PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Physical and functional properties of fish gelatin-based film incorporated with mangrove extracts
items: Depth effect on the prokaryotic community assemblage associated with sponges from different rocky reefs
items: Study on the mechanism of Danshen-Guizhi drug pair in the treatment of ovarian cancer based on network pharmacology and in vitro experiment
items: Transcriptome profiling reveals stress-responsive gene networks in cattle muscles
items: Life history and ossification patterns in Miguashaia bureaui reveal the early evolution of osteogenesis in coelacanths
items: False memories when viewing overlapping scenes
items: Early Pleistocene large mammals from Maka’amitalu, Hadar, lower Awash Valley, Ethiopia
items: A low-cost benthic incubation chamber for in-situ community metabolism measurements
items: RNA sequencing reveals novel LncRNA/mRNAs co-expression network associated with puerarin-mediated inhibition of cardiac hypertrophy in mice
items: Does size matter? An analysis of the niche width and vulnerability to climate change of fourteen species of the genus Crotalus from North America

Physical and functional properties of fish gelatin-based film incorporated with mangrove extracts
type: item
type: AcademicArticle
description: Background The fishery processing industry produces a remarkable number of by-products daily. Fish skin accounts for one of the significant wastes produced. Fish skin, however, can be subjected to extraction to yield gelatine and used as the primary raw material for edible film production. To increase the functionality of edible films, bioactive compounds can be incorporated into packaging. Mangroves produce potential bioactive compounds that are suitable as additional agents for active packaging. This study aimed to create a fish gelatine-based edible film enriched with mangrove extracts and to observe its mechanical and biological properties. Methods Two mangrove species (Bruguiera gymnorhiza and Sonneratia alba) with four extract concentrations (control, 0.05%, 0.15%, 0.25%, and 0.35%) were used to enrich edible films. The elongation, water vapour transmission, thickness, tensile strength, moisture content, antioxidant and antibacterial properties of the resulting packaging were analysed. Results The results showed that the mangrove species and extract concentration significantly affected (p < 0.05) the physical properties of the treated films such as elongation (16.89–19.38%), water vapour transmission (13.31–13.59 g/m2), and active packaging-antioxidant activities (12.36%–60.98%). The thickness, tensile strength, and water content were not significantly affected. Potent antioxidant activity and relatively weak antimicrobial activity of this active gelatine packaging were observed.
format: application/pdf
format: text/html
creator: Rahmi Nurdiani
creator: Rica D.A. Ma’rifah
creator: Ihda K. Busyro
creator: Abdul A. Jaziri
creator: Asep A. Prihanto
creator: Muhamad Firdaus
creator: Rosnita A. Talib
creator: Nurul Huda
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Food Science and Technology
description: doi:10.7717/peerj.13062
publisher: PeerJ Inc.
rights: © 2022 Nurdiani et al.
abstract: Background The fishery processing industry produces a remarkable number of by-products daily. Fish skin accounts for one of the significant wastes produced. Fish skin, however, can be subjected to extraction to yield gelatine and used as the primary raw material for edible film production. To increase the functionality of edible films, bioactive compounds can be incorporated into packaging. Mangroves produce potential bioactive compounds that are suitable as additional agents for active packaging. This study aimed to create a fish gelatine-based edible film enriched with mangrove extracts and to observe its mechanical and biological properties. Methods Two mangrove species (Bruguiera gymnorhiza and Sonneratia alba) with four extract concentrations (control, 0.05%, 0.15%, 0.25%, and 0.35%) were used to enrich edible films. The elongation, water vapour transmission, thickness, tensile strength, moisture content, antioxidant and antibacterial properties of the resulting packaging were analysed. Results The results showed that the mangrove species and extract concentration significantly affected (p < 0.05) the physical properties of the treated films such as elongation (16.89–19.38%), water vapour transmission (13.31–13.59 g/m2), and active packaging-antioxidant activities (12.36%–60.98%). The thickness, tensile strength, and water content were not significantly affected. Potent antioxidant activity and relatively weak antimicrobial activity of this active gelatine packaging were observed.
bibliographic citation: Nurdiani et al. (2022) Physical and functional properties of fish gelatin-based film incorporated with mangrove extracts. PeerJ 10:e13062 https://doi.org/10.7717/peerj.13062
date submitted: 2021-09-17
date accepted: 2022-02-14
issued: 2022-04-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nurdiani
  given name: Rahmi
author list: Agent
  family name: Ma’rifah
  given name: Rica D.A.
author list: Agent
  family name: Busyro
  given name: Ihda K.
author list: Agent
  family name: Jaziri
  given name: Abdul A.
author list: Agent
  family name: Prihanto
  given name: Asep A.
author list: Agent
  family name: Firdaus
  given name: Muhamad
author list: Agent
  family name: Talib
  given name: Rosnita A.
author list: Agent
  family name: Huda
  given name: Nurul
doi: 10.7717/peerj.13062
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-06
copyright: ©2022 Nurdiani et al.
attribution name: Nurdiani et al.

