Characterization of the complete mitochondrial genome of the Sunda stink-badger (Mydaus javanensis) from the island of Borneo
Background The Mephitidae is a family of skunks and stink-badgers that includes 12 extant species in four genera, namely, Mydaus, Conepatus, Mephitis and Spilogale. Mydaus is the only genus within Mephitidae found outside the American continent, with its distribution limited to the islands of Borneo, Indonesia and Philippines. There are two extant species of Mydaus i.e., javanensis and marchei. Currently, complete mitogenomes are unavailable for either species. Here, we present the characterization of the first complete mitogenome for the Sunda stink-badger (Mydaus javanensis) from the island of Borneo. Methods Muscle tissue was obtained and the DNA was sequenced using a combination of Illumina Barcode Tagged Sequence (BTSeq) and Sanger sequencing techniques. The genome was annotated with MITOS and manually checked for accuracy. A circular map of the mitogenome was constructed with Proksee. Relative synonymous codon usage (RSCU) and codon frequency were calculated using MEGA-X. The protein coding genes (PCGs) were aligned with reference sequences from GenBank and used for the construction of phylogenetic trees (maximum liklihood (ML) and Bayesian inference (BI)). Additionally, due to the lack of available complete genomes in public databases, we constructed another tree with the cyt b gene. Results The complete circular mitogenome was 16,391 base pairs in length. It comprises the typical 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes, one control region (CR) and an L-strand replication origin (OL). The G+C content was 38.1% with a clear bias towards A and T nucleotides. Of the 13 PGCs, only ND6 was positioned in the reverse direction, along with five other tRNAs. Five PCGs had incomplete stop codons and rely on post-transcriptional polyadenylation (TAA) for termination. Based on the codon count, Leucine was the most common amino acid (589), followed by Threonine (332) and Isoleucine (325). The ML and BI phylogenetic trees, based on concatenated PCGs and the cyt b gene, respectively, correctly clustered the species with other members of the Mephitidae family but were unique enough to set it apart from Conepatus, Mephitis and Spilogale. The results confirm Mydaus as a member of the mephitids and the mitogenome will be useful for evolutionary analysis and conservation of the species.
Subbiah et al. (2024) Characterization of the complete mitochondrial genome of the Sunda stink-badger (Mydaus javanensis) from the island of Borneo. PeerJ 12:e18190 https://doi.org/10.7717/peerj.18190
UV-B irradiation promotes anthocyanin biosynthesis in the leaves of Lycium ruthenicum Murray
Anthocyanins are the most valuable pigments in Lycium ruthenicum Murray (L. ruthenicum). Although ultraviolet-B (UV-B) irradiation is a key environmental factor influencing anthocyanin biosynthesis in L. ruthenicum, the deep molecular mechanism remains unclear. Herein, we examined the changes in the total anthocyanin content and transcriptomic characteristics of L. ruthenicum leaves following UV-B irradiation treatment. The results showed a twofold increase in anthocyanin content in the leaves of L. ruthenicum after the treatment. The transcriptome analysis showed that the expression of 24 structural genes identified in the anthocyanin synthesis pathway was up-regulated. In particular, F3’H (Unigene0009145) and C4H (Unigene0046607) exhibit notable up-regulation, suggesting their potential roles in anthocyanin synthesis. Protein interaction network results revealed that MYB1 (Unigene0047706) had the highest connectivity, followed by bHLH (Unigene0014085). Additionally, UVR8 (Unigene0067978) and COP1 (Unigene0008780) were found to be highly involved in UV-B signal transduction. These findings provide new insights into the genetic and biochemical mechanisms that regulate anthocyanin production, and could guide agricultural practices to reduce environmental impacts and improve crop yield and quality.
