Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay
Dysbiosis and acclimatization are two starkly opposing outcomes of altered holobiont associations in response to environmental pollution. This study assesses whether shifts in microbial taxonomic composition and functional profiles of the cosmopolitan sponge Hymeniacidon perlevis indicate dysbiotic or acclimatized responses to water pollution. To do so, sponge and water samples were collected in a semi-enclosed environment (San Antonio Bay, Patagonia, Argentina) from variably polluted sites (i.e., eutrophication, heavy metal contamination). We found significant differences in the microbiome of H. perlevis with respect to the pollution history of the sites. Several indicators suggested that acclimatization, rather than dysbiosis, explained the microbiome response to higher pollution: 1) the distinction of the sponge microbiome from the water microbiome; 2) low similarity between the sponge and water microbiomes at the most polluted site; 3) the change in microbiome composition between sponges from the different sites; 4) a high similarity in the microbiome among sponge individuals within sites; 5) a similar ratio of common sponge microbes to opportunistic microbes between sponges at the most and least polluted sites; and 6) a distinctive functional profile of the sponge microbiome at the most polluted site. This profile indicated a more expansive metabolic repertoire, including the degradation of pollutants and the biosynthesis of secondary metabolites, suggesting a relevant role of these microbial communities in the adaptation of the holobiont to organic pollution. Our results shed light on the rearrangement of the H. perlevis microbiome that could allow it to successfully colonize sites with high anthropogenic impact while resisting dysbiosis.
Gastaldi et al. (2024) Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay. PeerJ 12:e17707 https://doi.org/10.7717/peerj.17707
Validation of PozQoL scale in Turkish population living with HIV: a cross-cultural adaptation study
Background The increasing number of people living with HIV requires a simple and easy-to-use quality of life (QoL) scale for people living with HIV (PLWH). This study aims to adapt the PozQoL scale into Turkish and assess its reliability and validity for the PLWH population in Turkey. Methods Translation-back-translation methodology was employed, and face-to-face interviews were conducted with 130 patients using the PozQoL, socio-demographic, and clinical data questionnaire. Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) were utilized to identify the underlying factor structure and examine the validity of the measurement model, respectively. Cronbach’s alpha and intraclass correlation coefficients (ICCs) were used to assess internal consistency and test-retest reliability, respectively. Results EFA revealed four factors with an eigenvalue of 0.88, explaining 62.1% of the cumulative variance. CFA indicated that the four-factor solution achieved good levels of fit. The total Cronbach’s alpha was 0.81, indicating high internal consistency. The ICC for the total score was 0.92 (95% confidence interval (CI) [0.90–0.94]; p < 0.05), demonstrating high test-retest reliability. Conclusion The Turkish version of the PozQoL was found to be a valid and reliable tool for assessing the health-related QoL of PLWH in Turkey.
Atalay et al. (2024) Validation of PozQoL scale in Turkish population living with HIV: a cross-cultural adaptation study. PeerJ 12:e17873 https://doi.org/10.7717/peerj.17873
Focused ultrasound-induced cell apoptosis for the treatment of tumours
Cancer is a serious public health problem worldwide. Traditional treatments, such as surgery, radiotherapy, chemotherapy, and immunotherapy, do not always yield satisfactory results; therefore, an efficient treatment for tumours is urgently needed. As a convenient and minimally invasive modality, focused ultrasound (FUS) has been used not only as a diagnostic tool but also as a therapeutic tool in an increasing number of studies. FUS can help treat malignant tumours by inducing apoptosis. This review describes the three apoptotic pathways, apoptotic cell clearance, and how FUS affects these three apoptotic pathways. This review also discusses the role of thermal and cavitation effects on apoptosis, including caspase activity, mitochondrial dysfunction, and Ca2+ elease. Finally, this article reviews various aspects of FUS combination therapy, including sensitization by radiotherapy and chemotherapy, gene expression upregulation, and the introduction of therapeutic gases, to provide new ideas for clinical tumour therapy.
Wang et al. (2024) Focused ultrasound-induced cell apoptosis for the treatment of tumours. PeerJ 12:e17886 https://doi.org/10.7717/peerj.17886
Use of an age-simulation suit as an empathy-building method for dental students: a pre-post study
Background The aging of the population highlights the need to establish empathetic connections with older adults. To achieve this, age simulation suits have been designed, allowing users to experience the physical limitations associated with aging. This study aimed to evaluate the experience of dental students with these devices, using psychometric tools to measure the impact on their understanding and empathy. Methods A pre/post-test study was conducted with the participation of 63 dental students from Rey Juan Carlos University who were fitted with an age simulation suit and asked to perform different tasks. Psychometric tools were used to assess specific parameters. Empathy was measured using the Jefferson Empathy Scale, emotional intelligence was assessed with the Trait Meta-Mood Scale-24 (TMMS-24), and the emotional attention dimension was analyzed using the Positive and Negative Affect Schedule (PANAS). Results The scores on the Jefferson Empathy Scale significantly improved from 88.44 ± 6.8 to 91.06 ± 10.11 after using the simulation suit (P < 0.026). Pearson’s product moment correlation analysis showed no significant positive association or correlation between age and scores from the three questionnaires. In the rest, a positive and significant correlation was observed (P < 0.0001). Conclusions Age simulation activities effectively enhance empathy among dental students. However, more studies are needed to foster positive attitudes toward aging and prevent negative stereotypes.
