PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish
items: Childhood parasitic infections and gastrointestinal illness in indigenous communities at Lake Atitlán, Guatemala
items: Rumen bacterial community profile and fermentation in Barki sheep fed olive cake and date palm byproducts
items: Estimating the differences in critical thermal maximum and metabolic rate of Helicoverpa punctigera (Wallengren) (Lepidoptera: Noctuidae) across life stages
items: No evidence of effects or interaction between the widely used herbicide, glyphosate, and a common parasite in bumble bees
items: Circ_0030235 knockdown protects H9c2 cells against OGD/R-induced injury via regulation of miR-526b
items: Circular RNA RBM33 contributes to extracellular matrix degradation via miR-4268/EPHB2 axis in abdominal aortic aneurysm
items: Evolution of diverse host infection mechanisms delineates an adaptive radiation of lampsiline freshwater mussels centered on their larval ecology
items: Landscape and microhabitat features determine small mammal abundance in forest patches in agricultural landscapes
items: Performance in mortality prediction of SAPS 3 And MPM-III scores among adult patients admitted to the ICU of a private tertiary referral hospital in Tanzania: a retrospective cohort study

Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish
type: item
type: AcademicArticle
description: Background The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species’ vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE. Methods Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt. Results Overall, otolith size varied linearly with fish size (from 10–60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0–30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such …
format: application/pdf
format: text/html
creator: Wilson Xieu
creator: Levi S. Lewis
creator: Feng Zhao
creator: Rachel A. Fichman
creator: Malte Willmes
creator: Tien-Chieh Hung
creator: Luke Ellison
creator: Troy Stevenson
creator: Galen Tigan
creator: Andrew A. Schultz
creator: James A. Hobbs
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12280
publisher: PeerJ Inc.
rights: © 2021 Xieu et al.
abstract: Background The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species’ vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE. Methods Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt. Results Overall, otolith size varied linearly with fish size (from 10–60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0–30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such …
bibliographic citation: Xieu et al. (2021) Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish. PeerJ 9:e12280 https://doi.org/10.7717/peerj.12280
date submitted: 2021-02-24
date accepted: 2021-09-20
issued: 2021-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xieu
  given name: Wilson
author list: Agent
  family name: Lewis
  given name: Levi S.
author list: Agent
  family name: Zhao
  given name: Feng
author list: Agent
  family name: Fichman
  given name: Rachel A.
author list: Agent
  family name: Willmes
  given name: Malte
author list: Agent
  family name: Hung
  given name: Tien-Chieh
author list: Agent
  family name: Ellison
  given name: Luke
author list: Agent
  family name: Stevenson
  given name: Troy
author list: Agent
  family name: Tigan
  given name: Galen
author list: Agent
  family name: Schultz
  given name: Andrew A.
author list: Agent
  family name: Hobbs
  given name: James A.
doi: 10.7717/peerj.12280
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-17
copyright: ©2021 Xieu et al.
attribution name: Xieu et al.

Childhood parasitic infections and gastrointestinal illness in indigenous communities at Lake Atitlán, Guatemala
type: item
type: AcademicArticle
description: Lake Atitlán has experienced a decline in water quality resulting from cultural eutrophication. Indigenous Mayans who already face disproportionate health challenges rely directly on the lake water. Our objectives were to: (1) estimate prevalence of shedding of water-borne fecal parasites among children 5 years of age and younger, (2) assess household-reported incidence of gastrointestinal illness in children, and (3) characterize water sources, treatment, and sanitation conditions in households. We hypothesized that household use of untreated lake water results in increased risk of shedding of parasites and gastrointestinal symptoms. A cross-sectional fecal sampling and physical exam of 401 children were conducted along with WASH surveys in partnership with healthcare providers in seven communities. Fecal samples were screened for Giardia lamblia and Cryptosporidium parvum, using a rapid ELISA, with a portion examined by microscope. The prevalence of parasite shedding was 12.2% (9.7% for Giardia; 2.5% for Cryptosporidium). Risk factors for Giardia shedding included age 3 years or older (3.4 odds ratio, z-stat = 2.781 p = 0.0054), low height-for-age z-score (2.3 odds ratio, z-stat = 2.225, p = 0.0216), lack of any household water treatment (2.5 odds ratio, z-stat = 2.492, p < 0.0012), and open access to household latrine (2.04 odds ratio, z-stat = 1.992, p = 0.0464). The majority (77.3%) of households reported water treatment, boiling and gravity fed filters as the most widespread practices. The vast majority of households (92%) reported usage of a latrine, while 40% reported open and shared access beyond their household. An overwhelming majority of households reported diarrhea and fever several times per year or greater, with approximately half reporting vomiting at that frequency. Lake water use was identified as a risk factor for households reporting frequent gastrointestinal symptoms (odds ratio of 2.5, 4.4, and 2.6; z-stat of 3.10, 3.65, and 3.0; p-values of 0.…
format: application/pdf
format: text/html
creator: Amber Roegner
creator: Mónica N. Orozco
creator: Claudia Jarquin
creator: William Boegel
creator: Clara Secaira
creator: Marlin E. Caballeros
creator: Lujain Al-Saleh
creator: Eliška Rejmánková
subject: Parasitology
subject: Gastroenterology and Hepatology
subject: Global Health
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.12331
publisher: PeerJ Inc.
rights: © 2021 Roegner et al.
