PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Association between gonadal hormones and osteoporosis in schizophrenia patients undergoing risperidone monotherapy: a cross-sectional study
items: Identification of potential genes in upper tract urothelial carcinoma using next-generation sequencing with bioinformatics and in vitro analyses
items: Variation in purple sea urchin (Strongylocentrotus purpuratus) morphological traits in relation to resource availability
items: Comparison of morphology, development and expression patterns of hsf and hsp11.0 of Cotesia chilonis under normal and high temperature
items: A Python script to merge Sanger sequences
items: A novel one-step quick assay for detection of SARS-COV2 antibodies across mammalian species
items: HiCEnterprise: identifying long range chromosomal contacts in Hi-C data
items: Recruitment of toxin-like proteins with ancestral venom function supports endoparasitic lifestyles of Myxozoa
items: Hematological and cytochemical characteristics of peripheral blood cells in the argus snakehead (Ophiocephalus argus Cantor)
items: Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves

Association between gonadal hormones and osteoporosis in schizophrenia patients undergoing risperidone monotherapy: a cross-sectional study
type: item
type: AcademicArticle
description: Objective Patients with schizophrenia are at increased risk of osteoporosis. This study first determined the osteoporosis rate in patients with schizophrenia and then then explored the association between serum gonadal hormone levels and osteoporosis among these patients. Methods A total of 250 patients with schizophrenia and 288 healthy controls were recruited. Osteoporosis was defined by decreased bone mineral density (BMD) of the calcaneus. Serum fasting levels of gonadal hormones (prolactin, estradiol, testosterone, progesterone, follicle-stimulating hormone, luteinizing hormone) were determined. The relationship between osteoporosis and hormone levels was statistically analyzed by binary logistic regression analysis. Results Our results showed that patients with schizophrenia had a markedly higher rate of osteoporosis (24.4% vs. 10.1%) than healthy controls (P < 0.001). Patients with osteoporosis were older, had a longer disease course, and had a lower body mass index (BMI) than patients without osteoporosis (all P < 0.05). Regarding gonadal hormones, we found significantly higher prolactin, but lower estradiol, levels in patients with osteoporosis than in those without osteoporosis (both P < 0.05). The regression analysis revealed that PRL (OR = 1.1, 95% CI [1.08–1.15], P < 0.001) and E2 level (OR = 0.9, 95%CI [0.96–0.99], P = 0.011) were significantly associated with osteoporosis in patients with schizophrenia. Conclusion Our results indicate that patients with schizophrenia who are being treated with risperidone have a high rate of osteoporosis. Increased prolactin and reduced estradiol levels are significantly associated with osteoporosis.
format: application/pdf
format: text/html
creator: Yi Chen
creator: Yaoyao Zhang
creator: Kaili Fan
creator: Weiqian Xu
creator: Chao Teng
creator: Shuangshuang Wang
creator: Wei Tang
creator: Xiaomin Zhu
subject: Drugs and Devices
subject: Neurology
subject: Orthopedics
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.11332
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Objective Patients with schizophrenia are at increased risk of osteoporosis. This study first determined the osteoporosis rate in patients with schizophrenia and then then explored the association between serum gonadal hormone levels and osteoporosis among these patients. Methods A total of 250 patients with schizophrenia and 288 healthy controls were recruited. Osteoporosis was defined by decreased bone mineral density (BMD) of the calcaneus. Serum fasting levels of gonadal hormones (prolactin, estradiol, testosterone, progesterone, follicle-stimulating hormone, luteinizing hormone) were determined. The relationship between osteoporosis and hormone levels was statistically analyzed by binary logistic regression analysis. Results Our results showed that patients with schizophrenia had a markedly higher rate of osteoporosis (24.4% vs. 10.1%) than healthy controls (P < 0.001). Patients with osteoporosis were older, had a longer disease course, and had a lower body mass index (BMI) than patients without osteoporosis (all P < 0.05). Regarding gonadal hormones, we found significantly higher prolactin, but lower estradiol, levels in patients with osteoporosis than in those without osteoporosis (both P < 0.05). The regression analysis revealed that PRL (OR = 1.1, 95% CI [1.08–1.15], P < 0.001) and E2 level (OR = 0.9, 95%CI [0.96–0.99], P = 0.011) were significantly associated with osteoporosis in patients with schizophrenia. Conclusion Our results indicate that patients with schizophrenia who are being treated with risperidone have a high rate of osteoporosis. Increased prolactin and reduced estradiol levels are significantly associated with osteoporosis.
bibliographic citation: Chen et al. (2021) Association between gonadal hormones and osteoporosis in schizophrenia patients undergoing risperidone monotherapy: a cross-sectional study. PeerJ 9:e11332 https://doi.org/10.7717/peerj.11332
date submitted: 2020-10-29
date accepted: 2021-04-01
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yi
author list: Agent
  family name: Zhang
  given name: Yaoyao
author list: Agent
  family name: Fan
  given name: Kaili
author list: Agent
  family name: Xu
  given name: Weiqian
author list: Agent
  family name: Teng
  given name: Chao
author list: Agent
  family name: Wang
  given name: Shuangshuang
author list: Agent
  family name: Tang
  given name: Wei
author list: Agent
  family name: Zhu
  given name: Xiaomin
doi: 10.7717/peerj.11332
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Chen et al.
attribution name: Chen et al.