Depth effect on the prokaryotic community assemblage associated with sponges from different rocky reefs
type: item
type: AcademicArticle
description: Background Sponge microbiomes are essential for the function and survival of their host and produce biologically active metabolites, therefore, they are ideal candidates for ecological, pharmacologic and clinical research. Next-generation sequencing (NGS) has revealed that many factors, including the environment and host, determine the composition and structure of these symbiotic communities but the controls of this variation are not well described. This study assessed the microbial communities associated with two marine sponges of the genera Aplysina (Nardo, 1834) and Ircinia (Nardo, 1833) in rocky reefs from Punta Arena de la Ventana (Gulf of California) and Pichilingue (La Paz Bay) in the coast of Baja California Sur, México to determine the relative importance of environment and host in structuring the microbiome of sponges. Methods Specimens of Aplysina sp were collected by scuba diving at 10 m and 2 m; Ircinia sp samples were collected at 2 m. DNA of sponge-associated prokaryotes was extracted from 1 cm3 of tissue, purified and sent for 16S amplicon sequencing. Primer trimmed pair-ended microbial 16S rDNA gene sequences were merged using Ribosomal Database Project (RDP) Paired-end Reads Assembler. Chao1, Shannon and Simpson (alpha) biodiversity indices were estimated, as well permutational analysis of variance (PERMANOVA), and Bray-Curtis distances. Results The most abundant phyla differed between hosts. Those phyla were: Proteobacteria, Acidobacteria, Cyanobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes. In Ircinia sp the dominant phylum was Acidobacteria. Depth was the main factor influencing the microbial community, as analysis of similarities (ANOSIM) showed a significant difference between the microbial communities from different depths. Conclusion Microbial diversity analysis showed that depth was more important than host in structuring the Aplysina sp and Ircinia sp microbiome. This observation contrast with previous reports tha…
format: application/pdf
format: text/html
creator: Bárbara González-Acosta
creator: Aarón Barraza
creator: César Guadarrama-Analco
creator: Claudia J. Hernández-Guerrero
creator: Sergio Francisco Martínez-Díaz
creator: César Salvador Cardona-Félix
creator: Ruth Noemí Aguila-Ramírez
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.13133
publisher: PeerJ Inc.
rights: © 2022 González-Acosta et al.
abstract: Background Sponge microbiomes are essential for the function and survival of their host and produce biologically active metabolites, therefore, they are ideal candidates for ecological, pharmacologic and clinical research. Next-generation sequencing (NGS) has revealed that many factors, including the environment and host, determine the composition and structure of these symbiotic communities but the controls of this variation are not well described. This study assessed the microbial communities associated with two marine sponges of the genera Aplysina (Nardo, 1834) and Ircinia (Nardo, 1833) in rocky reefs from Punta Arena de la Ventana (Gulf of California) and Pichilingue (La Paz Bay) in the coast of Baja California Sur, México to determine the relative importance of environment and host in structuring the microbiome of sponges. Methods Specimens of Aplysina sp were collected by scuba diving at 10 m and 2 m; Ircinia sp samples were collected at 2 m. DNA of sponge-associated prokaryotes was extracted from 1 cm3 of tissue, purified and sent for 16S amplicon sequencing. Primer trimmed pair-ended microbial 16S rDNA gene sequences were merged using Ribosomal Database Project (RDP) Paired-end Reads Assembler. Chao1, Shannon and Simpson (alpha) biodiversity indices were estimated, as well permutational analysis of variance (PERMANOVA), and Bray-Curtis distances. Results The most abundant phyla differed between hosts. Those phyla were: Proteobacteria, Acidobacteria, Cyanobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes. In Ircinia sp the dominant phylum was Acidobacteria. Depth was the main factor influencing the microbial community, as analysis of similarities (ANOSIM) showed a significant difference between the microbial communities from different depths. Conclusion Microbial diversity analysis showed that depth was more important than host in structuring the Aplysina sp and Ircinia sp microbiome. This observation contrast with previous reports tha…
bibliographic citation: González-Acosta et al. (2022) Depth effect on the prokaryotic community assemblage associated with sponges from different rocky reefs. PeerJ 10:e13133 https://doi.org/10.7717/peerj.13133
date submitted: 2021-09-07
date accepted: 2022-02-26
issued: 2022-04-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: González-Acosta
  given name: Bárbara
author list: Agent
  family name: Barraza
  given name: Aarón
author list: Agent
  family name: Guadarrama-Analco
  given name: César
author list: Agent
  family name: Hernández-Guerrero
  given name: Claudia J.
author list: Agent
  family name: Martínez-Díaz
  given name: Sergio Francisco
author list: Agent
  family name: Cardona-Félix
  given name: César Salvador
author list: Agent
  family name: Aguila-Ramírez
  given name: Ruth Noemí
doi: 10.7717/peerj.13133
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-06
copyright: © 2022 González-Acosta et al.
attribution name: González-Acosta et al.

Study on the mechanism of Danshen-Guizhi drug pair in the treatment of ovarian cancer based on network pharmacology and in vitro experiment
type: item
type: AcademicArticle
description: Our study aims to explore the active components and mechanisms of the Danshen-Guizhi drug pair in treating ovarian cancer by network pharmacology and in vitro experiment. The “component-target-pathway” diagram of the Danshen-Guizhi drug pair was established by network pharmacology, and the effective active components, important targets as well as potential mechanisms of the Danshen-Guizhi drug pair were analyzed. The predicted results were verified by molecular docking and in vitro experiments. The main active components of the Danshen-Guizhi drug pair in the treatment of ovarian cancer are salviolone, luteolin, β-sitosterol and tanshinone IIA. The main core target is PTGS2. The pathways involved mainly include the cancer pathway, PI3K-Akt signaling pathway, and IL-17 signaling pathway. The molecular docking results showed that salviolone and tanshinone IIA had good binding ability to the target. The expression of PTGS2 mRNA and PGE2 in ovarian cells were significantly inhibited by salviolone. The mechanism of the Danshen-Guizhi drug pair in the treatment of ovarian cancer may be regulating cell proliferation, apoptosis and tumor immunity. This provides a theoretical basis for the clinical development and application of the Danshen-Guizhi drug pair.
