Doubling the known diversity of a remote island fauna: marine bivalves of the Juan Fernández and Desventuradas oceanic archipelagos (Southeastern Pacific Ocean)
Juan Fernández and Desventuradas are two oceanic archipelagos located in the southeastern Pacific Ocean far off the Chilean coast that received protected status as marine parks in 2016. Remoteness and access difficulty contributed to historically poor biodiversity sampling and limited associated research. This is particularly noticeable for bivalves, with most prior regional publications focused on single taxa or un-illustrated checklists. This study investigates marine bivalves collected between the intertidal and 415 m depth during (1) the 1997 IOC97 expedition aboard the M/V Carlos Porter, with special focus on scuba-collected micro-mollusks of both archipelagos, (2) two expeditions by the R/V Anton Bruun (Cruise 12/1965 and Cruise 17/1966), and (3) Cruise 21 of USNS Eltanin under the United States Antarctic Program, which sampled at Juan Fernández in 1965. Also, relevant historical material of the British H.M.S. Challenger Expedition (1873–1876), the Swedish Pacific Expedition (1916–1917), and by German zoologist Ludwig H. Plate (1893–1895) is critically revised. A total of 48 species are recognized and illustrated, including 19 new species (described herein) and six other potentially new species. The presence of two species mentioned in the literature for the region (Aulacomya atra and Saccella cuneata) could not be confirmed. The genera Verticipronus and Halonympha are reported for the first time from the Eastern Pacific, as are Anadara and Condylocardia from Chilean waters. Lectotypes are designated for Arca (Barbatia) platei and Mytilus algosus. These findings double the number of extant bivalve species known from the Juan Fernández and Desventuradas archipelagos, highlighting the lack of attention these islands groups have received in the past. A high percentage of species endemic to one or both archipelagos are recognized herein, accounting for almost 78% of the total. The newly recognized level of bivalve endemism supports the consideration of Juan Fernández and Desventuradas as two different biogeographic units (Provinces or Ecoregions) of the Eastern Pacific Ocean.
Zelaya et al. (2024) Doubling the known diversity of a remote island fauna: marine bivalves of the Juan Fernández and Desventuradas oceanic archipelagos (Southeastern Pacific Ocean). PeerJ 12:e17305 https://doi.org/10.7717/peerj.17305
Labeled-free quantitative proteomic analysis of cervical squamous cell carcinoma identifies potential protein biomarkers
Background Cervical cancer remains a prevalent cancer among women, and reliance on surgical and radio-chemical therapies can irreversibly affect patients’ life span and quality of life. Thus, early diagnosis and further exploration into the pathogenesis of cervical cancer are crucial. Mass spectrometry technology is widely applied in clinical practice and can be used to further investigate the protein alterations during the onset of cervical cancer. Methods Employing labeled-free quantitative proteomics technology and bioinformatics tools, we analyzed and compared the differential protein expression profiles between normal cervical squamous cell tissues and cervical squamous cell cancer tissues. GEPIA is an online website for analyzing the RNA sequencing expression data of tumor and normal tissue data from the TCGA and the GTEx databases. This approach aided in identifying qualitative and quantitative changes in key proteins related to the progression of cervical cancer. Results Compared to normal samples, a total of 562 differentially expressed proteins were identified in cervical cancer samples, including 340 up-regulated and 222 down-regulated proteins. Gene ontology functional annotation, and KEGG pathway, and enrichment analysis revealed that the differentially expressed proteins mainly participated in metabolic pathways, spliceosomes, regulation of the actin cytoskeleton, and focal adhesion signaling pathways. Specifically, desmoplakin (DSP), protein phosphatase 1, regulatory (inhibitor) subunit 13 like (PPP1R13L) and ANXA8 may be involved in cervical tumorigenesis by inhibiting apoptotic signal transmission. Moreover, we used GEPIA database to validate the expression of DSP, PPP1R13L and ANXA8 in human cancers and normal cervix. Conclusion In this study, we identified 562 differentially expressed proteins, and there were three proteins expressed higher in the cervical cancer tissues. The functions and signaling pathways of these differentially expressed proteins lay a theoretical foundation for elucidating the molecular mechanisms of cervical cancer.