Identification of potential genes in upper tract urothelial carcinoma using next-generation sequencing with bioinformatics and in vitro analyses
type: item
type: AcademicArticle
description: Background We aimed to identify prognostic biomarkers of upper tract urothelial carcinomas (UTUCs), including microRNAs (miRNAs) and genes which account for only 5% to 10% of all urothelial carcinomas (UCs). In Taiwan, this figure is markedly higher, where it can reach up to 30% of UC cases. Materials and Methods Using next-generation sequencing (NGS), we analyzed two pairs of renal pelvis tumors and adjacent normal urothelial tissues to screen miRNAs and messenger RNAs. By combining bioinformatics analysis from miRmap, Gene Expression Omnibus (GEO), and Oncomine and Ingenuity® Pathway Analysis databases, we identified candidate genes. To search for upstream miRNAs with exact target binding sites, we used miRmap, TargetScan, and miRDB to enforce evidence. Then, we clarified gene and protein expression through an in vitro study using western blot analysis and quantitative real-time reverse transcriptase-PCR. Results Interactions between selected target genes obtained using the NGS and miRmap methods were assessed through a Venn diagram analysis. Six potential genes, namely, PDE5A, RECK, ZEB2, NCALD, PLCXD3 and CYBRD1 showed significant differences. Further analysis of gene expression from the GEO dataset indicated lower expression of PDE5A, RECK, ZEB2, and CYBRD1 in bladder cancer tissue than in normal bladder mucosa, which indicated that PDE5A, RECK, ZEB2, and CYBRD1 may act as tumor suppressors in UTUC. In addition, we compared the expression of these genes in various UC cell lines (RT4, BFTC905, J82, T24, UMUC3, 5637, BFTC 909, UMUC14) and found decreased expression of PDE5A in muscle-invasive UC cells compared with the RT4 cell line. Furthermore, by using paired UTUC and normal tissues from 20 patients, lower PDE5A expression was also demonstrated in tumor specimens. Conclusions Our findings suggest these candidate genes may play some roles in UTUC progression. We propose that these markers may be potential targets clarified by in vitro and in vivo experiments. P…
format: application/pdf
format: text/html
creator: Hsiang-Ying Lee
creator: Ching-Chia Li
creator: Wei-Ming Li
creator: Ya-Ling Hsu
creator: Hsin-Chih Yeh
creator: Hung-Lung Ke
creator: Bi Wen Yeh
creator: Chun-Nung Huang
creator: Chien-Feng Li
creator: Po-Lin Kuo
creator: Wen-Jeng Wu
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.11343
publisher: PeerJ Inc.
rights: © 2021 Lee et al.
abstract: Background We aimed to identify prognostic biomarkers of upper tract urothelial carcinomas (UTUCs), including microRNAs (miRNAs) and genes which account for only 5% to 10% of all urothelial carcinomas (UCs). In Taiwan, this figure is markedly higher, where it can reach up to 30% of UC cases. Materials and Methods Using next-generation sequencing (NGS), we analyzed two pairs of renal pelvis tumors and adjacent normal urothelial tissues to screen miRNAs and messenger RNAs. By combining bioinformatics analysis from miRmap, Gene Expression Omnibus (GEO), and Oncomine and Ingenuity® Pathway Analysis databases, we identified candidate genes. To search for upstream miRNAs with exact target binding sites, we used miRmap, TargetScan, and miRDB to enforce evidence. Then, we clarified gene and protein expression through an in vitro study using western blot analysis and quantitative real-time reverse transcriptase-PCR. Results Interactions between selected target genes obtained using the NGS and miRmap methods were assessed through a Venn diagram analysis. Six potential genes, namely, PDE5A, RECK, ZEB2, NCALD, PLCXD3 and CYBRD1 showed significant differences. Further analysis of gene expression from the GEO dataset indicated lower expression of PDE5A, RECK, ZEB2, and CYBRD1 in bladder cancer tissue than in normal bladder mucosa, which indicated that PDE5A, RECK, ZEB2, and CYBRD1 may act as tumor suppressors in UTUC. In addition, we compared the expression of these genes in various UC cell lines (RT4, BFTC905, J82, T24, UMUC3, 5637, BFTC 909, UMUC14) and found decreased expression of PDE5A in muscle-invasive UC cells compared with the RT4 cell line. Furthermore, by using paired UTUC and normal tissues from 20 patients, lower PDE5A expression was also demonstrated in tumor specimens. Conclusions Our findings suggest these candidate genes may play some roles in UTUC progression. We propose that these markers may be potential targets clarified by in vitro and in vivo experiments. P…
bibliographic citation: Lee et al. (2021) Identification of potential genes in upper tract urothelial carcinoma using next-generation sequencing with bioinformatics and in vitro analyses. PeerJ 9:e11343 https://doi.org/10.7717/peerj.11343
date submitted: 2020-11-20
date accepted: 2021-04-03
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Hsiang-Ying
author list: Agent
  family name: Li
  given name: Ching-Chia
author list: Agent
  family name: Li
  given name: Wei-Ming
author list: Agent
  family name: Hsu
  given name: Ya-Ling
author list: Agent
  family name: Yeh
  given name: Hsin-Chih
author list: Agent
  family name: Ke
  given name: Hung-Lung
author list: Agent
  family name: Yeh
  given name: Bi Wen
author list: Agent
  family name: Huang
  given name: Chun-Nung
author list: Agent
  family name: Li
  given name: Chien-Feng
author list: Agent
  family name: Kuo
  given name: Po-Lin
author list: Agent
  family name: Wu
  given name: Wen-Jeng
doi: 10.7717/peerj.11343
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Lee et al.