format: application/pdf
format: text/html
creator: Chongzhen Qin
creator: Menglin Wu
creator: Xinru Wang
creator: Wenda Zhang
creator: Guangzhao Qi
creator: Na-Yi Wu
creator: Xiaoting Liu
creator: Yaoyao Lu
creator: Jingmin Zhang
creator: Yuna Chai
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13148
publisher: PeerJ Inc.
rights: © 2022 Qin et al.
abstract: Our study aims to explore the active components and mechanisms of the Danshen-Guizhi drug pair in treating ovarian cancer by network pharmacology and in vitro experiment. The “component-target-pathway” diagram of the Danshen-Guizhi drug pair was established by network pharmacology, and the effective active components, important targets as well as potential mechanisms of the Danshen-Guizhi drug pair were analyzed. The predicted results were verified by molecular docking and in vitro experiments. The main active components of the Danshen-Guizhi drug pair in the treatment of ovarian cancer are salviolone, luteolin, β-sitosterol and tanshinone IIA. The main core target is PTGS2. The pathways involved mainly include the cancer pathway, PI3K-Akt signaling pathway, and IL-17 signaling pathway. The molecular docking results showed that salviolone and tanshinone IIA had good binding ability to the target. The expression of PTGS2 mRNA and PGE2 in ovarian cells were significantly inhibited by salviolone. The mechanism of the Danshen-Guizhi drug pair in the treatment of ovarian cancer may be regulating cell proliferation, apoptosis and tumor immunity. This provides a theoretical basis for the clinical development and application of the Danshen-Guizhi drug pair.
bibliographic citation: Qin et al. (2022) Study on the mechanism of Danshen-Guizhi drug pair in the treatment of ovarian cancer based on network pharmacology and in vitro experiment. PeerJ 10:e13148 https://doi.org/10.7717/peerj.13148
date submitted: 2021-10-08
date accepted: 2022-03-01
issued: 2022-04-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Chongzhen
author list: Agent
  family name: Wu
  given name: Menglin
author list: Agent
  family name: Wang
  given name: Xinru
author list: Agent
  family name: Zhang
  given name: Wenda
author list: Agent
  family name: Qi
  given name: Guangzhao
author list: Agent
  family name: Wu
  given name: Na-Yi
author list: Agent
  family name: Liu
  given name: Xiaoting
author list: Agent
  family name: Lu
  given name: Yaoyao
author list: Agent
  family name: Zhang
  given name: Jingmin
author list: Agent
  family name: Chai
  given name: Yuna
doi: 10.7717/peerj.13148
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-06
copyright: © 2022 Qin et al.
attribution name: Qin et al.

Transcriptome profiling reveals stress-responsive gene networks in cattle muscles
type: item
type: AcademicArticle
description: In meat-producing animals, preslaughter operations (e.g., transportation, mixing unfamiliar animals, food and water deprivation) may be a source of stress with detrimental effects on meat quality. The objective of this work was to study the effect of emotional and physical stress by comparing the transcriptomes of two muscles (M. longissimus thoracis, LT and M. semitendinosus, ST) in Normand cows exposed to stress (n = 16) vs. cows handled with limited stress (n = 16). Using a microarray, we showed that exposure to stress resulted in differentially expressed genes (DEGs) in both muscles (62 DEGs in LT and 32 DEGs in ST, of which eight were common transcription factors (TFs)). Promoter analysis of the DEGs showed that 25 cis transcriptional modules were overrepresented, of which nine were detected in both muscles. Molecular interaction networks of the DEGs targeted by the most represented cis modules helped identify common regulators and common targets involved in the response to stress. They provided elements showing that the transcriptional response to stress is likely to (i) be controlled by regulators of energy metabolism, factors involved in the response to hypoxia, and inflammatory cytokines; and (ii) initiate metabolic processes, angiogenesis, corticosteroid response, immune system processes, and satellite cell activation/quiescence. The results of this study demonstrate that exposure to stress induced a core response to stress in both muscles, including changes in the expression of TFs. These factors could relay the physiological adaptive response of cattle muscles to cope with emotional and physical stress. The study provides information to further understand the consequences of these molecular processes on meat quality and find strategies to attenuate them.
format: application/pdf
format: text/html
creator: Isabelle Cassar-Malek
creator: Lise Pomiès
creator: Anne de la Foye
creator: Jérémy Tournayre
creator: Céline Boby
creator: Jean-François Hocquette
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13150
publisher: PeerJ Inc.
rights: © 2022 Cassar-Malek et al.
