Assessment of antimycobacterial activities of pure compounds extracted from Thai medicinal plants against clarithromycin-resistant Mycobacterium abscessus
Background Infection with Mycobacterium abscessus is usually chronic and is associated with clarithromycin resistance. Increasing drug resistance is a major public-health problem and has led to the search for new antimycobacterial agents. We evaluated the antimycobacterial activity, toxicity, and synergistic effects of several plant secondary metabolites against M. abscessus. Methods Twenty-three compounds were evaluated for antimycobacterial activity against thirty M. abscessus clinical isolates by broth microdilution to determine their minimum inhibitory concentration (MIC) values. Toxicity was evaluated using red and white blood cells (RBCs and WBCs). The compounds were used in combination with clarithromycin to investigate the possibility of synergistic activity. Results Five out of twenty-three compounds (RL008, RL009, RL011, RL012 and RL013) exhibited interesting antimycobacterial activity against M. abscessus, with MIC values ranging from <1 to >128 μg/mL. These extracts did not induce hemolytic effect on RBCs and displayed low toxicity against WBCs. The five least-toxic compounds were tested for synergism with clarithromycin against seven isolates with inducible clarithromycin resistance and seven with acquired clarithromycin resistance. The best synergistic results against these isolates were observed for RL008 and RL009 (8/14 isolates; 57%). Conclusions This study demonstrated antimycobacterial and synergistic activities of pure compounds extracted from medicinal plants against clarithromycin-resistant M. abscessus. This synergistic action, together with clarithromycin, may be effective for treating infections and should be further studied for the development of novel antimicrobial agents.
Sirichoat et al. (2021) Assessment of antimycobacterial activities of pure compounds extracted from Thai medicinal plants against clarithromycin-resistant Mycobacterium abscessus. PeerJ 9:e12391 https://doi.org/10.7717/peerj.12391
Blood cells and hematological parameters of the mountain dragon, Diploderma micangshanensis (Squamata: Lacertilia: Agamidae)
Hematological characteristics reflect the health status of animals and their physiological adaptation to the environment. However, few studies focused on the species of Diploderma. In this study, the blood cells and the hematological parameters of Diploderma micangshanensis, a species endemic to China, were examined based on 48 healthy adult (32 males and 16 females). The blood cells and hematological parameters of D. micangshanensis were similar to those of other lizard species. Although the values of erythrocyte morphometric characters and hematological parameters varied between males and females, the differences were only significant in the case of the hematocrit and erythrocyte size, which may allow for higher oxygen availability in males. Hemoglobin, mean corpuscular hemoglobin concentration, and mean corpuscle volume were strongly affected by the snout-vent length and/or body mass, which reflect the physiological adaptation to the oxygen requirement of different individuals. This is the first report of hematological data from a species of Diploderma, and the results will provide data for research on the adaptive evolution and health assessment in this species and other congeners.
Bai et al. (2021) Blood cells and hematological parameters of the mountain dragon, Diploderma micangshanensis (Squamata: Lacertilia: Agamidae). PeerJ 9:e12397 https://doi.org/10.7717/peerj.12397
Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization
Background Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. Methods We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. Results We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.