attribution name: Lee et al.

Variation in purple sea urchin (Strongylocentrotus purpuratus) morphological traits in relation to resource availability
type: item
type: AcademicArticle
description: Flexible resource investment is a risk sensitive reproductive strategy where individuals trade resources spent on reproduction for basic metabolic maintenance and survival. This study examined morphological variation in herbivorous sea urchin grazers across a mosaic landscape of macroalgae dominated habitats interspersed with patches of sea urchin barrens to determine whether sea urchins shift energy allocation in response to food limitation. Extensive underwater surveys of habitat attributes (e.g., sea urchin density, algae cover) were paired with detailed laboratory assays (e.g., sea urchin dissections) to determine how resource abundance affects energy allocation between reproductive capacity and body structure in the purple sea urchin, Strongylocentrotus purpuratus. We found that: (1) sea urchins had a more elongate jaw structure relative to body size in habitats void of macroalgae (i.e., barrens), (2) sea urchin reproductive capacity (i.e., gonad index) was lower in barrens and the barrens habitat was primarily comprised of encrusting algae, and (3) sea urchin jaw morphology (i.e., lantern index) and reproductive capacity (i.e., gonad index) were inversely related. These results suggest that sea urchins respond to macroalgae limited environments by shifting energy allocation between reproductive capacity and modifications of the foraging apparatus, which may explain the ability of sea urchins to acquire food in resource-limited environments.
format: application/pdf
format: text/html
creator: Joshua G. Smith
creator: Sabrina C. Garcia
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.11352
publisher: PeerJ Inc.
rights: © 2021 Smith and Garcia
abstract: Flexible resource investment is a risk sensitive reproductive strategy where individuals trade resources spent on reproduction for basic metabolic maintenance and survival. This study examined morphological variation in herbivorous sea urchin grazers across a mosaic landscape of macroalgae dominated habitats interspersed with patches of sea urchin barrens to determine whether sea urchins shift energy allocation in response to food limitation. Extensive underwater surveys of habitat attributes (e.g., sea urchin density, algae cover) were paired with detailed laboratory assays (e.g., sea urchin dissections) to determine how resource abundance affects energy allocation between reproductive capacity and body structure in the purple sea urchin, Strongylocentrotus purpuratus. We found that: (1) sea urchins had a more elongate jaw structure relative to body size in habitats void of macroalgae (i.e., barrens), (2) sea urchin reproductive capacity (i.e., gonad index) was lower in barrens and the barrens habitat was primarily comprised of encrusting algae, and (3) sea urchin jaw morphology (i.e., lantern index) and reproductive capacity (i.e., gonad index) were inversely related. These results suggest that sea urchins respond to macroalgae limited environments by shifting energy allocation between reproductive capacity and modifications of the foraging apparatus, which may explain the ability of sea urchins to acquire food in resource-limited environments.
bibliographic citation: Smith et al. (2021) Variation in purple sea urchin (Strongylocentrotus purpuratus) morphological traits in relation to resource availability. PeerJ 9:e11352 https://doi.org/10.7717/peerj.11352
date submitted: 2020-11-12
date accepted: 2021-04-05
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Joshua G.
author list: Agent
  family name: Garcia
  given name: Sabrina C.
doi: 10.7717/peerj.11352
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: © 2021 Smith and Garcia
attribution name: Smith and Garcia

Comparison of morphology, development and expression patterns of hsf and hsp11.0 of Cotesia chilonis under normal and high temperature
type: item
type: AcademicArticle
description: Cotesia chilonis (Munakata) is the dominant parasitic wasp of the rice pest, Chilo suppressalis (Walker), and is a valuable parasitic wasp for the prevention and control of C. suppressalis. In this study, developmental indicators and expression of Cchsp11.0 (heat shock protein 11.0) and Cchsf (heat shock factor) were compared for C. chilonis at 27 °C and 36 °C. Developmental duration, morphology, emergence rate, and number of C. chilonis offspring were shortened at 36 °C while the ratio of females to males increased. Cchsp11.0 and Cchsf were highly expressed in the 1st instar stage at 36 °C, and Cchsp11.0 expression gradually decreased as C. chilonis matured; Cchsf expression was not correlated with Cchsp11.0 expression. Compared with 27 °C, the expression pattern of Cchsp11.0 and Cchsf was also not consistent, and Cchsp11.0 expression increased significantly at the adult stage. In conclusion, mildly high temperatures impact growth, development and reproduction of C. chilonis and stimulate the expression of Cchsp11.0 and Cchsf, and Cchsp11.0 and Cchsf play different roles in different developmental stages of C. chilonis at normal and high temperature.