abstract: In meat-producing animals, preslaughter operations (e.g., transportation, mixing unfamiliar animals, food and water deprivation) may be a source of stress with detrimental effects on meat quality. The objective of this work was to study the effect of emotional and physical stress by comparing the transcriptomes of two muscles (M. longissimus thoracis, LT and M. semitendinosus, ST) in Normand cows exposed to stress (n = 16) vs. cows handled with limited stress (n = 16). Using a microarray, we showed that exposure to stress resulted in differentially expressed genes (DEGs) in both muscles (62 DEGs in LT and 32 DEGs in ST, of which eight were common transcription factors (TFs)). Promoter analysis of the DEGs showed that 25 cis transcriptional modules were overrepresented, of which nine were detected in both muscles. Molecular interaction networks of the DEGs targeted by the most represented cis modules helped identify common regulators and common targets involved in the response to stress. They provided elements showing that the transcriptional response to stress is likely to (i) be controlled by regulators of energy metabolism, factors involved in the response to hypoxia, and inflammatory cytokines; and (ii) initiate metabolic processes, angiogenesis, corticosteroid response, immune system processes, and satellite cell activation/quiescence. The results of this study demonstrate that exposure to stress induced a core response to stress in both muscles, including changes in the expression of TFs. These factors could relay the physiological adaptive response of cattle muscles to cope with emotional and physical stress. The study provides information to further understand the consequences of these molecular processes on meat quality and find strategies to attenuate them.
bibliographic citation: Cassar-Malek et al. (2022) Transcriptome profiling reveals stress-responsive gene networks in cattle muscles. PeerJ 10:e13150 https://doi.org/10.7717/peerj.13150
date submitted: 2021-12-16
date accepted: 2022-03-01
issued: 2022-04-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cassar-Malek
  given name: Isabelle
author list: Agent
  family name: Pomiès
  given name: Lise
author list: Agent
  family name: de la Foye
  given name: Anne
author list: Agent
  family name: Tournayre
  given name: Jérémy
author list: Agent
  family name: Boby
  given name: Céline
author list: Agent
  family name: Hocquette
  given name: Jean-François
doi: 10.7717/peerj.13150
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-06
copyright: © 2022 Cassar-Malek et al.
attribution name: Cassar-Malek et al.

Life history and ossification patterns in Miguashaia bureaui reveal the early evolution of osteogenesis in coelacanths
type: item
type: AcademicArticle
description: The study of development is critical for revealing the evolution of major vertebrate lineages. Coelacanths have one of the longest evolutionary histories among osteichthyans, but despite access to extant representatives, the onset of their weakly ossified endoskeleton is still poorly understood. Here we present the first palaeohistological and skeletochronological study of Miguashaia bureaui from the Upper Devonian of Canada, pivotal for exploring the palaeobiology and early evolution of osteogenesis in coelacanths. Cross sections of the caudal fin bones show that the cortex is made of layers of primary bone separated by lines of arrested growth, indicative of a cyclical growth. The medullary cavity displays remnants of calcified cartilage associated with bony trabeculae, characteristic of endochondral ossification. A skeletochronological analysis indicates that rapid growth during a short juvenile period was followed by slower growth in adulthood. Our new analysis highlights the life history and palaeoecology of Miguashaia bureaui and reveals that, despite differences in size and habitat, the poor endoskeletal ossification known in the extant Latimeria chalumnae can be traced back at least 375 million years ago.
format: application/pdf
format: text/html
creator: Jorge Mondéjar Fernández
creator: François J. Meunier
creator: Richard Cloutier
creator: Gaël Clément
creator: Michel Laurin
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.13175
publisher: PeerJ Inc.
rights: © 2022 Mondéjar Fernández et al.
abstract: The study of development is critical for revealing the evolution of major vertebrate lineages. Coelacanths have one of the longest evolutionary histories among osteichthyans, but despite access to extant representatives, the onset of their weakly ossified endoskeleton is still poorly understood. Here we present the first palaeohistological and skeletochronological study of Miguashaia bureaui from the Upper Devonian of Canada, pivotal for exploring the palaeobiology and early evolution of osteogenesis in coelacanths. Cross sections of the caudal fin bones show that the cortex is made of layers of primary bone separated by lines of arrested growth, indicative of a cyclical growth. The medullary cavity displays remnants of calcified cartilage associated with bony trabeculae, characteristic of endochondral ossification. A skeletochronological analysis indicates that rapid growth during a short juvenile period was followed by slower growth in adulthood. Our new analysis highlights the life history and palaeoecology of Miguashaia bureaui and reveals that, despite differences in size and habitat, the poor endoskeletal ossification known in the extant Latimeria chalumnae can be traced back at least 375 million years ago.
bibliographic citation: Mondéjar Fernández et al. (2022) Life history and ossification patterns in Miguashaia bureaui reveal the early evolution of osteogenesis in coelacanths. PeerJ 10:e13175 https://doi.org/10.7717/peerj.13175
date submitted: 2022-01-07
date accepted: 2022-03-06
issued: 2022-04-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mondéjar Fernández
  given name: Jorge
author list: Agent
  family name: Meunier
  given name: François J.
author list: Agent
  family name: Cloutier
  given name: Richard
author list: Agent
  family name: Clément
  given name: Gaël
author list: Agent
  family name: Laurin
  given name: Michel
doi: 10.7717/peerj.13175
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-06
copyright: © 2022 Mondéjar Fernández et al.
attribution name: Mondéjar Fernández et al.