abstract: Lake Atitlán has experienced a decline in water quality resulting from cultural eutrophication. Indigenous Mayans who already face disproportionate health challenges rely directly on the lake water. Our objectives were to: (1) estimate prevalence of shedding of water-borne fecal parasites among children 5 years of age and younger, (2) assess household-reported incidence of gastrointestinal illness in children, and (3) characterize water sources, treatment, and sanitation conditions in households. We hypothesized that household use of untreated lake water results in increased risk of shedding of parasites and gastrointestinal symptoms. A cross-sectional fecal sampling and physical exam of 401 children were conducted along with WASH surveys in partnership with healthcare providers in seven communities. Fecal samples were screened for Giardia lamblia and Cryptosporidium parvum, using a rapid ELISA, with a portion examined by microscope. The prevalence of parasite shedding was 12.2% (9.7% for Giardia; 2.5% for Cryptosporidium). Risk factors for Giardia shedding included age 3 years or older (3.4 odds ratio, z-stat = 2.781 p = 0.0054), low height-for-age z-score (2.3 odds ratio, z-stat = 2.225, p = 0.0216), lack of any household water treatment (2.5 odds ratio, z-stat = 2.492, p < 0.0012), and open access to household latrine (2.04 odds ratio, z-stat = 1.992, p = 0.0464). The majority (77.3%) of households reported water treatment, boiling and gravity fed filters as the most widespread practices. The vast majority of households (92%) reported usage of a latrine, while 40% reported open and shared access beyond their household. An overwhelming majority of households reported diarrhea and fever several times per year or greater, with approximately half reporting vomiting at that frequency. Lake water use was identified as a risk factor for households reporting frequent gastrointestinal symptoms (odds ratio of 2.5, 4.4, and 2.6; z-stat of 3.10, 3.65, and 3.0; p-values of 0.…
bibliographic citation: Roegner et al. (2021) Childhood parasitic infections and gastrointestinal illness in indigenous communities at Lake Atitlán, Guatemala. PeerJ 9:e12331 https://doi.org/10.7717/peerj.12331
date submitted: 2021-01-14
date accepted: 2021-09-27
issued: 2021-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roegner
  given name: Amber
author list: Agent
  family name: Orozco
  given name: Mónica N.
author list: Agent
  family name: Jarquin
  given name: Claudia
author list: Agent
  family name: Boegel
  given name: William
author list: Agent
  family name: Secaira
  given name: Clara
author list: Agent
  family name: Caballeros
  given name: Marlin E.
author list: Agent
  family name: Al-Saleh
  given name: Lujain
author list: Agent
  family name: Rejmánková
  given name: Eliška
doi: 10.7717/peerj.12331
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-17
copyright: ©2021 Roegner et al.
attribution name: Roegner et al.

Rumen bacterial community profile and fermentation in Barki sheep fed olive cake and date palm byproducts
type: item
type: AcademicArticle
description: Rumen bacteria make the greatest contribution to rumen fermentation that enables the host animal to utilize the ingested feeds. Agro-industrial byproducts (AIP) such as olive cake (OC) and date palm byproducts (discarded dates (DD), and date palm fronds (DPF)) represent a practical solution to the deficiency in common feed resources. In this study, thirty-six growing Barki lambs were divided into three groups to evaluate the effect of untraditional diets including the AIP on the growth performance. Subsequently, nine adult Barki rams were used to evaluate the effect of experimental diets on rumen fermentation and rumen bacteria. Three rations were used: common concentrate mixture (S1), common untraditional concentrate mixture including OC and DD (S2), and the same concentrate mixture in S2 supplemented with roughage as DPF enriched with 15% molasses (S3). The animals in S2 group showed higher dry matter intake (DMI) and lower relative growth rate (RGR) as compared to the animals in S1 group. However, the animals in S3 group were the lowest in DMI but achieved RGR by about 87.6% of that in the S1 group. Rumen pH, acetic and butyric acids were more prevalent in animals of S3 group and rumen ammonia (NH3-N), total volatile fatty acids (TVFA), propionic acid were higher in S1. Rumen enzymes activities were higher in S1 group followed by S3 and S2. The bacterial population was more prevalent in S1 and microbial diversity was higher in the S3 group. Principal coordinate analysis revealed clusters associated with diet type and the relative abundance of bacteria varied between sheep groups. The bacterial community was dominated by phylum Bacteroidetes and Firmicutes; whereas, Prevotella, Ruminococcus, and Butyrivibrio were the dominant genera. Results indicate that diet S3 supplemented by OC, DD, and DPF could replace the conventional feed mixture.
format: application/pdf
format: text/html
creator: Alaa Emara Rabee
creator: Khalid Z. Kewan
creator: Ebrahim A. Sabra
creator: Hassan M. El Shaer
creator: Mebarek Lamara
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.12447
publisher: PeerJ Inc.
rights: © 2021 Rabee et al.
