Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing
DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.
Hoban et al. (2022) Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ 10:e13790 https://doi.org/10.7717/peerj.13790
Epigenetic modification mechanism of histone demethylase KDM1A in regulating cardiomyocyte apoptosis after myocardial ischemia-reperfusion injury
Hypoxia and reoxygenation (H/R) play a prevalent role in heart-related diseases. Histone demethylases are involved in myocardial injury. In this study, the mechanism of the lysine-specific histone demethylase 1A (KDM1A/LSD1) on cardiomyocyte apoptosis after myocardial ischemia-reperfusion injury (MIRI) was investigated. Firstly, HL-1 cells were treated with H/R to establish the MIRI models. The expressions of KDM1A and Sex Determining Region Y-Box Transcription Factor 9 (SOX9) in H/R-treated HL-1 cells were examined. The cell viability, markers of myocardial injury (LDH, AST, and CK-MB) and apoptosis (Bax and Bcl-2), and Caspase-3 and Caspase-9 protein activities were detected, respectively. We found that H/R treatment promoted cardiomyocyte apoptosis and downregulated KDM1A, and overexpressing KDM1A reduced apoptosis in H/R-treated cardiomyocytes. Subsequently, tri-methylation of lysine 4 on histone H3 (H3K4me3) level on the SOX9 promoter region was detected. We found that KDM1A repressed SOX9 transcription by reducing H3K4me3. Then, HL-1 cells were treated with CPI-455 and plasmid pcDNA3.1-SOX9 and had joint experiments with pcDNA3.1-KDM1A. We disclosed that upregulating H3K4me3 or overexpressing SOX9 reversed the inhibitory effect of overexpressing KDM1A on apoptosis of H/R-treated cardiomyocytes. In conclusion, KDM1A inhibited SOX9 transcription by reducing the H3K4me3 on the SOX9 promoter region and thus inhibited H/R-induced apoptosis of cardiomyocytes.
He et al. (2022) Epigenetic modification mechanism of histone demethylase KDM1A in regulating cardiomyocyte apoptosis after myocardial ischemia-reperfusion injury. PeerJ 10:e13823 https://doi.org/10.7717/peerj.13823
Gender differences in demographic and clinical characteristics in patients with HBV-related liver diseases in China
Background The gender differences in demographic and clinical characteristics were examined in patients with hepatitis B virus (HBV)-related liver diseases. Methods Overall, 634 patients (44.7 ± 13.8 years) were consecutively included. Data of demographic and clinical characteristics were collected during an assessment interview. Comparisons between male and female patients in terms of demographic and clinical data were carried out using univariate analyses. The independent associations between the demographic and clinical variables and gender were examined with either logistic regression or analysis of covariance as appropriate. Results The study sample consisted of 452 male and 182 female patients. Multiple logistic regression analyses revealed that being employed (OR = 3.4), personal monthly income <3,000 yuan (OR = 0.3), being current alcohol users (OR = 6.4), Cirrhosis (OR = 5.9), Hepatocellular Carcinoma (HCC) (OR = 8.5) and having less severe insomnia (OR = 0.6) were independently associated with male gender. The analysis of covariance revealed that after controlling for other potential confounding variables, later onset of HBV-related diseases (F = 4.5, p = 0.03) and older age (F = 6.7, p = 0.009) were independently associated with male gender. Conclusions Given the significant clinical differences in male and female patients with HBV-related liver diseases, more attention should be given to gender-specific treatment and prevention for this population.