format: application/pdf
format: text/html
creator: Fu-Jing He
creator: Feng Zhu
creator: Ming-Xing Lu
creator: Yu-Zhou Du
subject: Agricultural Science
subject: Entomology
description: doi:10.7717/peerj.11353
publisher: PeerJ Inc.
rights: © 2021 He et al.
abstract: Cotesia chilonis (Munakata) is the dominant parasitic wasp of the rice pest, Chilo suppressalis (Walker), and is a valuable parasitic wasp for the prevention and control of C. suppressalis. In this study, developmental indicators and expression of Cchsp11.0 (heat shock protein 11.0) and Cchsf (heat shock factor) were compared for C. chilonis at 27 °C and 36 °C. Developmental duration, morphology, emergence rate, and number of C. chilonis offspring were shortened at 36 °C while the ratio of females to males increased. Cchsp11.0 and Cchsf were highly expressed in the 1st instar stage at 36 °C, and Cchsp11.0 expression gradually decreased as C. chilonis matured; Cchsf expression was not correlated with Cchsp11.0 expression. Compared with 27 °C, the expression pattern of Cchsp11.0 and Cchsf was also not consistent, and Cchsp11.0 expression increased significantly at the adult stage. In conclusion, mildly high temperatures impact growth, development and reproduction of C. chilonis and stimulate the expression of Cchsp11.0 and Cchsf, and Cchsp11.0 and Cchsf play different roles in different developmental stages of C. chilonis at normal and high temperature.
bibliographic citation: He et al. (2021) Comparison of morphology, development and expression patterns of hsf and hsp11.0 of Cotesia chilonis under normal and high temperature. PeerJ 9:e11353 https://doi.org/10.7717/peerj.11353
date submitted: 2021-01-14
date accepted: 2021-04-05
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Fu-Jing
author list: Agent
  family name: Zhu
  given name: Feng
author list: Agent
  family name: Lu
  given name: Ming-Xing
author list: Agent
  family name: Du
  given name: Yu-Zhou
doi: 10.7717/peerj.11353
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: © 2021 He et al.
attribution name: He et al.

A Python script to merge Sanger sequences
type: item
type: AcademicArticle
description: Merging Sanger sequences is frequently needed during the gene cloning process. In this study, we provide a Python script that is able to assemble multiple overlapping Sanger sequences. The script utilizes the overlapping regions within the tandem Sanger sequences to merge the Sanger sequences. The results demonstrate that the script can produce the merged sequence from the input Sanger sequences in a single run. The script offers a simple and free method for merging Sanger sequences and is useful for gene cloning.
format: application/pdf
format: text/html
creator: Cen Chen
creator: Bingguo Lu
creator: Xiaofang Huang
creator: Chuyun Bi
creator: Lili Zhao
creator: Yunzhuo Hu
creator: Xuanyang Chen
creator: Shiqiang Lin
creator: Kai Huang
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Computational Science
description: doi:10.7717/peerj.11354
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Merging Sanger sequences is frequently needed during the gene cloning process. In this study, we provide a Python script that is able to assemble multiple overlapping Sanger sequences. The script utilizes the overlapping regions within the tandem Sanger sequences to merge the Sanger sequences. The results demonstrate that the script can produce the merged sequence from the input Sanger sequences in a single run. The script offers a simple and free method for merging Sanger sequences and is useful for gene cloning.
bibliographic citation: Chen et al. (2021) A Python script to merge Sanger sequences. PeerJ 9:e11354 https://doi.org/10.7717/peerj.11354
date submitted: 2020-12-15
date accepted: 2021-04-05
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Cen
author list: Agent
  family name: Lu
  given name: Bingguo
author list: Agent
  family name: Huang
  given name: Xiaofang
author list: Agent
  family name: Bi
  given name: Chuyun
author list: Agent
  family name: Zhao
  given name: Lili
author list: Agent
  family name: Hu
  given name: Yunzhuo
author list: Agent
  family name: Chen
  given name: Xuanyang
author list: Agent
  family name: Lin
  given name: Shiqiang
author list: Agent
  family name: Huang
  given name: Kai
doi: 10.7717/peerj.11354
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: © 2021 Chen et al.
attribution name: Chen et al.

