The biomarkers discovery of hyperuricemia and gout: proteomics and metabolomics
Background Hyperuricemia and gout are a group of disorders of purine metabolism. In recent years, the incidence of hyperuricemia and gout has been increasing, which is a severe threat to people’s health. Several studies on hyperuricemia and gout in proteomics and metabolomics have been conducted recently. Some literature has identified biomarkers that distinguish asymptomatic hyperuricemia from acute gout or remission of gout. We summarize the physiological processes in which these biomarkers may be involved and their role in disease progression. Methodology We used professional databases including PubMed, Web of Science to conduct the literature review. This review addresses the current landscape of hyperuricemia and gout biomarkers with a focus on proteomics and metabolomics. Results Proteomic methods are used to identify differentially expressed proteins to find specific biomarkers. These findings may be suggestive for the diagnosis and treatment of hyperuricemia and gout to explore the disease pathogenesis. The identified biomarkers may be mediators of the link between hyperuricemia, gout and kidney disease, metabolic syndrome, diabetes and hypertriglyceridemia. Metabolomics reveals the main influential pathways through small molecule metabolites, such as amino acid metabolism, lipid metabolism, or other characteristic metabolic pathways. These studies have contributed to the discovery of Chinese medicine. Some traditional Chinese medicine compounds can improve the metabolic disorders of the disease. Conclusions We suggest some possible relationships of potential biomarkers with inflammatory episodes, complement activation, and metabolic pathways. These biomarkers are able to distinguish between different stages of disease development. However, there are relatively few proteomic as well as metabolomic studies on hyperuricemia and gout, and some experiments are only primary screening tests, which need further in-depth study.
Wu et al. (2023) The biomarkers discovery of hyperuricemia and gout: proteomics and metabolomics. PeerJ 11:e14554 https://doi.org/10.7717/peerj.14554
On the origin of mitochondria: a multilayer network approach
Backgound The endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method. Methods We used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa. Results In our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades. Conclusion By leveraging complex networks methods to the challenging question of circumscribing mitochondrial origin, we suggest that the entire Alphaproteobacteria clade is the closest relative to mitochondria (Alphaproteobacterial-sister hypothesis), echoing recent findings based on different datasets and methodologies.
Borges et al. (2023) On the origin of mitochondria: a multilayer network approach. PeerJ 11:e14571 https://doi.org/10.7717/peerj.14571
Stem transcriptome screen for selection in wild and cultivated pitahaya (Selenicereus undatus): an epiphytic cactus with edible fruit
Dragon fruit, pitahaya or pitaya are common names for the species in the Hylocereus group of Selenicereus that produce edible fruit. These Neotropical epiphytic cacti are considered promising underutilized crops and are currently cultivated around the world. The most important species, S. undatus, has been managed in the Maya domain for centuries and is the focus of this article. Transcriptome profiles from stems of wild and cultivated plants of this species were compared. We hypothesized that differences in transcriptomic signatures could be associated with genes related to drought stress. De novo transcriptome assembly and the analysis of differentially expressed genes (DEGs) allowed us to identify a total of 9,203 DEGs in the Hunucmá cultivar relative of wild Mozomboa plants. Of these, 4,883 represent up-regulated genes and 4,320, down-regulated genes. Additionally, 6,568 DEGs were identified from a comparison between the Umán cultivar and wild plants, revealing 3,286 up-regulated and 3,282 down-regulated genes. Approximately half of the DEGs are shared by the two cultivated plants. Differences between the two cultivars that were collected in the same region could be the result of differences in management. Metabolism was the most representative functional category in both cultivars. The up-regulated genes of both cultivars formed a network related to the hormone-mediated signaling pathway that includes cellular responses to auxin stimulus and to hormone stimulus. These cellular reactions have been documented in several cultivated plants in which drought-tolerant cultivars modify auxin transport and ethylene signaling, resulting in a better redistribution of assimilates.