abstract: Rumen bacteria make the greatest contribution to rumen fermentation that enables the host animal to utilize the ingested feeds. Agro-industrial byproducts (AIP) such as olive cake (OC) and date palm byproducts (discarded dates (DD), and date palm fronds (DPF)) represent a practical solution to the deficiency in common feed resources. In this study, thirty-six growing Barki lambs were divided into three groups to evaluate the effect of untraditional diets including the AIP on the growth performance. Subsequently, nine adult Barki rams were used to evaluate the effect of experimental diets on rumen fermentation and rumen bacteria. Three rations were used: common concentrate mixture (S1), common untraditional concentrate mixture including OC and DD (S2), and the same concentrate mixture in S2 supplemented with roughage as DPF enriched with 15% molasses (S3). The animals in S2 group showed higher dry matter intake (DMI) and lower relative growth rate (RGR) as compared to the animals in S1 group. However, the animals in S3 group were the lowest in DMI but achieved RGR by about 87.6% of that in the S1 group. Rumen pH, acetic and butyric acids were more prevalent in animals of S3 group and rumen ammonia (NH3-N), total volatile fatty acids (TVFA), propionic acid were higher in S1. Rumen enzymes activities were higher in S1 group followed by S3 and S2. The bacterial population was more prevalent in S1 and microbial diversity was higher in the S3 group. Principal coordinate analysis revealed clusters associated with diet type and the relative abundance of bacteria varied between sheep groups. The bacterial community was dominated by phylum Bacteroidetes and Firmicutes; whereas, Prevotella, Ruminococcus, and Butyrivibrio were the dominant genera. Results indicate that diet S3 supplemented by OC, DD, and DPF could replace the conventional feed mixture.
bibliographic citation: Rabee et al. (2021) Rumen bacterial community profile and fermentation in Barki sheep fed olive cake and date palm byproducts. PeerJ 9:e12447 https://doi.org/10.7717/peerj.12447
date submitted: 2021-09-02
date accepted: 2021-10-18
issued: 2021-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rabee
  given name: Alaa Emara
author list: Agent
  family name: Kewan
  given name: Khalid Z.
author list: Agent
  family name: Sabra
  given name: Ebrahim A.
author list: Agent
  family name: El Shaer
  given name: Hassan M.
author list: Agent
  family name: Lamara
  given name: Mebarek
doi: 10.7717/peerj.12447
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-17
copyright: © 2021 Rabee et al.
attribution name: Rabee et al.

Estimating the differences in critical thermal maximum and metabolic rate of Helicoverpa punctigera (Wallengren) (Lepidoptera: Noctuidae) across life stages
type: item
type: AcademicArticle
description: Temperature is a crucial driver of insect activity and physiological processes throughout their life-history, and heat stress may impact life stages (larvae, pupae and adult) in different ways. Using thermolimit respirometry, we assessed the critical thermal maxima (CTmax-temperature at which an organism loses neuromuscular control), CO2 emission rate (V́CO2) and Q10 (a measure of V́CO2 temperature sensitivity) of three different life stages of Helicoverpa punctigera (Wallengren) by increasing their temperature exposure from 25 °C to 55 °C at a rate of 0.25 °C min−1. We found that the CTmax of larvae (49.1 °C ± 0.3 °C) was higher than pupae (47.4 °C ± 0.2 °C) and adults (46.9 °C ± 0.2 °C). The mean mass-specific CO2 emission rate (ml V́CO2 h−1) of larvae (0.26 ± 0.03 ml V́CO2 h−1) was also higher than adults (0.24 ± 0.04 ml V́CO2 h−1) and pupae (0.06 ± 0.02 ml V́CO2 h−1). The Q10: 25–35 °C for adults (2.01 ± 0.22) was significantly higher compared to larvae (1.40 ± 0.06) and Q10: 35–45 °C for adults (3.42 ± 0.24) was significantly higher compared to larvae (1.95 ± 0.08) and pupae (1.42 ± 0.98) respectively. We have established the upper thermal tolerance of H. punctigera, which will lead to a better understanding of the thermal physiology of this species both in its native range, and as a pest species in agricultural systems.
format: application/pdf
format: text/html
creator: Samuel A. Bawa
creator: Peter C. Gregg
creator: Alice P. Del Soccoro
creator: Cara Miller
creator: Nigel R. Andrew
subject: Agricultural Science
subject: Entomology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.12479
publisher: PeerJ Inc.
rights: © 2021 Bawa et al.
abstract: Temperature is a crucial driver of insect activity and physiological processes throughout their life-history, and heat stress may impact life stages (larvae, pupae and adult) in different ways. Using thermolimit respirometry, we assessed the critical thermal maxima (CTmax-temperature at which an organism loses neuromuscular control), CO2 emission rate (V́CO2) and Q10 (a measure of V́CO2 temperature sensitivity) of three different life stages of Helicoverpa punctigera (Wallengren) by increasing their temperature exposure from 25 °C to 55 °C at a rate of 0.25 °C min−1. We found that the CTmax of larvae (49.1 °C ± 0.3 °C) was higher than pupae (47.4 °C ± 0.2 °C) and adults (46.9 °C ± 0.2 °C). The mean mass-specific CO2 emission rate (ml V́CO2 h−1) of larvae (0.26 ± 0.03 ml V́CO2 h−1) was also higher than adults (0.24 ± 0.04 ml V́CO2 h−1) and pupae (0.06 ± 0.02 ml V́CO2 h−1). The Q10: 25–35 °C for adults (2.01 ± 0.22) was significantly higher compared to larvae (1.40 ± 0.06) and Q10: 35–45 °C for adults (3.42 ± 0.24) was significantly higher compared to larvae (1.95 ± 0.08) and pupae (1.42 ± 0.98) respectively. We have established the upper thermal tolerance of H. punctigera, which will lead to a better understanding of the thermal physiology of this species both in its native range, and as a pest species in agricultural systems.
bibliographic citation: Bawa et al. (2021) Estimating the differences in critical thermal maximum and metabolic rate of Helicoverpa punctigera (Wallengren) (Lepidoptera: Noctuidae) across life stages. PeerJ 9:e12479 https://doi.org/10.7717/peerj.12479
date submitted: 2021-03-17
date accepted: 2021-10-21
issued: 2021-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bawa
  given name: Samuel A.
author list: Agent
  family name: Gregg
  given name: Peter C.
author list: Agent
  family name: Del Soccoro
  given name: Alice P.
author list: Agent
  family name: Miller
  given name: Cara
author list: Agent
  family name: Andrew
  given name: Nigel R.
doi: 10.7717/peerj.12479
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-17
copyright: © 2021 Bawa et al.
attribution name: Bawa et al.

