title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=750 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth. link: https://peerj.com/articles/12940 last-modified: 2022-02-22 description: BackgroundPogostemon cablin (Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, P. cablin is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil.MethodsTo better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed de novo transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads.ResultsIn this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of P. cablin. We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were “terpenoid backbone biosynthesis”, “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “sesquiterpenoid and triterpenoid biosynthesis”, “ubiquinone and other terpenoid-quinone biosynthesis”, “flavonoid biosynthesis”, and “flavone and flavonol biosynthesis”. However, the main pathways of the patchouliol-type also included “diterpene biosynthesis” and “monoterpene biosynthesis”. Additionally, by comparing the expression levels of the three tissues verified by qRT-PCR, more DEGs in the roots were upregulated in the mevalonate (MVA) pathway in the cytoplasm, but more DEGs in the leaves were upregulated in the methylerythritol phosphate (MEP) pathway in the plastid, both of which are important pathways for terpenoids biosynthesis. These findings promote the study of further genome annotation and transcriptome research in P. cablin. creator: Hongyi Zhang creator: Wenjing Deng creator: Changhua Lu creator: Mengling He creator: Hanjing Yan uri: https://doi.org/10.7717/peerj.12940 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study link: https://peerj.com/articles/12973 last-modified: 2022-02-22 description: BackgroundIn the United States, state-level policies requiring vaccination of school-going children constitute a critical strategy for improving vaccination coverage. However, policies allowing vaccination exemptions have also been implemented and contribute to reductions in vaccination coverage and potential increases in the burden of vaccine-preventable diseases. Understanding the geographic disparities in the distribution of vaccination exemptions and identifying high risk areas is necessary for guiding resource allocation and public health control strategies. This study investigated geographic disparities in vaccination exemptions as well as socioeconomic and demographic predictors of vaccination exemptions in Florida.MethodsVaccination exemption data were obtained from the Florida Department of Health’s Florida HealthCHARTS web interface. Spatial patterns in geographic distribution of total and non-medical vaccination exemptions were assessed using county-level choropleth maps. Negative binomial models were used to identify significant predictors of county-level risks of both total and non-medical vaccination exemptions.ResultsTotal exemptions varied from 0 to 30.2 per 10,000 people. Nine counties had exemption risks in the top two classes (10.4–15.9 and 15.9–30.2 exemptions per 10,000 people). These counties were distributed in five distinct areas: Western Panhandle, central northern area, central, South-eastern coastal area, and the southern coastal border of the state. Non-medical exemptions varied from 0 to 10.4 per 10,000 people. Fifteen counties had exemption risks in the top two classes (3.7–5.6 and 5.6–10.4 exemptions per 10,000 people), and were located in six distinct areas: Western and Central Panhandle, Northeastern, Central-eastern coastal area, Central-western coastal area, and the South-western coastal border of the state. Predictors of high risk of total vaccination exemptions were high density of primary care providers (p < 0.001), high median income (p = 0.001), high percentage of Hispanic population (p = 0.046), and low percentage of population with a college education (p = 0.013). A predictor of high risk of non-medical vaccination exemptions was high percentage of White population (p = 0.045). However, predictors of low risks of non-medical exemptions were high percentages of population: living in rural areas (p = 0.023), with college education (p = 0.013), with high school education (p = 0.009), and with less than high school education (p < 0.001).ConclusionsThere is evidence of county-level geographic disparities in both total and non-medical vaccination exemption risks in Florida. These disparities are explained by differences in county-level socioeconomic and