title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=515 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Autistic traits are associated with individual differences in finger tapping: an online study link: https://peerj.com/articles/15406 last-modified: 2023-05-16 description: In a novel online study, we explored whether finger tapping differences are evident in people with autistic traits in the general population. We hypothesised that those with higher autistic traits would show more impairment in finger tapping, and that age would moderate tapping output. The study included a non-diagnosed population of 159 participants aged 18–78 who completed an online measure of autistic traits (the AQ-10) and a measure of finger tapping (the FTT). Results showed those with higher AQ-10 scores recorded lower tapping scores in both hands. Moderation analysis showed younger participants with more autistic traits recorded lower tapping scores for the dominant hand. This suggests motor differences seen in autism studies are evident in the general population. creator: Alycia Messing creator: Deborah Apthorp uri: https://doi.org/10.7717/peerj.15406 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Messing and Apthorp title: Impact of mini-driver genes in the prognosis and tumor features of colorectal cancer samples: a novel perspective to support current biomarkers link: https://peerj.com/articles/15410 last-modified: 2023-05-16 description: BackgroundColorectal cancer (CRC) is the second leading cause of cancer-related deaths, and its development is associated with the gains and/or losses of genetic material, which leads to the emergence of main driver genes with higher mutational frequency. In addition, there are other genes with mutations that have weak tumor-promoting effects, known as mini-drivers, which could aggravate the development of oncogenesis when they occur together. The aim of our work was to use computer analysis to explore the survival impact, frequency, and incidence of mutations of possible mini-driver genes to be used for the prognosis of CRC.MethodsWe retrieved data from three sources of CRC samples using the cBioPortal platform and analyzed the mutational frequency to exclude genes with driver features and those mutated in less than 5% of the original cohort. We also observed that the mutational profile of these mini-driver candidates is associated with variations in the expression levels. The candidate genes obtained were subjected to Kaplan–Meier curve analysis, making a comparison between mutated and wild-type samples for each gene using a p-value threshold of 0.01.ResultsAfter gene filtering by mutational frequency, we obtained 159 genes of which 60 were associated with a high accumulation of total somatic mutations with Log2 (fold change) > 2 and p values < 10−5. In addition, these genes were enriched to oncogenic pathways such as epithelium-mesenchymal transition, hsa-miR-218-5p downregulation, and extracellular matrix organization. Our analysis identified five genes with possible implications as mini-drivers: DOCK3, FN1, PAPPA2, DNAH11, and FBN2. Furthermore, we evaluated a combined classification where CRC patients with at least one mutation in any of these genes were separated from the main cohort obtaining a p-value < 0.001 in the evaluation of CRC prognosis.ConclusionOur study suggests that the identification and incorporation of mini-driver genes in addition to known driver genes could enhance the accuracy of prognostic biomarkers for CRC. creator: Anthony Vladimir Campos Segura creator: Mariana Belén Velásquez Sotomayor creator: Ana Isabel Flor Gutiérrez Román creator: César Alexander Ortiz Rojas creator: Alexis Germán Murillo Carrasco uri: https://doi.org/10.7717/peerj.15410 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Campos Segura et al. title: Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane link: https://peerj.com/articles/14973 last-modified: 2023-05-15 description: De novo synthesis of thiamine (vitamin B1) in plants depends on the action of thiamine thiazole synthase, which synthesizes the thiazole ring, and is encoded by the THI1 gene. Here, we investigated the evolution and diversity of THI1 in Poaceae, where C4 and C3 photosynthetic plants co-evolved. An ancestral duplication of THI1 is observed in Panicoideae that remains in many modern monocots, including sugarcane. In addition to the two sugarcane copies (ScTHI1-1 and ScTHI1-2), we identified ScTHI1-2 alleles showing differences in their sequence, indicating divergence between ScTHI1-2a and ScTHI1-2b. Such variations are observed only in the Saccharum complex, corroborating the phylogeny. At least five THI1 genomic environments were found in Poaceae, two in sugarcane, M. sinensis, and S. bicolor. The THI1 promoter in Poaceae is highly conserved at 300 bp upstream of the start codon ATG and has cis-regulatory elements that putatively bind to transcription factors associated with development, growth, development and biological rhythms. An experiment set to compare gene expression levels in different