Machine learning: a powerful tool for identifying key microbial agents associated with specific cancer types
Machine learning (ML) includes a broad class of computer programs that improve with experience and shows unique strengths in performing tasks such as clustering, classification and regression. Over the past decade, microbial communities have been implicated in influencing the onset, progression, metastasis, and therapeutic response of multiple cancers. Host-microbe interaction may be a physiological pathway contributing to cancer development. With the accumulation of a large number of high-throughput data, ML has been successfully applied to the study of human cancer microbiomics in an attempt to reveal the complex mechanism behind cancer. In this review, we begin with a brief overview of the data sources included in cancer microbiomics studies. Then, the characteristics of the ML algorithm are briefly introduced. Secondly, the application progress of ML in cancer microbiomics is also reviewed. Finally, we highlight the challenges and future prospects facing ML in cancer microbiomics. On this basis, we conclude that the development of cancer microbiomics can not be achieved without ML, and that ML can be used to develop tumor-targeting microbial therapies, ultimately contributing to personalized and precision medicine.
Feng et al. (2023) Machine learning: a powerful tool for identifying key microbial agents associated with specific cancer types. PeerJ 11:e16304 https://doi.org/10.7717/peerj.16304
De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb. (Balsaminaceae) using nanopore long-read sequencing
The plant family Balsaminaceae comprises only two genera, and they are a study in contrasts. While Impatiens is an impressively prolific genus, with over 1,000 species and more being discovered each year, its sister genus, Hydrocera, has one solitary species, H. triflora. The two genera also differ in geographic distribution and habitat type (Impatiens species are widely distributed in much of the Old World and N. America, while H. triflora is confined to wetlands specific to S. India, Sri Lanka, and SE Asia). Other contrasting features include plant habit, habitat, floral architecture, mode of seed dispersal, and a host of other traits. The family Balsaminaceae is therefore an excellent model for studying speciation and character evolution as well as understanding the proximal and evolutionary forces that have driven the two genera to adopt such contrasting evolutionary paths. Various species of the Impatiens genus are also commercially important in the ornamental flower industry and as sources of phytochemicals that are of medicinal and other commercial value. As a preliminary step towards studying the genomic basis of the contrasting features of the two genera, we have sequenced and assembled, de novo, the genome of an iconic Impatiens species from N. America, namely I. capensis, and report our findings here.
Gadagkar et al. (2023) De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb. (Balsaminaceae) using nanopore long-read sequencing. PeerJ 11:e16328 https://doi.org/10.7717/peerj.16328
Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR
Citrus crops are affected by many fungal diseases. Among them, Citrus Black Spot caused by the ascomycete Phyllosticta citricarpa is particularly economically damaging wherever it occurs. Many other species of Phyllosticta are described on Citrus, but only P. citricarpa is considered a quarantine pest on the European continent. In order to prevent the introduction of this species into Europe, it is essential to have a detection test which can reliably identify it, and not confuse it with other species present on citrus, notably P. paracitricarpa. The latter taxon has recently been described as very close to P. citricarpa, and most detection tests do not allow to distinguish the two species. In this work, we exploited the genomic data of 37 isolates of Phyllosticta spp. from citrus, firstly to assess their phylogenetic relationships, and secondly to search for genomic regions that allowed the definition of species-specific markers of P. citricarpa. Analysis of 51 concatenated genes separated P. citricarpa and P. paracitricarpa in two phylogenetic clades. A locus was selected to define a hydrolysis probe and primers combination that could be used in real-time PCR for the specific detection of the quarantine species, to the exclusion of all others present on Citrus. This test was then thoroughly validated on a set of strains covering a wide geographical diversity, and on numerous biological samples to demonstrate its reliability for regulatory control. The validation data highlighted the need to check the reliability of the test in advance, when a change of reagents was being considered.
