Aichi Target 18 beyond 2020: mainstreaming Traditional Biodiversity Knowledge in the conservation and sustainable use of marine and coastal ecosystems
Indigenous Peoples and Local Communities (IPLCs) have inhabited coastal areas, the seas, and remote islands for millennia, and developed place-based traditional ancestral knowledge and diversified livelihoods associated with the biocultural use of marine and coastal ecosystems. Through their cultural traditions, customary wise practices, and holistic approaches to observe, monitor, understand, and appreciate the Natural World, IPLCs have been preserving, managing, and sustainably using seascapes and coastal landscapes, which has been essential for biodiversity conservation. The international community has more than ever recognized the central role of IPLCs in the conservation of biodiversity-rich ecosystems, in particular, for the achievement of the Global Biodiversity Targets determined by the Parties to the United Nations Convention on Biological Diversity to tackle biodiversity loss. However, much remains to be done to fully recognize and protect at national levels IPLCs’ Traditional Biodiversity Knowledge (TBK), ways of life, and their internationally recognized rights to inhabit, own, manage and govern traditional lands, territories, and waters, which are increasingly threatened. At the 2018 4th World Conference on Marine Biodiversity held in Montréal, Canada, eight themed working groups critically discussed progress to date and barriers that have prevented the achievement of the Aichi Biodiversity Targets agreed for the period 2011–2020, and priority actions for the Post-2020 Global Biodiversity Framework. Discussions in the “Application of Biodiversity Knowledge” working group focused on Targets 11 and 18 and the equal valuation of diverse Biodiversity Knowledge Systems (BKS). This Perspective Paper summarizes the 10 Priority Actions identified for a holistic biodiversity conservation, gender equality and human rights-based approach that strengthens the role of IPLCs as biodiversity conservation decision-makers and managers at national and international levels. Furthermore, the Perspective proposes a measurable Target 18 post-2020 and discusses actions to advance the recognition of community-based alternative conservation schemes and TBK to ensure the long-lasting conservation, customary biocultural use, and sustainable multi-functional management of nature around the globe.
Fajardo et al. (2021) Aichi Target 18 beyond 2020: mainstreaming Traditional Biodiversity Knowledge in the conservation and sustainable use of marine and coastal ecosystems. PeerJ 9:e9616 https://doi.org/10.7717/peerj.9616
Expression of vitamin D 1α-hydroxylase in human gingival fibroblasts in vivo
Background Vitamin D 1α-hydroxylase CYP27B1 is the key factor in the vitamin D pathway. Previously, we analyzed the expression of CYP27B1 in human gingival fibroblasts in vitro. In the present study, we analyzed the gingival expression of CYP27B1 in vivo. Methods Forty-two patients with periodontitis Stage IV Grade C and 33 controls were recruited. All patients with periodontitis had unsalvageable teeth and part of the wall of the periodontal pocket was resected and obtained after tooth extraction. All controls needed crown-lengthening surgery, and samples of gingiva resected during surgery were also harvested. All the individuals’ gingivae were used for immunohistochemistry and immunofluorescence. In addition, gingivae from seventeen subjects of the diseased group and twelve subjects of the control group were analyzed by real-time PCR. Results Expression of CYP27B1 was detected both in gingival epithelia and in gingival connective tissues, and the expression in connective tissues colocalized with vimentin, indicating that CYP27B1 protein is expressed in gingival fibroblasts. The expression of CYP27B1 mRNA in gingival connective tissues and the CYP27B1 staining scores in gingival fibroblasts in the diseased group were significantly higher than those in the control group. Conclusions Expression of CYP27B1 in human gingival tissues was detected, not only in the fibroblasts of gingival connective tissues, but also in the gingival epithelial cells, and might be positively correlated with periodontal inflammation.
Liu et al. (2021) Expression of vitamin D 1α-hydroxylase in human gingival fibroblasts in vivo. PeerJ 9:e10279 https://doi.org/10.7717/peerj.10279
Analysis of synonymous codon usage of transcriptome database in Rheum palmatum
Background Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. Methods In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. Results The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.