Bai et al. (2024) Labeled-free quantitative proteomic analysis of cervical squamous cell carcinoma identifies potential protein biomarkers. PeerJ 12:e17444 https://doi.org/10.7717/peerj.17444
A taxonomic revision of Rhizophora L. (Rhizophoraceae) in Thailand
A taxonomic revision of Rhizophora L. (Rhizophoraceae) in Thailand is presented. Two species, R. apiculata Blume and R. mucronata Poir., are enumerated with updated morphological descriptions, illustrations and a taxonomic identification key, together with notes on distributions, habitats and ecology, phenology, conservation assessments, etymology, vernacular names, uses, and specimens examined. Three names in Rhizophora, are lectotypified: R. apiculata and two associated synonyms of R. mucronata (i.e., R. latifolia Miq. and R. macrorrhiza Griff.). R. longissima Blanco, a synonym of R. mucronata, is neotypified. All two Rhizophora species have a conservation assessment of Least Concern (LC). Based on the morphological identification, these two species can be distinguished from one another by the shape and width of the leaf laminae and the length of a terminal stiff point of the leaf laminae; the type and position of the inflorescences and the number of flowers per inflorescence; the character and color of the bracteoles; the presence or absence of the flower pedicels; the shape of the mature flower buds; the shape, color, and texture of the sepals; the shape, character, and the presence or absence of hairs of the petals; the number of stamens per flower; the size of the fruits; the color and size of the hypocotyls; the color and diameter of the cotyledonous cylindrical tubes; and the color of the colleters and exudate. The thick cuticles, sunken stomata, large hypodermal cells, and cork warts are adaptive anatomical features of leaves in Rhizophora that live in the mangrove environments. The pollen grains of Thai Rhizophora species are tricolporate, prolate spheroidal or oblate spheroidal shapes, small-sized, and reticulate exine sculpturing.
Ngernsaengsaruay et al. (2024) A taxonomic revision of Rhizophora L. (Rhizophoraceae) in Thailand. PeerJ 12:e17460 https://doi.org/10.7717/peerj.17460
Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress
Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety ‘Jingu 21’ (Setaria italica) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly (p < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1).
Environmental Contamination and Remediation
Zhao et al. (2024) Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress. PeerJ 12:e17461 https://doi.org/10.7717/peerj.17461
Restoring South African subtropical succulent thicket using Portulacaria afra: root growth of cuttings differs depending on the harvest site during a drought
The restoration of succulent thicket (the semi-arid components of the Albany Subtropical Thicket biome endemic to South Africa) has largely focused on the reintroduction of Portulacaria afra L. Jacq—a leaf- and stem-succulent shrub—through the planting of unrooted cuttings directly into field sites. However, there has been inconsistent establishment and survival rates, with low rates potentially due to a range of factors (e.g., post-planting drought, frost or herbivory), including the poor condition of source material used. Here we test the effect of parent-plant and harvesting site on the root development of P. afra cuttings in a common garden experiment. Ten sites were selected along a ∼110 km transect, with cuttings harvested from five parent-plants per site. Leaf moisture content was determined for each parent-plant at the time of harvesting as a proxy for plant condition. Root development—percentage of rooted cuttings and mean root dry weight—was recorded for a subset of cuttings from each parent-plant after 35, 42, 48, 56, and 103 days after planting in a common garden setting. We found evidence for cutting root development (rooting percentage and root dry mass) to be strongly associated with harvesting site across all sampling days (p < 0.005 for all tests). These differences are likely a consequence of underlying physiological factors; this was supported by the significant but weak correlation (r2 = 0.10–0.26) between the leaf moisture content of the parent-plant (at the time of harvesting) and dry root mass of the cuttings (at each of the sampling days). Our findings demonstrate that varying plant condition across sites can significantly influence root development during dry phases (i.e., intra- and inter-annual droughts) and that this may be a critical component that needs to be understood as part of any restoration programme. Further work is required to identify the environmental conditions that promote or impede root development in P. afra cuttings.