demographic factors. Study findings are important in guiding resource allocation for health planning aimed at improving vaccination rates and reducing incidence of vaccine-preventable diseases. creator: Corinne B. Tandy creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.12973 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tandy and Odoi title: Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition link: https://peerj.com/articles/12991 last-modified: 2022-02-22 description: BackgroundOral squamous cell carcinoma (OSCC), the most common type of primary malignant tumor in the oral cavity, is a lethal disease with high recurrence and mortality rates. Butyrate, a metabolite produced by periodontal pathogens, has been linked to oral diseases. The purpose of this study was to evaluate the effect of sodium butyrate (NaB) on the proliferation, migration, and invasion of OSCC cells in vitro and to explore the potential mechanism.MethodsTwo OSCC cell lines (HSC-4 and SCC-9) were treated with NaB at different concentrations. The cell proliferation was assayed by CCK-8, ethylene deoxyuridine (EdU), and flow cytometry. Wound healing and transwell assay were performed to detect cell migration and invasion. Changes in epithelial-mesenchymal transition (EMT) markers, including E-cadherin, Vimentin, and SNAI1, were evaluated by quantitative real-time PCR (qRT-PCR), western blot, and immunofluorescent staining. The expression levels of matrix metalloproteinases (MMPs) were analyzed by qRT-PCR and gelatin zymography.ResultsOur results showed that NaB inhibited the proliferation of OSCC cells and induced cell cycle arrest at G1 phase, but NaB significantly enhanced cell migration and invasion compared with the control group. Further mechanistic investigation demonstrated that NaB induced EMT by increasing the expression of Vimentin and SNAI1, decreasing the expression of membrane-bound E-cadherin, and correspondingly promoting E-cadherin translocation from the membrane to the cytoplasm. In addition, the overexpression of MMP1/2/9/13 was closely related to NaB treatment.ConclusionsOur study conclude that butyrate may promote the migration and invasion of OSCC cells by inducing EMT. These findings indicate that butyrate may contribute to OSCC metastasis. creator: Wenli Zang creator: Junchao Liu creator: Fengxue Geng creator: Dongjuan Liu creator: Shuwei Zhang creator: Yuchao Li creator: Yaping Pan uri: https://doi.org/10.7717/peerj.12991 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zang et al. title: Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish link: https://peerj.com/articles/12992 last-modified: 2022-02-22 description: The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish. creator: Lasse Nyholm creator: Iñaki Odriozola creator: Garazi Martin Bideguren creator: Ostaizka Aizpurua creator: Antton Alberdi uri: https://doi.org/10.7717/peerj.12992 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nyholm et al. title: Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans) link: https://peerj.com/articles/12993 last-modified: 2022-02-22 description: Toads release toxic dry secretions from glands in their skin. Toxin possesses a wide range of biological effects, but little is known about its specific gene expression pattern and regulatory mechanisms. The Asiatic toad (Bufo gargarizans) is widely used to produce toxin. Here, we explored the gene expression of 30 tissue samples from three different skin sites (parotoid gland, dorsal skin, and abdomen skin) of B. gargarizans. After de novo assembly, 783,130 unigenes with an average length of 489 bp (N50 = 556 bp) were obtained. A total of 9,248 significant differentially expressed genes (DEGs) were detected. There were 8,819 DEGs between the parotoid gland and abdomen skin and 1,299 DEGs between the dorsal skin and abdomen skin, while only 1,283 DEGs were obtained between the parotoid gland and dorsal skin. Through enrichment analysis, it was found that the detected differential gene expressions corresponded to the different functions of different skin sites. Our key findings were the genetic expression of toxin secretion, the protection function of skin, and the related genes such as HSD3B, Cyp2c, and CAT, LGALS9. In conclusion, we provide useful transcript resources to study the gene expression and gene function of B. gargarizans and other amphibians. The detected DEGs between different sites of the skin provided better insights into the genetic mechanisms