False memories when viewing overlapping scenes
type: item
type: AcademicArticle
description: Humans can memorize and later recognize many objects and complex scenes. In this study, we prepared large photographs and presented participants with only partial views to test the fidelity of their memories. The unpresented parts of the photographs were used as a source of distractors with similar semantic and perceptual information. Additionally, we presented overlapping views to determine whether the second presentation provided a memory advantage for later recognition tests. Experiment 1 (N = 28) showed that while people were good at recognizing presented content and identifying new foils, they showed a remarkable level of uncertainty about foils selected from the unseen parts of presented photographs (false alarm, 59%). The recognition accuracy was higher for the parts that were shown twice, irrespective of whether the same identical photograph was viewed twice or whether two photographs with overlapping content were observed. In Experiment 2 (N = 28), the memorability of the large image was estimated by a pre-trained deep neural network. Neither the recognition accuracy for an image part nor the tendency for false alarms correlated with the memorability. Finally, in Experiment 3 (N = 21), we repeated the experiment while measuring eye movements. Fixations were biased toward the center of the original large photograph in the first presentation, and this bias was repeated during the second presentation in both identical and overlapping views. Altogether, our experiments show that people recognize parts of remembered photographs, but they find it difficult to reject foils from unseen parts, suggesting that their memory representation is not sufficiently detailed to rule them out as distractors.
format: application/pdf
format: text/html
creator: Filip Děchtěrenko
creator: Jiří Lukavský
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13187
publisher: PeerJ Inc.
rights: © 2022 Děchtěrenko and Lukavský
abstract: Humans can memorize and later recognize many objects and complex scenes. In this study, we prepared large photographs and presented participants with only partial views to test the fidelity of their memories. The unpresented parts of the photographs were used as a source of distractors with similar semantic and perceptual information. Additionally, we presented overlapping views to determine whether the second presentation provided a memory advantage for later recognition tests. Experiment 1 (N = 28) showed that while people were good at recognizing presented content and identifying new foils, they showed a remarkable level of uncertainty about foils selected from the unseen parts of presented photographs (false alarm, 59%). The recognition accuracy was higher for the parts that were shown twice, irrespective of whether the same identical photograph was viewed twice or whether two photographs with overlapping content were observed. In Experiment 2 (N = 28), the memorability of the large image was estimated by a pre-trained deep neural network. Neither the recognition accuracy for an image part nor the tendency for false alarms correlated with the memorability. Finally, in Experiment 3 (N = 21), we repeated the experiment while measuring eye movements. Fixations were biased toward the center of the original large photograph in the first presentation, and this bias was repeated during the second presentation in both identical and overlapping views. Altogether, our experiments show that people recognize parts of remembered photographs, but they find it difficult to reject foils from unseen parts, suggesting that their memory representation is not sufficiently detailed to rule them out as distractors.
bibliographic citation: Děchtěrenko et al. (2022) False memories when viewing overlapping scenes. PeerJ 10:e13187 https://doi.org/10.7717/peerj.13187
date submitted: 2021-04-08
date accepted: 2022-03-08
issued: 2022-04-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Děchtěrenko
  given name: Filip
author list: Agent
  family name: Lukavský
  given name: Jiří
doi: 10.7717/peerj.13187
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-06
copyright: © 2022 Děchtěrenko and Lukavský
attribution name: Děchtěrenko and Lukavský

Early Pleistocene large mammals from Maka’amitalu, Hadar, lower Awash Valley, Ethiopia
type: item
type: AcademicArticle
description: The Early Pleistocene was a critical time period in the evolution of eastern African mammal faunas, but fossil assemblages sampling this interval are poorly known from Ethiopia’s Afar Depression. Field work by the Hadar Research Project in the Busidima Formation exposures (~2.7–0.8 Ma) of Hadar in the lower Awash Valley, resulted in the recovery of an early Homo maxilla (A.L. 666-1) with associated stone tools and fauna from the Maka’amitalu basin in the 1990s. These assemblages are dated to ~2.35 Ma by the Bouroukie Tuff 3 (BKT-3). Continued work by the Hadar Research Project over the last two decades has greatly expanded the faunal collection. Here, we provide a comprehensive account of the Maka’amitalu large mammals (Artiodactyla, Carnivora, Perissodactyla, Primates, and Proboscidea) and discuss their paleoecological and biochronological significance. The size of the Maka’amitalu assemblage is small compared to those from the Hadar Formation (3.45–2.95 Ma) and Ledi-Geraru (2.8–2.6 Ma) but includes at least 20 taxa. Bovids, suids, and Theropithecus are common in terms of both species richness and abundance, whereas carnivorans, equids, and megaherbivores are rare. While the taxonomic composition of the Maka’amitalu fauna indicates significant species turnover from the Hadar Formation and Ledi-Geraru deposits, turnover seems to have occurred at a constant rate through time as taxonomic dissimilarity between adjacent fossil assemblages is strongly predicted by their age difference. A similar pattern characterizes functional ecological turnover, with only subtle changes in dietary proportions, body size proportions, and bovid abundances across the composite lower Awash sequence. Biochronological comparisons with other sites in eastern Africa suggest that the taxa recovered from the Maka’amitalu are broadly consistent with the reported age of the BKT-3 tuff. Considering the age of BKT-3 and biochronology, a range of 2.4–1.9 Ma is most likely for the faunal assemblage.
format: application/pdf
format: text/html
creator: John Rowan
creator: Ignacio A. Lazagabaster
creator: Christopher J. Campisano
creator: Faysal Bibi
creator: René Bobe
creator: Jean-Renaud Boisserie
creator: Stephen R. Frost
creator: Tomas Getachew
creator: Christopher C. Gilbert
creator: Margaret E. Lewis
creator: Sahleselasie Melaku
creator: Eric Scott
creator: Antoine Souron
creator: Lars Werdelin
creator: William H. Kimbel
creator: Kaye E. Reed
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13210
publisher: PeerJ Inc.
