PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Management of recurrent ureteral stricture: a retrospectively comparative study with robot-assisted laparoscopic surgery versus open approach
items: The response of fine root morphological and physiological traits to added nitrogen in Schrenk’s spruce (Picea schrenkiana) of the Tianshan mountains, China
items: Migraine aura, a predictor of near-death experiences in a crowdsourced study
items: Amino acids and acylcarnitine production by Chlorella vulgaris and Chlorella sorokiniana microalgae from wastewater culture
items: The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes (Coregonus lavaretus): one story more
items: Phospholipase A2 from krait Bungarus fasciatus venom induces human cancer cell death in vitro
items: Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge Isodictya sp.
items: Effectiveness of water-saving technologies during early stages of restoration of endemic Opuntia cacti in the Galápagos Islands, Ecuador
items: Different distant metastasis patterns based on tumor size could be found in extensive-stage small cell lung cancer patients: a large, population-based SEER study
items: Switching between standard coral reef benthic monitoring protocols is complicated: proof of concept

Management of recurrent ureteral stricture: a retrospectively comparative study with robot-assisted laparoscopic surgery versus open approach
type: item
type: AcademicArticle
description: Background Management of recurrent ureteral stricture is challenging. Consensus on the best surgical choice has not been demonstrated. In this study, we aim to report our experience in treating recurrent ureteral stricture and demonstrate whether robot-assisted procedure for redo ureteral surgery is as effective as open procedure while remaining less invasive. Methods We retrospectively assessed 41 patients (22 robot-assisted surgeries and 19 open surgeries) who underwent consecutive robot-assisted and open procedures for redo ureteral surgery from January 2014 to 2018 in our institution. Perioperative outcomes, including demographics, operative time, estimated blood loss, complications, pain scores, success rate and cost, were compared between two groups. Results There was no significant intergroup difference in terms of age, body mass index, gender composition and American Society of Anesthesiologists scores. A total of 31 patients underwent redo pyeloplasty and ten underwent redo uretero-ureterostomy. Compared with open group, robot-assisted group showed shorter operative time (124.55 min vs. 185.11 min, p < 0.0001), less estimated blood loss (100.00 mL vs. 182.60 mL, p = 0.008) and higher cost (61161.77¥ vs. 39470.79¥, p < 0.0001). Complication rate and pain scores were similar between two groups. Median follow-up periods were 30 and 48 months for robot-assisted and open group respectively. Success rate in the robot-assisted (85.71%) and the open group (82.35%) was not significantly different. Conclusions Robot-assisted surgery for recurrent stricture after previous ureteral reconstruction is as effective as open procedure and is associated with shorter operative time and less estimated blood loss.
format: application/pdf
format: text/html
creator: Qing Wang
creator: Yuchao Lu
creator: Henglong Hu
creator: Jiaqiao Zhang
creator: Baolong Qin
creator: Jianning Zhu
creator: Najib Isse Dirie
creator: Zongbiao Zhang
creator: Shaogang Wang
subject: Surgery and Surgical Specialties
subject: Urology
description: doi:10.7717/peerj.8166
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Management of recurrent ureteral stricture is challenging. Consensus on the best surgical choice has not been demonstrated. In this study, we aim to report our experience in treating recurrent ureteral stricture and demonstrate whether robot-assisted procedure for redo ureteral surgery is as effective as open procedure while remaining less invasive. Methods We retrospectively assessed 41 patients (22 robot-assisted surgeries and 19 open surgeries) who underwent consecutive robot-assisted and open procedures for redo ureteral surgery from January 2014 to 2018 in our institution. Perioperative outcomes, including demographics, operative time, estimated blood loss, complications, pain scores, success rate and cost, were compared between two groups. Results There was no significant intergroup difference in terms of age, body mass index, gender composition and American Society of Anesthesiologists scores. A total of 31 patients underwent redo pyeloplasty and ten underwent redo uretero-ureterostomy. Compared with open group, robot-assisted group showed shorter operative time (124.55 min vs. 185.11 min, p < 0.0001), less estimated blood loss (100.00 mL vs. 182.60 mL, p = 0.008) and higher cost (61161.77¥ vs. 39470.79¥, p < 0.0001). Complication rate and pain scores were similar between two groups. Median follow-up periods were 30 and 48 months for robot-assisted and open group respectively. Success rate in the robot-assisted (85.71%) and the open group (82.35%) was not significantly different. Conclusions Robot-assisted surgery for recurrent stricture after previous ureteral reconstruction is as effective as open procedure and is associated with shorter operative time and less estimated blood loss.
bibliographic citation: Wang et al. (2019) Management of recurrent ureteral stricture: a retrospectively comparative study with robot-assisted laparoscopic surgery versus open approach. PeerJ 7:e8166 https://doi.org/10.7717/peerj.8166
date submitted: 2019-07-08
date accepted: 2019-11-05
issued: 2019-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qing
author list: Agent
  family name: Lu
  given name: Yuchao
author list: Agent
  family name: Hu
  given name: Henglong
author list: Agent
  family name: Zhang
  given name: Jiaqiao
author list: Agent
  family name: Qin
  given name: Baolong
author list: Agent
  family name: Zhu
  given name: Jianning
author list: Agent
  family name: Dirie
  given name: Najib Isse
author list: Agent
  family name: Zhang
  given name: Zongbiao
author list: Agent
  family name: Wang
  given name: Shaogang
doi: 10.7717/peerj.8166
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-04
copyright: © 2019 Wang et al.
attribution name: Wang et al.