Liu et al. (2022) Gender differences in demographic and clinical characteristics in patients with HBV-related liver diseases in China. PeerJ 10:e13828 https://doi.org/10.7717/peerj.13828
In silico testing of flavonoids as potential inhibitors of protease and helicase domains of dengue and Zika viruses
Background Dengue and Zika are two major vector-borne diseases. Dengue causes up to 25,000 deaths and nearly a 100 million cases worldwide per year, while the incidence of Zika has increased in recent years. Although Zika has been associated to fetal microcephaly and Guillain-Barré syndrome both it and dengue have common clinical symptoms such as severe headache, retroocular pain, muscle and join pain, nausea, vomiting, and rash. Currently, vaccines have been designed and antivirals have been identified for these diseases but there still need for more options for treatment. Our group previously obtained some fractions from medicinal plants that blocked dengue virus (DENV) infection in vitro. In the present work, we explored the possible targets by molecular docking a group of molecules contained in the plant fractions against DENV and Zika virus (ZIKV) NS3-helicase (NS3-hel) and NS3-protease (NS3-pro) structures. Finally, the best ligands were evaluated by molecular dynamic simulations. Methods To establish if these molecules could act as wide spectrum inhibitors, we used structures from four DENV serotypes and from ZIKV. ADFR 1.2 rc1 software was used for docking analysis; subsequently molecular dynamics analysis was carried out using AMBER20. Results Docking suggested that 3,5-dicaffeoylquinic acid (DCA01), quercetin 3-rutinoside (QNR05) and quercetin 3,7-diglucoside (QND10) can tightly bind to both NS3-hel and NS3-pro. However, after a molecular dynamics analysis, tight binding was not maintained for NS3-hel. In contrast, NS3-pro from two dengue serotypes, DENV3 and DENV4, retained both QNR05 and QND10 which converged near the catalytic site. After the molecular dynamics analysis, both ligands presented a stable trajectory over time, in contrast to DCA01. These findings allowed us to work on the design of a molecule called MOD10, using the QND10 skeleton to improve the interaction in the active site of the NS3-pro domain, which was verified through molecular dynamics simulation, turning out to be better than QNR05 and QND10, both in interaction and in the trajectory. Discussion Our results suggests that NS3-hel RNA empty binding site is not a good target for drug design as the binding site located through docking is too big. However, our results indicate that QNR05 and QND10 could block NS3-pro activity in DENV and ZIKV. In the interaction with these molecules, the sub-pocket-2 remained unoccupied in NS3-pro, leaving opportunity for improvement and drug design using the quercetin scaffold. The analysis of the NS3-pro in complex with MOD10 show a molecule that exerts contact with sub-pockets S1, S1’, S2 and S3, increasing its affinity and apparent stability on NS3-pro.
Cruz-Arreola et al. (2022) In silico testing of flavonoids as potential inhibitors of protease and helicase domains of dengue and Zika viruses. PeerJ 10:e13650 https://doi.org/10.7717/peerj.13650
Randomized feasibility trial of the Scleroderma Patient-centered Intervention Network hand exercise program (SPIN-HAND)
Purpose The Scleroderma Patient-centered Intervention Network (SPIN) online hand exercise program (SPIN-HAND), is an online self-help program of hand exercises designed to improve hand function for people with scleroderma. The objective of this feasibility trial was to evaluate aspects of feasibility for conducting a full-scale randomized controlled trial of the SPIN-HAND program. Materials and Methods The feasibility trial was embedded in the SPIN cohort and utilized the cohort multiple randomized controlled trial (cmRCT) design. In the cmRCT design, at the time of cohort enrollment, cohort participants consent to be assessed for trial eligibility and randomized prior to being informed about trials conducted using the cohort. When trials were conducted in the cohort, participants randomized to the intervention were informed and consented to access the intervention. Participants randomized to control were not informed that they have not received an intervention. All participants eligible and randomized to participate in the trial were included in analyses on an intent-to-treat basis. Cohort participants with a Cochin Hand Function Scale score ≥ 3/90 and an interest in using an online hand-exercise intervention were randomized (1:1 ratio) to be offered as usual care plus the SPIN-HAND Program or usual care for 3 months. User satisfaction was assessed with semi-structured interviews. Results Of the 40 randomized participants, 24 were allocated to SPIN-HAND and 16 to usual care. Of 24 participants randomized to be offered SPIN-HAND, 15 (63%) consented to use the program. Usage of SPIN-HAND content among the 15 participants who consented to use the program was low; only five (33%) logged in more than twice. Participants found the content relevant and easy to understand (satisfaction rating 8.5/10, N = 6). Automated eligibility and randomization procedures via the SPIN Cohort platform functioned properly. The required technical support was minimal. Conclusions Trial methodology functioned as designed, and the SPIN-HAND Program was feasibly delivered; however, the acceptance of the offer and use of program content among accepters were low. Adjustments to information provided to potential participants will be implemented in the full-scale SPIN-HAND trial to attempt to increase offer acceptance.