of toxin secretion and the protection function of skin for amphibians. creator: Yue Lan creator: Lewei He creator: Xue Dong creator: Ruixiang Tang creator: Wanyu Li creator: Jiao Wang creator: Lei Wang creator: Bisong Yue creator: Megan Price creator: Tao Guo creator: Zhenxin Fan uri: https://doi.org/10.7717/peerj.12993 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lan et al. title: Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow link: https://peerj.com/articles/12998 last-modified: 2022-02-22 description: ObjectiveThe purpose of the present study was to determine the effects of starch sugar by-product (SSB) feeding on the rumen in-vitro digestibility, in situ disappearance rate, and lactating dairy cow.MethodsTo determine the rumen in vitro digestibility, 50 mL of the buffer-rumen fluid mixture was dispensed into a 125 mL serum bottle containing 0.5 g of dry matter (DM) of substrates. Nitrogen gas (N2, 99.9% pure) was flushed into the serum bottles and three replications were incubated at 0, 2, 4, 8, 16, 24, and 48 h. To determine the in-situ disappearance rate, SSB was incubated for 0, 2, 4, 8, 16, 24, and 48 hours in nylon bags (5 × 10 cm, 45*m pore size) placed within the ventral sac of two cannulated Holstein cows.. A total of sixteen Holstein Friesian cows (60.5 ± 20.4 months old, 706.8 ± 3.4 kg initial body wieght) fed experimental diets during the experimental periods. The treatments were basal diet (control) and 3.0% DM of SSB, with the diet formulated according to national research council (NRC) nutrient requirements of dairy cattle guideline. An experiment was conducted with a randomized block design for six weeks based on body weight.ResultsSoluble fraction (fraction a) of DM and crude protein (CP) was 28.99 and 11.92%DM, fraction b of DM and CP was 44.63 and 31.61% DM, and c value of DM and CP was 26.38 and 56.47%DM. As an increase SSB level in total mixed ration (TMR), there was a decrease in gas production at 0, 16, and 48 h (p < 0.05). As an increase SSB level in TMR, there was a decrease in acetate to propionate ratio at 8, 16, 24, and 48 h (p < 0.05). Dry matter intake, milk production, and milk composition did not differ between the treatments. All blood profile contents did not differ between treatments.ConclusionA diet containing 3.0% SSB could be fed to ruminants without adverse effects on rumen fermentation. creator: Yongjun Choi creator: Suhun Kim creator: Sangrak Lee creator: Youngjun Na uri: https://doi.org/10.7717/peerj.12998 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Choi et al. title: Functional network motifs defined through integration of protein-protein and genetic interactions link: https://peerj.com/articles/13016 last-modified: 2022-02-22 description: Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data. creator: Amruta Sahoo creator: Sebastian Pechmann uri: https://doi.org/10.7717/peerj.13016 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sahoo and Pechmann title: Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat link: https://peerj.com/articles/12808 last-modified: 2022-02-21 description: Shrimp aquaculture has been accomplished with breeding and nursing of shrimp in an artificial environment to fulfill the increasing demand of shrimp consumption worldwide. However, the microbial diseases appear as a serious problem in this industry. The study was designed to identify the diverse bacteria from shrimp PL (post-larvae) nurseries and to profile antibiotic resistance patterns. The rearing water (raw seawater, treated and outlet water) and shrimp PL were collected from eight nurseries of south-west Bangladesh. Using selective agar plates, thirty representative isolates were selected for 16S rRNA gene sequencing, antibiotic susceptibility test and MAR index calculation. Representative isolates were identified as Aeromonas caviae, Pseudomonas monteilii, Shewanella algae, Vibrio alginolyticus, V. brasiliensis, V. natriegens, V. parahaemolyticus, V. shilonii, V. xuii, Zobellella denitrificans which are Gram-negative, and Bacillus licheniformis and B. pumilus which are Gram-positive. Notably, six strains identified as Acinetobacter venetianus might be a concern of risk for shrimp industry. The antibiotic resistance pattern reveals that the strain YWO8-97 (identified as P. monteilii) was resistant to all twelve antibiotics. Ceftazidime was the most powerful antibiotic since most of the studied strains were sensitive against it. The six strains of