tissues across the sugarcane R570 life cycle showed that ScTHI1-1 was expressed mainly in leaves regardless of age. Furthermore, ScTHI1 displayed relatively high expression levels in meristem and culm, which varied with the plant age. Finally, yeast complementation studies with THI4-defective strain demonstrate that only ScTHI1-1 and ScTHI1-2b isoforms can partially restore thiamine auxotrophy, albeit at a low frequency. Taken together, the present work supports the existence of multiple origins of THI1 harboring genomic regions in Poaceae with predicted functional redundancy. In addition, it questions the contribution of the levels of the thiazole ring in C4 photosynthetic plant tissues or potentially the relevance of the THI1 protein activity. creator: Henrique Moura Dias creator: Andreia Prata Vieira creator: Erika Maria de Jesus creator: Nathalia de Setta creator: Gesiele Barros creator: Marie-Anne Van Sluys uri: https://doi.org/10.7717/peerj.14973 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Moura Dias et al. title: Prevalence and risk factors of recurrent aphthous stomatitis among college students at Mangalore, India link: https://peerj.com/articles/14998 last-modified: 2023-05-15 description: BackgroundRecurrent aphthous stomatitis (RAS) is one of the most common oral mucosal diseases affecting an approximate 25% of the world’s population. Some common etiological factors are genetics, nutritional deficiencies, stress and immune dysfunction. There is currently no specific medication to treat the condition but RAS tends to heal by itself within a week or two. We aimed to explore about the prevalence and related risk factors of recurrent aphthous ulcers among college students aged 18–30 years who had been affected within the preceding six months prior to the study duration.MethodsA questionnaire survey was conducted among 681 students from four colleges in Mangalore, Karnataka, India after obtaining the approval for the same from the respective colleges. Consenting participants returned a survey containing various questions. The collected data was then analyzed using descriptive statistics. The study was approved by the Institutional Ethics Committee.ResultsOf the 681 participants, 322 (47.2%) were affected with RAS in the past six months which included 131 (40.6%) males and 191 (59.3%) females. Single mouth ulcers were the most common presentation seen among the study participants (74.2%). Factors showing statistically significant association were: family history of RAS (P < 0.001), known diabetics (P < 0.001), history of smoking (P < 0.001), oral trauma (P < 0.001), history of wearing braces/dentures (P < 0.001) as well as those using toothpastes containing sodium lauryl sulphate (P < 0.001), stress and lack of sleep (P < 0.001). The most common form of medication used were topical agents (43.1%) (P < 0.001).ConclusionsThere was a statistically significant association between the occurrence of RAS and family history of RAS, diabetes, smoking, history of braces/dentures, oral trauma, sodium lauryl sulphate toothpastes, lack of sleep, stress, menstruation, consumption of particular foods and beverages. Further research is needed in this field to truly understand the prevalence and risk factors of RAS and to help in discovering a treatment modality for this condition. creator: Matthew Antony Manoj creator: Animesh Jain creator: Saanchia Andria Madtha creator: Tina Mary Cherian uri: https://doi.org/10.7717/peerj.14998 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Manoj et al. title: Antibiotic use in infants within the first year of life is associated with the appearance of antibiotic-resistant genes in their feces link: https://peerj.com/articles/15015 last-modified: 2023-05-15 description: BackgroundAntibiotic resistance, an increasing challenge, is not only a national threat but also a global threat. Carriage of resistance genes is not limited to adults alone, various microbiota niches present in the body system of children have been found to harbor bacteria carrying resistant genes, especially, their gut microbiota. This study aims to identify selected antibiotic-resistant genes from the fecal samples of infants and the association of antibiotics use with the occurrence of resistant genes in the infant’s gut.MethodsA total number of 172 metagenomic DNA samples previously extracted from stool samples of 28 Nigerian babies longitudinally within their first year of life were screened for the presence of ESBL genes (blaSHV, blaTEM, and blaCTX-M), PMQR genes (qnrA, qnrB, qnrS, qepA), ribosomal protection protein tetracycline resistance gene, (RPP) β-lactamase (blaZ), macrolide (ermA, ermB, mefA/E), aminoglycoside modifying enzymes gentR (aac(6′)/aph(2″)) and dfrA genes by PCR. Nineteen (19) of the 28 babies used antibiotics during the study. The association between antibiotic use by the babies within the first year of life and occurrence of resistant genes were analyzed by Spearman rank correlation.ResultsOne hundred and twenty-two (122) samples (71%) out of the 172 isolates had antibiotic-resistance