A novel one-step quick assay for detection of SARS-COV2 antibodies across mammalian species
type: item
type: AcademicArticle
description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) has so far infected almost a hundred of millions of people and caused more than a million of death across the world. Many serological tests have been developed to track down virus infection in community via identification of antibodies against SARS-CoV2 virus. However, the tests vary in sensitivity, specificity, complexity, and speed. Here, I developed a simple, one-step, quick test to detect antibodies against SARS-CoV2 N (scN) nucleocapsid protein via direct visualization of antigen-antibody reaction. A total of 40 serum samples of SARS-CoV2 patients were purchased from RayBiotech. A total of 50 pre-pandemic human serum samples from San Diego Blood Bank were used as negative controls. After performing the one-step quick test of these 90 serum samples, I found that 39 samples are positive for anti-scN antibodies. All of the 39 positives are from the 40 SARS-CoV2 patients, suggesting that the one-step test is more sensitive than the lateral flow immunoassay (LFIA), the most widely used rapid antibody test. None of the 50 pre-pandemic samples is positive for anti-scN antibodies, indicating that the one-step test has an excellent specificity. The one-step test takes only ~5 min to detect the antibodies; and 1 ml of Escherichia coli culture can produce reagent proteins sufficient for thousands of the tests. Since the one-step test does not need a secondary antibody, it can be used as a universal test for anti-scN antibodies across different mammalian species to track down both human infection and the animal reservoir of SARS-CoV2 virus.
format: application/pdf
format: text/html
creator: Xianjin Zhou
subject: Biotechnology
subject: Virology
subject: Hematology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.11381
publisher: PeerJ Inc.
rights: © 2021 Zhou
abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) has so far infected almost a hundred of millions of people and caused more than a million of death across the world. Many serological tests have been developed to track down virus infection in community via identification of antibodies against SARS-CoV2 virus. However, the tests vary in sensitivity, specificity, complexity, and speed. Here, I developed a simple, one-step, quick test to detect antibodies against SARS-CoV2 N (scN) nucleocapsid protein via direct visualization of antigen-antibody reaction. A total of 40 serum samples of SARS-CoV2 patients were purchased from RayBiotech. A total of 50 pre-pandemic human serum samples from San Diego Blood Bank were used as negative controls. After performing the one-step quick test of these 90 serum samples, I found that 39 samples are positive for anti-scN antibodies. All of the 39 positives are from the 40 SARS-CoV2 patients, suggesting that the one-step test is more sensitive than the lateral flow immunoassay (LFIA), the most widely used rapid antibody test. None of the 50 pre-pandemic samples is positive for anti-scN antibodies, indicating that the one-step test has an excellent specificity. The one-step test takes only ~5 min to detect the antibodies; and 1 ml of Escherichia coli culture can produce reagent proteins sufficient for thousands of the tests. Since the one-step test does not need a secondary antibody, it can be used as a universal test for anti-scN antibodies across different mammalian species to track down both human infection and the animal reservoir of SARS-CoV2 virus.
bibliographic citation: Zhou (2021) A novel one-step quick assay for detection of SARS-COV2 antibodies across mammalian species. PeerJ 9:e11381 https://doi.org/10.7717/peerj.11381
date submitted: 2021-01-25
date accepted: 2021-04-09
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Xianjin
doi: 10.7717/peerj.11381
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: © 2021 Zhou
attribution name: Zhou

HiCEnterprise: identifying long range chromosomal contacts in Hi-C data
type: item
type: AcademicArticle
description: Motivation Computational analysis of chromosomal contact data is currently gaining popularity with the rapid advance in experimental techniques providing access to a growing body of data. An important problem in this area is the identification of long range contacts between distinct chromatin regions. Such loops were shown to exist at different scales, either mediating relatively short range interactions between enhancers and promoters or providing interactions between much larger, distant chromosome domains. A proper statistical analysis as well as availability to a wide research community are crucial in a tool for this task. Results We present HiCEnterprise, a first freely available software tool for identification of long range chromatin contacts not only between small regions, but also between chromosomal domains. It implements four different statistical tests for identification of significant contacts for user defined regions or domains as well as necessary functions for input, output and visualization of chromosome contacts. Availability The software and the corresponding documentation are available at: github.com/regulomics/HiCEnterprise. Supplementary information Supplemental data are available in the online version of the article and at the website regulomics.mimuw.edu.pl/wp/hicenterprise.
format: application/pdf
format: text/html
creator: Hanna Kranas
creator: Irina Tuszynska
creator: Bartek Wilczynski
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Statistics
description: doi:10.7717/peerj.10558
publisher: PeerJ Inc.
rights: © 2021 Kranas et al.
abstract: Motivation Computational analysis of chromosomal contact data is currently gaining popularity with the rapid advance in experimental techniques providing access to a growing body of data. An important problem in this area is the identification of long range contacts between distinct chromatin regions. Such loops were shown to exist at different scales, either mediating relatively short range interactions between enhancers and promoters or providing interactions between much larger, distant chromosome domains. A proper statistical analysis as well as availability to a wide research community are crucial in a tool for this task. Results We present HiCEnterprise, a first freely available software tool for identification of long range chromatin contacts not only between small regions, but also between chromosomal domains. It implements four different statistical tests for identification of significant contacts for user defined regions or domains as well as necessary functions for input, output and visualization of chromosome contacts. Availability The software and the corresponding documentation are available at: github.com/regulomics/HiCEnterprise. Supplementary information Supplemental data are available in the online version of the article and at the website regulomics.mimuw.edu.pl/wp/hicenterprise.