The response of fine root morphological and physiological traits to added nitrogen in Schrenk’s spruce (Picea schrenkiana) of the Tianshan mountains, China
type: item
type: AcademicArticle
description: Fine roots are essential for water and nutrient uptake in plants, but little is known about the variation in fine root traits and the underlying mechanisms that drive it. Understanding the responses of fine root function traits to changing environmental conditions and the role of fine root traits as drivers of forest ecosystem processes are critical for informing physiological and ecological theory as well as ecosystem management. We measured morphological and physiological traits of fine roots from six soil layers and three diameter classes in Schrenk’s spruce (Picea shrenkiana) forests of the Tianshan mountains, China. We found significant effects of nitrogen addition on these morphological and physiological traits, which varied by soil layer and root diameter. Specifically, specific root length (SRL) was higher in medium N addition group (N2) than in control group (N0). Specific root area (SRA) was higher in the control group (N0) than fertilized groups (N1, N2 and N3). Root tissue density (RTD) was higher in low N addition group (N1) than in the other group. Root dry matter content had no significant difference among four treatment groups. SRL, SRA, and RTD of fine roots in different diameter classes were all significantly different between high N addition (N3) and the control (N0) groups. The physiological characteristics of fine roots showed that soluble sugar (SS), fine root vitality (FRV), and tissue water content (TWC) in different soil layers were higher in the control group than in the fertilized groups. While soluble protein (SP), malondialdehyde (MDA) and free proline (FP) were lower in the control group (N0) than in the fertilized groups. In addition, SS, FRV, SP, TWC, FP, and MDA in all N addition treatments groups were significantly different from the control group. Fine root morphological traits were closely related to physiological traits, and added nitrogen inputs change these correlations. Our study confirms that nitrogen addition has specific ef…
format: application/pdf
format: text/html
creator: Lu Gong
creator: Jingjing Zhao
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.8194
publisher: PeerJ Inc.
rights: © 2019 Gong and Zhao
abstract: Fine roots are essential for water and nutrient uptake in plants, but little is known about the variation in fine root traits and the underlying mechanisms that drive it. Understanding the responses of fine root function traits to changing environmental conditions and the role of fine root traits as drivers of forest ecosystem processes are critical for informing physiological and ecological theory as well as ecosystem management. We measured morphological and physiological traits of fine roots from six soil layers and three diameter classes in Schrenk’s spruce (Picea shrenkiana) forests of the Tianshan mountains, China. We found significant effects of nitrogen addition on these morphological and physiological traits, which varied by soil layer and root diameter. Specifically, specific root length (SRL) was higher in medium N addition group (N2) than in control group (N0). Specific root area (SRA) was higher in the control group (N0) than fertilized groups (N1, N2 and N3). Root tissue density (RTD) was higher in low N addition group (N1) than in the other group. Root dry matter content had no significant difference among four treatment groups. SRL, SRA, and RTD of fine roots in different diameter classes were all significantly different between high N addition (N3) and the control (N0) groups. The physiological characteristics of fine roots showed that soluble sugar (SS), fine root vitality (FRV), and tissue water content (TWC) in different soil layers were higher in the control group than in the fertilized groups. While soluble protein (SP), malondialdehyde (MDA) and free proline (FP) were lower in the control group (N0) than in the fertilized groups. In addition, SS, FRV, SP, TWC, FP, and MDA in all N addition treatments groups were significantly different from the control group. Fine root morphological traits were closely related to physiological traits, and added nitrogen inputs change these correlations. Our study confirms that nitrogen addition has specific ef…
bibliographic citation: Gong et al. (2019) The response of fine root morphological and physiological traits to added nitrogen in Schrenk’s spruce (Picea schrenkiana) of the Tianshan mountains, China. PeerJ 7:e8194 https://doi.org/10.7717/peerj.8194
date submitted: 2019-07-17
date accepted: 2019-11-11
issued: 2019-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gong
  given name: Lu
author list: Agent
  family name: Zhao
  given name: Jingjing
doi: 10.7717/peerj.8194
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-04
copyright: © 2019 Gong and Zhao
attribution name: Gong and Zhao

Migraine aura, a predictor of near-death experiences in a crowdsourced study
type: item
type: AcademicArticle
description: Background Near-death experiences (NDE) occur with imminent death and in situations of stress and danger but are poorly understood. Evidence suggests that NDE are associated with rapid eye movement (REM) sleep intrusion, a feature of narcolepsy. Previous studies further found REM abnormalities and an increased frequency of dream-enacting behavior in migraine patients, as well as an association between migraine with aura and narcolepsy. We therefore investigated if NDE are more common in people with migraine aura. Methods We recruited 1,037 laypeople from 35 countries and five continents, without any filters except for English language and age ≥18 years, via a crowdsourcing platform. Reports were validated using the Greyson NDE Scale. Results Eighty-one of 1,037 participants had NDE (7.8%; CI [6.3–9.7%]). There were no significant associations between NDE and age (p > 0.6, t-test independent samples) or gender (p > 0.9, Chi-square test). The only significant association was between NDE and migraine aura: 48 (6.1%) of 783 subjects without migraine aura and 33 (13.0%) of 254 subjects with migraine aura had NDE (p < 0.001, odds ratio (OR) = 2.29). In multiple logistic regression analysis, migraine aura remained significant after adjustment for age (p < 0.001, OR = 2.31), gender (p < 0.001, OR = 2.33), or both (p < 0.001, OR = 2.33). Conclusions In our sample, migraine aura was a predictor of NDE. This indirectly supports the association between NDE and REM intrusion and might have implications for the understanding of NDE, because a variant of spreading depolarization (SD), terminal SD, occurs in humans at the end of life, while a short-lasting variant of SD is considered the pathophysiological correlate of migraine aura.