Chen et al. (2024) UV-B irradiation promotes anthocyanin biosynthesis in the leaves of Lycium ruthenicum Murray. PeerJ 12:e18199 https://doi.org/10.7717/peerj.18199
Exploring the density and morphology of coconut structures at two locations: a time-based analysis using computer tomography
Background The study aimed to observe the internal structure of coconuts from two locations (coastal and non-coastal) using computed tomography (CT). Methods Seventy-six mature coconuts were collected from Wenchang and Ding’an cities in Hainan Province. These coconuts were scanned four times using CT, with a two-week interval between each scan. CT data were post-processed to reconstruct two-dimensional slices and three-dimensional models. The density and morphological parameters of coconut structures were measured, and the differences in these characteristics between the two groups and the changes over time were analyzed. Results Time and location had interactive effects on CT values of embryos, solid endosperms and mesocarps, morphological information such as major axis of coconut, thickness of mesocarp, volume of coconut water and height of bud (p < 0.05). Conclusions Planting location and observation time can affect the density and morphology of some coconut structures.
Lin et al. (2024) Exploring the density and morphology of coconut structures at two locations: a time-based analysis using computer tomography. PeerJ 12:e18206 https://doi.org/10.7717/peerj.18206
Effects of different ratios of nitrogen base fertilizer to topdressing on soil nitrogen form and enzyme activity in sugar beet under shallow drip irrigation
Sugar beets account for 30% of global sugar production each year, and their byproducts are an important source of bioethanol and animal feed. Sugar beet is an important cash crop in Inner Mongolia, China. To achieve high yields and sugar content, it is essential to supply nitrogen fertilizer in accordance with the growth characteristics of sugar beet, thereby enhancing the efficiency of nitrogen fertilizer utilization. A two-year experiment was carried out in the experimental field of the Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences. The impact of varying ratios of nitrogen-based fertilizer to topdressing on nitrate nitrogen and ammonium nitrogen levels in the 20–60 cm soil layer, as well as the activities of protease, urease, catalase, and sucrose in the 20–40 cm soil layer were investigated during the rapid leaf growth period and root and sugar growth period. Results indicated that different ratios of nitrogen-based fertilizer to topdressing significantly influenced the levels of nitrate nitrogen and ammonium nitrogen, and the activities of protease and urease in the 0–20 cm soil layer, with these effects diminishing as soil depth increased. The activities of catalase and sucrose were minimally impacted. Nitrogen was applied at 150 kg/ha during the growth period of sugar beet, according to the growth characteristics of sugar beet to maximize nitrogen utilization efficiency. Topdressing was completed with irrigation at the rapid growth stage. The nitrogen-based fertilizer to topdressing ratio of 6:4 resulted in optimal crop yield and sugar yield of sugar beet under shallow drip irrigation. Additionally, the activities of protease and urease in different soil treatments were significantly different, and the activities of protease and urease in the 0–40 cm soil layer were identified as useful soil physiological indicators for nitrogen utilization in sugar beet.
Li et al. (2024) Effects of different ratios of nitrogen base fertilizer to topdressing on soil nitrogen form and enzyme activity in sugar beet under shallow drip irrigation. PeerJ 12:e18219 https://doi.org/10.7717/peerj.18219
World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens
Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.
Ion et al. (2024) World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens. PeerJ 12:e18229 https://doi.org/10.7717/peerj.18229
The impact of scabies in tent cities in Kahramanmaraş after the Turkish earthquakes: oral pharmacologic treatment efficacy
Background Our study was conducted to determine the impact of scabies in people living in collective living areas such as tent cities and container cities after the February 6 Kahramanmaraş earthquakes and to show the effectiveness of oral ivermectin treatment on scabies cases because topical treatments could not be used in this period when access to water was limited. Methods Among 233 patients diagnosed and treated with scabies in tent and container cities, 192 patients who met the criteria were included in the study. Descriptive statistics were given as number (n), percentage (%), mean, median, standard deviation (SD). In the comparison of categorical data, the chi-square test was applied; in the comparison of numerical data ANOVA analyses was applied. Results A total of 192 scabies patients (82.4%), 47.9% (N:92) of whom were women, were included in the study. The frequency of scabies in the total population in tent cities and container cities was found to be at least 0.54%. The most common symptoms were pruritis (99.0%) and rash (97.9%). The most common sites of lesion involvement were the umbilicus (87.0.%), forearm (75.0%), and back (70.3%). After the first dose of ivermectin, 159 (82.8%) patients showed complete recovery, while 30 (15.6%) patients showed partial recovery. 3 (1.6%) patients showed no improvement. After the second dose of ivermectin, 173 (90.1%) patients showed complete recovery. There were two (1.0%) patients who did not show improvement after two doses. Due to the deterioration of urban infrastructure after devastating earthquakes, the irregularity of mass living areas, the lack of hygiene conditions, and the difficulty of accessing clean, usable water, oral ivermectin may be the first choice for treatment in terms of ease of use and effectiveness.