Potts et al. (2024) Restoring South African subtropical succulent thicket using Portulacaria afra: root growth of cuttings differs depending on the harvest site during a drought. PeerJ 12:e17471 https://doi.org/10.7717/peerj.17471
Combined uranium-series and electron spin resonance dating from the Pliocene fossil sites of Aves and Milo’s palaeocaves, Bolt’s Farm, Cradle of Humankind, South Africa
Bolt’s Farm is the name given to a series of non-hominin bearing fossil sites that have often been suggested to be some of the oldest Pliocene sites in the Cradle of Humankind, South Africa. This article reports the results of the first combined Uranium-Series and Electron Spin Resonance (US-ESR) dating of bovid teeth at Milo’s Cave and Aves Cave at Bolt’s Farm. Both tooth enamel fragments and tooth enamel powder ages were presented for comparison. US-ESR, EU and LU models are calculated. Overall, the powder ages are consistent with previous uranium-lead and palaeomagnetic age estimates for the Aves Cave deposit, which suggest an age between ~3.15 and 2.61 Ma and provide the first ages for Milo’s Cave dates to between ~3.1 and 2.7 Ma. The final ages were not overly dependent on the models used (US-ESR, LU or EU), which all overlap within error. These ages are all consistent with the biochronological age estimate (<3.4–>2.6 Ma) based on the occurrence of Stage I Metridiochoerus andrewsi. Preliminary palaeomagnetic analysis from Milo’s Cave indicates a reversal takes place at the site with predominantly intermediate directions, suggesting the deposit may date to the period between ~3.03 and 3.11 Ma within error of the ESR ages. This further suggests that there are no definitive examples of palaeocave deposits at Bolt’s Farm older than 3.2 Ma. This research indicates that US-ESR dating has the potential to date fossil sites in the Cradle of Humankind to over 3 Ma. However, bulk sample analysis for US-ESR dating is recommended for sites over 3 Ma.
Yu et al. (2024) Combined uranium-series and electron spin resonance dating from the Pliocene fossil sites of Aves and Milo’s palaeocaves, Bolt’s Farm, Cradle of Humankind, South Africa. PeerJ 12:e17478 https://doi.org/10.7717/peerj.17478
Internet addiction among adolescents during the COVID-19 pandemic: Associations with sociodemographic and psychological distress
Background The COVID-19 pandemic has had tremendous implications for billions of adolescents worldwide due to school closures, forcing students to embrace internet usage for daily tasks. Uncontrolled use of the internet among adolescents makes them vulnerable to internet addiction (IA). This study aims to determine the prevalence of IA among adolescents and assess its association with sociodemographic factors, smartphone use, and psychological distress during the pandemic. Method A cross-sectional self-administered online survey was conducted among students aged 13–17 from May 15th, 2021, until May 30th, 2021, using the Malay version of the Internet Addiction Test (MVIAT), the Depression, Anxiety, and Stress Scale (DASS-21), and the Coronavirus Impacts Questionnaires, as well as a sociodemographic information form. The data was analyzed with IBM SPSS Statistics version 23. Results A total of 420 adolescents participated in the survey. The majority of them (70.7%) were female, with a mean age of 15.47 years (±1.49 years old). About 45.5% of the respondents were classified as internet addicted users. The Chi-square test analysis showed that age (p = 0.002), smartphone usage (p = 0.010), rate of midnight use (p < 0.001), frequency (p < 0.001), duration (p < 0.001) of device usage, and presence of depression, anxiety, and stress (p < 0.001) were all significantly associated with IA. Multiple logistic regression showed age (aOR = 1.16, 95% CI [1.00–1.35], p = 0.048), smartphone usage (aOR =3.52, 95% CI [1.43–8.67], p = 0.006), mild or moderate depression (aOR = 2.43, 95% CI [1.36–4.34], p = 0.003), severe or extremely severe stress (aOR = 6.41, 95% CI [2.18–18.82], p = 0.001) were significantly related to IA. Conclusions Late adolescence, the use of smartphones, and the presence of psychological distress like depression, and stress were potentially associated with IA. Wise use of smartphones and early identification of any psychological distress among adolescents are warranted, especially during the pandemic.