Huo et al. (2021) Analysis of synonymous codon usage of transcriptome database in Rheum palmatum. PeerJ 9:e10450 https://doi.org/10.7717/peerj.10450
A nature-based health intervention at a military healthcare center: a randomized, controlled, cross-over study
We describe a mixed qualitative and quantitative research study in a military facility regarding the role of nature in well-being. Study intervention included two 20-minute walks. One walk was in an intentionally designed woodland environment (Green Road) and the other was on a busy campus road in a medical treatment facility (Urban Road). Twelve volunteers from a military facility participated in both walks in a cross-over experimental design. The two walking sessions were randomly ordered and preceded by pre-walk instructions appropriate to each road’s characteristics and incorporated focused attention and present moment orientation. A semi-structured post-walk interview, the primary outcome, was conducted after the conclusion of each walk. Qualitative data analyses consisted of sentiments and themes by using NVivo 12 software. The Green Road was unanimously rated as positive (100%). Responses to Urban Road were evenly distributed among positive (33.3%), negative (33.3%), and neutral/mixed (33.3%) sentiments. The Green Road yielded predominantly positive themes such as enjoyment of nature, relaxation, and feelings of privacy and safety. Urban Road produced significantly more negative themes such as concerns for safety, dislike of noise and other noxious experiences. Quantitative assessment of distress and mindfulness with Distress Thermometer (DT) and Mindful Attention Awareness Scale-state version (MAAS) demonstrated that a walk on the Green Road significantly decreased distress and increased mindfulness compared to a walk on the Urban Road. We also observed that pre-walk instructions could direct attention to both obvious and subtle elements of experience and enhance awareness. Results support the notion that an intentional nature-based environment may produce significantly more positive experiences and result in health-promoting benefits in a military health-care setting compared to an urban environment. Future studies with clinical populations could advance our understanding of the healing value of nature-based interventions. The impact of intentional green environments may be enhanced by well-designed instructions for both recreational and therapeutic use.
Ameli et al. (2021) A nature-based health intervention at a military healthcare center: a randomized, controlled, cross-over study. PeerJ 9:e10519 https://doi.org/10.7717/peerj.10519
Limited effect of a highway barrier on the genetic structure of a gypsum soil specialist
Background Gypsum ecosystems are edaphic islands surrounded by a matrix that is inhospitable to gypsum soil plant specialists. These naturally fragmented landscapes are currently exacerbated due to man-made disturbances, jeopardising their valuable biodiversity. Concomitant action of other fragmentation drivers such as linear infrastructures may increase the already high threat to these specialists. Although some evidence suggest that gypsophytes are not evolutionary dead-ends and can respond to fragmentation by means of phenotypic plasticity, the simultaneous action of barriers to genetic flow can pose a severe hazard to their viability. Here, we evaluated the effect of a highway with heavy traffic on the genetic flow and diversity in the species Lepidium subulatum, a dominant Iberian shrubby gypsophyte. Methods We tested the possible existence of bottlenecks, and estimated the genetic diversity, gene flow and genetic structure in the remnant populations, exploring in detail the effect of a highway as a possible barrier. Results Results showed variability in genetic diversity, migrants and structure. The highway had a low impact on the species since populations can retain high levels of genetic diversity and genetic parameter, like FST and FIS, did not seem to be affected. The presence of some level of genetic flow in both sides along the highway could explain the relatively high genetic diversity in the habitat remnants. Discussion Natural fragmentation and their exacerbation by agriculture and linear infrastructures seem to be negligible for this species and do not limit its viability. The biological features, demographic dynamics and population structures of gypsum species seem to be a valuable, adaptive pre-requisite to be a soil specialist and to maintain its competitiveness with other species in such adverse stressful conditions.