rights: © 2022 Rowan et al.
abstract: The Early Pleistocene was a critical time period in the evolution of eastern African mammal faunas, but fossil assemblages sampling this interval are poorly known from Ethiopia’s Afar Depression. Field work by the Hadar Research Project in the Busidima Formation exposures (~2.7–0.8 Ma) of Hadar in the lower Awash Valley, resulted in the recovery of an early Homo maxilla (A.L. 666-1) with associated stone tools and fauna from the Maka’amitalu basin in the 1990s. These assemblages are dated to ~2.35 Ma by the Bouroukie Tuff 3 (BKT-3). Continued work by the Hadar Research Project over the last two decades has greatly expanded the faunal collection. Here, we provide a comprehensive account of the Maka’amitalu large mammals (Artiodactyla, Carnivora, Perissodactyla, Primates, and Proboscidea) and discuss their paleoecological and biochronological significance. The size of the Maka’amitalu assemblage is small compared to those from the Hadar Formation (3.45–2.95 Ma) and Ledi-Geraru (2.8–2.6 Ma) but includes at least 20 taxa. Bovids, suids, and Theropithecus are common in terms of both species richness and abundance, whereas carnivorans, equids, and megaherbivores are rare. While the taxonomic composition of the Maka’amitalu fauna indicates significant species turnover from the Hadar Formation and Ledi-Geraru deposits, turnover seems to have occurred at a constant rate through time as taxonomic dissimilarity between adjacent fossil assemblages is strongly predicted by their age difference. A similar pattern characterizes functional ecological turnover, with only subtle changes in dietary proportions, body size proportions, and bovid abundances across the composite lower Awash sequence. Biochronological comparisons with other sites in eastern Africa suggest that the taxa recovered from the Maka’amitalu are broadly consistent with the reported age of the BKT-3 tuff. Considering the age of BKT-3 and biochronology, a range of 2.4–1.9 Ma is most likely for the faunal assemblage.
bibliographic citation: Rowan et al. (2022) Early Pleistocene large mammals from Maka’amitalu, Hadar, lower Awash Valley, Ethiopia. PeerJ 10:e13210 https://doi.org/10.7717/peerj.13210
date submitted: 2021-12-03
date accepted: 2022-03-10
issued: 2022-04-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rowan
  given name: John
author list: Agent
  family name: Lazagabaster
  given name: Ignacio A.
author list: Agent
  family name: Campisano
  given name: Christopher J.
author list: Agent
  family name: Bibi
  given name: Faysal
author list: Agent
  family name: Bobe
  given name: René
author list: Agent
  family name: Boisserie
  given name: Jean-Renaud
author list: Agent
  family name: Frost
  given name: Stephen R.
author list: Agent
  family name: Getachew
  given name: Tomas
author list: Agent
  family name: Gilbert
  given name: Christopher C.
author list: Agent
  family name: Lewis
  given name: Margaret E.
author list: Agent
  family name: Melaku
  given name: Sahleselasie
author list: Agent
  family name: Scott
  given name: Eric
author list: Agent
  family name: Souron
  given name: Antoine
author list: Agent
  family name: Werdelin
  given name: Lars
author list: Agent
  family name: Kimbel
  given name: William H.
author list: Agent
  family name: Reed
  given name: Kaye E.
doi: 10.7717/peerj.13210
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-06
copyright: © 2022 Rowan et al.
attribution name: Rowan et al.

A low-cost benthic incubation chamber for in-situ community metabolism measurements
type: item
type: AcademicArticle
description: Benthic incubation chambers facilitate in-situ metabolism studies in shallow water environments. They are used to isolate the water surrounding a study organism or community so that changes in water chemistry can be quantified to characterise physiological processes such as photosynthesis, respiration, and calcification. Such field measurements capture the biological processes taking place within the benthic community while incorporating the influence of environmental variables that are often difficult to recreate in ex-situ settings. Variations in benthic chamber designs have evolved for a range of applications. In this study, we built upon previous designs to create a novel chamber, which is (1) low-cost and assembled without specialised equipment, (2) easily reproducible, (3) minimally invasive, (4) adaptable to varied substrates, and (5) comparable with other available designs in performance. We tested the design in the laboratory and field and found that it achieved the outlined objectives. Using non-specialised materials, we were able to construct the chamber at a low cost (under $20 USD per unit), while maintaining similar performance and reproducibility with that of existing designs. Laboratory and field tests demonstrated minimal leakage (2.08 ± 0.78% water exchange over 4 h) and acceptable light transmission (86.9 ± 1.9%), results comparable to those reported for other chambers. In the field, chambers were deployed in a shallow coastal environment in Akumal, Mexico, to measure productivity of seagrass, and coral-, algae-, and sand-dominated reef patches. In both case studies, production rates aligned with those of comparable benthic chamber deployments in the literature and followed established trends with light, the primary driver of benthic metabolism, indicating robust performance under field conditions. We demonstrate that our low-cost benthic chamber design uses locally accessible and minimal resources, is adaptable for a variety of field settings, an…
format: application/pdf
format: text/html
creator: Jennifer Mallon
creator: Anastazia T. Banaszak
creator: Lauren Donachie
creator: Dan Exton
creator: Tyler Cyronak
creator: Thorsten Balke
creator: Adrian M. Bass
subject: Marine Biology
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
description: doi:10.7717/peerj.13116
publisher: PeerJ Inc.