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format: text/html
creator: Daniel Kondziella
creator: Markus Harboe Olsen
creator: Coline L. Lemale
creator: Jens P. Dreier
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Emergency and Critical Care
subject: Neurology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8202
publisher: PeerJ Inc.
rights: © 2019 Kondziella et al.
abstract: Background Near-death experiences (NDE) occur with imminent death and in situations of stress and danger but are poorly understood. Evidence suggests that NDE are associated with rapid eye movement (REM) sleep intrusion, a feature of narcolepsy. Previous studies further found REM abnormalities and an increased frequency of dream-enacting behavior in migraine patients, as well as an association between migraine with aura and narcolepsy. We therefore investigated if NDE are more common in people with migraine aura. Methods We recruited 1,037 laypeople from 35 countries and five continents, without any filters except for English language and age ≥18 years, via a crowdsourcing platform. Reports were validated using the Greyson NDE Scale. Results Eighty-one of 1,037 participants had NDE (7.8%; CI [6.3–9.7%]). There were no significant associations between NDE and age (p > 0.6, t-test independent samples) or gender (p > 0.9, Chi-square test). The only significant association was between NDE and migraine aura: 48 (6.1%) of 783 subjects without migraine aura and 33 (13.0%) of 254 subjects with migraine aura had NDE (p < 0.001, odds ratio (OR) = 2.29). In multiple logistic regression analysis, migraine aura remained significant after adjustment for age (p < 0.001, OR = 2.31), gender (p < 0.001, OR = 2.33), or both (p < 0.001, OR = 2.33). Conclusions In our sample, migraine aura was a predictor of NDE. This indirectly supports the association between NDE and REM intrusion and might have implications for the understanding of NDE, because a variant of spreading depolarization (SD), terminal SD, occurs in humans at the end of life, while a short-lasting variant of SD is considered the pathophysiological correlate of migraine aura.
bibliographic citation: Kondziella et al. (2019) Migraine aura, a predictor of near-death experiences in a crowdsourced study. PeerJ 7:e8202 https://doi.org/10.7717/peerj.8202
date submitted: 2019-09-06
date accepted: 2019-11-13
issued: 2019-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kondziella
  given name: Daniel
author list: Agent
  family name: Olsen
  given name: Markus Harboe
author list: Agent
  family name: Lemale
  given name: Coline L.
author list: Agent
  family name: Dreier
  given name: Jens P.
doi: 10.7717/peerj.8202
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-04
copyright: © 2019 Kondziella et al.
attribution name: Kondziella et al.

Amino acids and acylcarnitine production by Chlorella vulgaris and Chlorella sorokiniana microalgae from wastewater culture
type: item
type: AcademicArticle
description: Background Microalgae are a widely distributed group of prokaryotic and eukaryotic photosynthetic microorganisms that use a number of substances present in wastewater to produce a variety of biotechnological and nutritional biomolecules. Methods Production ofamino acids and acylcarnitine by Chlorella vulgaris and Chlorella sorokiniana was determined after 13 d of culture in wastewater, under various culture conditions. Wastewater was collected from “La Encantada” stream, located in Saltillo, Coahuila, Mexico. Microalgae was cultured at 23°C and natural day light, including the use of the following conditions: (1) extra light (12:12 light:dark cycles, 1,380 lumens), (2) agitation (130 rpm), and (3) both conditions, until exponential phase. Supernatant products were then analyzed by liquid chromatograph coupled to mass spectrometry. In addition, metabolomic profiles related to growing conditions were evaluated. Results Amino acids and acylcarnitine production by C. sorokiniana and C. vulgaris resulted in higher Ala and Leu concentrations by C. vulgaris compared with control, where control produced Gly and Pro in higher amounts compared with C. sorokiniana. Tyr, Phe, Val, and Cit were detected in lower amounts under light and shaking culture conditions. High concentrations of C0 acylcarnitines were produced by both microalgae compared with control, where C. sorokiniana production was independent of culture conditions, whereas C. vulgaris one was stimulated by shaking. C4 production was higher by C. sorokiniana compared with control. Furthermore, C4, C6DC, C14:1, C14:2, and C18:1OH production by microalga was low in all culture conditions. Conclusion Microalgae produced essential amino acids and nutritionally important carnitines from wastewater. In addition, C. sorokiniana biomass has higher potential as animal nutrient supplement, as compared with that of C. vulgaris.
format: application/pdf
format: text/html
creator: Juan M. Ballesteros-Torres
creator: Luis Samaniego-Moreno
creator: Ricardo Gomez-Flores
creator: Reyes S. Tamez-Guerra
creator: Cristina Rodríguez-Padilla
creator: Patricia Tamez-Guerra
subject: Biochemistry
subject: Biotechnology
subject: Ecology
subject: Microbiology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.7977
publisher: PeerJ Inc.
rights: © 2019 Ballesteros-Torres et al.
abstract: Background Microalgae are a widely distributed group of prokaryotic and eukaryotic photosynthetic microorganisms that use a number of substances present in wastewater to produce a variety of biotechnological and nutritional biomolecules. Methods Production ofamino acids and acylcarnitine by Chlorella vulgaris and Chlorella sorokiniana was determined after 13 d of culture in wastewater, under various culture conditions. Wastewater was collected from “La Encantada” stream, located in Saltillo, Coahuila, Mexico. Microalgae was cultured at 23°C and natural day light, including the use of the following conditions: (1) extra light (12:12 light:dark cycles, 1,380 lumens), (2) agitation (130 rpm), and (3) both conditions, until exponential phase. Supernatant products were then analyzed by liquid chromatograph coupled to mass spectrometry. In addition, metabolomic profiles related to growing conditions were evaluated. Results Amino acids and acylcarnitine production by C. sorokiniana and C. vulgaris resulted in higher Ala and Leu concentrations by C. vulgaris compared with control, where control produced Gly and Pro in higher amounts compared with C. sorokiniana. Tyr, Phe, Val, and Cit were detected in lower amounts under light and shaking culture conditions. High concentrations of C0 acylcarnitines were produced by both microalgae compared with control, where C. sorokiniana production was independent of culture conditions, whereas C. vulgaris one was stimulated by shaking. C4 production was higher by C. sorokiniana compared with control. Furthermore, C4, C6DC, C14:1, C14:2, and C18:1OH production by microalga was low in all culture conditions. Conclusion Microalgae produced essential amino acids and nutritionally important carnitines from wastewater. In addition, C. sorokiniana biomass has higher potential as animal nutrient supplement, as compared with that of C. vulgaris.