No evidence of effects or interaction between the widely used herbicide, glyphosate, and a common parasite in bumble bees
type: item
type: AcademicArticle
description: Background Glyphosate is the world’s most used pesticide and it is used without the mitigation measures that could reduce the exposure of pollinators to it. However, studies are starting to suggest negative impacts of this pesticide on bees, an essential group of pollinators. Accordingly, whether glyphosate, alone or alongside other stressors, is detrimental to bee health is a vital question. Bees are suffering declines across the globe, and pesticides, including glyphosate, have been suggested as being factors in these declines. Methods Here we test, across a range of experimental paradigms, whether glyphosate impacts a wild bumble bee species, Bombus terrestris. In addition, we build upon existing work with honey bees testing glyphosate-parasite interactions by conducting fully crossed experiments with glyphosate and a common bumble bee trypanosome gut parasite, Crithidia bombi. We utilised regulatory acute toxicity testing protocols, modified to allow for exposure to multiple stressors. These protocols are expanded upon to test for effects on long term survival (20 days). Microcolony testing, using unmated workers, was employed to measure the impacts of either stressor on a proxy of reproductive success. This microcolony testing was conducted with both acute and chronic exposure to cover a range of exposure scenarios. Results We found no effects of acute or chronic exposure to glyphosate, over a range of timespans post-exposure, on mortality or a range of sublethal metrics. We also found no interaction between glyphosate and Crithidia bombi in any metric, although there was conflicting evidence of increased parasite intensity after an acute exposure to glyphosate. In contrast to published literature, we found no direct impacts of this parasite on bee health. Our testing focussed on mortality and worker reproduction, so impacts of either or both of these stressors on other sublethal metrics could still exist. Conclusions Our results expand the current knowledge on…
format: application/pdf
format: text/html
creator: Edward A. Straw
creator: Mark J.F. Brown
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Parasitology
subject: Toxicology
description: doi:10.7717/peerj.12486
publisher: PeerJ Inc.
rights: © 2021 Straw and Brown
abstract: Background Glyphosate is the world’s most used pesticide and it is used without the mitigation measures that could reduce the exposure of pollinators to it. However, studies are starting to suggest negative impacts of this pesticide on bees, an essential group of pollinators. Accordingly, whether glyphosate, alone or alongside other stressors, is detrimental to bee health is a vital question. Bees are suffering declines across the globe, and pesticides, including glyphosate, have been suggested as being factors in these declines. Methods Here we test, across a range of experimental paradigms, whether glyphosate impacts a wild bumble bee species, Bombus terrestris. In addition, we build upon existing work with honey bees testing glyphosate-parasite interactions by conducting fully crossed experiments with glyphosate and a common bumble bee trypanosome gut parasite, Crithidia bombi. We utilised regulatory acute toxicity testing protocols, modified to allow for exposure to multiple stressors. These protocols are expanded upon to test for effects on long term survival (20 days). Microcolony testing, using unmated workers, was employed to measure the impacts of either stressor on a proxy of reproductive success. This microcolony testing was conducted with both acute and chronic exposure to cover a range of exposure scenarios. Results We found no effects of acute or chronic exposure to glyphosate, over a range of timespans post-exposure, on mortality or a range of sublethal metrics. We also found no interaction between glyphosate and Crithidia bombi in any metric, although there was conflicting evidence of increased parasite intensity after an acute exposure to glyphosate. In contrast to published literature, we found no direct impacts of this parasite on bee health. Our testing focussed on mortality and worker reproduction, so impacts of either or both of these stressors on other sublethal metrics could still exist. Conclusions Our results expand the current knowledge on…
bibliographic citation: Straw et al. (2021) No evidence of effects or interaction between the widely used herbicide, glyphosate, and a common parasite in bumble bees. PeerJ 9:e12486 https://doi.org/10.7717/peerj.12486
date submitted: 2021-08-26
date accepted: 2021-10-22
issued: 2021-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Straw
  given name: Edward A.
author list: Agent
  family name: Brown
  given name: Mark J.F.
