic revision of the Temnothorax salvini clade (Hymenoptera: Formicidae), with a key to the clades of New World Temnothorax
link: https://peerj.com/articles/11514
last-modified: 2021-06-30
description: Temnothorax is a large myrmicine ant genus with a range spanning the northern hemisphere, including the northern half of the Neotropics. Many of the Neotropical species were originally placed in the now defunct genus Macromischa. Recent molecular work has revealed that distinct lineages of Neotropical Temnothorax have arrived by evolutionary convergenceat a morphological syndrome with characteristics that were used to diagnose the former genus Macromischa. One such lineage is the salvini clade, which in this study is redefined to contain 63 species, 35 of which are described as new. A key to all species of the salvini clade based on the worker caste is provided; additionally, a worker-based key to all clades of the New World is provided. The following species are redescribed: T. albispinus (Wheeler), T. androsanus (Wheeler), T. annexus (Baroni Urbani), T. augusti (Baroni Urbani), T. aztecus (Wheeler), T. ciferrii (Menozzi & Russo), T. flavidulus (Wheeler & Mann), T. fuscatus (Mann), T. goniops (Baroni Urbani), T. huehuetenangoi (Baroni Urbani), T. ixili (Baroni Urbani), T. leucacanthus (Baroni Urbani), T. nigricans (Baroni Urbani), T. ocarinae (Baroni Urbani), T. pastinifer (Emery), T. pergandei (Emery), T. politus (Smith), T. pulchellus (Emery), T. rugosus (Mackay), T. salvini (Forel), T. schwarzi (Mann), T. skwarrae (Wheeler), T. subditivus (Wheeler), T. tenuisculptus (Baroni Urbani), T. terricola (Mann), T. terrigena (Wheeler), T. torrei (Aguayo). The gynes of T. ciferrii, T. fuscatus, T. ixili, T. politus, T. rugosus, T. salvini, T. tenuisculptus and T. torrei are described. The males of T. albispinus and T. fuscatus are described. Lectotypes are designated for T. androsanus, T. annexus, T. augusti, T. aztecus, T. flavidulus, T. fuscatus, T. nigricans, T. pastinifer, T. pergandei, T. politus, T. pulchellus, T. salvini, T. skwarrae, T. subditivus, T. terricola, and T. terrigena. A neotype for Temnothorax salvini obscurior (Forel) is designated, the taxon is raised to species, and a replacement name is designated: T. longicaulisstat. nov., nom. nov. The following species are described as new: T. achiisp. nov., T. acuminatussp. nov., T. acutispinosussp. nov., T. agavicolasp. nov., T. altinodussp. nov., T. arbustussp. nov., T. aureussp. nov., T. aztecoidessp. nov., T. bahorucosp. nov., T. balaclavasp. nov., T. balneariussp. nov., T. bisonsp. nov., T. casanovaisp. nov., T. fortispinosussp. nov., T. harlequinasp. nov., T. hippolytussp. nov., T. laticrussp. nov., T. leucacanthoidessp. nov., T. longinoisp. nov., T. magnabullasp. nov., T. misomoschussp. nov., T. nebliselvasp. nov., T. obtusigastersp. nov., T. paraztecussp. nov., T. parralensissp. nov., T. parvidentatussp. nov., T. pilicornissp. nov., T. quercicolasp. nov., T. quetzalsp. nov., T. rutabulafersp. nov., T. terraztecussp. nov., T. tuxtlanussp. nov., T. wettererisp. nov., T. wilsonisp. nov., T. xincaisp. nov.
creator: Matthew M. Prebus
uri: https://doi.org/10.7717/peerj.11514
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Prebus

title: The impact of PIT tags on the growth and survival of pythons is insignificant in randomised controlled trial
link: https://peerj.com/articles/11531
last-modified: 2021-06-30
description: Individual identification is fundamental to the study of captive and wild animals but can have adverse impacts if the method of identification is inappropriate for the species or question of interest. We conducted a randomised controlled trial to test whether passive integrated transponder (PIT) tags reduced the growth or survival of pythons. We randomly allocated 200 captive-bred Burmese python (Python bivittatus) hatchlings into two groups, tagged versus untagged. Hatchlings were individually identified using a combination of PIT tags and unique colour patterns, and their mass, snout-vent length (SVL) and body condition measured at 9, 73, 134, 220, 292 and 385 days of age. We recorded the date of all mortalities. Python morphometrics and their rate of change increased or fluctuated non-linearly with age. The impact of PIT tagging on python body mass and body mass growth over the 376 day study period was insignificant. PIT tagging additionally had an insignificant impact on python survival. However, we found minor differences in SVL growth between tagged and untagged pythons. These differences peaked at approximately 0.5 mm/day and appeared to drive similar, but more pronounced, differences between tagged and untagged pythons in their rate of change in body condition; peaking at approximately 3–4 g/day. While we cannot be certain that these small differences are, or are not, biologically meaningful, they nonetheless appear to be short-term and readily resolved. Unsurprisingly, the strongest driver of python growth was their age, with growth rapidly increasing or highest amongst younger snakes for all measures of size. Python sex was associated with their body mass and survival, with higher mass but lower survival amongst females. Python size at hatching did not impact on their growth or survival. Our results confirm that PIT tags are a valuable and effective tool for the identification and tracking of captive pythons, and snakes generally, and meet high safety and animal welfare standards.
creator: Patrick L. Taggart
creator: Stephen Morris
creator: Charles G.B. Caraguel
uri: https://doi.org/10.7717/peerj.11531
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Taggart et al.