bibliographic citation: Kranas et al. (2021) HiCEnterprise: identifying long range chromosomal contacts in Hi-C data. PeerJ 9:e10558 https://doi.org/10.7717/peerj.10558
date submitted: 2020-07-07
date accepted: 2020-11-22
issued: 2021-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kranas
  given name: Hanna
author list: Agent
  family name: Tuszynska
  given name: Irina
author list: Agent
  family name: Wilczynski
  given name: Bartek
doi: 10.7717/peerj.10558
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-26
copyright: © 2021 Kranas et al.
attribution name: Kranas et al.

Recruitment of toxin-like proteins with ancestral venom function supports endoparasitic lifestyles of Myxozoa
type: item
type: AcademicArticle
description: Cnidarians are the oldest lineage of venomous animals and use nematocysts to discharge toxins. Whether venom toxins have been recruited to support parasitic lifestyles in the Endocnidozoa (Myxozoa + Polypodium) is, however, unknown. To examine this issue we variously employed transcriptomic, proteomic, associated molecular phylogenies, and localisation studies on representative primitive and derived myxozoans (Malacosporea and Myxosporea, respectively), Polypodium hydriforme, and the free-living staurozoan Calvadosia cruxmelitensis. Our transcriptomics and proteomics analyses provide evidence for expression and translation of venom toxin homologs in myxozoans. Phylogenetic placement of Kunitz type serine protease inhibitors and phospholipase A2 enzymes reveals modification of toxins inherited from ancestral free-living cnidarian toxins, and that venom diversity is reduced in myxozoans concordant with their reduced genome sizes. Various phylogenetic analyses of the Kunitz-type toxin family in Endocnidozoa suggested lineage-specific gene duplications, which offers a possible mechanism for enhancing toxin diversification. Toxin localisation in the malacosporean Buddenbrockia plumatellae substantiates toxin translation and thus illustrates a repurposing of toxin function for endoparasite development and interactions with hosts, rather than for prey capture or defence. Whether myxozoan venom candidates are expressed in transmission stages (e.g. in nematocysts or secretory vesicles) requires further investigation.
format: application/pdf
format: text/html
creator: Ashlie Hartigan
creator: Adrian Jaimes-Becerra
creator: Beth Okamura
creator: Liam B. Doonan
creator: Malcolm Ward
creator: Antonio C. Marques
creator: Paul F. Long
subject: Environmental Sciences
subject: Marine Biology
subject: Molecular Biology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.11208
publisher: PeerJ Inc.
rights: © 2021 Hartigan et al.
abstract: Cnidarians are the oldest lineage of venomous animals and use nematocysts to discharge toxins. Whether venom toxins have been recruited to support parasitic lifestyles in the Endocnidozoa (Myxozoa + Polypodium) is, however, unknown. To examine this issue we variously employed transcriptomic, proteomic, associated molecular phylogenies, and localisation studies on representative primitive and derived myxozoans (Malacosporea and Myxosporea, respectively), Polypodium hydriforme, and the free-living staurozoan Calvadosia cruxmelitensis. Our transcriptomics and proteomics analyses provide evidence for expression and translation of venom toxin homologs in myxozoans. Phylogenetic placement of Kunitz type serine protease inhibitors and phospholipase A2 enzymes reveals modification of toxins inherited from ancestral free-living cnidarian toxins, and that venom diversity is reduced in myxozoans concordant with their reduced genome sizes. Various phylogenetic analyses of the Kunitz-type toxin family in Endocnidozoa suggested lineage-specific gene duplications, which offers a possible mechanism for enhancing toxin diversification. Toxin localisation in the malacosporean Buddenbrockia plumatellae substantiates toxin translation and thus illustrates a repurposing of toxin function for endoparasite development and interactions with hosts, rather than for prey capture or defence. Whether myxozoan venom candidates are expressed in transmission stages (e.g. in nematocysts or secretory vesicles) requires further investigation.
bibliographic citation: Hartigan et al. (2021) Recruitment of toxin-like proteins with ancestral venom function supports endoparasitic lifestyles of Myxozoa. PeerJ 9:e11208 https://doi.org/10.7717/peerj.11208
date submitted: 2020-12-07
date accepted: 2021-03-12
issued: 2021-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hartigan
  given name: Ashlie
author list: Agent
  family name: Jaimes-Becerra
  given name: Adrian
author list: Agent
  family name: Okamura
  given name: Beth
author list: Agent
  family name: Doonan
  given name: Liam B.
author list: Agent
  family name: Ward
  given name: Malcolm
author list: Agent
  family name: Marques
  given name: Antonio C.
author list: Agent
  family name: Long
  given name: Paul F.
doi: 10.7717/peerj.11208
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-26
copyright: © 2021 Hartigan et al.
attribution name: Hartigan et al.