Kwakkenbos et al. (2022) Randomized feasibility trial of the Scleroderma Patient-centered Intervention Network hand exercise program (SPIN-HAND). PeerJ 10:e13471 https://doi.org/10.7717/peerj.13471
Molecular identification and first demographic insights of sharks based on artisanal fisheries bycatch in the Pacific Coast of Colombia: implications for conservation
The Pacific coast of Colombia is characterized by mangrove ecosystems which play a crucial role as possible nurseries for juvenile sharks. However, trophic food webs from coastal ecosystems are heavily disturbed by increased fishing pressure, which affects numerous shark species. In this region of the Eastern Tropical Pacific (ETP), fisheries’ data from coastal areas are scarce and unspecific, as most sharks from artisanal fisheries are landed decapitated and finless, making their morphological identification difficult. For the establishment and implementation of effective regional conservation and management policies, information on the diversity and population dynamics of shark species is crucial. We therefore sequenced the mitochondrial NADH2 gene of 696 samples taken from fishermen’s landings of shark’s bycatch along the Colombian north Pacific coast. We were able to identify 14 species of sharks, two of the most abundant species were Sphyrna lewini and Carcharhinus falciformis, both evaluated on IUCN the Red List of Threatened species (Critically Endangered and Vulnerable) and CITES regulated. We found low genetic diversity in the sampled area increasing the concern for both species in the region, even more considering that the majority of individuals were juveniles. Our results showed the importance of genetic markers for first population genetic insights as a complementary tool during the decision-making process in management plans. For this specific region, strategies such as the delimitation of conservation priority areas or the regulation of fishing gears could help improve the sustainability of shark populations in the Colombian Pacific.
Villate-Moreno et al. (2022) Molecular identification and first demographic insights of sharks based on artisanal fisheries bycatch in the Pacific Coast of Colombia: implications for conservation. PeerJ 10:e13478 https://doi.org/10.7717/peerj.13478
Factors limiting reproductive success in urban Greylag Geese (Anser anser)
In the late eighties, Greylag Geese (Anser anser) started to colonise an urban area previously void of geese in southwestern Germany. Between 2004 and 2020, in a period of steady population increase with subsequent population stagnation, we analysed two measures of reproductive success: (1) the relation between freshly hatched to fledged young for each brood and (2) the probability of a hatchling to survive to fledging. We were able to show that the dispersal of pairs from the nesting site to a different brood rearing area resulted in higher reproductive success. However, the increasing population size of Greylag Geese and the number of breeding pairs of recently immigrated Egyptian Geese (Alopochen aegyptiaca) had a negative impact on reproductive success, indicating density dependence. Our results show that newly established populations in urban settings do not grow indefinitely, which is an important fact that should be taken into account by wildlife managers.
Mai et al. (2022) Factors limiting reproductive success in urban Greylag Geese (Anser anser). PeerJ 10:e13685 https://doi.org/10.7717/peerj.13685
The COVID-19 infodemic in Brazil: trends in Google search data
Background Since the beginning of the new coronavirus pandemic, there has been much information about the disease and the virus has been in the spotlight, shared and commented upon on the Internet. However, much of this information is infodemics and can interfere with the advancement of the disease and that way that populations act. Thus, Brazil is a country that requires attention, as despite the fact that in almost two years of pandemic it has shown a devastating numbers of deaths and number of cases, and generates false, distorted and malicious news about the pandemic. This work intends to understand the attitudes of the Brazilian population using infodemic queries from the Google Trends search tool and social and income variables. Methods Data from infodemic research carried out on Google Trends, between January 1, 2020 and June 30, 2021, with socioeconomic data, such as income and education, were unified in a single database: standardization and exploratory and multivalued techniques based on grouping were used in the study. Results In the analysis of the search trend of infodemic terms, it is clear that the categories of Prevention and Beliefs should stand out in Brazil, where there is a diverse culture. It is followed by the COVID-19 Treatment category, with treatments that were not those recommended by the authorities. Income transfer programs and information on socioeconomic variables did not have much impact on infodemic surveys, but it was observed that states where President Bolsonaro has more supporters had researched more infodemic information. Conclusions In a country as geographically large as Brazil, it is important that political authorities go to great lengths to disseminate reliable information and monitor the infodemic in the media and on the internet. It was concluded that the denial of the pandemic and the influence of political leaders influenced the search for infodemic information, contributing to a disorganization in the control of the disease and prevention measures.