Oltehua-López et al. (2023) Stem transcriptome screen for selection in wild and cultivated pitahaya (Selenicereus undatus): an epiphytic cactus with edible fruit. PeerJ 11:e14581 https://doi.org/10.7717/peerj.14581
The role of subjective significance, valence and arousal in the explicit processing of emotion-laden words
Emotional categorisation (deciding whether a word is emotional or not) is a task that employs the explicit analysis of the emotional meaning of words. Therefore, it allows for assessing the role of emotional factors, i.e., valence, arousal, and subjective significance, in emotional word processing. The aim of the current experiment was to investigate the role of subjective significance, a reflective form of activation that is similar to arousal (the automatic form), in the processing of emotional meaning. We applied the orthogonal manipulation of three emotional factors. Thus, we were able to precisely differentiate the effects of each factor and search for interactions between them. We expected valence to shape the late positive complex LPC component, while subjective significance and arousal were expected to shape the P300 and N400 components. We observed the effects of subjective significance throughout the whole span of processing, while the arousal effect was present only in the LPC component. We also observed that amplitudes for N400 and LPC discriminated negative from positive valence. The results showed that all factors included in the analysis should be taken into account while explaining the processing of emotion-laden words; especially interesting is the subjective significance, which was shown to shape processing individually, as well as to come into interaction with valence and arousal.
Imbir et al. (2023) The role of subjective significance, valence and arousal in the explicit processing of emotion-laden words. PeerJ 11:e14583 https://doi.org/10.7717/peerj.14583
No effect of attentional modulation by spatial cueing in a masked numerical priming paradigm using continuous flash suppression (CFS)
One notion emerging from studies on unconscious visual processing is that different “blinding techniques” seem to suppress the conscious perception of stimuli at different levels of the neurocognitive architecture. However, even when only the results from a single suppression method are compared, the picture of the scope and limits of unconscious visual processing remains strikingly heterogeneous, as in the case of continuous flash suppression (CFS). To resolve this issue, it has been suggested that high-level semantic processing under CFS is facilitated whenever interocular suppression is attenuated by the removal of visuospatial attention. In this behavioral study, we aimed to further investigate this “CFS-attenuation-by-inattention” hypothesis in a numerical priming study using spatial cueing. Participants performed a number comparison task on a visible target number (“compare number to five”). Prime-target pairs were either congruent (both numbers smaller, or both larger than five) or incongruent. Based on the “CFS-attenuation-by-inattention” hypothesis, we predicted that reaction times (RTs) for congruent prime-target pairs should be faster than for incongruent ones, but only when the prime was presented at the uncued location. In the invisible condition, we observed no priming effects and thus no evidence in support of the “CFS-attenuation-by-inattention” hypothesis. In the visible condition, we found an inverse effect of prime-target congruency. Our results agree with the notion that the representation of CF-suppressed stimuli is fractionated, and limited to their basic, elemental features, thus precluding semantic processing.
Handschack et al. (2023) No effect of attentional modulation by spatial cueing in a masked numerical priming paradigm using continuous flash suppression (CFS). PeerJ 11:e14607 https://doi.org/10.7717/peerj.14607
A novel fatty acid metabolism-related gene prognostic signature and candidate drugs for patients with hepatocellular carcinoma
Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Fatty acid metabolism (FAM) is associated with the development and treatment of HCC. This study aimed to build a FAM-related gene model to assess the prognosis of HCC and provide guidance for individual treatment. RNA-sequencing data of patients with HCC from The Cancer Genome Atlas and Gene Expression Omnibus database (GSE14520) were extracted as the training and validation sets, respectively. A FAM-related gene predictive signature was built, and the performance of prognostic model was assessed. The immune infiltration and drug sensitivity were also evaluated. Quantitative real-time polymerase chain reaction and western blot were performed to evaluate the levels of the model genes. A 12-gene FAM-related risk signature was constructed; patients with a higher risk score had poorer prognosis than those with a lower risk score. Risk score was shown as an independent risk factor for overall survival of HCC, and the signature was further confirmed as an effective and accurate model. A nomogram was constructed, and it exhibited the good performance in the prognostic prediction. In addition, the immune cell infiltration and sensitivity to chemotherapy drugs were correlated with different risk levels. Finally, quantitative real-time polymerase chain reaction and western blot proved the changes of above genes. Differential expression of FAM-related genes can be used to predict response to immunotherapy and chemotherapy, and improve the clinical prognosis evaluation of patients with HCC, which provides new clues for further experimental exploration and verification on FAM-related genes in HCC.