rights: © 2022 Mallon et al.
abstract: Benthic incubation chambers facilitate in-situ metabolism studies in shallow water environments. They are used to isolate the water surrounding a study organism or community so that changes in water chemistry can be quantified to characterise physiological processes such as photosynthesis, respiration, and calcification. Such field measurements capture the biological processes taking place within the benthic community while incorporating the influence of environmental variables that are often difficult to recreate in ex-situ settings. Variations in benthic chamber designs have evolved for a range of applications. In this study, we built upon previous designs to create a novel chamber, which is (1) low-cost and assembled without specialised equipment, (2) easily reproducible, (3) minimally invasive, (4) adaptable to varied substrates, and (5) comparable with other available designs in performance. We tested the design in the laboratory and field and found that it achieved the outlined objectives. Using non-specialised materials, we were able to construct the chamber at a low cost (under $20 USD per unit), while maintaining similar performance and reproducibility with that of existing designs. Laboratory and field tests demonstrated minimal leakage (2.08 ± 0.78% water exchange over 4 h) and acceptable light transmission (86.9 ± 1.9%), results comparable to those reported for other chambers. In the field, chambers were deployed in a shallow coastal environment in Akumal, Mexico, to measure productivity of seagrass, and coral-, algae-, and sand-dominated reef patches. In both case studies, production rates aligned with those of comparable benthic chamber deployments in the literature and followed established trends with light, the primary driver of benthic metabolism, indicating robust performance under field conditions. We demonstrate that our low-cost benthic chamber design uses locally accessible and minimal resources, is adaptable for a variety of field settings, an…
bibliographic citation: Mallon et al. (2022) A low-cost benthic incubation chamber for in-situ community metabolism measurements. PeerJ 10:e13116 https://doi.org/10.7717/peerj.13116
date submitted: 2022-01-17
date accepted: 2022-02-23
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mallon
  given name: Jennifer
author list: Agent
  family name: Banaszak
  given name: Anastazia T.
author list: Agent
  family name: Donachie
  given name: Lauren
author list: Agent
  family name: Exton
  given name: Dan
author list: Agent
  family name: Cyronak
  given name: Tyler
author list: Agent
  family name: Balke
  given name: Thorsten
author list: Agent
  family name: Bass
  given name: Adrian M.
doi: 10.7717/peerj.13116
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: © 2022 Mallon et al.
attribution name: Mallon et al.

RNA sequencing reveals novel LncRNA/mRNAs co-expression network associated with puerarin-mediated inhibition of cardiac hypertrophy in mice
type: item
type: AcademicArticle
description: Background Evidence has demonstrated that puerarin is a potential medicine for the treatment of cardiac hypertrophy. However, the precise underlying molecular mechanisms of the protective effect of puerarin are still unclear. Here, we aimed to explore the regulatory mechanisms of lncRNAs/mRNAs co-expression network in a cardiac hypertrophy mouse model after puerarin treatment. Methods A mouse model of cardiac hypertrophy was established by transverse aortic constriction (TAC). The echocardiography, tissue staining and western blot were used to examine the protective effect of puerarin. Then RNA sequencing (RNA-seq) was carried out to analyze systematically mRNAs and lncRNAs expression. The target lncRNA were confirmed using qRT-PCR. Moreover, a coding/non-coding gene co-expression network were established to find the interaction of lncRNA and mRNAs. The biological process, cellular component, molecular function and pathways of different expression mRNAs targeted by lncRNA were explored using Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis. Results Puerarin exhibited an obvious inhibitory effect in cardiac hypertrophy in TAC model. RNA-seq analysis was performed to investigate the lncRNAs and mRNAs expression patterns of cardiomyocytes in sham and TAC groups treated with or without puerarin. RNA-seq identified that TAC downregulated four lncRNAs, which could be revised by puerarin treatment (|log2 Fold change| > 2 and FDR < 0.05). Among them, expression alterations of lncRNA Airn (antisense of Igf2r non-protein coding RNA) was confirmed by qRT-PCR. Pearson’s correlation coefficients of co-expression levels suggested that there was an interactive relationship between Airn and 2,387 mRNAs (r > 0.95 or r < −0.95). Those co-expressed mRNAs were enriched in some important biological processes such as translational initiation, cell proliferation, insulin-like growth factor binding and poly(A) RNA binding. KEGG analyses sugge…
format: application/pdf
format: text/html
creator: Shan Ye
creator: Weiyan Chen
creator: Caiwen Ou
creator: Min-Sheng Chen
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Cardiology
description: doi:10.7717/peerj.13144
publisher: PeerJ Inc.
rights: © 2022 Ye et al.