Hematological and cytochemical characteristics of peripheral blood cells in the argus snakehead (Ophiocephalus argus Cantor)
type: item
type: AcademicArticle
description: Background The argus snakehead (Ophiocephalus argus Cantor) is a highly nutritious, freshwater, cultured bony fish with a high economic value. The health of the fish is closely related to its blood cells, which are critical for oxygen transport, natural defense, and immunity. We investigated the morphometry, microstructure, and cytochemical characteristics of the peripheral blood cells of O. argus. Our results may provide the basic reference values needed to monitor the health of this fish for large-scale cultivation. Methods The number of blood cells in O. argus were counted on a hemocytometer and their size was measured using a micrometer under light microscope. The morphology and classification of the blood cells were studied using Wright’s staining and the cytochemical characteristics were studied using seven chemical stains including peroxidase (POX), Sudan black B (SBB), periodic acid-Schiff (PAS), acid phosphatase (ACP), alkaline phosphatase (ALP), chloroacetic acid AS-D naphthol esterase (AS-D), and α-naphthol acetate esterase (α-NAE). Results The peripheral blood cells in O. argus can be classified as erythrocytes, leukocytes, and thrombocytes; of which, females had 2.9597 million/mm3, 88,400/mm3, and 43,600/mm3, respectively, and males had 3.0105 million/mm3, 105,500/mm3, and 34,000/mm3, respectively. Leukocytes consisted of neutrophils, monocytes, large lymphocytes, and small lymphocytes. Eosinophils and basophils were not found. Monocytes were the most numerous leukocytes identified, followed by neutrophils and small lymphocytes, while large lymphocytes were the least frequently identified. Cytochemical staining showed that erythrocytes were only positive for PAS staining. Neutrophils were strongly positive for POX, SBB, and ACP, and positive for all the other cytochemical stains. Monocytes were positive for PAS and α-NAE and were weakly positive for ACP and AS-D staining. Large lymphocytes were positive for PAS and were weakly positive for ALP, AS-D, an…
format: application/pdf
format: text/html
creator: Xue Wang
creator: Zhengjie Wu
creator: Shengmei Wu
creator: Xianxian Chen
creator: Misbah Hanif
creator: Shengzhou Zhang
subject: Aquaculture, Fisheries and Fish Science
subject: Veterinary Medicine
subject: Zoology
subject: Histology
subject: Freshwater Biology
description: doi:10.7717/peerj.11234
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background The argus snakehead (Ophiocephalus argus Cantor) is a highly nutritious, freshwater, cultured bony fish with a high economic value. The health of the fish is closely related to its blood cells, which are critical for oxygen transport, natural defense, and immunity. We investigated the morphometry, microstructure, and cytochemical characteristics of the peripheral blood cells of O. argus. Our results may provide the basic reference values needed to monitor the health of this fish for large-scale cultivation. Methods The number of blood cells in O. argus were counted on a hemocytometer and their size was measured using a micrometer under light microscope. The morphology and classification of the blood cells were studied using Wright’s staining and the cytochemical characteristics were studied using seven chemical stains including peroxidase (POX), Sudan black B (SBB), periodic acid-Schiff (PAS), acid phosphatase (ACP), alkaline phosphatase (ALP), chloroacetic acid AS-D naphthol esterase (AS-D), and α-naphthol acetate esterase (α-NAE). Results The peripheral blood cells in O. argus can be classified as erythrocytes, leukocytes, and thrombocytes; of which, females had 2.9597 million/mm3, 88,400/mm3, and 43,600/mm3, respectively, and males had 3.0105 million/mm3, 105,500/mm3, and 34,000/mm3, respectively. Leukocytes consisted of neutrophils, monocytes, large lymphocytes, and small lymphocytes. Eosinophils and basophils were not found. Monocytes were the most numerous leukocytes identified, followed by neutrophils and small lymphocytes, while large lymphocytes were the least frequently identified. Cytochemical staining showed that erythrocytes were only positive for PAS staining. Neutrophils were strongly positive for POX, SBB, and ACP, and positive for all the other cytochemical stains. Monocytes were positive for PAS and α-NAE and were weakly positive for ACP and AS-D staining. Large lymphocytes were positive for PAS and were weakly positive for ALP, AS-D, an…
bibliographic citation: Wang et al. (2021) Hematological and cytochemical characteristics of peripheral blood cells in the argus snakehead (Ophiocephalus argus Cantor). PeerJ 9:e11234 https://doi.org/10.7717/peerj.11234
date submitted: 2020-07-30
date accepted: 2021-03-17
issued: 2021-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xue
author list: Agent
  family name: Wu
  given name: Zhengjie
author list: Agent
  family name: Wu
  given name: Shengmei
author list: Agent
  family name: Chen
  given name: Xianxian
author list: Agent
  family name: Hanif
  given name: Misbah
author list: Agent
  family name: Zhang
  given name: Shengzhou
doi: 10.7717/peerj.11234