Ioos et al. (2023) Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR. PeerJ 11:e16354 https://doi.org/10.7717/peerj.16354
Evaluation of crystalline amino acids as potent stimulatory chemoattractants for the slipper lobster Thenus orientalis
Intensive research on the effectiveness of chemoattractants has been widely explored to improve the feed qualities in expanding crustacean farming. Taste preferences in slipper lobster remained unknown despite their significant contribution to the lobster fisheries. Chemoattractants allow better performance in aquaculture species by increasing food attractiveness and palatability. Amino acids (AA) have been leading in previous research on crustacean feeding behavior. Given that slipper lobster possesses chemoreceptors to detect and orient towards food, this study investigated an approach to identify the AA with the most potent chemoattractant in eliciting a response from slipper lobster. Behavioral assays were performed to evaluate the responses of slipper lobster Thenus orientalis (carapace length, 52.34 ± 1.52 mm) on 15 crystalline AA and three derivatives of AA (DAA) at three concentrations between 10−1 and 10−3 M as test substances (TS). Meretrix sp. extract was used as a positive control and clean filtered seawater as a negative control. The behavioral responses of 14 T. orientalis were evaluated based on their antennular flicking rate, third maxillipeds activity, and substrate probing by the pereiopods. T. orientalis responded to the solutions of single AA down to a concentration of 10−3 M, excluding histidine and serine. The behavioral activity displayed by T. orientalis increased with the TS concentrations. L-glutamic acid monosodium salt monohydrate, betaine, and glycine solutions elicited the most behavioral responses, whereas histidine exhibited the lowest behavioral responses. Conclusively, L-glutamic acid monosodium salt monohydrate, betaine, and glycine can be potential chemoattractants for T. orientalis.
Teoh et al. (2023) Evaluation of crystalline amino acids as potent stimulatory chemoattractants for the slipper lobster Thenus orientalis. PeerJ 11:e15607 https://doi.org/10.7717/peerj.15607
Validating a re-implementation of an algorithm to integrate transcriptome and ChIP-seq data
Transcription factor binding to a gene regulatory region induces or represses its expression. Binding and expression target analysis (BETA) integrates the binding and gene expression data to predict this function. First, the regulatory potential of the factor is modeled based on the distance of its binding sites from the transcription start sites in a decay function. Then the differential expression statistics from an experiment where this factor was perturbed represent the binding effect. The rank product of the two values is employed to order in importance. This algorithm was originally implemented in Python. We reimplemented the algorithm in R to take advantage of existing data structures and other tools for downstream analyses. Here, we attempted to replicate the findings in the original BETA paper. We applied the new implementation to the same datasets using default and varying inputs and cutoffs. We successfully replicated the original results. Moreover, we showed that the method was appropriately influenced by varying the input and was robust to choices of cutoffs in statistical testing.
Ahmed et al. (2023) Validating a re-implementation of an algorithm to integrate transcriptome and ChIP-seq data. PeerJ 11:e16318 https://doi.org/10.7717/peerj.16318
Analysis of the apoplast fluid proteome during the induction of systemic acquired resistance in Arabidopsis thaliana
Background Plant-pathogen interactions occur in the apoplast comprising the cell wall matrix and the fluid in the extracellular space outside the plasma membrane. However, little is known regarding the contribution of the apoplastic proteome to systemic acquired resistance (SAR). Methods Specifically, SAR was induced by inoculating plants with Pst DC3000 avrRps4. The apoplast washing fluid (AWF) was collected from the systemic leaves of the SAR-induced or mock-treated plants. A label free quantitative proteomic analysis was performed to identified the proteins related to SAR in AWF. Results A total of 117 proteins were designated as differentially accumulated proteins (DAPs), including numerous pathogenesis-related proteins, kinases, glycosyl hydrolases, and redox-related proteins. Functional enrichment analyses shown that these DAPs were mainly enriched in carbohydrate metabolic process, cell wall organization, hydrogen peroxide catabolic process, and positive regulation of catalytic activity. Comparative analysis of proteome data indicated that these DAPs were selectively enriched in the apoplast during the induction of SAR. Conclusions The findings of this study indicate the apoplastic proteome is involved in SAR. The data presented herein may be useful for future investigations on the molecular mechanism mediating the establishment of SAR.