abstract: Background Evidence has demonstrated that puerarin is a potential medicine for the treatment of cardiac hypertrophy. However, the precise underlying molecular mechanisms of the protective effect of puerarin are still unclear. Here, we aimed to explore the regulatory mechanisms of lncRNAs/mRNAs co-expression network in a cardiac hypertrophy mouse model after puerarin treatment. Methods A mouse model of cardiac hypertrophy was established by transverse aortic constriction (TAC). The echocardiography, tissue staining and western blot were used to examine the protective effect of puerarin. Then RNA sequencing (RNA-seq) was carried out to analyze systematically mRNAs and lncRNAs expression. The target lncRNA were confirmed using qRT-PCR. Moreover, a coding/non-coding gene co-expression network were established to find the interaction of lncRNA and mRNAs. The biological process, cellular component, molecular function and pathways of different expression mRNAs targeted by lncRNA were explored using Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis. Results Puerarin exhibited an obvious inhibitory effect in cardiac hypertrophy in TAC model. RNA-seq analysis was performed to investigate the lncRNAs and mRNAs expression patterns of cardiomyocytes in sham and TAC groups treated with or without puerarin. RNA-seq identified that TAC downregulated four lncRNAs, which could be revised by puerarin treatment (|log2 Fold change| > 2 and FDR < 0.05). Among them, expression alterations of lncRNA Airn (antisense of Igf2r non-protein coding RNA) was confirmed by qRT-PCR. Pearson’s correlation coefficients of co-expression levels suggested that there was an interactive relationship between Airn and 2,387 mRNAs (r > 0.95 or r < −0.95). Those co-expressed mRNAs were enriched in some important biological processes such as translational initiation, cell proliferation, insulin-like growth factor binding and poly(A) RNA binding. KEGG analyses sugge…
bibliographic citation: Ye et al. (2022) RNA sequencing reveals novel LncRNA/mRNAs co-expression network associated with puerarin-mediated inhibition of cardiac hypertrophy in mice. PeerJ 10:e13144 https://doi.org/10.7717/peerj.13144
date submitted: 2021-10-01
date accepted: 2022-03-01
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Shan
author list: Agent
  family name: Chen
  given name: Weiyan
author list: Agent
  family name: Ou
  given name: Caiwen
author list: Agent
  family name: Chen
  given name: Min-Sheng
doi: 10.7717/peerj.13144
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: © 2022 Ye et al.
attribution name: Ye et al.

Does size matter? An analysis of the niche width and vulnerability to climate change of fourteen species of the genus Crotalus from North America
type: item
type: AcademicArticle
description: The niche comprises the set of abiotic and biotic environmental conditions in which a species can live. Consequently, those species that present broader niches are expected to be more tolerant to changes in climatic variations than those species that present reduced niches. In this study, we estimate the amplitude of the climatic niche of fourteen species of rattlesnakes of the genus Crotalus to evaluate whether those species that present broader niches are less susceptible to the loss of climatically suitable zones due to the projected climate change for the time period 2021–2040. Our results suggest that for the species under study, the breadth of the niche is not a factor that determines their vulnerability to climatic variations. However, 71.4% of the species will experience increasingly inadequate habitat conditions, mainly due to the increase in temperature and the contribution that this variable has in the creation of climatically suitable zones for most of these species.
format: application/pdf
format: text/html
creator: Jorge Luis Becerra-López
creator: Raciel Cruz-Elizalde
creator: Aurelio Ramírez-Bautista
creator: Itzel Magno-Benítez
creator: Claudia Ballesteros-Barrera
creator: Javier Alvarado-Díaz
creator: Robert W. Bryson Jr
creator: Uriel Hernández-Salinas
creator: César A. Díaz-Marín
creator: Christian Berriozabal-Islas
creator: Karen Fraire-Galindo
creator: Juan Tello-Ruiz
creator: Alexander Czaja
creator: María Guadalupe Torres-Delgado
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.13154
publisher: PeerJ Inc.
rights: © 2022 Becerra-López et al.
abstract: The niche comprises the set of abiotic and biotic environmental conditions in which a species can live. Consequently, those species that present broader niches are expected to be more tolerant to changes in climatic variations than those species that present reduced niches. In this study, we estimate the amplitude of the climatic niche of fourteen species of rattlesnakes of the genus Crotalus to evaluate whether those species that present broader niches are less susceptible to the loss of climatically suitable zones due to the projected climate change for the time period 2021–2040. Our results suggest that for the species under study, the breadth of the niche is not a factor that determines their vulnerability to climatic variations. However, 71.4% of the species will experience increasingly inadequate habitat conditions, mainly due to the increase in temperature and the contribution that this variable has in the creation of climatically suitable zones for most of these species.
bibliographic citation: Becerra-López et al. (2022) Does size matter? An analysis of the niche width and vulnerability to climate change of fourteen species of the genus Crotalus from North America. PeerJ 10:e13154 https://doi.org/10.7717/peerj.13154
date submitted: 2021-10-21
date accepted: 2022-03-01
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Becerra-López
  given name: Jorge Luis
author list: Agent
  family name: Cruz-Elizalde
  given name: Raciel
author list: Agent
  family name: Ramírez-Bautista
  given name: Aurelio
author list: Agent
  family name: Magno-Benítez
  given name: Itzel
author list: Agent
  family name: Ballesteros-Barrera
  given name: Claudia
author list: Agent
  family name: Alvarado-Díaz
  given name: Javier
author list: Agent
  family name: Bryson Jr
  given name: Robert W.
author list: Agent
  family name: Hernández-Salinas
  given name: Uriel
author list: Agent
  family name: Díaz-Marín
  given name: César A.
author list: Agent
  family name: Berriozabal-Islas
  given name: Christian
author list: Agent
  family name: Fraire-Galindo
  given name: Karen
author list: Agent
  family name: Tello-Ruiz
  given name: Juan
author list: Agent
  family name: Czaja
  given name: Alexander
author list: Agent
  family name: Torres-Delgado
  given name: María Guadalupe
doi: 10.7717/peerj.13154
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Becerra-López et al.
attribution name: Becerra-López et al.

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