bibliographic citation: Ballesteros-Torres et al. (2019) Amino acids and acylcarnitine production by Chlorella vulgaris and Chlorella sorokiniana microalgae from wastewater culture. PeerJ 7:e7977 https://doi.org/10.7717/peerj.7977
date submitted: 2019-05-04
date accepted: 2019-10-02
issued: 2019-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ballesteros-Torres
  given name: Juan M.
author list: Agent
  family name: Samaniego-Moreno
  given name: Luis
author list: Agent
  family name: Gomez-Flores
  given name: Ricardo
author list: Agent
  family name: Tamez-Guerra
  given name: Reyes S.
author list: Agent
  family name: Rodríguez-Padilla
  given name: Cristina
author list: Agent
  family name: Tamez-Guerra
  given name: Patricia
doi: 10.7717/peerj.7977
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-03
copyright: ©2019 Ballesteros-Torres et al.
attribution name: Ballesteros-Torres et al.

The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes (Coregonus lavaretus): one story more
type: item
type: AcademicArticle
description: In the Coregonus lavaretus complex may be found lacustrine sympatric pairs, which serves as an intriguing model for studying different aspects of fish evolutionary biology. One such sympatric whitefish pair inhabits Teletskoye Lake (West Siberia, Russia) and includes a “large” form (Coregonus lavaretus pidschian (Gmelin, 1789)) and a “small” form (C. l. pravdinellus (Dulkeit, 1949)). C. l. pravdinellus has a narrow trophic specialization and feeds on zooplankton, whereas the diet of C. l. pidschian is based on benthic prey. In the present study we aimed to address the question of how the gut microbial community reflects the divergence in diet of a sympatric pair of whitefish. Studied samples included the mucosa and content were collected for cardiac and pyloric stomach, anterior, middle, and posterior intestine, but only mucosa was collected for the pyloric caeca. In addition, water, sediment, macrophyte (environmental microbiota) and invertebrate (microbiota of prey) samples were collected in the same location. The V3–V4 region of the 16S rRNA genes was chosen for microbiome analysis and the software PICRUSt used to estimate the difference functional roles of the microbiota. The number of OTUs and Chao1 index in mucosa and content of cardiac and pyloric stomach were significantly different between whitefish. Significant differences were observed between whitefish for content from different parts of the intestine in terms of OTU number and Chao1 indices, whereas for mucosa from the same parts of intestine these differences were absent. No significant differences were found for diversity estimates of mucosa and content of different parts of the gut (there were a few exceptions) between whitefish. The form of whitefish and the segment of the digestive system were factors with a significant determinative effect on the structure of the microbiota from gut mucosa and content. The most dominant phyla in mucosa and content of cardiac and pyloric stomach was Proteobacteria …
format: application/pdf
format: text/html
creator: Mikhail M. Solovyev
creator: Elena N. Kashinskaya
creator: Nickolai A. Bochkarev
creator: Karl B. Andree
creator: Evgeniy Simonov
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.8005
publisher: PeerJ Inc.
rights: © 2019 Solovyev et al.
abstract: In the Coregonus lavaretus complex may be found lacustrine sympatric pairs, which serves as an intriguing model for studying different aspects of fish evolutionary biology. One such sympatric whitefish pair inhabits Teletskoye Lake (West Siberia, Russia) and includes a “large” form (Coregonus lavaretus pidschian (Gmelin, 1789)) and a “small” form (C. l. pravdinellus (Dulkeit, 1949)). C. l. pravdinellus has a narrow trophic specialization and feeds on zooplankton, whereas the diet of C. l. pidschian is based on benthic prey. In the present study we aimed to address the question of how the gut microbial community reflects the divergence in diet of a sympatric pair of whitefish. Studied samples included the mucosa and content were collected for cardiac and pyloric stomach, anterior, middle, and posterior intestine, but only mucosa was collected for the pyloric caeca. In addition, water, sediment, macrophyte (environmental microbiota) and invertebrate (microbiota of prey) samples were collected in the same location. The V3–V4 region of the 16S rRNA genes was chosen for microbiome analysis and the software PICRUSt used to estimate the difference functional roles of the microbiota. The number of OTUs and Chao1 index in mucosa and content of cardiac and pyloric stomach were significantly different between whitefish. Significant differences were observed between whitefish for content from different parts of the intestine in terms of OTU number and Chao1 indices, whereas for mucosa from the same parts of intestine these differences were absent. No significant differences were found for diversity estimates of mucosa and content of different parts of the gut (there were a few exceptions) between whitefish. The form of whitefish and the segment of the digestive system were factors with a significant determinative effect on the structure of the microbiota from gut mucosa and content. The most dominant phyla in mucosa and content of cardiac and pyloric stomach was Proteobacteria …
bibliographic citation: Solovyev et al. (2019) The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes (Coregonus lavaretus): one story more. PeerJ 7:e8005 https://doi.org/10.7717/peerj.8005
date submitted: 2019-03-27
date accepted: 2019-10-07
issued: 2019-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Solovyev
  given name: Mikhail M.
author list: Agent
  family name: Kashinskaya
  given name: Elena N.
author list: Agent
  family name: Bochkarev
  given name: Nickolai A.
author list: Agent
  family name: Andree
  given name: Karl B.
author list: Agent
  family name: Simonov
  given name: Evgeniy
doi: 10.7717/peerj.8005
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-03
copyright: ©2019 Solovyev et al.
attribution name: Solovyev et al.