Rodriguez-Molinero et al. (2024) Use of an age-simulation suit as an empathy-building method for dental students: a pre-post study. PeerJ 12:e17908 https://doi.org/10.7717/peerj.17908
Association between NKILA and some apoptotic gene expression in atherosclerosis
Oxidized light-density lipoprotein (ox-LDL) causes endothelial dysfunction, which is an important determinant of atherogenesis, and subsequently leads to apoptosis. Atherosclerosis is one of the most significant cardiovascular diseases (CVDs) threatening human health and causes death worldwide. Recently, long noncoding RNAs (lncRNAs) have been suggested to involved in vascular biology. Ox-LDL activates nuclear factor kappa-B (NF-κB), and NF-κB interacting lncRNA (NKILA) inhibits NF-κB signaling. In this study, the hypothesis is that NKILA may regulate endothelial cell (EC) apoptosis and, therefore, play a role in the pathogenesis of atherosclerosis. This hypothesis is based on the knowledge that EC apoptosis contributes to atherosclerosis development and that NKILA has become a prominent lncRNA in CVDs. The expression of Bcl-2-associated X protein (BAX), caspase 9 (CASP9), cytochrome c (Cyt c, CYCS), apoptotic protease activating factor 1 (APAF1), and B-cell lymphoma 2 (BCL-2) genes in human umbilical vein endothelial cells (HUVEC) treated with ox-LDL and transfected with NKILA siRNA was analyzed using quantitative reverse transcription polymerase chain reaction (RT-qPCR). BAX, CASP9, CYCS, APAF1, and BCL-2 gene expression was downregulated in ox-LDL and NKILA siRNA-treated HUVEC. In addition, when threshold/quantification cycle (Cq) values of NKILA gene expression increased, Cq values of BAX, CASP9, APAF1, and BCL-2 gene expression increased statistics significantly. The expression detection of all these genes, resulting from NKILA gene silencing, may provide guidance for epigenetic studies on EC apoptosis in atherosclerosis.
Bayyurt et al. (2024) Association between NKILA and some apoptotic gene expression in atherosclerosis. PeerJ 12:e17915 https://doi.org/10.7717/peerj.17915
Comparison of visual quality after wavefront-guided LASIK in patients with different levels of preoperative total ocular higher-order aberrations: a retrospective study
Purpose To compare the visual quality after wavefront-guided femtosecond LASIK (WFG FS-LASIK) in patients with different levels of preoperative total ocular higher-order aberrations to guide clinical decision-making regarding patient selection and treatment strategies. Methods This study included 112 right eyes of 112 patients who previously underwent WFG FS-LASIK for correcting myopia and myopic astigmatism. The patients were divided into two groups based on the mean values of preoperative total ocular HOAs (0.30 ± 0.09 µm): HOA ≤ 0.3 and > 0.3 groups. The visual acuity, manifest refraction, corneal Strehl ratio (SR), root mean square (RMS) of corneal and ocular aberrations, and area under the log contrast sensitivity function (AULCSF) of both groups were compared preoperatively and at 1, 3, 6, and 12 months postoperatively. Results The induced ocular HOAs and coma (Δ = 1 mo − Preop) were significantly lower in the HOAs > 0.3 group than in the HOAs ≤ 0.3 group (ΔHOAs: 0.39 ± 0.19 vs. 0.29 ± 0.18 μm, t = 2.797, P = 0.006; Δ coma: 0.30 ± 0.19 vs. 0.20 ± 0.21 μm, t = 2.542, P = 0.012). In the HOAs > 0.3 group, ΔHOAs were negatively correlated with the preoperative ocular HOAs (r = −0.315, P = 0.019). In the HOAs ≤ 0.3 group, the regression equation for Δ HOAs = 0.098 + 0.053 |SE| (F = 21.756, P < 0.001). In the HOAs > 0.3 group, the regression equation for ΔHOAs = 0.534 − 1.081 HOAs + 0.038|Sphere| (F = 7.954, P = 0.001). The postoperative uncorrected distance visual acuity, spherical equivalent, corneal aberrations, SR and AULCSF of both groups were similar (all P > 0.05). Furthermore, the ocular aberrations were not significantly different between both groups at 3, 6, and 12 months postoperatively (all P > 0.05). In addition, compared with the preoperative period, the AULCSF of both groups were significantly increased in the postoperative period (all P < 0.05). Conclusions The induced ocular HOAs and coma in HOAs > 0.3 group were lower. However, both groups achieved equivalent and excellent visual quality after WFG FS-LASIK. WFG FS-LASIK may provide significant visual benefits for a wider range of patients.