Yang et al. (2023) A novel fatty acid metabolism-related gene prognostic signature and candidate drugs for patients with hepatocellular carcinoma. PeerJ 11:e14622 https://doi.org/10.7717/peerj.14622
Evaluating the effect of the incidence angle of ALOS-2 PALSAR-2 on detecting aquaculture facilities for sustainable use of coastal space and resources
Background Driven by the growing world population, aquaculture plays a key role in meeting the increasing demand for food. However, aquaculture facilities in Japan are widely installed in coastal waters where natural disasters, such as typhoons and tsunamis, might wash these facilities away, thereby interfering with maritime navigation safety. Therefore, it is imperative to efficiently monitor the state of aquaculture facilities daily, particularly after a disaster in real time. To this end, several new space-borne L-band synthetic aperture radars (SARs) continue to be launched now and in the future, whose utilizations are expected to increase nationally and internationally. An example is the Japan Aerospace Exploration Agency, currently operating a SAR that can be operated day and night, and even under cloudy conditions, called ALOS-2 PALSAR-2. Methods Based on the above facts, this study evaluated the effect of the incidence angle of ALOS-2 PALSAR-2 HH single-polarization data, using 3 m spatial resolution, on aquaculture raft detection. As the study site, we selected Ago Bay, located on the Pacific coast of Mie Prefecture in central Japan since the Nankai Trough Megathrust Earthquake and tsunamis have been predicted to occur in the future around this area. Then, we analyzed the sigma zero (backscattering coefficient) of aquaculture rafts and their surrounding sea surfaces, including the relationships between satellite orbits and aquaculture raft directions. Results Investigations revealed that the optimum incidence angle for detecting aquaculture rafts in this study was 33.8°–45.1°. Differences in the sigma zero values existed between the ascending and descending orbits. However, the incidence angles differed on the orbits. Then, differences in the median sigma zero values across a range of incidence angles were evaluated under the descending orbit. In addition, when the directions of the aquaculture rafts were closely perpendicular to the satellite orbit, aquaculture rafts tended to show the highest values of sigma zero due to Bragg resonance scattering. Hence, this knowledge may allow for the rapid detection of aquaculture rafts during an emergency without going on-site.
Spatial and Geographic Information Science
Murata et al. (2023) Evaluating the effect of the incidence angle of ALOS-2 PALSAR-2 on detecting aquaculture facilities for sustainable use of coastal space and resources. PeerJ 11:e14649 https://doi.org/10.7717/peerj.14649
Depletion of PSMD14 suppresses bladder cancer proliferation by regulating GPX4
Objective The aim of this study was to investigate the role of deubiquitinase (DUB) 26S proteasome non-ATPase regulatory subunit 14 (PSMD14) in patients with bladder cancer. Methods From 2016 to 2018, 181 patients diagnosed with primary bladder cancer at the Affiliated Hospital of Qingdao University were recruited. The expression of PSMD14 in bladder cancer tissues was tested by immunochemistry. The association between PSMD14 expression and clinical and pathological data and outcomes of bladder cancer patients was determined. Overexpression and knockdown cells were constructed to evaluate the effects of PSMD14 on proliferation of bladder cancer cells. Results Our results showed that PSMD14 was significantly overexpressed in bladder cancer tissues compared to adjacent non-tumor tissues (76.24% vs 23.76%, P = 0.02). The expression of PSMD14 was significantly higher in patients with larger tumor diameters (85.14% vs 70.09%, P = 0.019) and patients with a family history of cancer (92.16% vs 70.00%, P = 0.002). Patients with high expression of PSMD14 had poor disease-free survival (DFS) (HR = 2.89, 95% CI [1.247–6.711], P = 0.013). Gain and loss of function experiments demonstrated that PSMD14 deficiency inhibited bladder cancer cell proliferation. Additionally, depletion of PSMD14 suppressed bladder cancer cell growth via down-regulation of GPX4, and the promotion of PSMD14-induced cell growth was observably reversed by the GPX4 inhibitor RSL3. Conclusion We determined that PSMD14 is highly expressed in bladder cancer tissues, and that PSMD14 expression correlated with poor disease-free survival. Depletion of PSMD14 could inhibit the proliferation of bladder cancer cells through the downregulation of GPX4. Therefore, PSMD14 may be an effective target for the treatment of bladder cancer.