Martín-Rodríguez et al. (2021) Limited effect of a highway barrier on the genetic structure of a gypsum soil specialist. PeerJ 9:e10533 https://doi.org/10.7717/peerj.10533
A feasibility study to determine the use of baited pots in Greenland halibut (Reinhardtius hippoglossoides) fisheries, supported by the use of underwater video observations
High incidental catches of Greenland shark (Somniosus microcephalus) in Nunavut’s Greenland halibut (Reinhardtius hippoglossoides) fishery has led to studies on the feasibility of capturing Greenland halibut with baited pots. In this study, catch rates among six experimental pots are compared. In addition to this, underwater video observations of Greenland halibut interacting with two of these experimental pot types are quantified in order to help provide recommendations on future pot designs. Catch rates of Greenland halibut differed among pots with different entrance mesh types, and none of the pots produced substantial amounts of bycatch. Strings of pots were deployed within a narrow corridor between baited gillnets targeting Greenland halibut, which may have affected catch results. Video observations revealed Greenland halibut entangled by their teeth significantly more often in entrance funnels constructed with 50 mm than with 19 mm clear monofilament netting and the entrance rate was 45% higher with the 19 mm netting. Greenland halibut that successfully entered a pot repeatedly became entangled by their teeth in 58 mm netting used in the side and end panels and in a horizontal panel used to separate the pot into a lower and upper chamber. The majority (80%) of Greenland halibut were observed to approach a pot against the current. The downstream entrance was aligned with the current in 52% of the observed Greenland halibut approaches. Seventy percent of entry attempts and 67% of successful entries occurred when fish approached against the current and when the entrance was aligned with the current. These observations lead to recommendations that future studies consider developing a four entrance pot to ensure an entrance is always aligned with bottom currents. Based on these observations of entanglements, it is recommended to use 19 mm clear monofilament netting in the entrance funnel, 100 mm polyethylene netting in the exterior panels, and 19 mm polypropylene netting in the horizontal panel when targeting Greenland halibut. Three Greenland sharks were observed interacting with the pots in the video sets, but none were captured or damaged the pots during the potting experiments, providing validity to the use of pots to mitigate the capture of Greenland shark in Nunavut territorial waters.
Folkins et al. (2021) A feasibility study to determine the use of baited pots in Greenland halibut (Reinhardtius hippoglossoides) fisheries, supported by the use of underwater video observations. PeerJ 9:e10536 https://doi.org/10.7717/peerj.10536
Soluble expression and purification of Bluetongue Virus Type 1 (BTV1) structure protein VP2 in Escherichia coli and its immunogenicity in mice
Background The VP2 on the surface of the virus particle is the main structural protein of BTV, which can induce the host to produce neutralizing antibodies and play an important role in the antiviral immunity process. This study aimed to obtain the soluble VP2 and analyze its immunogenicity. Methods The gene encoding the full-length VP2 of BTV1 was amplified by PCR. The products from restriction enzyme digestion and ligase reaction between VP2 and vector pET-28a were transformed into E.coli DH5α. After PCR and sequencing detection, the positive plasmid PET28a-VP2 was transformed into E.coli BL21(DE3) and Rosetta(DE3) competent cells, expression induced by IPTG. The fusion protein was expressed in the optimized conditions with the induction of IPTG, purified by affinity chromatography and identified by SDS-PAGE and Western blotting. A total of 5 Balb/c mice aged 6–8 weeks were immunized with the fusion protein at a dose of 30 µg per mouse. Each mouse was immunized three times at an interval of 3 weeks. Results The recombinant plasmid PET28a-VP2 was successfully constructed. The expression strains were induced by 0.4 mmol/L IPTG at 16 °C for 10 h, and BTV1 VP2 was expressed in a soluble form. The purity of the recombinant VP2 protein (∼109 kDa) was about 90% in the concentration at 0.2 mg/ml afterpurification. The purified VP2 had good immunoreactivity with BTV1 positive serum. Taken together, thisstudy offered a route for producing soluble BTV VP2, which retains activity and immunogenicity, to bebeneficial to the research on developing BTV vaccine, and lay the foundation for further research on BTV.