Beyoğlu et al. (2024) The impact of scabies in tent cities in Kahramanmaraş after the Turkish earthquakes: oral pharmacologic treatment efficacy. PeerJ 12:e18242 https://doi.org/10.7717/peerj.18242
Comparative transcriptome and hormone analyses of roots in apple among three rootstocks with different rooting abilities
Background Root plays an important role in the growth and development of fruit trees; however, the molecular mechanisms behind the differences among rootstock varie-ties remain unclear. Methods This study examined the effects of different rootstocks on root structure and the endogenous hormone content of 1-year old apple seedlings in combinations of Tianhong 2 (T2)/Malus robusta (HT), T2/G935, and T2/Jizhen 2 (J2). Results The results showed that the T2/HT treatment had greater root length, surface area, volume, average diameter, tips and forks, followed by G935 and J2. In T2/HT leaves and roots, the indole-3-acetic acid (IAA) and gibberellins (GA3) levels were highest, and the abscisic acid (ABA) levels were the lowest. A root transcriptome analysis detected 10,064, 10,511, and 8,719 differentially expressed genes in T2/HT vs. T2/G935, T2/HT vs. T2/J2, and T2/J2 vs. T2/G935, respectively. The analysis of Gene Ontology (GO) terms indicated a significant enrichment in biological processes, cellular components, and molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that plant hormone signaling, MAPK signaling pathway–plant, and plant–pathogen interaction played important roles in differences in the rooting ability of different rootstocks. In addition, some key differential genes were associated with root growth and development and were involved in these metabolic pathways. This study is important for enriching theoretical studies of fruit tree roots.
Li et al. (2024) Comparative transcriptome and hormone analyses of roots in apple among three rootstocks with different rooting abilities. PeerJ 12:e18244 https://doi.org/10.7717/peerj.18244
Association of serum Metrnl levels and high-density lipoprotein cholesterol in patients with type 2 diabetes mellitus: a cross-sectional study
Purpose Meteorin-like (Metrnl) is a novel adipokine which is highly expressed in adipose tissue and has a beneficial effect on glucose and lipid metabolism. High density lipoprotein cholesterol (HDL-C) is well recognized to be inversely associated with cardiovascular events. However, the relationship between serum Metrnl levels and HDL-C in the type 2 diabetes mellitus (T2DM) remains unclear. Therefore, the present study aimed to evaluate the association of serum Metrnl with HDL-C levels in T2DM. Materials and Methods Eighty participants with T2DM were included in this cross-sectional study. They were divided into two groups according to HDL-C levels: Group1 (lower HDL-C group): HDL-C < 1.04 mmol/L; Group2 (higher HDL-C group): HDL-C ≥ 1.04 mmol/L. Serum Metrnl levels were measured by enzyme-linked immunosorbent assay (ELISA). Results As compared with lower HDL-C levels groups, serum Metrnl levels were significantly higher in the group with higher HDL-C. Binary logistic regression analysis showed serum Metrnl levels were positively associated with HDL-C group after adjustment with sex, age, body mass index (BMI), mean arterial pressure (MAP), fasting blood glucose (FPG), triglyceride (TG). Furthermore, serum Metrnl levels were inversely correlated with insulin resistance index (HOMA-IR). HDL-C levels were lowest in the group with the lowest Metrnl levels group and remained positively associated with Metrnl after adjustment for sex, age, BMI, TG, and HOMA-IR by using multivariate logistic regression analysis. Conclusion Serum Metrnl levels were positively associated with HDL-C levels in patients with T2DM.This suggests that increasing serum Metrnl levels maybe a candidate for improving lipid metabolism and preventing cardiovascular events in T2DM. Registry and the Registration No. of the Study/Trial The study was registered in the Chinese clinical trial registry (ChiCTR- 2100047148).