doi: 10.7717/peerj.12486
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-17
copyright: ©2021 Straw and Brown
attribution name: Straw and Brown

Circ_0030235 knockdown protects H9c2 cells against OGD/R-induced injury via regulation of miR-526b
type: item
type: AcademicArticle
description: Backgrounds Acute myocardial infarction (MI) is the common clinical manifestation of coronary heart disease. Circular RNAs (circRNAs) act key roles in cardiomyocytes growth and angiogenesis. However, their functions in MI are not entirely clear. This research intended to investigate the role and underlying mechanisms of circ_0030235 in H9c2 cells. Methods H9c2 cells were conducted to oxygen glucose deprivation/reperfusion (OGD/R) inducement to establish the MI model. Circ_0030235 and miR-526b expression was tested and altered by qRT-PCR and transfection. Cell viability, apoptosis and reactive oxygen species (ROS) injury were tested by CCK-8 assay, TUNEL assay kit, and ROS Detection Assay Kit, respectively. Assessment of cell injury-related factors was performed by employing ELISA, Mitochondrial Viability Staining and the JC-1-Mitochondrial Membrane Potential Assay Kit. The relationship between circ_0030235 and miR-526b was analyzed by dual luciferase reporter assay. The expression of key proteins was analyzed by western blot. Results Circ_0030235 was highly expressed in OGD/R-induced H9c2 cells. OGD/R inducement cell viability, while accelerated apoptosis. Besides, the level ROS, cell injury-related factors, mitochondrial membrane potential were notably elevated by OGD/R inducement, while mitochondrial viability was remarkably declined. Whereas, these impacts were all noticeably remitted by circ_0030235 knockdown. miR-526b was a target of circ_0030235. Circ_0030235 knockdown-induced impacts were all notably abrogated by miR-526b inhibition, including the activating impacts on PI3K/AKT and MEK/ERK pathways. Conclusions This research implied that circ_0030235 knockdown might remit OGD/R-induced impacts via activation of PI3K/AKT and MEK/ERK pathways and regulation of miR-526b.
format: application/pdf
format: text/html
creator: Yuquan Zhang
creator: Shuzhu Liu
creator: Limin Ding
creator: Dawei Wang
creator: Qiangqiang Li
creator: Dongdong Li
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.11482
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Backgrounds Acute myocardial infarction (MI) is the common clinical manifestation of coronary heart disease. Circular RNAs (circRNAs) act key roles in cardiomyocytes growth and angiogenesis. However, their functions in MI are not entirely clear. This research intended to investigate the role and underlying mechanisms of circ_0030235 in H9c2 cells. Methods H9c2 cells were conducted to oxygen glucose deprivation/reperfusion (OGD/R) inducement to establish the MI model. Circ_0030235 and miR-526b expression was tested and altered by qRT-PCR and transfection. Cell viability, apoptosis and reactive oxygen species (ROS) injury were tested by CCK-8 assay, TUNEL assay kit, and ROS Detection Assay Kit, respectively. Assessment of cell injury-related factors was performed by employing ELISA, Mitochondrial Viability Staining and the JC-1-Mitochondrial Membrane Potential Assay Kit. The relationship between circ_0030235 and miR-526b was analyzed by dual luciferase reporter assay. The expression of key proteins was analyzed by western blot. Results Circ_0030235 was highly expressed in OGD/R-induced H9c2 cells. OGD/R inducement cell viability, while accelerated apoptosis. Besides, the level ROS, cell injury-related factors, mitochondrial membrane potential were notably elevated by OGD/R inducement, while mitochondrial viability was remarkably declined. Whereas, these impacts were all noticeably remitted by circ_0030235 knockdown. miR-526b was a target of circ_0030235. Circ_0030235 knockdown-induced impacts were all notably abrogated by miR-526b inhibition, including the activating impacts on PI3K/AKT and MEK/ERK pathways. Conclusions This research implied that circ_0030235 knockdown might remit OGD/R-induced impacts via activation of PI3K/AKT and MEK/ERK pathways and regulation of miR-526b.
bibliographic citation: Zhang et al. (2021) Circ_0030235 knockdown protects H9c2 cells against OGD/R-induced injury via regulation of miR-526b. PeerJ 9:e11482 https://doi.org/10.7717/peerj.11482
date submitted: 2020-12-22
date accepted: 2021-04-27
issued: 2021-11-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yuquan
author list: Agent
  family name: Liu
  given name: Shuzhu
author list: Agent
  family name: Ding
  given name: Limin
author list: Agent
  family name: Wang
  given name: Dawei
author list: Agent
  family name: Li
  given name: Qiangqiang
author list: Agent
  family name: Li
  given name: Dongdong
doi: 10.7717/peerj.11482
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-16
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Circular RNA RBM33 contributes to extracellular matrix degradation via miR-4268/EPHB2 axis in abdominal aortic aneurysm
type: item
type: AcademicArticle
description: Background Abdominal aortic aneurysm (AAA) is a complex vascular disease involving expansion of the abdominal aorta. Extracellular matrix (ECM) degradation is crucial to AAA pathogenesis, however, the specific molecular mechanism remains unclear. This study aimed to investigate differentially expressed circular RNAs (DEcircRNAs) involved in ECM degradation of AAA. Methods Transcriptome sequencing was used to analyze the DEcircRNAs between the AAA tissues and normal tissues. The expression of circRNAs in tissues and cells was validated using quantitative reverse transcription PCR (RT-qPCR). Overexpression of circRNAs in vascular smooth muscle cells (VSMCs) treated with angiotensin II (Ang II) was employed to explore its effect on ECM degradation of AAA. Bioinformatic technology, luciferase reporter gene assay, RT-qPCR, and rescue experiment were employed to evaluate the regulatory mechanism of circRNA. Results We identified 65 DEcircRNAs in AAA tissues compared with normal abdominal aortic tissues, including 30 up-regulated and 35 down-regulated circRNAs, which were mainly involved in inflammation and ECM-related functions and pathways. Moreover, circRBM33 was significantly increased in AAA tissues and Ang II-induced VSMCs compared with control samples. Overexpression of circRBM33 increased the expression of ECM-related molecule matrix metalloproteinase-2 and reduced the tissue inhibitor of matrix metalloproteinases-1 expression. Mechanistically, miR-4268 targeted binding to circRBM33 and inhibited the luciferase activity of circRBM33. Overexpression of circRBM33 induced the expression of EPH receptor B2 (EPHB2), and this effect was countered by miR-4268 mimics. Conclusions Overall, our data suggest that circRBM33 might be involved in AAA progression by regulating ECM degradation via the miR-4268/EPHB2 axis.