Md Bukhori et al. (2024) Internet addiction among adolescents during the COVID-19 pandemic: Associations with sociodemographic and psychological distress. PeerJ 12:e17489 https://doi.org/10.7717/peerj.17489
Impact of white blood cell count on the development of contrast-induced acute kidney injury in patients receiving percutaneous coronary intervention
This study aimed to investigate the efficacy of a pre-procedural white blood cell (WBC) count in the prediction of contrast-induced acute kidney injury (CI-AKI) risk in coronary artery disease patients receiving a percutaneous coronary intervention (PCI). This observational study comprises a sample of 1,013 coronary artery disease patients (including ACS and stable angina) receiving PCI, gathered from September 2015 to July 2017. CI-AKI incidence in the study population was 4.8% (49/1013). Patients in the CI-AKI group had significantly higher WBC counts than those in the non-CI-AKI group (10.41 ± 5.37 vs. 8.09 ± 3.10, p = 0.004). Logistic analysis showed that WBC count (odds ratio [OR]: 1.12, 95% CI [1.03–1.21], P = 0.006) was a significant and independent predictor of CI-AKI risk in patients receiving PCI, Receiver-operating characteristic (ROC) curve analysis found that pre-procedural WBC count ≥11.03*109/L was the optimal cut-off value in the prediction of CI-AKI risk with a sensitivity of 41.0% and a specificity of 86.5%. Patients with CI-AKI had a significantly worse 1-year survival rate than patients without CI-AKI (91.8% vs. 97.6%, P = 0.012). In summary, increased pre-procedural WBC count is associated with an increased risk of developing CI-AKI in patients receiving PCI.
Fu et al. (2024) Impact of white blood cell count on the development of contrast-induced acute kidney injury in patients receiving percutaneous coronary intervention. PeerJ 12:e17493 https://doi.org/10.7717/peerj.17493
Wing mechanics and acoustic communication of a new genus of sylvan katydid (Orthoptera: Tettigoniidae: Pseudophyllinae) from the Central Cordillera cloud forest of Colombia
Stridulation is used by male katydids to produce sound via the rubbing together of their specialised forewings, either by sustained or interrupted sweeps of the file producing different tones and call structures. There are many species of Orthoptera that remain undescribed and their acoustic signals are unknown. This study aims to measure and quantify the mechanics of wing vibration, sound production and acoustic properties of the hearing system in a new genus of Pseudophyllinae with taxonomic descriptions of two new species. The calling behaviour and wing mechanics of males were measured using micro-scanning laser Doppler vibrometry, microscopy, and ultrasound sensitive equipment. The resonant properties of the acoustic pinnae of the ears were obtained via μ-CT scanning and 3D printed experimentation, and numerical modelling was used to validate the results. Analysis of sound recordings and wing vibrations revealed that the stridulatory areas of the right tegmen exhibit relatively narrow frequency responses and produce narrowband calls between 12 and 20 kHz. As in most Pseudophyllinae, only the right mirror is activated for sound production. The acoustic pinnae of all species were found to provide a broadband increased acoustic gain from ~40–120 kHz by up to 25 dB, peaking at almost 90 kHz which coincides with the echolocation frequency of sympatric bats. The new genus, named Satizabalus n. gen., is here derived as a new polytypic genus from the existing genus Gnathoclita, based on morphological and acoustic evidence from one described (S. sodalis n. comb.) and two new species (S. jorgevargasi n. sp. and S. hauca n. sp.). Unlike most Tettigoniidae, Satizabalus exhibits a particular form of sexual dimorphism whereby the heads and mandibles of the males are greatly enlarged compared to the females. We suggest that Satizabalus is related to the genus Trichotettix, also found in cloud forests in Colombia, and not to Gnathoclita.