title: Whole blood fatty acid concentrations in the San Cristóbal Galápagos tortoise (Chelonoidis chathamensis)
link: https://peerj.com/articles/11582
last-modified: 2021-06-30
description: To continue releasing San Cristóbal Galápagos tortoises housed in managed-care facilities at the Giant Tortoise Breeding Center of Galápagos National Park (Galapaguera de Cerro Colorado) to the Otoy Ecological Farm, health assessments and physical examinations were conducted. As a part of these wellness examinations, blood was drawn from 11 tortoises to analyze fatty acid concentrations. Fatty acid levels can provide insight into the nutritional profiles, immune status, and reproductive health of vertebrates. To the co-author’s knowledge, there is no current information about fatty acids in this species. It was hypothesized that there would be inherent differences based on the different geographic ranges, diets, sex, and age of turtles. It was noted that the ω-6/ω-3 ratio was higher for the breeding center than for the ecological farm and that overall polyunsaturated fatty acids (PUFAs) did not have any significant differences. The ω-6/ω-3 findings can contribute to a global picture of these fatty acids across taxa, as reptiles are underrepresented in this area of research. Additional results are a resourceful starting point for future investigations into how fatty acids are affected in Galápagos tortoises.
creator: Khushboo Dass
creator: Gregory A. Lewbart
creator: Juan Pablo Muñoz-Pérez
creator: Maryuri I. Yépez
creator: Andrea Loyola
creator: Emile Chen
creator: Diego Páez-Rosas
uri: https://doi.org/10.7717/peerj.11582
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Dass et al.

title: Effects of mannan oligosaccharides on growth performance, nutrient digestibility, ruminal fermentation and hematological parameters in sheep
link: https://peerj.com/articles/11631
last-modified: 2021-06-30
description: BackgroundMannan oligosaccharides (MOS) are a promising feed additive in animal husbandry due to mainly improving animal health status. The purpose of this study was to investigate the effects of MOS on growth performance, nutrient digestibility, ruminal fermentation, and twelve hematological parameters in sheep.MethodsNinety-six healthy Hu rams with similar body weights were chosen and divided into four treatment groups (twenty-four rams in each group), in which four different doses of MOS were tested: 0%, 0.8%, 1.6% and 2.4% of the basal diet (on an as-fed basis).ResultsThe results showed that supplementation dietary MOS did not affect feed intake, body weight, average daily weight gain, or ruminal short-chain fatty acids (SCFAs) concentration; the ratio of individual fatty acids to total SCFAs, the C2/C3 ratio, and the hematological parameters in the sheep were also unaltered (P > 0.05). Conversely, supplementation dietary MOS increased the dry matter, organic matter, crude protein, neutral detergent fiber, acid detergent fiber, and ash apparent digestibility (P < 0.05), and decreased the ruminal ammonia concentration in the sheep (P < 0.05), especially at a dose of 1.6%.ConclusionsThis indicates that supplementation dietary MOS improved nutrient utilization by the sheep and nitrogen metabolism in the rumen; however, the effects are too slight to interfere with the basal metabolism in the sheep.
creator: Chen Zheng
creator: Juwang Zhou
creator: Yanqin Zeng
creator: Ting Liu
uri: https://doi.org/10.7717/peerj.11631
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Zheng et al.