format: application/pdf
format: text/html
creator: Shizhi Wang
creator: Qingwen Yuan
creator: Wenpeng Zhao
creator: Weimin Zhou
subject: Cardiology
subject: Oncology
subject: Pathology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.12232
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background Abdominal aortic aneurysm (AAA) is a complex vascular disease involving expansion of the abdominal aorta. Extracellular matrix (ECM) degradation is crucial to AAA pathogenesis, however, the specific molecular mechanism remains unclear. This study aimed to investigate differentially expressed circular RNAs (DEcircRNAs) involved in ECM degradation of AAA. Methods Transcriptome sequencing was used to analyze the DEcircRNAs between the AAA tissues and normal tissues. The expression of circRNAs in tissues and cells was validated using quantitative reverse transcription PCR (RT-qPCR). Overexpression of circRNAs in vascular smooth muscle cells (VSMCs) treated with angiotensin II (Ang II) was employed to explore its effect on ECM degradation of AAA. Bioinformatic technology, luciferase reporter gene assay, RT-qPCR, and rescue experiment were employed to evaluate the regulatory mechanism of circRNA. Results We identified 65 DEcircRNAs in AAA tissues compared with normal abdominal aortic tissues, including 30 up-regulated and 35 down-regulated circRNAs, which were mainly involved in inflammation and ECM-related functions and pathways. Moreover, circRBM33 was significantly increased in AAA tissues and Ang II-induced VSMCs compared with control samples. Overexpression of circRBM33 increased the expression of ECM-related molecule matrix metalloproteinase-2 and reduced the tissue inhibitor of matrix metalloproteinases-1 expression. Mechanistically, miR-4268 targeted binding to circRBM33 and inhibited the luciferase activity of circRBM33. Overexpression of circRBM33 induced the expression of EPH receptor B2 (EPHB2), and this effect was countered by miR-4268 mimics. Conclusions Overall, our data suggest that circRBM33 might be involved in AAA progression by regulating ECM degradation via the miR-4268/EPHB2 axis.
bibliographic citation: Wang et al. (2021) Circular RNA RBM33 contributes to extracellular matrix degradation via miR-4268/EPHB2 axis in abdominal aortic aneurysm. PeerJ 9:e12232 https://doi.org/10.7717/peerj.12232
date submitted: 2021-05-07
date accepted: 2021-09-09
issued: 2021-11-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Shizhi
author list: Agent
  family name: Yuan
  given name: Qingwen
author list: Agent
  family name: Zhao
  given name: Wenpeng
author list: Agent
  family name: Zhou
  given name: Weimin
doi: 10.7717/peerj.12232
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-16
copyright: © 2021 Wang et al.
attribution name: Wang et al.

Evolution of diverse host infection mechanisms delineates an adaptive radiation of lampsiline freshwater mussels centered on their larval ecology
type: item
type: AcademicArticle
description: North American watersheds contain a high diversity of freshwater mussels (Unionoida). During the long-lived, benthic phase of their life cycle, up to 40 species can co-occur in a single riffle and there is typically little evidence for major differences in their feeding ecology or microhabitat partitioning. In contrast, their brief parasitic larval phase involves the infection of a wide diversity of fish hosts and female mussels have evolved a spectrum of adaptations for infecting host fish with their offspring. Many species use a passive broadcast strategy: placing high numbers of larvae in the water column and relying on chance encounters with potential hosts. Many other species, including most members of the Lampsilini, have a proactive strategy that entails the use of prey-mimetic lures to change the behavior of the hosts, i.e., eliciting a feeding response through which they become infected. Two main lure types are collectively produced: mantle tissue lures (on the female’s body) and brood lures, containing infective larvae, that are released into the external environment. In this study, we used a phylogenomic approach (ddRAD-seq) to place the diversity of infection strategies used by 54 North American lampsiline mussels into an evolutionary context. Ancestral state reconstruction recovered evidence for the early evolution of mantle lures in this clade, with brood lures and broadcast infection strategies both being independently derived twice. The most common infection strategy, occurring in our largest ingroup clade, is a mixed one in which mimetic mantle lures are apparently the predominant infection mechanism, but gravid females also release simple, non-mimetic brood lures at the end of the season. This mixed infection strategy clade shows some evidence of an increase in diversification rate and most members use centrarchids (Micropterus & Lepomis spp.) as their predominant fish hosts. Broad linkage between infection strategies and predominant fish host gene…
format: application/pdf
format: text/html
creator: Trevor L. Hewitt
creator: Amanda E. Haponski
creator: Diarmaid Ó. Foighil
subject: Biodiversity
subject: Evolutionary Studies
subject: Genomics
subject: Freshwater Biology
description: doi:10.7717/peerj.12287
publisher: PeerJ Inc.
rights: © 2021 Hewitt et al.