A. venetianus showed multiple antibiotic resistance patterns. MAR index were ranged from 0.08 to 1.0, and values of 26 isolates were more than 0.2 which means prior high exposure to the antibiotics. From the present study, it can be concluded that shrimp PL nurseries in southern part of Bangladesh are getting contaminated with antibiotic resistant pathogenic bacteria. creator: Abdullah Yasin creator: Mst. Khadiza Begum creator: Md. Mostavi Enan Eshik creator: Nusrat Jahan Punom creator: Shawon Ahmmed creator: Mohammad Shamsur Rahman uri: https://doi.org/10.7717/peerj.12808 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yasin et al. title: Removal of Microcystis aeruginosa cells using the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1 link: https://peerj.com/articles/12867 last-modified: 2022-02-21 description: Inorganic and synthetic flocculants are widely investigated for removing harmful microalgae, such as Microcystis aeruginosa. However, their toxicity and non-biodegradability are shortcomings. Bioflocculants based on extracellular polysaccharides have attracted much attention as alternative flocculants. However, its high production cost is a limiting factor for applying bioflocculants. Here, we investigate the potential of the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1, as a novel flocculant on M. aeruginosa cells. The removal efficiency of M. aeruginosa cells by the dead cells was measured by mixing and shaking both components in a buffer with 5 mM CaCl2 in different incubation times and concentrations of the dead cells. After that, the minimum effective concentration of CaCl2 was determined. The combination effect of FeCl3 and the dead cells on the removal efficiency was tested. The structure of cell aggregates consisted of the dead cells and M. aeruginosa cells were also observed using a scanning electron microscope. The maximum removal efficiency (75.39%) was reached within 3 min in the presence of CaCl2 when 5 mg/ml of the dead cells (wet cells) were added. The optimal concentration of CaCl2 was 5 mM. The combination of the dead cells and a low concentration of FeCl3 (10 mg/L) with 5 mM of CaCl2 significantly improved the removal efficiency by about 1.2 times (P < 0.05). This result indicates that the combination usage of the dead cells can reduce the use of FeCl3. These results indicated that the dead cells could potentially be a novel biolfocculant to remove M. aeruginosa cells. creator: Go Furusawa creator: Koji Iwamoto uri: https://doi.org/10.7717/peerj.12867 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Furusawa and Iwamoto title: Genome-wide identification and characterization of laccase family members in eggplant (Solanum melongena L.) link: https://peerj.com/articles/12922 last-modified: 2022-02-21 description: Laccase, as a copper-containing polyphenol oxidase, primarily functions in the process of lignin, anthocyanin biosynthesis, and various abiotic/biotic stresses. In this study, forty-eight laccase members were identified in the eggplant genome. Only forty-two laccase genes from eggplant (SmLACs) were anchored unevenly in 12 chromosomes, the other six SmLACs were mapped on unanchored scaffolds. Phylogenetic analysis indicated that only twenty-five SmLACs were divided into six different groups on the basis of groups reported in Arabidopsis. Gene structure analysis revealed that the number of exons ranged from one to 13. Motif analysis revealed that SmLACs included six conserved motifs. In aspects of gene duplication analysis, twenty-one SmLACs were collinear with LAC genes from Arabidopsis, tomato or rice. Cis-regulatory elements analysis indicated many SmLACs may be involved in eggplant morphogenesis, flavonoid biosynthesis, diverse stresses and growth/development processes. Expression analysis further confirmed that a few SmLACs may function in vegetative and reproductive organs at different developmental stages and also in response to one or multiple stresses. This study would help to further understand and enrich the physiological function of the SmLAC gene family in eggplant, and may provide high-quality genetic resources for eggplant genetics and breeding. creator: Faxiang Wan creator: Linqing Zhang creator: Mengying Tan creator: Xiaohua Wang creator: Guang-Long Wang creator: Mengru Qi creator: Bingxin Liu creator: Jun Gao creator: Yu Pan creator: Yongqing Wang uri: https://doi.org/10.7717/peerj.12922 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wan et al.