Harb et al. (2022) The COVID-19 infodemic in Brazil: trends in Google search data. PeerJ 10:e13747 https://doi.org/10.7717/peerj.13747
Environmental detection of Fasciola hepatica by loop-mediated isothermal amplification
Fasciola hepatica, commonly referred to as liver flukes, is a substantial zoonotic parasitic disease of humans and livestock globally. While infection is readily controlled by anthelmintics, namely triclabendazole, the heavy reliance on triclabendazole has resulted in drug resistance appearing worldwide. Due to drug resistance, it is imperative to adopt an integrated parasite management program to preserve the efficacy of currently available anthelmintics. A integrated liver fluke management plan would benefit from a simple rapid, field-deployable diagnostic for detection of F. hepatica in environment and the host. Therefore, a rapid DNA test using loop-mediated isothermal amplification was developed and optimised for the detection of F. hepatica from faecal and water samples to enable the detection of parasites both within the host and from the environment. The assay presented here is fast, with amplification in ≤20 min, and highly sensitive, with a detection limit of 5 × 10−4 ng/µL. The workflow presented here provides a time to result of ≤60 min without requiring a commercial kit for the extraction of DNA from faecal and water samples, and pending further validation from field-samples, could potentially be used to enable real-time decision making to mitigate parasite prevalence on a farming property and with no requirement for sample transportation.
Tran et al. (2022) Environmental detection of Fasciola hepatica by loop-mediated isothermal amplification. PeerJ 10:e13778 https://doi.org/10.7717/peerj.13778
HMGB1-activatied NLRP3 inflammasome induces thrombocytopenia in heatstroke rat
Background Thrombocytopenia, an early common complication in heatstroke (HS), has been widely considered as a mortality predictor of HS. The mechanism underlying thrombocytopenia in HS remains unknown. It is not known whether NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome is activated in HS platelet, which, in turn, induces platelet activation and thrombocytopenia. This study tried to clarify the activation of the NOD-like receptor signaling pathway under HS conditions and investigate its roles in mediating HS-induced thrombocytopenia. Methods Rat HS models were established in a certain ambient temperature and humidity. Platelets, isolated from blood, were counted and CD62P, an index of platelet activation, was measured by flow cytometry in all rats. The colocalization of NLRP3 inflammasome in platelet was detected by confocal fluorescence microscopy. Mitochondrial-derived reactive oxygen species (ROS) was detected using the molecular probes. Plasma HMGB1 and IL-1β levels were measured by ELISA. Results Platelet activation, showed by upregulated CD62P, and thrombocytopenia were observed in HS rats. HS activated the NLRP3 inflammasome, which was induced by elevated levels of ROS, while the upregulated CD62P and thrombocytopenia triggered by NLRP3 inflammasome were attributed to the high mobility group box protein 1 (HMGB1) inplasma. Moreover, inhibition of the NOD-like receptor signaling pathway in rats with HS suppressed platelet activation and the decline of platelet count. Similar results were obtained when the receptor toll-like receptor 4 (TLR4)/advanced glycation end product (RAGE) was blocked. Conclusions The NOD-like receptor signaling pathway induces platelet activation and thrombocytopenia in HS rats. These findings suggested that the NLRP3 inflammasome might be the potential target for HS treatment.
Yin et al. (2022) HMGB1-activatied NLRP3 inflammasome induces thrombocytopenia in heatstroke rat. PeerJ 10:e13799 https://doi.org/10.7717/peerj.13799