Liston et al. (2021) Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization. PeerJ 9:e12418 https://doi.org/10.7717/peerj.12418
Modernising tactile acuity assessment; clinimetrics of semi-automated tests and effects of age, sex and anthropometry on performance
Background Reduced tactile acuity has been observed in several chronic pain conditions and has been proposed as a clinical indicator of somatosensory impairments related to the condition. As some interventions targeting these impairments have resulted in pain reduction, assessing tactile acuity may have significant clinical potential. While two-point discrimination threshold (TPDT) is a popular method of assessing tactile acuity, large measurement error has been observed (impeding responsiveness) and its validity has been questioned. The recently developed semi-automated ‘imprint Tactile Acuity Device’ (iTAD) may improve tactile acuity assessment, but clinimetric properties of its scores (accuracy score, response time and rate correct score) need further examination. Aims Experiment 1: To determine inter-rater reliability and measurement error of TPDT and iTAD assessments. Experiment 2: To determine internal consistencies and floor or ceiling effects of iTAD scores, and investigate effects of age, sex, and anthropometry on performance. Methods Experiment 1: To assess inter-rater reliability (ICC(2,1)) and measurement error (coefficient of variation (CoV)), three assessors each performed TPDT and iTAD assessments at the neck in forty healthy participants. Experiment 2: To assess internal consistency (ICC(2,k)) and floor or ceiling effects (skewness z-scores), one hundred healthy participants performed the iTAD’s localisation and orientation tests. Balanced for sex, participants were equally divided over five age brackets (18–30, 31–40, 41–50, 51–60 and 61–70). Age, sex, body mass index (BMI) and neck surface area were assessed to examine their direct (using multiple linear regression analysis) and indirect (using sequential mediation analysis) relationship with iTAD scores. Results Mean ICC(2,1) was moderate for TPDT (0.70) and moderate-to-good for the various iTAD scores (0.65–0.86). The CoV was 25.3% for TPDT and ranged from 6.1% to 16.5% for iTAD scores. Internal consistency was high for both iTAD accuracy scores (ICC(2,6) = 0.84; ICC(2,4) = 0.86). No overt floor or ceiling effects were detected (all skewness z-scores < 3.29). Accuracy scores were only directly related to age (decreasing with increasing age) and sex (higher for men). Discussion Although reliability was similar, iTAD scores demonstrated less measurement error than TPDT indicating a potential for better responsiveness to treatment effects. Further, unlike previously reported for TPDT, iTAD scores appeared independent of anthropometry, which simplifies interpretation. Additionally, the iTAD assesses multiple aspects of tactile processing which may provide a more comprehensive evaluation of tactile acuity. Taken together, the iTAD shows promise in measuring tactile acuity, but patient studies are needed to verify clinical relevance.
Olthof et al. (2021) Modernising tactile acuity assessment; clinimetrics of semi-automated tests and effects of age, sex and anthropometry on performance. PeerJ 9:e12192 https://doi.org/10.7717/peerj.12192
Salinity effects on water potential and the normalized difference vegetation index in four species of a saline semi-arid ecosystem
This study was carried out during January 2020–December 2020 in a semi-desert ecosystem in southern Sonora, Mexico, to determine the annual and daily variations in water potential and the normalized difference vegetation index (NDVI) of Bursera fagaroides Engl., Monogr. Phan., Parkinsonia aculeata L., Sp. Pl.; Prosopis laevigata (Humb. & Bonpl. ex Willd.), and Atriplex canescens (Pursh) Nutt. Soil electrical conductivity, cation content, and physical characteristics were determined at two depths, and water potential (ψ) was measured in roots, stems, and leaves. The daily leaf ψ was measured every 15 days each month to determine the duration of stress (hours) and the stress intensity (SI). The electrical conductivity determinations classified the soil in the experimental area as strongly saline. A significant difference was noted in electrical conductivity between soil depths. The four studied species showed significant gradients of ψ in their organs. In this soil, all four species remained in a stressed condition for approximately 11 h per day. The mean SI was 27%, and B. fagaroides Engl., Monogr. Phan. showed the lowest value. The four species showed increased NDVI values during the rainy months, with P. laevigata (Humb. & Bonpl. ex Willd.) and Parkinsonia aculeata L., Sp. Pl. showing the highest values. The capacity for ψ decrease under saline conditions identified A. canescens (Pursh) Nutt., B. fagaroides Engl., Monogr. Phan. and P. aculeata L., Sp. Pl. as practical and feasible alternatives for establishment in saline soils in southern Sonora for purposes of soil recovery and reforestation.
Soto Gonzáles et al. (2021) Salinity effects on water potential and the normalized difference vegetation index in four species of a saline semi-arid ecosystem. PeerJ 9:e12297 https://doi.org/10.7717/peerj.12297
Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus (Nelumbo nucifera)
Lotus (Nelumbo nucifera) is a highly recognized flower with high ornamental value. Flower color and flower morphology are two main factors for flower lotus breeding. Petaloidy is a universal phenomenon in lotus flowers. However, the genetic regulation of floral organ petaloidy in lotus remains elusive. In this study, the transcriptomic analysis was performed among three organs, including petal, carpel petaloidy, and carpel in lotus. A total of 1,568 DEGs related to carpel petaloidy were identified. Our study identified one floral homeotic gene encoded by the MADS-box transcription factor, AGAMOUS (AG) as the candidate gene for petaloid in lotus. Meanwhile, a predicted labile boundary in floral organs of N. nucifera was hypothesized. In summary, our results explored the candidate genes related to carpel petaloidy, setting a theoretical basis for the molecular regulation of petaloid phenotype.