Jiang et al. (2023) Analysis of the apoplast fluid proteome during the induction of systemic acquired resistance in Arabidopsis thaliana. PeerJ 11:e16324 https://doi.org/10.7717/peerj.16324
Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens
Background The Kashmir red deer or Hangul (Cervus hanglu hanglu) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species. Methods Blood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14× and ~10× coverage, respectively) from Dachigam National Park. Results The annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies C. hanglu yarkandensis and is sister to the Hungarian red deer (C. elaphus hippelaphus). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related C. yarkandensis, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species.
Ahmad et al. (2023) Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens. PeerJ 11:e15746 https://doi.org/10.7717/peerj.15746
Assessment tools and incidence of hospital-associated disability in older adults: a rapid systematic review
Background During hospitalization older adults have a high risk of developing functional impairments unrelated to the reasons for their admission. This is termed hospital-associated disability (HAD). This systematic review aimed to assess the incidence of HAD in older adults admitted to acute care with two outcomes: firstly in at least one activity of daily living from a set of functional tasks (e.g., Katz Index) and secondly the incidence of functional decline in an individual functional task (e.g., bathing), and to identify any tools or functional tasks used to assess activities of daily living (ADL) in hospitalized older patients. Methods A rapid systematic review was performed according to the recommendations of the Cochrane Rapid Reviews Methods Group and reported the data according the PRISMA statement. A literature search was performed in Medline (via Ovid), EMBASE, and Cochrane Central Register of Controlled Trials databases on 26 August 2021. Inclusion criteria: older adults (≥65 years), assessment of individual items of activities of daily living at baseline and discharge. Exclusion criterion: studies investigating a specific condition that could affect functional decline and studies that primarily examined a population with cognitive impairment. The protocol was registered on OSF registries (https://osf.io/9jez4/) identifier: DOI 10.17605/OSF.IO/9JEZ4. Results Ten studies were included in the final review. Incidence of HAD (overall score) was 37% (95% CI 0.30–0.43). Insufficient data prevented meta-analysis of the individual items. One study provided sufficient data to calculate incidence, with the following values for patients’ self-reported dependencies: 32% for bathing, 27% for dressing, 27% for toileting, 30% for eating and 27% for transferring. The proxy reported the following values for patients’ dependencies: 70% for bathing, 66% for dressing, 70% for toileting, 61% for eating and 59% for transferring. The review identified four assessment tools, two sets of tasks, and individual items assessing activities of daily living in such patients. Conclusions Incidence of hospital-associated disability in older patients might be overestimated, due to the combination of disease-related disability and hospital-associated disability. The tools used to assess these patients presented some limitations. These results should be interpreted with caution as only one study reported adequate information to assess the HAD incidence. At the item level, the latter was higher when disability was reported by the proxies than when it was reported by patients. This review highlights the lack of systematic reporting of data used to calculate HAD incidence. The methodological quality and the risk of bias in the included studies raised some concerns.