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-26
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves
type: item
type: AcademicArticle
description: Background Vernonia amygdalina as a tropical horticultural crop has been widely used for medicinal herb, feed, and vegetable. Recently, increasing studies revealed that this species possesses multiple pharmacological properties. Notably, V. amygdalina leaves possess an abundance of flavonoids, but the specific profiles of flavonoids and the mechanisms of fl avonoid bi osynthesis in developing leaves are largely unknown. Methods The total flavonoids of V. amygdalina leaves were detected using ultraviolet spectrophotometer. The temporal flavonoid profiles of V. amygdalina leaves were analyzed by LC-MS. The transcriptome analysis of V. amygdalina leaves was performed by Illumina sequencing. Functional annotation and differential expression analysis of V. amygdalina genes were performed by Blast2GO v2.3.5 and RSEM v1.2.31, respectively. qRT-PCR analysis was used to verify the gene expressions in developing V. amygdalina leaves. Results By LC-MS analysis, three substrates (p-coumaric acid, trans-cinnamic acid, and phenylalanine) for flavonoid biosynthesis were identified in V. amygdalina leaves. Additionally, 42 flavonoids were identified from V. amygdalina leaves, including six dihydroflavones, 14 flavones, eight isoflavones, nine flavonols, two xanthones, one chalcone, one cyanidin, and one dihydroflavonol. Glycosylation and methylation were common at the hydroxy group of C3, C7, and C4’ positions. Moreover, dynamic patterns of different flavonoids showed diversity. By Illumina sequencing, the obtained over 200 million valid reads were assembled into 60,422 genes. Blast analysis indicated that 31,872 genes were annotated at least in one of public databases. Greatly increasing molecular resources makes up for the lack of gene information in V. amygdalina. By digital expression profiling and qRT-PCR, we specifically characterized some key enzymes, such as Va-PAL1, Va-PAL4, Va-C4H1, Va-4CL3, Va-ACC1, Va-CHS1, Va-CHI, Va-FNSII, and Va-IFS3, involved in flavonoid biosynthes…
format: application/pdf
format: text/html
creator: Lanya Shui
creator: Kaisen Huo
creator: Yan Chen
creator: Zilin Zhang
creator: Yanfang Li
creator: Jun Niu
subject: Agricultural Science
subject: Food Science and Technology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11239
publisher: PeerJ Inc.
rights: © 2021 Shui et al.
abstract: Background Vernonia amygdalina as a tropical horticultural crop has been widely used for medicinal herb, feed, and vegetable. Recently, increasing studies revealed that this species possesses multiple pharmacological properties. Notably, V. amygdalina leaves possess an abundance of flavonoids, but the specific profiles of flavonoids and the mechanisms of fl avonoid bi osynthesis in developing leaves are largely unknown. Methods The total flavonoids of V. amygdalina leaves were detected using ultraviolet spectrophotometer. The temporal flavonoid profiles of V. amygdalina leaves were analyzed by LC-MS. The transcriptome analysis of V. amygdalina leaves was performed by Illumina sequencing. Functional annotation and differential expression analysis of V. amygdalina genes were performed by Blast2GO v2.3.5 and RSEM v1.2.31, respectively. qRT-PCR analysis was used to verify the gene expressions in developing V. amygdalina leaves. Results By LC-MS analysis, three substrates (p-coumaric acid, trans-cinnamic acid, and phenylalanine) for flavonoid biosynthesis were identified in V. amygdalina leaves. Additionally, 42 flavonoids were identified from V. amygdalina leaves, including six dihydroflavones, 14 flavones, eight isoflavones, nine flavonols, two xanthones, one chalcone, one cyanidin, and one dihydroflavonol. Glycosylation and methylation were common at the hydroxy group of C3, C7, and C4’ positions. Moreover, dynamic patterns of different flavonoids showed diversity. By Illumina sequencing, the obtained over 200 million valid reads were assembled into 60,422 genes. Blast analysis indicated that 31,872 genes were annotated at least in one of public databases. Greatly increasing molecular resources makes up for the lack of gene information in V. amygdalina. By digital expression profiling and qRT-PCR, we specifically characterized some key enzymes, such as Va-PAL1, Va-PAL4, Va-C4H1, Va-4CL3, Va-ACC1, Va-CHS1, Va-CHI, Va-FNSII, and Va-IFS3, involved in flavonoid biosynthes…
bibliographic citation: Shui et al. (2021) Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves. PeerJ 9:e11239 https://doi.org/10.7717/peerj.11239
date submitted: 2020-11-26
date accepted: 2021-03-17
issued: 2021-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shui
  given name: Lanya
author list: Agent
  family name: Huo
  given name: Kaisen
author list: Agent
  family name: Chen
  given name: Yan
author list: Agent
  family name: Zhang
  given name: Zilin
author list: Agent
  family name: Li
  given name: Yanfang
author list: Agent
  family name: Niu
  given name: Jun
doi: 10.7717/peerj.11239
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-26
copyright: ©2021 Shui et al.
attribution name: Shui et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359