Phospholipase A2 from krait Bungarus fasciatus venom induces human cancer cell death in vitro
type: item
type: AcademicArticle
description: Background Snake venoms are the complex mixtures of different compounds manifesting a wide array of biological activities. The venoms of kraits (genus Bungarus, family Elapidae) induce mainly neurological symptoms; however, these venoms show a cytotoxicity against cancer cells as well. This study was conducted to identify in Bungarus fasciatus venom an active compound(s) exerting cytotoxic effects toward MCF7 human breast cancer cells and A549 human lung cancer cells. Methods The crude venom of B. fasciatus was separated by gel-filtration on Superdex HR 75 column and reversed phase HPLC on C18 column. The fractions obtained were screened for cytotoxic effect against MCF7, A549, and HK2 cell lines using colorimetric assay with the tetrazolium dye MTT- 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. The primary structure of active protein was established by ultra high resolution LC-MS/MS. The molecular mechanism of the isolated protein action on MCF7 cells was elucidated by flow cytometry. Results MTT cell viability assays of cancer cells incubated with fractions isolated from B. fasciatus venom revealed a protein with molecular mass of about 13 kDa possessing significant cytotoxicity. This protein manifested the dose and time dependent cytotoxicity for MCF7 and A549 cell lines while showed no toxic effect on human normal kidney HK2 cells. In MCF7, flow cytometry analysis revealed a decrease in the proportion of Ki-67 positive cells. As Ki-67 protein is a cellular marker for proliferation, its decline indicates the reduction in the proliferation of MCF7 cells treated with the protein. Flow cytometry analysis of MCF7 cells stained with propidium iodide and Annexin V conjugated with allophycocyanin showed that a probable mechanism of cell death is apoptosis. Mass spectrometric studies showed that the cytotoxic protein was phospholipase A2. The amino acid sequence of this enzyme earlier was deduced from cloned cDNA, and in this work it was isolated from the…
format: application/pdf
format: text/html
creator: Thien V. Tran
creator: Andrei E. Siniavin
creator: Anh N. Hoang
creator: My T.T. Le
creator: Chuong D. Pham
creator: Trung V. Phung
creator: Khoa C. Nguyen
creator: Rustam H. Ziganshin
creator: Victor I. Tsetlin
creator: Ching-Feng Weng
creator: Yuri N. Utkin
subject: Biochemistry
subject: Toxicology
description: doi:10.7717/peerj.8055
publisher: PeerJ Inc.
rights: © 2019 Tran et al.
abstract: Background Snake venoms are the complex mixtures of different compounds manifesting a wide array of biological activities. The venoms of kraits (genus Bungarus, family Elapidae) induce mainly neurological symptoms; however, these venoms show a cytotoxicity against cancer cells as well. This study was conducted to identify in Bungarus fasciatus venom an active compound(s) exerting cytotoxic effects toward MCF7 human breast cancer cells and A549 human lung cancer cells. Methods The crude venom of B. fasciatus was separated by gel-filtration on Superdex HR 75 column and reversed phase HPLC on C18 column. The fractions obtained were screened for cytotoxic effect against MCF7, A549, and HK2 cell lines using colorimetric assay with the tetrazolium dye MTT- 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. The primary structure of active protein was established by ultra high resolution LC-MS/MS. The molecular mechanism of the isolated protein action on MCF7 cells was elucidated by flow cytometry. Results MTT cell viability assays of cancer cells incubated with fractions isolated from B. fasciatus venom revealed a protein with molecular mass of about 13 kDa possessing significant cytotoxicity. This protein manifested the dose and time dependent cytotoxicity for MCF7 and A549 cell lines while showed no toxic effect on human normal kidney HK2 cells. In MCF7, flow cytometry analysis revealed a decrease in the proportion of Ki-67 positive cells. As Ki-67 protein is a cellular marker for proliferation, its decline indicates the reduction in the proliferation of MCF7 cells treated with the protein. Flow cytometry analysis of MCF7 cells stained with propidium iodide and Annexin V conjugated with allophycocyanin showed that a probable mechanism of cell death is apoptosis. Mass spectrometric studies showed that the cytotoxic protein was phospholipase A2. The amino acid sequence of this enzyme earlier was deduced from cloned cDNA, and in this work it was isolated from the…
bibliographic citation: Tran et al. (2019) Phospholipase A2 from krait Bungarus fasciatus venom induces human cancer cell death in vitro. PeerJ 7:e8055 https://doi.org/10.7717/peerj.8055
date submitted: 2019-04-12
date accepted: 2019-10-17
issued: 2019-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tran
  given name: Thien V.
author list: Agent
  family name: Siniavin
  given name: Andrei E.
author list: Agent
  family name: Hoang
  given name: Anh N.
author list: Agent
  family name: Le
  given name: My T.T.
author list: Agent
  family name: Pham
  given name: Chuong D.
author list: Agent
  family name: Phung
  given name: Trung V.
author list: Agent
  family name: Nguyen
  given name: Khoa C.
author list: Agent
  family name: Ziganshin
  given name: Rustam H.
author list: Agent
  family name: Tsetlin
  given name: Victor I.
author list: Agent
  family name: Weng
  given name: Ching-Feng
author list: Agent
  family name: Utkin
  given name: Yuri N.
doi: 10.7717/peerj.8055
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-03
copyright: © 2019 Tran et al.
attribution name: Tran et al.

Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge Isodictya sp.
type: item
type: AcademicArticle
description: Although the cellular and molecular responses to exposure to relatively high temperatures (acute thermal stress or heat shock) have been studied previously, only sparse empirical evidence of how it affects cold-water species is available. As climate change becomes more pronounced in areas such as the Western Antarctic Peninsula, both long-term and occasional acute temperature rises will impact species found there, and it has become crucial to understand the capacity of these species to respond to such thermal stress. Here, we use the Antarctic sponge Isodictya sp. to investigate how sessile organisms (particularly Porifera) can adjust to acute short-term heat stress, by exposing this species to 3 and 5 °C for 4 h, corresponding to predicted temperatures under high-end 2080 IPCC-SRES scenarios. Assembling a de novo reference transcriptome (90,188 contigs, >93.7% metazoan BUSCO genes) we have begun to discern the molecular response employed by Isodictya to adjust to heat exposure. Our initial analyses suggest that TGF-β, ubiquitin and hedgehog cascades are involved, alongside other genes. However, the degree and type of response changed little from 3 to 5 °C in the time frame examined, suggesting that even moderate rises in temperature could cause stress at the limits of this organism’s capacity. Given the importance of sponges to Antarctic ecosystems, our findings are vital for discerning the consequences of short-term increases in Antarctic ocean temperature on these and other species.
format: application/pdf
format: text/html
creator: Marcelo González-Aravena
creator: Nathan J. Kenny
creator: Magdalena Osorio
creator: Alejandro Font
creator: Ana Riesgo
creator: César A. Cárdenas
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.8088
publisher: PeerJ Inc.
rights: © 2019 González-Aravena et al.
abstract: Although the cellular and molecular responses to exposure to relatively high temperatures (acute thermal stress or heat shock) have been studied previously, only sparse empirical evidence of how it affects cold-water species is available. As climate change becomes more pronounced in areas such as the Western Antarctic Peninsula, both long-term and occasional acute temperature rises will impact species found there, and it has become crucial to understand the capacity of these species to respond to such thermal stress. Here, we use the Antarctic sponge Isodictya sp. to investigate how sessile organisms (particularly Porifera) can adjust to acute short-term heat stress, by exposing this species to 3 and 5 °C for 4 h, corresponding to predicted temperatures under high-end 2080 IPCC-SRES scenarios. Assembling a de novo reference transcriptome (90,188 contigs, >93.7% metazoan BUSCO genes) we have begun to discern the molecular response employed by Isodictya to adjust to heat exposure. Our initial analyses suggest that TGF-β, ubiquitin and hedgehog cascades are involved, alongside other genes. However, the degree and type of response changed little from 3 to 5 °C in the time frame examined, suggesting that even moderate rises in temperature could cause stress at the limits of this organism’s capacity. Given the importance of sponges to Antarctic ecosystems, our findings are vital for discerning the consequences of short-term increases in Antarctic ocean temperature on these and other species.
bibliographic citation: González-Aravena et al. (2019) Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge Isodictya sp.. PeerJ 7:e8088 https://doi.org/10.7717/peerj.8088
date submitted: 2019-08-12
date accepted: 2019-10-23
issued: 2019-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: González-Aravena
  given name: Marcelo
author list: Agent
  family name: Kenny
  given name: Nathan J.
author list: Agent
  family name: Osorio
  given name: Magdalena
author list: Agent
  family name: Font
  given name: Alejandro
author list: Agent
  family name: Riesgo
  given name: Ana
author list: Agent
  family name: Cárdenas
  given name: César A.
doi: 10.7717/peerj.8088
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-03
copyright: © 2019 González-Aravena et al.
attribution name: González-Aravena et al.

Effectiveness of water-saving technologies during early stages of restoration of endemic Opuntia cacti in the Galápagos Islands, Ecuador
type: item
type: AcademicArticle
description: Restoration of keystone species is a primary strategy used to combat biodiversity loss and recover ecological services. This is particularly true for oceanic islands, which despite their small land mass, host a large fraction of the planet’s imperiled species. The endemic Opuntia spp. cacti are one example and a major focus for restoration in the Galápagos archipelago, Ecuador. These cacti are keystone species that support much of the unique vertebrate animal community in arid zones, yet human activities have substantially reduced Opuntia populations. Extreme aridity poses an obstacle for quickly restoring Opuntia populations though water-saving technologies may provide a solution. The aim of this study was to evaluate current restoration efforts and the utility of two water-saving technologies as tools for the early stages of restoring Opuntia populations in the Galápagos archipelago. We planted 1,425 seedlings between 2013 and 2018, of which 66% had survived by the end of 2018. Compared with no-technology controls, seedlings planted with Groasis Waterboxx® water-saving technology (polypropylene trays with water reservoir and protective refuge for germinants) had a greater rate of survival in their first two-years of growth on one island (Plaza Sur) and greater growth rate on four islands whereas the “Cocoon” water-saving technology (similar technology but made of biodegradable fiber) did not affect growth and actually reduced seedling survival. Survival and growth rate were also influenced by vegetation zone, elevation, and precipitation in ways largely contingent on island. Overall, our findings suggest that water-saving technologies are not always universally applicable but can substantially increase the survival and growth rate of seedlings in certain conditions, providing in some circumstances a useful tool for improving restoration outcomes for rare plants of arid ecosystems.