genes. PMQR genes were absent in all the samples. Three isolates had blaTEM gene, nine isolates had blaSHV gene, six isolates had blaCTX-M gene and 19 isolates had dfrA gene, 31 samples had tet gene, 29 samples had mef gene, 27 samples had ermB gene, four samples had ermA gene, 13 samples had blaZ gene and 16 samples had aac gene. The babies whose samples had resistant genes used antibiotics in the same months the samples were collected. Interestingly, the 11 babies whose samples had the dfrA gene all used antibiotics in the same months their samples were collected but none of them used trimethoprim/sulfamethoxazole antibiotic. The overall correlation matrix of the babies showed a strong association between antibiotic use (AU) and antibiotic use presence of resistance genes (AUPRG) with a coefficient of 0.89. Antibiotic-resistant genes are present in the gut of infants and their occurrence is strongly connected with antibiotic use by infants. creator: Tolulope Elizabeth Fadeyi creator: Omolanke Temitope Oyedemi creator: Olushina Olawale Awe creator: Funmilola Ayeni uri: https://doi.org/10.7717/peerj.15015 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Fadeyi et al. title: An overview of the osseous palmar sesamoid in Anura, with the particular case of some Rhinella species link: https://peerj.com/articles/15063 last-modified: 2023-05-15 description: BackgroundSesamoids are generally regarded as structures that are not part of the tetrapod body plan. The presence of a palmar sesamoid is assumed to serve as a distribution point for the forces of the flexor digitorum communis muscle to the flexor tendons of the digits, which are embedded in the flexor plate. It has been considered that the palmar sesamoid is present in most anuran groups, and it has been suggested that it acts by inhibiting the closing of the palm, preventing grasping. Typical arboreal anuran groups lack a palmar sesamoid and flexor plate, a pattern shared with other tetrapod groups, which can retain a reduced sesamoid and flexor plate. We focus on the anatomical structure of the Rhinella group, which includes species that present an osseous palmar sesamoid and climb bushes or trees to avoid depredation or escape dangerous situations, and can exhibit scansorial and arboreal behaviors. We also add data on the bony sesamoids of 170 anuran species to study the anatomy and evolution of the osseous palmar sesamoid within this amphibian group. Our objective is to bring an overview of the osseous palmar sesamoid in anurans, unveiling the relationship between this element of the manus, its phylogeny, and the anuran habitat use.MethodsSkeletal whole-mount specimens of Rhinella were cleared and double-dyed to describe the sesamoid anatomy and related tissues. We review and describe the palmar sesamoid of 170 anuran species from CT images downloaded from Morphosource.org, representing almost all Anuran families. We performed an standard ancestral state reconstruction by optimizing two selected characters (osseous palmar sesamoid presence, distal carpal palmar surface) along with the habitat use of the sampled taxa, using parsimony with Mesquite 3.7.ResultsOur primary finding is that sesamoid optimization in the anuran phylogeny revealed that its presence is associated with certain clades and not as widespread as previously anticipated. Additionally, we will also be delving into other important outcomes of our study that are relevant to those working in the field of anuran sesamoids. The osseous palmar sesamoid is present in the clade Bufonidae-Dendrobatidae-Leptodactylidae-Brachicephalidae that we named as PS clade, and also in the archeobatrachian pelobatoid Leptobranchium, all strongly terrestrial and burrowing species, though with exceptions. The osseous palmar sesamoid is always present in Bufonidae, but varies in form and size, depending on the mode that they use their manus, such as in the Rhinella margaritifera which has a cylindrical one and also grasping abilities that involve closing the manus. The scattered presence of the bony palmar sesamoid among anuran clades raises the question whether this sesamoid can be present with a different tissular composition in other groups. creator: Adriana Manzano creator: Virginia Abdala uri: https://doi.org/10.7717/peerj.15063 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Manzano et al. title: The effectiveness of hepatitis B vaccine in toddlers based on the five-year period national basic health research (Riskesdas 2007, 2013 and 2018) in Indonesia link: https://peerj.com/articles/15199 last-modified: 2023-05-15 description: BackgroundHepatitis B is a viral infection that has a high prevalence in Indonesia. The Ministry of Health of Indonesia has conducted a national vaccination program for hepatitis B. In order to evaluate the success of the hepatitis B vaccination in Indonesia, a community study based on basic health research (Riskesdas) was performed nationwide since 2007 for five year period in 2007, 2013, and 2018.MethodsFurther statistical analysis was performed specifically for the