abstract: North American watersheds contain a high diversity of freshwater mussels (Unionoida). During the long-lived, benthic phase of their life cycle, up to 40 species can co-occur in a single riffle and there is typically little evidence for major differences in their feeding ecology or microhabitat partitioning. In contrast, their brief parasitic larval phase involves the infection of a wide diversity of fish hosts and female mussels have evolved a spectrum of adaptations for infecting host fish with their offspring. Many species use a passive broadcast strategy: placing high numbers of larvae in the water column and relying on chance encounters with potential hosts. Many other species, including most members of the Lampsilini, have a proactive strategy that entails the use of prey-mimetic lures to change the behavior of the hosts, i.e., eliciting a feeding response through which they become infected. Two main lure types are collectively produced: mantle tissue lures (on the female’s body) and brood lures, containing infective larvae, that are released into the external environment. In this study, we used a phylogenomic approach (ddRAD-seq) to place the diversity of infection strategies used by 54 North American lampsiline mussels into an evolutionary context. Ancestral state reconstruction recovered evidence for the early evolution of mantle lures in this clade, with brood lures and broadcast infection strategies both being independently derived twice. The most common infection strategy, occurring in our largest ingroup clade, is a mixed one in which mimetic mantle lures are apparently the predominant infection mechanism, but gravid females also release simple, non-mimetic brood lures at the end of the season. This mixed infection strategy clade shows some evidence of an increase in diversification rate and most members use centrarchids (Micropterus & Lepomis spp.) as their predominant fish hosts. Broad linkage between infection strategies and predominant fish host gene…
bibliographic citation: Hewitt et al. (2021) Evolution of diverse host infection mechanisms delineates an adaptive radiation of lampsiline freshwater mussels centered on their larval ecology. PeerJ 9:e12287 https://doi.org/10.7717/peerj.12287
date submitted: 2021-03-03
date accepted: 2021-09-21
issued: 2021-11-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hewitt
  given name: Trevor L.
author list: Agent
  family name: Haponski
  given name: Amanda E.
author list: Agent
  family name: Foighil
  given name: Diarmaid Ó.
doi: 10.7717/peerj.12287
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-16
copyright: ©2021 Hewitt et al.
attribution name: Hewitt et al.

Landscape and microhabitat features determine small mammal abundance in forest patches in agricultural landscapes
type: item
type: AcademicArticle
description: Intensification of agricultural landscapes represent a major threat for biodiversity conservation also affecting several ecosystem services. The natural and semi-natural remnants, available in the agricultural matrix, represent important sites for small mammals and rodents, which are fundamental for sustaining various ecosystem functions and trophic chains. We studied the populations of two small mammals (Apodemus agrarius, A. sylvaticus) to evaluate the effects of landscape and habitat features on species abundance along a gradient of agricultural landscape intensification. The study was performed in Friuli Venezia Giulia (north-eastern Italy) during 19 months, in 19 wood remnants. Species abundance was determined using Capture-Mark-Recapture (CMR) techniques. In the same plots, main ecological parameters of the habitat (at microhabitat and patch scale) and landscape were considered. Abundance of A. agrarius increased in landscapes with high extent of permanent crops (i.e., orchards and poplar plantations) and low content of undecomposed litter in the wood understory. Instead, A. sylvaticus, a more generalist species, showed an opposite, albeit less strong, relationship with the same variables. Both species were not affected by any landscape structural feature (e.g., patch shape, isolation). Our findings showed that microhabitat features and landscape composition rather than wood and landscape structure affect populations’ abundance and species interaction. The opposite response of the two study species was probably because of their specific ecological requirements. In this light, conservation management of agricultural landscapes should consider the ecological needs of species at both landscape and habitat levels, by rebalancing composition patterns in the context of ecological intensification, and promoting a sustainable forest patch management.
format: application/pdf
format: text/html
creator: Luca Dorigo
creator: Francesco Boscutti
creator: Maurizia Sigura
subject: Agricultural Science
subject: Animal Behavior
subject: Ecology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12306
publisher: PeerJ Inc.
rights: © 2021 Dorigo et al.
abstract: Intensification of agricultural landscapes represent a major threat for biodiversity conservation also affecting several ecosystem services. The natural and semi-natural remnants, available in the agricultural matrix, represent important sites for small mammals and rodents, which are fundamental for sustaining various ecosystem functions and trophic chains. We studied the populations of two small mammals (Apodemus agrarius, A. sylvaticus) to evaluate the effects of landscape and habitat features on species abundance along a gradient of agricultural landscape intensification. The study was performed in Friuli Venezia Giulia (north-eastern Italy) during 19 months, in 19 wood remnants. Species abundance was determined using Capture-Mark-Recapture (CMR) techniques. In the same plots, main ecological parameters of the habitat (at microhabitat and patch scale) and landscape were considered. Abundance of A. agrarius increased in landscapes with high extent of permanent crops (i.e., orchards and poplar plantations) and low content of undecomposed litter in the wood understory. Instead, A. sylvaticus, a more generalist species, showed an opposite, albeit less strong, relationship with the same variables. Both species were not affected by any landscape structural feature (e.g., patch shape, isolation). Our findings showed that microhabitat features and landscape composition rather than wood and landscape structure affect populations’ abundance and species interaction. The opposite response of the two study species was probably because of their specific ecological requirements. In this light, conservation management of agricultural landscapes should consider the ecological needs of species at both landscape and habitat levels, by rebalancing composition patterns in the context of ecological intensification, and promoting a sustainable forest patch management.
bibliographic citation: Dorigo et al. (2021) Landscape and microhabitat features determine small mammal abundance in forest patches in agricultural landscapes. PeerJ 9:e12306 https://doi.org/10.7717/peerj.12306
date submitted: 2021-04-27
date accepted: 2021-09-22
issued: 2021-11-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dorigo
  given name: Luca
author list: Agent
  family name: Boscutti
  given name: Francesco
author list: Agent
  family name: Sigura
  given name: Maurizia
doi: 10.7717/peerj.12306
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-16
copyright: ©2021 Dorigo et al.
attribution name: Dorigo et al.