Lin et al. (2021) Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus (Nelumbo nucifera). PeerJ 9:e12322 https://doi.org/10.7717/peerj.12322
Integrating microRNA expression, miRNA-mRNA regulation network and signal pathway: a novel strategy for lung cancer biomarker discovery
Background Since there are inextricably connections among molecules in the biological networks, it would be a more efficient and accurate research strategy to screen microRNA (miRNA) markers combining with miRNA-mRNA regulatory networks. The independent regulation mode is more “fragile” and “influential” than the co-regulation mode. miRNAs can be used as biomarkers if they can independently regulate hub genes with important roles in the PPI network, simultaneously the expression products of the regulated hub genes play important roles in the signaling pathways of related tissue diseases. Methods We collected miRNA expression of non-small cell lung cancer (NSCLC) from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Volcano plot and signal-to-noise ratio (SNR) methods were used to obtain significant differentially expressed (SDE) miRNAs from the TCGA database and GEO database, respectively. A human miRNA-mRNA regulatory network was constructed and the number of genes uniquely targeted (NOG) by a certain miRNA was calculated. The area under the curve (AUC) values were used to screen for clinical sensitivity and specificity. The candidate markers were obtained using the criteria of the top five maximum AUC values and NOG ≥ 3. The protein–protein interaction (PPI) network was constructed and independently regulated hub genes were obtained. Gene Ontology (GO) analysis and KEGG pathway analysis were used to identify genes involved in cancer-related pathways. Finally, the miRNA which can independently regulate a hub gene and the hub gene can participate in an important cancer-related pathway was considered as a biomarker. The AUC values and gene expression profile analysis from two external GEO datasets as well as literature validation were used to verify the screening capability and reliability of this marker. Results Fifteen SDE miRNAs in lung cancer were obtained from the intersection of volcano plot and SNR based on the GEO database and the TCGA database. Five miRNAs with the top five maximum AUC values and NOG ≥ 3 were screened out. A total of 61 hub genes were obtained from the PPI network. It was found that the hub gene GTF2F2 was independently regulated by miR-708-5p. Further pathway analysis indicated that GTF2F2 participates in protein expression by binding with polymerase II, and it can regulate transcription and accelerate tumor growth. Hence, miR-708-5p could be used as a biomarker. The good screening capability and reliability of miR-708-5p as a lung cancer marker were confirmed by AUC values and gene expression profiling of external datasets, and experimental literature. The potential mechanism of miR-708-5p was proposed. Conclusions This study proposes a new idea for lung cancer marker screening by integrating microRNA expression, regulation network and signal pathway. miR-708-5p was identified as a biomarker using this novel strategy. This study may provide some help for cancer marker screening.
Nie et al. (2021) Integrating microRNA expression, miRNA-mRNA regulation network and signal pathway: a novel strategy for lung cancer biomarker discovery. PeerJ 9:e12369 https://doi.org/10.7717/peerj.12369
Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanxi, China
Objectives We carried out a retrospective study to investigate the drug susceptibility and genetic relationship of clinical Escherichia coli isolates from patients with BSIs in Shanxi, China. Methods E. coli isolates causing BSIs were consecutively collected from June 2019 to March 2020. Antimicrobial susceptibility testing was performed by broth microdilution method. PCR was used to detect antimicrobial resistance genes coding for extended-spectrum β-lactamases (ESBLs), phylogenetic groups and seven housekeeping genes of E. coli. Results A total of 76 E. coli were collected. Antimicrobial susceptibility testing revealed that the top six E. coli resistant antibiotics were ampicillin (90.7%), ciprofloxacin (69.7%), cefazolin (65.7%), levofloxacin (63.1%), ceftriaxone and cefotaxime (56.5%). Among the 76 isolates, 43 produced ESBLs. Molecular analysis showed that CTX-M-14 was the most common ESBLs, followed by CTX-M-15 and CTX-M-55. Phylogenetic group D (42.2%) predominated, followed by group B2 (34.2%), group A (18.4%) and group B1 (5.2%). The most prevalent sequence types (STs) were ST131 (15/76), ST69 (12/76) and ST38 (6/76). Conclusions This study is the first to report the phenotypic and molecular characteristics of E. coli isolated from BSIs in Shanxi, China. Our results indicated a high prevalence of MDR in E. coli strains isolated from BSIs and a serious spread of ESBL genes in Shanxi, especially the epidemiological blaCTX-M. Phylogenetic analysis indicated genetic diversity among E. coli BSIs isolates.