Giacomino et al. (2023) Assessment tools and incidence of hospital-associated disability in older adults: a rapid systematic review. PeerJ 11:e16036 https://doi.org/10.7717/peerj.16036
Differences in lumbar spine intradiscal pressure between standing and sitting postures: a comprehensive literature review
Background Musculoskeletal disorders (MSDs), especially in the lumbar spine, are a leading concern in occupational health. Work activities associated with excessive exposure are a source of risk for MSDs. The optimal design of workplaces requires changes in both sitting and standing postures. In order to secure such a design scientifically proved quantitative data are needed that would allow for the assessment of differences in spine load due to body posture and/or exerted force. Intradiscal pressure (IP) measurement in the lumbar spine is the most direct method of estimating spinal loads. Hence, this study aims at the quantitative evaluation of differences in lumbar spine load due to body posture and exerted forces, based on IP reported in publications obtained from a comprehensive review of the available literature. Methodology In order to collect data from studies measuring IP in the lumbar spine, three databases were searched. Studies with IP for living adults, measured in various sitting and standing postures, where one of these was standing upright, were included in the analysis. For data to be comparable between studies, the IP for each position was referenced to upright standing. Where different studies presented IP for the same postures, those relative IPs (rIP) were merged. Then, an analysis of the respective outcomes was conducted to find the possible relationship of IPs dependent on a specific posture. Results A preliminary analysis of the reviewed papers returned nine items fulfilling the inclusion and exclusion criteria. After merging relative IPs from different studies, rIP for 27 sitting and 26 standing postures was yielded. Some of the data were useful for deriving mathematical equations expressing rIP as a function of back flexion angle and exerted force in the form of a second degree polynomial equation for the standing and sitting positions. The equations showed that for the standing posture, the increase in IP with increasing back flexion angle is steeper when applying an external force than when maintaining body position only. In a sitting position with the back flexed at 20°, adding 10 kg to each hand increases the IP by about 50%. According to the equations developed, for back flexion angles less than 20°, the IP is greater in sitting than in standing. When the angle is greater than 20°, the IP in the sitting position is less than in the standing position at the same angle of back flexion. Conclusions Analysis of the data from the reviewed papers showed that: sitting without support increases IP by about 30% in relation to upright standing; a polynomial of the second degree defines changes in IP as a function of back flexion for for both postures. There are differences in the pattern of changes in IP with a back flexion angle between sitting and standing postures, as back flexion in standing increases IP more than in sitting.
Roman-Liu et al. (2023) Differences in lumbar spine intradiscal pressure between standing and sitting postures: a comprehensive literature review. PeerJ 11:e16176 https://doi.org/10.7717/peerj.16176
Transcriptome analysis reveals the mechanism of pyroptosis-related genes in septic cardiomyopathy
Background Septic cardiomyopathy (SC) is characterized by myocardial dysfunction caused by sepsis and constitutes one of the serious complications of sepsis. Pyroptosis is a unique proinflammatory programmed cell death process. However, the role of pyroptosis in the development of SC remains unclear, and further study is required. The purpose of this study is to identify pyroptosis-related genes (PRGs) in SC and explore the mechanism of pyroptosis involved in the regulation of SC formation and progression. Methods Differential expression analysis and enrichment analysis were performed on the SC-related dataset GSE79962 to identify differentially expressed genes (DEGs). PRGs were screened by intersecting genes associated with pyroptosis in previous studies with the DEGs obtained from GSE79962. The expression pattern of them was studied based on their raw expression data. Additionally, corresponding online databases were used to predict miRNAs, transcription factors (TFs) and therapeutic agents of PRGs. Lipopolysaccharide (LPS)-induced cell damage models in H9C2 and AC16 cell lines were constructed, cell activity was detected by CCK-8 and cell pyroptosis were detected by Hoechst33342/PI staining. Furthermore, these PRGs were verified in the external datasets (GSE53007 and GSE142615) and LPS-induced cell damage model. Finally, the effect of siRNA-mediated PRGs knockdown on the pyroptosis phenotype was examined. Results A total of 1,206 DEGs were screened, consisting of 663 high-expressed genes and 543 low-expressed genes. Among them, ten PRGs (SOD2, GJA1, TIMP3, TAP1, TIMP1, NOD1, TP53, CPTP, CASP1 and SAT1) were identified, and they were mainly enriched in “Pyroptosis”, “Ferroptosis”, “Longevity regulating pathway”, and “NOD-like receptor signaling pathway”. A total of 147 miRNAs, 31 TFs and 13 therapeutic drugs were predicted targeting the PRGs. The expression trends of SOD2 were confirmed in both the external datasets and LPS-induced cell damage models. Knockdown of SOD2 induced increased pyroptosis in the AC16 LPS-induced cell damage model. Conclusions In this study, we demonstrated that SOD2 is highly expressed in both the SC and LPS-induced cell damage models. Knockdown of SOD2 led to a significant increase in pyroptosis in the AC16 LPS-induced cell damage model. These findings suggest that SOD2 may serve as a potential target for the diagnosis and treatment of SC.
Zhu et al. (2023) Transcriptome analysis reveals the mechanism of pyroptosis-related genes in septic cardiomyopathy. PeerJ 11:e16214 https://doi.org/10.7717/peerj.16214