Performance in mortality prediction of SAPS 3 And MPM-III scores among adult patients admitted to the ICU of a private tertiary referral hospital in Tanzania: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Illness predictive scoring systems are significant and meaningful adjuncts of patient management in the Intensive Care Unit (ICU). They assist in predicting patient outcomes, improve clinical decision making and provide insight into the effectiveness of care and management of patients while optimizing the use of hospital resources. We evaluated mortality predictive performance of Simplified Acute Physiology Score (SAPS 3) and Mortality Probability Models (MPM0-III) and compared their performance in predicting outcome as well as identifying disease pattern and factors associated with increased mortality. Methods This was a retrospective cohort study of adult patients admitted to the ICU of the Aga Khan Hospital, Dar- es- Salaam, Tanzania between August 2018 and April 2020. Demographics, clinical characteristics, outcomes, source of admission, primary admission category, length of stay and the support provided with the worst physiological data within the first hour of ICU admission were extracted. SAPS 3 and MPM0-III scores were calculated using an online web-based calculator. The performance of each model was assessed by discrimination and calibration. Discrimination between survivors and non–survivors was assessed by the area under the receiver operator characteristic curve (ROC) and calibration was estimated using the Hosmer-Lemeshow goodness-of-fit test. Results A total of 331 patients were enrolled in the study with a median age of 58 years (IQR 43-71), most of whom were male (n = 208, 62.8%), of African origin (n = 178, 53.8%) and admitted from the emergency department (n = 306, 92.4%). In- hospital mortality of critically ill patients was 16.1%. Discrimination was very good for all models, the area under the receiver-operating characteristic (ROC) curve for SAPS 3 and MPM0-III was 0.89 (95% CI [0.844–0.935]) and 0.90 (95% CI [0.864–0.944]) respectively. Calibration as calculated by Hosmer-Lemeshow goodness-of-fit test showed good calibration for SAPS…
format: application/pdf
format: text/html
creator: Nadeem Kassam
creator: Eric Aghan
creator: Samina Somji
creator: Omar Aziz
creator: James Orwa
creator: Salim R. Surani
subject: Emergency and Critical Care
subject: Internal Medicine
description: doi:10.7717/peerj.12332
publisher: PeerJ Inc.
rights: © 2021 Kassam et al.
abstract: Background Illness predictive scoring systems are significant and meaningful adjuncts of patient management in the Intensive Care Unit (ICU). They assist in predicting patient outcomes, improve clinical decision making and provide insight into the effectiveness of care and management of patients while optimizing the use of hospital resources. We evaluated mortality predictive performance of Simplified Acute Physiology Score (SAPS 3) and Mortality Probability Models (MPM0-III) and compared their performance in predicting outcome as well as identifying disease pattern and factors associated with increased mortality. Methods This was a retrospective cohort study of adult patients admitted to the ICU of the Aga Khan Hospital, Dar- es- Salaam, Tanzania between August 2018 and April 2020. Demographics, clinical characteristics, outcomes, source of admission, primary admission category, length of stay and the support provided with the worst physiological data within the first hour of ICU admission were extracted. SAPS 3 and MPM0-III scores were calculated using an online web-based calculator. The performance of each model was assessed by discrimination and calibration. Discrimination between survivors and non–survivors was assessed by the area under the receiver operator characteristic curve (ROC) and calibration was estimated using the Hosmer-Lemeshow goodness-of-fit test. Results A total of 331 patients were enrolled in the study with a median age of 58 years (IQR 43-71), most of whom were male (n = 208, 62.8%), of African origin (n = 178, 53.8%) and admitted from the emergency department (n = 306, 92.4%). In- hospital mortality of critically ill patients was 16.1%. Discrimination was very good for all models, the area under the receiver-operating characteristic (ROC) curve for SAPS 3 and MPM0-III was 0.89 (95% CI [0.844–0.935]) and 0.90 (95% CI [0.864–0.944]) respectively. Calibration as calculated by Hosmer-Lemeshow goodness-of-fit test showed good calibration for SAPS…
bibliographic citation: Kassam et al. (2021) Performance in mortality prediction of SAPS 3 And MPM-III scores among adult patients admitted to the ICU of a private tertiary referral hospital in Tanzania: a retrospective cohort study. PeerJ 9:e12332 https://doi.org/10.7717/peerj.12332
date submitted: 2021-04-20
date accepted: 2021-09-27
issued: 2021-11-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kassam
  given name: Nadeem
author list: Agent
  family name: Aghan
  given name: Eric
author list: Agent
  family name: Somji
  given name: Samina
author list: Agent
  family name: Aziz
  given name: Omar
author list: Agent
  family name: Orwa
  given name: James
author list: Agent
  family name: Surani
  given name: Salim R.
doi: 10.7717/peerj.12332
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-16
copyright: ©2021 Kassam et al.
attribution name: Kassam et al.

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