Zhang et al. (2024) Comparison of visual quality after wavefront-guided LASIK in patients with different levels of preoperative total ocular higher-order aberrations: a retrospective study. PeerJ 12:e17940 https://doi.org/10.7717/peerj.17940
Plant growth promoting bacteria (PGPB)-induced plant adaptations to stresses: an updated review
Plants and bacteria are co-evolving and interact with one another in a continuous process. This interaction enables the plant to assimilate the nutrients and acquire protection with the help of beneficial bacteria known as plant growth-promoting bacteria (PGPB). These beneficial bacteria naturally produce bioactive compounds that can assist plants’ stress tolerance. Moreover, they employ various direct and indirect processes to induce plant growth and protect plants against pathogens. The direct mechanisms involve phytohormone production, phosphate solubilization, zinc solubilization, potassium solubilization, ammonia production, and nitrogen fixation while, the production of siderophores, lytic enzymes, hydrogen cyanide, and antibiotics are included under indirect mechanisms. This property can be exploited to prepare bioformulants for biofertilizers, biopesticides, and biofungicides, which are convenient alternatives for chemical-based products to achieve sustainable agricultural practices. However, the application and importance of PGPB in sustainable agriculture are still debatable despite its immense diversity and plant growth-supporting activities. Moreover, the performance of PGPB varies greatly and is dictated by the environmental factors affecting plant growth and development. This review emphasizes the role of PGPB in plant growth-promoting activities (stress tolerance, production of bioactive compounds and phytohormones) and summarises new formulations and opportunities.
Fanai et al. (2024) Plant growth promoting bacteria (PGPB)-induced plant adaptations to stresses: an updated review. PeerJ 12:e17882 https://doi.org/10.7717/peerj.17882
Simplifying the Centrolene buckleyi complex (Amphibia: Anura: Centrolenidae): a taxonomic review and description of two new species
Centrolenidae is a Neotropical family widely distributed in Central and South America, with its species richness concentrated in the tropical Andes. Several taxonomic problems have been identified within this family, mostly related to species with broad geographic distributions. In this study, we assessed and redefined the species boundaries of the Centrolene buckleyi species complex, and formally described two new species from the Andes of Ecuador. These new taxa are recognized by a combination of morphometric, osteological, acoustic, and genetic data. Following IUCN criteria, we propose that the two new species should to be considered as Endangered (EN), mainly because of their small distributions and habitat loss. The C. buckleyi complex provides insights into the biogeography of closely related Andean species. As in other glassfrogs, speciation in Centrolene seems to be mediated by the linearity of the Andes, where gene flow can be restricted by topography and, also, local extinctions.
Franco-Mena et al. (2024) Simplifying the Centrolene buckleyi complex (Amphibia: Anura: Centrolenidae): a taxonomic review and description of two new species. PeerJ 12:e17712 https://doi.org/10.7717/peerj.17712
Historic checklist, core species and temporal composition turnover of birds in an urban protected natural area in central México over 50 years
The Pedregal de San Ángel Ecological Reserve (REPSA) is located within the central campus of the National Autonomous University of Mexico (UNAM), in southwestern Mexico City. This area is known for its bird richness, which has been documented over time. However, this historical information has not been compiled, nor has it been assessed whether species composition has changed over time. In this study, we generated the historical checklist of avifauna in the REPSA by integrating data from systematic monitoring, bibliographic review and citizen science. Additionally, we calculated Jaccard’s dissimilarity Index (nestedness and species turnover) among bird checklists from each year and evaluated whether this index and its components changed over time. In addition, we estimate whether the proportion of species arriving and becoming extinct in the REPSA is influenced by time (census interval) and by the migratory status of the species. Finally, we identified the core species of the REPSA. Our results indicate that from 1967 to 2023, 258 bird species have been recorded in the REPSA. The Jaccard’s dissimilarity and turnover increased and reached an asymptotic trend over time while nestedness showed similar values throughout time. The time and species residency status did not have significant effect on the proportion of species that arrival and become extinct in the reserve. We identified 58 core species based on their persistence; 35 of these are residents, 22 have some migratory movement and one exotic species. Our results highlight the importance of the REPSA as a fundamental habitat for the avifauna of Mexico City, including a wide variety of migratory bird species.
Márquez-Luna et al. (2024) Historic checklist, core species and temporal composition turnover of birds in an urban protected natural area in central México over 50 years. PeerJ 12:e17888 https://doi.org/10.7717/peerj.17888
Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa ‘ja ‘ag hydrothermal vent fields in the Pescadero Basin, Gulf of California
Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa ‘ja ‘ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.
Peña-Salinas et al. (2024) Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa ‘ja ‘ag hydrothermal vent fields in the Pescadero Basin, Gulf of California. PeerJ 12:e17724 https://doi.org/10.7717/peerj.17724