Holmes et al. (2024) Wing mechanics and acoustic communication of a new genus of sylvan katydid (Orthoptera: Tettigoniidae: Pseudophyllinae) from the Central Cordillera cloud forest of Colombia. PeerJ 12:e17501 https://doi.org/10.7717/peerj.17501
Utilization of ripe coconut water in the development of probiotic gelatin
Background Desserts with vegetable ingredients are a constantly expanding global market due to the search for alternatives to cow’s milk. Fermentation of these matrices by lactic acid bacteria can add greater functionality to the product, improving its nutritional, sensory, and food safety characteristics, as well as creating bioactive components with beneficial effects on health. Concern for health and well-being has aroused interest in byproducts of the industry that have functional properties for the body, such as mature coconut water, a normally discarded residue that is rich in nutrients. This study aimed to develop a probiotic gelatin based on pulp and water from mature coconuts and evaluate the physicochemical characteristics, viability of the Lacticaseibacillus rhamnosus LR32 strain in the medium, as well as the texture properties of the product. Methods After collection and cleaning, the physicochemical characterization, mineral analysis, analysis of the total phenolic content and antioxidant activity of mature coconut water were carried out, as well as the centesimal composition of its pulp. Afterwards, the gelling was developed with the addition of modified corn starch, gelatin, sucrose, and probiotic culture, being subjected to acidity analysis, texture profile and cell count, on the first day and every 7 days during 21 days of storage, under refrigeration at 5 °C. An analysis of the centesimal composition was also carried out. Results The main minerals in coconut water were potassium (1,932.57 mg L−1), sodium (19.57 mg L−1), magnesium (85.13 mg L−1) calcium (279.93 mg L−1) and phosphorus (11.17 mg L−1), while the pulp had potassium (35.96 g kg−1), sodium (0.97 g kg−1), magnesium (2.18 g kg−1), 37 calcium (1.64 g kg−1), and phosphorus (3.32 g kg−1). The phenolic content of the water and pulp was 5.72 and 9.77 mg gallic acid equivalent (GAE) 100 g−1, respectively, and the antioxidant capacity was 1.67 and 0.98 39 g of 2, 2-diphenyl-1-picrylhydrazyl (DPPH) mg−1, respectively. The coconut pulp had 2.81 g 100 g−1of protein, 1.11 g 100 g−1 of 40 ash, 53% moisture, and 5.81 g 100 g−1 of carbohydrates. The gelatin produced during the storage period presented firmness parameters ranging from 145.82 to 206.81 grams-force (gf), adhesiveness from 692.85 to 1,028.63 gf sec, cohesiveness from 0.604 to 0.473, elasticity from 0.901 to 0.881, gumminess from 86.27 to 97.87 gf, and chewiness from 77.72 to 91.98 gf. Regarding the viability of the probiotic microorganism, the dessert had 7.49 log CFU g−1 that remained viable during the 21-day storage, reaching 8.51 CFU g−1. Acidity ranged from 0.15 to 0.64 g of lactic acid 100 g−1. The centesimal composition of the product showed 4.88 g 100 g−1 of protein, 0.54 g 100 g−1 of ash, 85.21% moisture, and 5.37g 100 g−1 of carbohydrates. The development of the gelatin made it possible to obtain a differentiated product, contributing to diversification in the food sector, providing a viable alternative for maintaining consumer health and reducing costs compared to desserts already available on the market.
Patricio Rocha et al. (2024) Utilization of ripe coconut water in the development of probiotic gelatin. PeerJ 12:e17502 https://doi.org/10.7717/peerj.17502