children under 59 months old (toddlers) immunized in both urban and rural areas in 2007, 2013, and 2018 based on certain characteristics by examining antibodies against HBsAg (anti-HBs), IgG antibodies against the core antigen (HBcAb), surface antigen (HBsAg) of hepatitis B virus (HBV). The data obtained from the data management laboratory of Ministry of Health, Indonesia, was analyzed with Bivariate analysis with continuity correction chi-square or Pearson chi-square using Stata software version 16.ResultsThis study showed an increase in hepatitis B coverage of complete immunization (30% in 2007, 60.3% in 2013, and 57% in 2018), which was also influenced by mothers’ level of education (Pearson chi-square , p ¡ 0.05) and access to health service points within 30 minutes (OR = 1.3–2.8, p ¡ 0.05). The trend of the percentage of immune status (anti-HBs) was increased (41.8% in 2007; 56.1% in 2013; and 79.1% in 2018). The higher anti-HBs was found in complete hepatitis B immunization status (OR = 1.5–2, p ¡ 0.05) and in good nutritional status (p ¡ 0.05). However, the anti-HBs was found decreased with increasing age (p ¡ 0.05). The trend of positive HBcAb (exposure to HBV infection) showed a decrease gradually of almost ten times from 2007 (8.6%-13.5%) compared to 2013 (2.6%-11.1%) and 2018 (1.1%-2%). Urban areas were at higher risk of hepatitis B exposure (OR = 1.4–2.2) than rural areas (OR = 0.37–0.80). The HBsAg data were only available in 2013 and 2018. Riskesdas data analysis showed the prevalence of hepatitis B (HBsAg) was lower in complete immunization status than that in incomplete one (p ¡ 0.05), but with an increase from 3.9% (2013) to 9.3% (2018), possibly due to inappropriate implementation of birth dose immunization or a vaccine-escape mutant from the HBV variants.ConclusionsThe effectiveness of hepatitis B vaccine obtained from the three Riskesdas periods in Indonesia showed an improvement, with an increase in immune status, reduced exposure to HBV and a lower prevalence of hepatitis B in children with complete vaccination. However, there is still an increase in hepatitis B infection, especially in urban areas. Therefore, a long-term evaluation of immunization coverage especially ensuring that the initial dose of immunization was given within the first 24 h of birth, HBsAg and HBcAb, nutritional status, genomic surveillance of HBV, and other aspects of program quality evaluation are needed to ensure that elimination efforts have been implemented properly. creator: Christina Safira Whinie Lestari creator: Rita Marleta Dewi creator: Sunarno Sunarno creator: Armedy Ronny Hasugian creator: Sarwo Handayani creator: Masri Sembiring Maha creator: Novaria Sari Dewi Panjaitan creator: Nathalia Ningrum creator: Meiriani Sari creator: Firda Fairuza uri: https://doi.org/10.7717/peerj.15199 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lestari et al. title: Identification and functional analysis of non-coding regulatory small RNA FenSr3 in Bacillus amyloliquefaciens LPB-18 link: https://peerj.com/articles/15236 last-modified: 2023-05-15 description: Bacillus amyloliquefaciens is an interesting microbe in the food processing and manufacturing industries. Non-coding small RNAs (sRNAs) have been shown to play a crucial role in the physiology and metabolism of bacteria by post-transcriptionally regulating gene expression. This study investigated the function of novel sRNA FenSr3 by constructing fenSr3 deficient strain and complementary strains in B. amyloliquefaciens LPB-18 , which were named LPN-18N and LPB-18P, respectively. The result showed significant differences in fengycin yield between strain LPB -18N and LPB-18P. The production of fengycin was significantly enhanced in B. amyloliquefaciens LPB-18N, compared with that of the strain LPB-18 from 190.908 mg/L to 327.598 mg/L. Moreover, the production of fengycin decreased from 190.464 mg/L to 38.6 mg/L in B . amyloliquefaciens LPB-18P. A comparative transcriptome sequencing was carried out to better understand the complex regulatory mechanism. Transcription analysis revealed that 1037 genes were differentially expressed between B. amyloliquefaciens LPB-18 and B. amyloliquefaciens LPB-18N, including the key regulatory genes in fatty acid, amino acid biosynthesis, and central carbon metabolism, which could provide sufficient quantities of building precursors for fengycin biosynthesis. The biofilm formation and sporulation was also enhanced in the strain LPB-18N, which indicates that FenSr3 could play a vital role in stress resistance and promotes survival in B. amyloliquefaciens. Some sRNAs involved in stress response have been identified in the literature, but their regulatory roles in fengycin production remain unclear. The study will contribute a novel perspective to the regulation mechanism of biosynthesis and the optimization of key metabolites of B. amyloliquefaciens. creator: Panping Yang creator: Chengxin Geng creator: Shaohui Zhu creator: Zhen Zhou creator: Muhammad Bilal creator: Chengyuan Gu creator: Hai Xu creator: Linchun Ji creator: Benchang Xiao