Wang et al. (2021) Soluble expression and purification of Bluetongue Virus Type 1 (BTV1) structure protein VP2 in Escherichia coli and its immunogenicity in mice. PeerJ 9:e10543 https://doi.org/10.7717/peerj.10543
In vitro anticandidal activity and gas chromatography-mass spectrometry (GC-MS) screening of Vitex agnus-castus leaf extracts
Background Candida infections are becoming more drug resistant; it is necessary to search for alternative medications to treat them. Therefore, the present study estimates the anticandidal activity of Vitex agnus-castus (VA-C) leaf extracts. Methods We used the agar well diffusion method to assess the anticandidal activity of three different VA-C leaf extracts (ethanol, methanol, and water) against three Candida species (Candida tropicalis, Candida albicans, and Candida ciferrii). The minimum inhibitory concentration (MIC) was estimated using the two-fold dilution method and the minimum fungicidal concentration (MFC) was determined using the classic pour plate technique. The MFC/MIC ratio was calculated to estimate the microbicidal or microbiostatic activity. A gas chromatography mass spectrometer was used to screen the phytochemicals of the VA-C leaf extracts (ethanol, methanol, and water). Results All VA-C extracts ethanol, methanol, and water were significantly inhibited the growth of the test Candida species and the inhibition activity depended on the solvent used and the Candida species. The results showed that C. tropicalis was the most highly inhibited by all extracts followed by C. albicans and C. ciferrii. The MIC values were 12.5–25 µg/ml, and MFC values were 25–100 µg/ml. The ratios of MFC/MIC were two-fold to four-fold which was considered candidacidal activity. Ninety-five phytochemical compounds were identified by the GC-MS assay for the VA-C leaf extracts. The total number of compounds per extract differed. Methanol had 43 compounds, ethanol had 47 compounds, and water had 52 compounds. The highest compound concentrations were: 4,5-Dichloro-1,3-dioxolan-2-one in ethanol and methanol, 1H-Indene, 2,3-dihydro-1,1,2,3,3-pentamethyl in ethanol, Isobutyl 4-hydroxybenzoate in methanol, and Benzoic acid and 4-hydroxy- in water. These phytochemical compounds belong to different bioactive chemical group such as polyphenols, fatty acids, terpenes, terpenoids, steroids, aldehydes, alcohols, and esters, and most of which have anticandidal activity. Conclusions VA-C leaf extracts may be useful alternatives to anticandidal drugs, based on their effectiveness against all test Candida species at low concentrations. However, appropriate toxicology screening should be conducted before use.
Ababutain et al. (2021) In vitro anticandidal activity and gas chromatography-mass spectrometry (GC-MS) screening of Vitex agnus-castus leaf extracts. PeerJ 9:e10561 https://doi.org/10.7717/peerj.10561
Serum metabolite profiling of a 4-Nitroquinoline-1-oxide-induced experimental oral carcinogenesis model using gas chromatography-mass spectrometry
Background Oral cancer progresses from hyperplastic epithelial lesions through dysplasia to invasive carcinoma. The critical needs in oral cancer treatment are expanding our knowledge of malignant tumour progression and the development of useful approaches to prevent dysplastic lesions. This study was designed to gain insights into the underlying metabolic transformations that occur during the process of oral carcinogenesis. Methods We used gas chromatography-mass spectrometry (GC-MS) in conjunction with multivariate statistical techniques to observe alterations in serum metabolites in a 4-Nitroquinoline 1-oxide (4NQO)-induced rat tongue carcinogenesis model. Thirty-eight male rats were randomly divided into two groups, including the 4NQO-induced model group of 30 rats and the healthy control group of five rats. Animals were sacrificed at weeks 9, 13, 20, 24, and 32, post-4NQO treatment. Tissue samples were collected for histopathological examinations and blood samples were collected for metabolomic analysis. Partial least squares discriminate analysis (PLS-DA) models generated from GC-MS metabolic profile data showed robust discrimination from rats with oral premalignant and malignant lesions induced by 4NQO, and normal controls. Results The results found 16 metabolites associated with 4NQO-induced rat tongue carcinogenesis. Dysregulated arachidonic acid, fatty acid, and glycine metabolism, as well as disturbed tricarboxylic acid (TCA) cycle and mitochondrial respiratory chains were observed in the animal model. The PLS-DA models of metabolomic results demonstrated good separations between the 4NQO-induced model group and the normal control group. Conclusion We found several metabolites modulated by 4NQO and provide a good reference for further study of early diagnosis in oral cancer.
Ge et al. (2021) Serum metabolite profiling of a 4-Nitroquinoline-1-oxide-induced experimental oral carcinogenesis model using gas chromatography-mass spectrometry. PeerJ 9:e10619 https://doi.org/10.7717/peerj.10619
Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2
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.
Azad (2021) Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2. PeerJ 9:e10666 https://doi.org/10.7717/peerj.10666