format: application/pdf
format: text/html
creator: Patricia Isabela Tapia
creator: Luka Negoita
creator: James P. Gibbs
creator: Patricia Jaramillo
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Environmental Impacts
description: doi:10.7717/peerj.8156
publisher: PeerJ Inc.
rights: © 2019 Tapia et al.
abstract: Restoration of keystone species is a primary strategy used to combat biodiversity loss and recover ecological services. This is particularly true for oceanic islands, which despite their small land mass, host a large fraction of the planet’s imperiled species. The endemic Opuntia spp. cacti are one example and a major focus for restoration in the Galápagos archipelago, Ecuador. These cacti are keystone species that support much of the unique vertebrate animal community in arid zones, yet human activities have substantially reduced Opuntia populations. Extreme aridity poses an obstacle for quickly restoring Opuntia populations though water-saving technologies may provide a solution. The aim of this study was to evaluate current restoration efforts and the utility of two water-saving technologies as tools for the early stages of restoring Opuntia populations in the Galápagos archipelago. We planted 1,425 seedlings between 2013 and 2018, of which 66% had survived by the end of 2018. Compared with no-technology controls, seedlings planted with Groasis Waterboxx® water-saving technology (polypropylene trays with water reservoir and protective refuge for germinants) had a greater rate of survival in their first two-years of growth on one island (Plaza Sur) and greater growth rate on four islands whereas the “Cocoon” water-saving technology (similar technology but made of biodegradable fiber) did not affect growth and actually reduced seedling survival. Survival and growth rate were also influenced by vegetation zone, elevation, and precipitation in ways largely contingent on island. Overall, our findings suggest that water-saving technologies are not always universally applicable but can substantially increase the survival and growth rate of seedlings in certain conditions, providing in some circumstances a useful tool for improving restoration outcomes for rare plants of arid ecosystems.
bibliographic citation: Tapia et al. (2019) Effectiveness of water-saving technologies during early stages of restoration of endemic Opuntia cacti in the Galápagos Islands, Ecuador. PeerJ 7:e8156 https://doi.org/10.7717/peerj.8156
date submitted: 2019-07-09
date accepted: 2019-11-04
issued: 2019-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tapia
  given name: Patricia Isabela
author list: Agent
  family name: Negoita
  given name: Luka
author list: Agent
  family name: Gibbs
  given name: James P.
author list: Agent
  family name: Jaramillo
  given name: Patricia
doi: 10.7717/peerj.8156
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-03
copyright: ©2019 Tapia et al.
attribution name: Tapia et al.

Different distant metastasis patterns based on tumor size could be found in extensive-stage small cell lung cancer patients: a large, population-based SEER study
type: item
type: AcademicArticle
description: Background Small-cell lung cancer (SCLC) is a malignant cancer with the ability to metastasize quickly. The relationship between tumor size and the distant metastasis patterns of Extensive-Stage Small Cell Lung Cancer (ES-SCLC) has not been reported. Objectives The aim of this study was to determine the different distant metastasis patterns as they related to tumor size in ES-SCLC. Patients and Methods We used Surveillance, Epidemiology, and End Results (SEER) population-based data collected from 2010 through 2013 to identify 11058 ES-SCLC patients with definite evidence of distant metastases. Multivariate logistic regression analysis was used to demonstrate the association between tumor size and distant metastasis patterns including bone, liver, brain, and lung metastases. Age, race, sex, and N stage were also selected in the logistic regression model. Results Subtle differences in metastasis patterns were found among patients based on different tumor sizes. Patients with tumors 3–7 cm have a higher risk of bone metastasis compared with those that have tumors ≤3 cm (OR 1.165, 95% CI [1.055–1.287], P = 0.003) and patients with tumors ≥7 cm have a higher risk of lung metastasis (OR 1.183, 95% CI [1.039–1.347], P = 0.011). In addition, patients with tumors ≥7 cm had a lower risk of brain metastasis and liver metastasis than patients with tumors ≤3 cm (OR 0.799, 95% CI [0.709–0.901], P < 0.001; OR 0.747, 95% CI [0.672–0.830], P < 0.001). Interestingly, there was no correlation between a larger tumor and a higher risk of metastasis. However, the tumor metastasis pattern did have some correlation with age, gender, race and N-status. Conclusion The pattern of distant metastasis of ES-SCLC is related to the tumor size and the tumor size is indicative of the metastatic site. Larger tumor sizes did not correlate with a higher risk of distant metastasis, but the size is related to the pattern of distant metastasis. The study of different distant metastasis patterns based on t…
format: application/pdf
format: text/html
creator: Jia Li
creator: Feng Liu
creator: Haining Yu
creator: Chenglong Zhao
creator: Zhenxiang Li
creator: Haiyong Wang
subject: Clinical Trials
subject: Epidemiology
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.8163
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Small-cell lung cancer (SCLC) is a malignant cancer with the ability to metastasize quickly. The relationship between tumor size and the distant metastasis patterns of Extensive-Stage Small Cell Lung Cancer (ES-SCLC) has not been reported. Objectives The aim of this study was to determine the different distant metastasis patterns as they related to tumor size in ES-SCLC. Patients and Methods We used Surveillance, Epidemiology, and End Results (SEER) population-based data collected from 2010 through 2013 to identify 11058 ES-SCLC patients with definite evidence of distant metastases. Multivariate logistic regression analysis was used to demonstrate the association between tumor size and distant metastasis patterns including bone, liver, brain, and lung metastases. Age, race, sex, and N stage were also selected in the logistic regression model. Results Subtle differences in metastasis patterns were found among patients based on different tumor sizes. Patients with tumors 3–7 cm have a higher risk of bone metastasis compared with those that have tumors ≤3 cm (OR 1.165, 95% CI [1.055–1.287], P = 0.003) and patients with tumors ≥7 cm have a higher risk of lung metastasis (OR 1.183, 95% CI [1.039–1.347], P = 0.011). In addition, patients with tumors ≥7 cm had a lower risk of brain metastasis and liver metastasis than patients with tumors ≤3 cm (OR 0.799, 95% CI [0.709–0.901], P < 0.001; OR 0.747, 95% CI [0.672–0.830], P < 0.001). Interestingly, there was no correlation between a larger tumor and a higher risk of metastasis. However, the tumor metastasis pattern did have some correlation with age, gender, race and N-status. Conclusion The pattern of distant metastasis of ES-SCLC is related to the tumor size and the tumor size is indicative of the metastatic site. Larger tumor sizes did not correlate with a higher risk of distant metastasis, but the size is related to the pattern of distant metastasis. The study of different distant metastasis patterns based on t…
bibliographic citation: Li et al. (2019) Different distant metastasis patterns based on tumor size could be found in extensive-stage small cell lung cancer patients: a large, population-based SEER study. PeerJ 7:e8163 https://doi.org/10.7717/peerj.8163
date submitted: 2019-07-01
date accepted: 2019-11-05
issued: 2019-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jia
author list: Agent
  family name: Liu
  given name: Feng
author list: Agent
  family name: Yu
  given name: Haining
author list: Agent
  family name: Zhao
  given name: Chenglong
author list: Agent
  family name: Li
  given name: Zhenxiang
author list: Agent
  family name: Wang
  given name: Haiyong
doi: 10.7717/peerj.8163
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-03
copyright: ©2019 Li et al.