Zhou et al. (2024) Association of serum Metrnl levels and high-density lipoprotein cholesterol in patients with type 2 diabetes mellitus: a cross-sectional study. PeerJ 12:e18264 https://doi.org/10.7717/peerj.18264
Ultra-rapid detection of nuclear protein of severe fever with thrombocytopenia syndrome virus by colloidal gold immunochromatography assay
In 2009, severe fever with thrombocytopenia syndrome virus (SFTSV), also known as the Dabie bandavirus (DBV), was first discovered in Henan, China. It is a tick-borne zoonotic virus with a fatality rate ranging from 6% to 30%. Currently, we lack safe and effective vaccines or antiviral drugs to treat SFTSV infection. Therefore, the development of a specific, sensitive, and cost-effective detection method is crucial. Using inactivated SFTSV and recombinant SFTSV nucleocapsid protein (SFTSV-NP), we repeatedly immunized mice with different adjuvants and obtained two monoclonal antibodies against SFTSV-NP, which were used to develop a colloidal gold immunochromatographic assay (ICA) rapid test kit for SFTSV. Compared with nucleic acid testing (gold standard), the ICA test strips are 97.67% accurate in testing clinical serum samples (36 cases of clinical serum samples and seven cases of whole blood samples). The test kit was 100% accurate in detecting different SFTSV strains. No false-positive results were generated when detecting other arboviruses. Therefore, our developed SFTSV test kit conveniently, rapidly, and effectively detects SFTSV.
Huang et al. (2024) Ultra-rapid detection of nuclear protein of severe fever with thrombocytopenia syndrome virus by colloidal gold immunochromatography assay. PeerJ 12:e18275 https://doi.org/10.7717/peerj.18275
A small venomous reptile from the Late Triassic (Norian) of the southwestern United States
Reptile feeding strategies encompass a wide variety of diets and accompanying diversity in methods for subduing prey. One such strategy, the use of venom for prey capture, is found in living reptile clades like helodermatid (beaded) lizards and some groups of snakes, and venom secreting glands are also present in some monitor lizards and iguanians. The fossil record of some of these groups shows strong evidence for venom use, and this feeding strategy also has been hypothesized for a variety of extinct reptiles (e.g., archosauromorphs, anguimorphs, and a sphenodontian). However, evidence of systems for venom delivery in extinct groups and its evolutionary origins has been scarce, especially when based on more than isolated teeth. Here, we describe a potentially venomous new reptile, Microzemiotes sonselaensis gen. et sp. nov., from a partial left dentary recovered from the Sonsela Member of the Chinle Formation (middle Norian, Upper Triassic) of northeastern Arizona, U.S.A. The three dentary teeth have apices that are distally reclined relative to their bases and the tip of the posteriormost tooth curves mesially. The teeth show subthecodont implantation and are interspaced by empty sockets that terminate above the Meckelian canal, which is dorsoventrally expanded posteriorly. Replacement tooth sockets are positioned distolingually to the active teeth as in varanid-like replacement. We identify this new specimen as a diapsid reptile based on its monocuspid teeth that lack carinae and serrations. A more exclusive phylogenetic position within Diapsida is not well supported and remains uncertain. Several features of this new taxon, such as the presence of an intramandibular septum, are shared with some anguimorph squamates; however, these likely evolved independently. The teeth of the new taxon are distinctively marked by external grooves that occur on the entire length of the crown on the labial and lingual sides, as seen in the teeth of living beaded lizards. If these grooves are functionally similar to those of beaded lizards, which use the grooves to deliver venom, this new taxon represents the oldest known reptile where venom-conducting teeth are preserved within a jaw. The teeth of the new species are anatomically distinct from and ~10x smaller than those of the only other known Late Triassic hypothesized venomous reptile, Uatchitodon, supporting venom use across multiple groups of different body size classes. This new species represents the third Late Triassic reptile species to possibly have used envenomation as a feeding (and/or defensive) strategy, adding to the small number of venomous reptiles known from the Mesozoic Era.
Burch et al. (2024) A small venomous reptile from the Late Triassic (Norian) of the southwestern United States. PeerJ 12:e18279 https://doi.org/10.7717/peerj.18279