Zhang et al. (2021) Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanxi, China. PeerJ 9:e12371 https://doi.org/10.7717/peerj.12371
Association between IL-1B (-511)/IL-1RN (VNTR) polymorphisms and type 2 diabetes: a systematic review and meta-analysis
Interleukin-1 (IL-1) plays an essential role in the immune pro-inflammatory process, which is regarded as one of many factors in the development of type 2 diabetes mellitus (T2DM). Several case-control studies have illustrated the association of the IL-1B (-511) (rs16944, Chr 2:112,837,290, C/T Intragenic, Transition Substitution) and IL-1RN (VNTR) (gene for IL-1 receptor antagonist, IL-1RA, 86 bp tandem repeats in intron 2) polymorphisms with T2DM risk. However, the results were inconsistent and inconclusive. We performed a meta-analysis (registry number: CRD42021268494) to assess the association of the IL-1B (-511) and IL-1RN (VNTR) polymorphisms with T2DM risk. Random-effects models were applied to calculate the pooled ORs (odds ratios) and 95% CIs (confidence intervals) to test the strength of the association in the overall group and subgroups stratified by ethnicity, respectively. Between-study heterogeneity and publication bias were evaluated by the Q-test, I2 statistic, Harbord test, and Peters test accordingly. Sensitivity analyses were also performed. A total of 12 publications evaluating the association of IL-1B (-511) and IL-1RN (VNTR) polymorphisms with the risk of T2DM development were included. The meta-analysis showed that IL-1RN (VNTR) was related to the increasing development of T2DM risk in the recessive model (OR = 1.62, 95% CI [1.09–2.42], Phet = 0.377, Pz = 0.018) and in the homozygous model (OR = 2.02, 95% CI [1.07–3.83], Phet = 0.085, Pz = 0.031), and the IL-1RN 2* allele was found a significant association with evaluated T2DM risk in all ethnicities (OR = 2.08, 95% CI [1.43–3.02], Phet < 0.001, Pz < 0.001) and in EA (OR = 2.01, 95% CI [1.53–2.66], Phet = 0.541, Pz < 0.001). Moreover, stratification by ethnicity revealed that IL-1B (-511) was associated with a decreased risk of T2DM in the dominant model (OR=0.76, 95% CI [0.59–0.97], Phet = 0.218, Pz = 0.027) and codominant model (OR = 0.73, 95% CI [0.54–0.99], Phet = 0.141, Pz = 0.040) in the East Asian (EA) subgroup. Our results suggest that the IL-1RN 2* allele and 2*2* homozygous polymorphism are strongly associated with increasing T2DM risk and that the IL-1B (-511) T allele polymorphism is associated with decreasing T2DM risk in the EA subgroup.
Jiao et al. (2021) Association between IL-1B (-511)/IL-1RN (VNTR) polymorphisms and type 2 diabetes: a systematic review and meta-analysis. PeerJ 9:e12384 https://doi.org/10.7717/peerj.12384
Nitzschia anatoliensis sp. nov., a cryptic diatom species from the highly alkaline Van Lake (Turkey)
In this article we describe Nitzschia anatoliensis Górecka, Gastineau & Solak sp. nov., an example of a diatom species inhabiting extreme habitats. The new species has been isolated and successfully grown from the highly alkaline Van Lake in East Turkey. The description is based on morphology (light and scanning electron microscopy), the sequencing of its organellar genomes and several molecular phylogenies. This species could easily be overlooked because of its extreme similarity to Nitzschia aurariae but molecular phylogenies indicate that they are only distantly related. Furthermore, molecular data suggest that N. anatoliensis may occur in several alkaline lakes of Asia Minor and Siberia, but was previously misidentified as Nitzschia communis. It also revealed the very close genetic proximity between N. anatoliensis and the endosymbiont of the dinotom Kryptoperidinium foliaceum, providing additional clues on what might have been the original species of diatoms to enter symbiosis.
Solak et al. (2021) Nitzschia anatoliensis sp. nov., a cryptic diatom species from the highly alkaline Van Lake (Turkey). PeerJ 9:e12220 https://doi.org/10.7717/peerj.12220