title: Heterogeneity of gut microbial responses in healthy household dogs transitioning from an extruded to a mildly cooked diet
link: https://peerj.com/articles/11648
last-modified: 2021-06-30
description: BackgroundThe gut microbiota (GM) is associated with canine health and can be impacted by diet. Dog owners in the U.S. have increasingly shown an interest in feeding their dogs a mildly cooked (MC) diet. However, its impact on canine GM and health remains largely unknown.MethodsHealthy household dogs were tracked upon switching from various brands of extruded to MC diets for four weeks. A health assessment was completed and stool samples were collected by each owner before (day 0) and after the diet transition (day 28). Shotgun metagenomic sequencing was performed at both time points to characterize the GM.ResultsDogs completed the study by either completing the health assessments (n = 31) or providing stool samples at both time points (n = 28). All owners reported either better or no change in overall health at the end of the study (61% and 39%, respectively), and none reported worse overall health. Defecation frequency was also reported to be lower (58%) or about the same (35%). Principal coordinate (PCo) analysis showed a significant shift (p = 0.004) in the β-diversity of the GM upon diet transition (34.2% and 10.3% explained by the first two axes). The abundances of 70 species increased after the diet change (adjusted p < 0.05), 67% and 24% of which belonged to the Lactobacillales and the Enterobacterales orders respectively. The abundances of 28 species decreased (adjusted p < 0.05), 46%, 18%, and 11% of which belonged to the Clostridiales, Bacillales, and Bacteroidales orders, respectively. Lower Lactobacillales and Enterobacterales, and higher Bacteroidales at baseline were associated with a greater shift along the PCo1 axis. Protein content of the baseline diet was correlated with the shift along the PCo1 axis (ρ = 0.67, p = 0.006).ConclusionOwners reported either improvement or no change in health in dogs transitioning from extruded kibble to MC diets for 4 weeks, but this report of health perception requires further exploration in a controlled trial. Diet change also led to a significant shift in the GM profile of healthy dogs. The magnitude of shift was associated with baseline GM and dietary protein, and warrants further examination of individualized responses and personalized nutrition in companion dogs. These results also support future investigation of the impact of a MC diet on health maintenance given its increasing popularity.
creator: Jirayu Tanprasertsuk
creator: Justin Shmalberg
creator: Heather Maughan
creator: Devon E. Tate
creator: LeeAnn M. Perry
creator: Aashish R. Jha
creator: Ryan W. Honaker
uri: https://doi.org/10.7717/peerj.11648
license: https://creativecommons.org/licenses/by-nc/4.0
rights: © 2021 Tanprasertsuk et al.

title: Biosynthesized selenium nanoparticles: characterization, antimicrobial, and antibiofilm activity against Enterococcus faecalis
link: https://peerj.com/articles/11653
last-modified: 2021-06-30
description: BackgroundControl over microbial growth is a crucial factor in determining the success of endodontic therapy. Enterococcus faecalis is the most resistant biofilm-forming species leading to endodontic failure. Hence, the current researches are directed towards discovering materials with superior disinfection properties and lesser cytotoxicity. This study aimed to synthesize and characterize biogenically produced Selenium Nanoparticles, and to evaluate the antimicrobial and antibiofilm efficacy, against Enterococcus Faecalis, for the following test groups: Group I: Distilled water (control), Group II: SeNPs (1 mg/ml), Group III: Calcium hydroxide (1 mg/ml), Group IV: 2% Chlorhexidine gluconate (CHX), Group V: 5.25% Sodium hypochlorite (NaOCl).Materials and MethodsSelenium nanoparticles were derived using fresh guava leaves (Psidium guajava) and were characterized. The antibacterial efficacy against E. faecalis was evaluated by agar well diffusion method. The antibiofilm efficacy of the test groups was observed by viable cell count, antibiofilm assay, and Anthrone and Bradford’s tests. The morphology of the biofilms was analysed using the Scanning Electron Microscope and Fourier Transform Infrared spectroscopy.ResultsAntibacterial and antibiofilm efficacy of all tested solutions showed superior antibacterial and antibiofilm efficacy when compared to the control group. Overall, SeNPs (Group II) was the most effective against E. faecalis biofilm, followed by NaOCl (Group V), CHX (Group IV), and Ca(OH)2 (Group III).ConclusionBiogenically produced SeNPs emerged as a novel antibacterial and antibiofilm agent against E. faecalis. This nano-formulation demonstrates the potential to be developed as a root canal disinfectant combating bacterial biofilm in endodontics after the results have been clinically extrapolated.
creator: Sanjay Miglani
creator: Nobuyuki Tani-Ishii
uri: https://doi.org/10.7717/peerj.11653
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Miglani and Tani-Ishii

title: New austrolimulid from Russia supports role of Early Triassic horseshoe crabs as opportunistic taxa
link: https://peerj.com/articles/11709
last-modified: 2021-06-30
description: Horseshoe crabs are extant marine euchelicerates that have a fossil record extending well into the Palaeozoic. Extreme xiphosurid morphologies arose during this evolutionary history. These forms often reflected the occupation of freshwater or marginal conditions. This is particularly the case for Austrolimulidae—a xiphosurid family that has recently been subject to thorough taxonomic examination. Expanding the austrolimulid record, we present new material from the Olenekian-aged Petropavlovka Formation in European Russia and assign this material to Attenborolimulus superspinosus gen. et sp. nov. A geometric morphometric analysis of 23 horseshoe crab genera illustrates that the new taxon is distinct from limulid and paleolimulid morphologies, supporting the assignment within Austrolimulidae. In considering Triassic austrolimulids, we suggest that the hypertrophy or reduction in exoskeletal sections illustrate how species within the family evolved as opportunistic taxa after the end-Permian extinction.
creator: Russell D.C. Bicknell
creator: Dmitry E. Shcherbakov
uri: https://doi.org/10.7717/peerj.11709
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Bicknell and Shcherbakov