Jia et al. (2023) Depletion of PSMD14 suppresses bladder cancer proliferation by regulating GPX4. PeerJ 11:e14654 https://doi.org/10.7717/peerj.14654
Immune fitness and lifestyle habits of Saudi medical students: a cross sectional study
Introduction Immune function reaches an optimum level in young adults. However, young adults are more likely to adopt potentially harmful habits that may pose a risk to their long-term health and immune fitness, and which eventually may put a substantial burden on the healthcare system. This study aimed to assess the status of medical students’ immune fitness, using the immune status questionnaire (ISQ) and exploring the association with the commonly adopted lifestyle habits hypothesized to have an impact on immune functions. Methods A descriptive, cross-sectional study was conducted among preclinical students attending the medical school of King Abdulaziz University. An online self-reported questionnaire was used to assess the immune status (ISQ), perceived (momentary) immune fitness, general health, lifestyle habits and students’ perception of these lifestyle-associated impacts on immune fitness. Descriptive, Spearman’s correlation and stepwise linear regression analyses were performed. Results In a pooled sample of 211 participants, the overall ISQ score was 6.00 ± 5.0 with statistically significant abnormally lower scores in females (ISQ 5.00 ± 5.0, p < 0.001). 49.29% of respondents experienced poor immune fitness as measured by the ISQ (<6). The ISQ score was significantly correlated with fast and fatty food consumption (p = 0.003), daytime sleepiness (p = 0.001), and BMI subgroups (p = 0.028) negatively and positively correlated with adherence to a program of exercise (p = 0.005). A total of 41.23% of participants who reported a normal immune health, rated at ≥6 were graded below 6 on the ISQ score. Only 62.6% of students were able to correctly identify the effects of fast and fatty food consumption on immune fitness. Conclusion Poor immune fitness was common among medical students in KAU and associated significantly with their adopted lifestyle habits. Although, other factors can be significant contributors, biased immune health perception and lack of awareness of these lifestyle-associated impacts on immune fitness and general health may hinder the adoption of healthier habits. Immune biomarkers should be implemented in future work.
Alharbi (2023) Immune fitness and lifestyle habits of Saudi medical students: a cross sectional study. PeerJ 11:e14363 https://doi.org/10.7717/peerj.14363
Serratia marcescens antibiotic resistance mechanisms of an opportunistic pathogen: a literature review
Serratia marcescens is a ubiquitous bacterium from order Enterobacterales displaying a high genetic plasticity that allows it to adapt and persist in multiple niches including soil, water, plants, and nosocomial environments. Recently, S. marcescens has gained attention as an emerging pathogen worldwide, provoking infections and outbreaks in debilitated individuals, particularly newborns and patients in intensive care units. S. marcescens isolates recovered from clinical settings are frequently described as multidrug resistant. High levels of antibiotic resistance across Serratia species are a consequence of the combined activity of intrinsic, acquired, and adaptive resistance elements. In this review, we will discuss recent advances in the understanding of mechanisms guiding resistance in this opportunistic pathogen.
Tavares-Carreon et al. (2023) Serratia marcescens antibiotic resistance mechanisms of an opportunistic pathogen: a literature review. PeerJ 11:e14399 https://doi.org/10.7717/peerj.14399