creator: Jingye Wang creator: Zhoujie Qian creator: Li Zhao creator: Yuping Zhao creator: Hedong Lu uri: https://doi.org/10.7717/peerj.15236 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al. title: Responses of soil organic carbon cycle to land degradation by isotopically tracing in a typical karst area, southwest China link: https://peerj.com/articles/15249 last-modified: 2023-05-15 description: BackgroundThe loss of soil organic carbon (SOC) under land degradation threatens crop production and reduces soil fertility and stability, which is more reflected in eco-sensitive environments. However, fewer studies simultaneously compared SOC variations and δ13CSOC compositions under diverse land uses, especially in karst areas.MethodsSoil profiles from two agricultural lands and a secondary forest land were selected to analyze SOC contents and their stable isotope composition (δ13CSOC) in a typical karst area located in southwest China to understand the response of the SOC cycle to land degradation. Moreover, the relationships between SOC contents and mean weight diameter (MWD) and soil erodibility (K) factor were comprehensively analyzed for assessing the response of SOC to soil degradation risk.ResultsThe mean SOC content was found to be the lowest in abandoned cropland (6.91 g/kg), followed by secondary forest land (9.31 g/kg) and grazing shrubland (34.80 g/kg), respectively. Meanwhile, the δ13CSOC values exhibited the following trend: secondary forest land (mean: −23.79‰) ≈abandoned cropland (mean: −23.76‰) >shrubland (mean: −25.33‰). The isotopic tracing results suggested that plant litter was the main contributor to SOC in the secondary forest land. Whereas abundant nitrogen from goat feces enhanced plant productivity and resulted in additional accumulation of SOC in the grazing shrubland. Conversely, long-term cultivation led to the depletion of SOC sequestration by the loss of calcium. In surface soils, the fractionation of δ13CSOC were considerably affected by the decomposition of SOC by soil microorganisms and covered vegetation rather than agricultural influences.ConclusionsThe findings indicate that the cycling of SOC and soil stability in the calcareous soil of southwest China are largely regulated by different land uses and the presence of vegetation cover. The depletion of SOC and soil physical degradation pose significant challenges for abandoned cropland, particularly in the karst area, where land degradation is inevitable. Nevertheless, moderate grazing enhances SOC levels, which is beneficial to the land fertility maintenance in the karst region. Therefore, more emphasis should be placed on the cultivation methods and management strategies for abandoned cropland in the karst area. creator: Ruiyin Han creator: Qian Zhang creator: Zhifang Xu uri: https://doi.org/10.7717/peerj.15249 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Han et al. title: Characterisation of pellicle-forming ability in clinical carbapenem-resistant Acinetobacter baumannii link: https://peerj.com/articles/15304 last-modified: 2023-05-15 description: BackgroundAcinetobacter baumannii was reported to have resistance towards carbapenems and the ability to form an air-liquid biofilm (pellicle) which contributes to their virulence. The GacSA two-component system has been previously shown to play a role in pellicle formation. Therefore, this study aims to detect the presence of gacA and gacS genes in carbapenem-resistant Acinetobacter baumannii (CRAB) isolates recovered from patients in intensive care units and to investigate their pellicle forming ability.MethodsThe gacS and gacA genes were screened in 96 clinical CRAB isolates using PCR assay. Pellicle formation assay was performed in Mueller Hinton medium and Luria Bertani medium using borosilicate glass tubes and polypropylene plastic tubes. The biomass of the pellicle was quantitated using the crystal violet staining assay. The selected isolates were further assessed for their motility using semi-solid agar and monitored in real-time using real-time cell analyser (RTCA).ResultsAll 96 clinical CRAB isolates carried the gacS and gacA genes, however, only four isolates (AB21, AB34, AB69 and AB97) displayed the ability of pellicle-formation phenotypically. These four pellicle-forming isolates produced robust pellicles in Mueller Hinton medium with better performance in borosilicate glass tubes in which biomass with OD570 ranging from 1.984 ± 0.383 to 2.272 ± 0.376 was recorded. The decrease in cell index starting from 13 hours obtained from the impedance-based RTCA showed that pellicle-forming isolates had entered the growth stage of pellicle development.ConclusionThese four pellicle-forming clinical CRAB isolates could be potentially more virulent, therefore further investigation is warranted to provide insights into their pathogenic mechanisms. creator: Heng Kang Ng creator: Suat Moi Puah creator: Cindy Shuan Ju Teh creator: Nuryana Idris creator: Kek Heng Chua uri: https://doi.org/10.7717/peerj.15304 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ng et al.