attribution name: Li et al.

Switching between standard coral reef benthic monitoring protocols is complicated: proof of concept
type: item
type: AcademicArticle
description: Monitoring the state of coral reefs is necessary to identify drivers of change and assess effectiveness of management actions. There are several widely-used survey methods, each of which is likely to exhibit different biases that should be quantified if the purpose is to combine datasets obtained via different survey methods. The latter is a particularly important consideration when switching methodologies in long-term monitoring programs and is highly relevant to the Caribbean today. This is because of the continuing need for regionally comparable coral reef monitoring datasets and the fact that the Global Coral Reef Monitoring Network (GCRMN)-Caribbean node is now recommending a photoquadrat (PQ) method over the chain intercept transect method widely adopted by the members of the first truly regional monitoring network, Caribbean Coastal Marine Productivity Program (CARICOMP), in the early-1990s. Barbados, a member of the CARICOMP network, has been using a variation of the chain intercept method in its long-term coral reef monitoring program for more than two decades. Now a member of GCRMN-Caribbean, Barbados is considering switching to the PQ method in conformity with other regional members. Since we expect differences between methods, this study seeks to quantify the nature of those differences to inform Barbados and others considering switching methods. In 2017, both methods were concurrently implemented at 21 permanent monitoring plots across three major reef types in Barbados. Differences in % cover estimates for the six major benthic components, that is, hard corals, sponges, gorgonians, macroalgae, turf algae and crustose coralline algae, were examined within and among reef types. Overall, we found a complex pattern of differences between methods that depended on the benthic component, its relative abundance, and the reef type. We conclude that most benthic components would require a different conversion procedure depending on the reef type, and we provide …
format: application/pdf
format: text/html
creator: Henri Vallès
creator: Hazel A. Oxenford
creator: Alex Henderson
subject: Computational Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.8167
publisher: PeerJ Inc.
rights: © 2019 Vallès et al.
abstract: Monitoring the state of coral reefs is necessary to identify drivers of change and assess effectiveness of management actions. There are several widely-used survey methods, each of which is likely to exhibit different biases that should be quantified if the purpose is to combine datasets obtained via different survey methods. The latter is a particularly important consideration when switching methodologies in long-term monitoring programs and is highly relevant to the Caribbean today. This is because of the continuing need for regionally comparable coral reef monitoring datasets and the fact that the Global Coral Reef Monitoring Network (GCRMN)-Caribbean node is now recommending a photoquadrat (PQ) method over the chain intercept transect method widely adopted by the members of the first truly regional monitoring network, Caribbean Coastal Marine Productivity Program (CARICOMP), in the early-1990s. Barbados, a member of the CARICOMP network, has been using a variation of the chain intercept method in its long-term coral reef monitoring program for more than two decades. Now a member of GCRMN-Caribbean, Barbados is considering switching to the PQ method in conformity with other regional members. Since we expect differences between methods, this study seeks to quantify the nature of those differences to inform Barbados and others considering switching methods. In 2017, both methods were concurrently implemented at 21 permanent monitoring plots across three major reef types in Barbados. Differences in % cover estimates for the six major benthic components, that is, hard corals, sponges, gorgonians, macroalgae, turf algae and crustose coralline algae, were examined within and among reef types. Overall, we found a complex pattern of differences between methods that depended on the benthic component, its relative abundance, and the reef type. We conclude that most benthic components would require a different conversion procedure depending on the reef type, and we provide …
bibliographic citation: Vallès et al. (2019) Switching between standard coral reef benthic monitoring protocols is complicated: proof of concept. PeerJ 7:e8167 https://doi.org/10.7717/peerj.8167
date submitted: 2019-08-05
date accepted: 2019-11-05
issued: 2019-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vallès
  given name: Henri
author list: Agent
  family name: Oxenford
  given name: Hazel A.
author list: Agent
  family name: Henderson
  given name: Alex
doi: 10.7717/peerj.8167
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-03
copyright: © 2019 Vallès et al.
attribution name: Vallès et al.

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