PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: In vitro effect of resin infiltrant on resistance of sound enamel surfaces in permanent teeth to demineralization
items: Regeneration and growth in crowns and rhizome fragments of Japanese knotweed (Reynoutria japonica) and desiccation as a potential control strategy
items: Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk
items: Comparative survival analyses among captive chimpanzees (Pan troglodytes) in America and Japan
items: Quantifying bite force in coexisting tayassuids and feral suids: a comparison between morphometric functional proxies and in vivo measurements
items: Development and validation of a novel survival model for acute myeloid leukemia based on autophagy-related genes
items: Muvi schmallenbergi gen. nov., sp. nov. (Crustacea, Tanaidacea) from the southeast Australian coast, with comments on the distribution and habitat preferences of Chondropodinae
items: Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species
items: Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India
items: Transport of biodeposits and benthic footprint around an oyster farm, Damariscotta Estuary, Maine

In vitro effect of resin infiltrant on resistance of sound enamel surfaces in permanent teeth to demineralization
type: item
type: AcademicArticle
description: Objective To investigate the effect of resin infiltrant on resistance of sound permanent enamel surfaces to demineralization. Method Eighty healthy premolars were sectioned to obtain enamel blocks from the buccal surface. Specimens with baseline surface microhardness values of 320–370 were selected. The experimental group were treated with resin infiltrant, while the control group was not. Specimens from each group were artificially demineralized and the surface microhardness values were measured again. Confocal laser scanning microscopy was used to measure the depth of demineralization and detect the penetration ability of the resin infiltrant. The specimens were subjected to a simulated toothbrushing abrasion test. Scanning electron microscopy was used to observe changes in the surface morphology of specimens after each of these procedures. Results No significant differences between the experimental and control groups were observed in the baseline microhardness values or in the experimental group after resin infiltration compared with the baseline conditions. After artificial demineralization, the microhardness value in the control group was significantly lower than that in the experimental group (266.0 (±34.5) compared with 304.0 (±13.0), P = 0.017). Confocal laser scanning microscopy results showed that the demineralization depth in the control group was significantly deeper than that in the experimental group (97.9 (±22.8) µm vs. 50.4 (±14.3) µm, P < 0.001), and that resin infiltrant completely penetrated the acid-etched demineralized area of the tooth enamel with a mean penetration depth of 31.6 (±9.0) µm. Scanning electron microscopy showed that the surface morphology was more uniform and smoother after simulated toothbrushing. The enamel surface structure was more severely destroyed in the control group after artificial demineralization compared with that of the experimental group. Conclusion Resin infiltrant can completely penetrate an acid-etched demineral…
format: application/pdf
format: text/html
creator: Meng Li
creator: Zhengyan Yang
creator: Yajing Huang
creator: Yueheng Li
creator: Zhi Zhou
subject: Dentistry
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.12008
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Objective To investigate the effect of resin infiltrant on resistance of sound permanent enamel surfaces to demineralization. Method Eighty healthy premolars were sectioned to obtain enamel blocks from the buccal surface. Specimens with baseline surface microhardness values of 320–370 were selected. The experimental group were treated with resin infiltrant, while the control group was not. Specimens from each group were artificially demineralized and the surface microhardness values were measured again. Confocal laser scanning microscopy was used to measure the depth of demineralization and detect the penetration ability of the resin infiltrant. The specimens were subjected to a simulated toothbrushing abrasion test. Scanning electron microscopy was used to observe changes in the surface morphology of specimens after each of these procedures. Results No significant differences between the experimental and control groups were observed in the baseline microhardness values or in the experimental group after resin infiltration compared with the baseline conditions. After artificial demineralization, the microhardness value in the control group was significantly lower than that in the experimental group (266.0 (±34.5) compared with 304.0 (±13.0), P = 0.017). Confocal laser scanning microscopy results showed that the demineralization depth in the control group was significantly deeper than that in the experimental group (97.9 (±22.8) µm vs. 50.4 (±14.3) µm, P < 0.001), and that resin infiltrant completely penetrated the acid-etched demineralized area of the tooth enamel with a mean penetration depth of 31.6 (±9.0) µm. Scanning electron microscopy showed that the surface morphology was more uniform and smoother after simulated toothbrushing. The enamel surface structure was more severely destroyed in the control group after artificial demineralization compared with that of the experimental group. Conclusion Resin infiltrant can completely penetrate an acid-etched demineral…
bibliographic citation: Li et al. (2021) In vitro effect of resin infiltrant on resistance of sound enamel surfaces in permanent teeth to demineralization. PeerJ 9:e12008 https://doi.org/10.7717/peerj.12008
date submitted: 2020-11-27
date accepted: 2021-07-27
issued: 2021-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Meng
author list: Agent
  family name: Yang
  given name: Zhengyan
author list: Agent
  family name: Huang
  given name: Yajing
author list: Agent
  family name: Li
  given name: Yueheng
author list: Agent
  family name: Zhou
  given name: Zhi
doi: 10.7717/peerj.12008
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-13
copyright: ©2021 Li et al.
attribution name: Li et al.

Regeneration and growth in crowns and rhizome fragments of Japanese knotweed (Reynoutria japonica) and desiccation as a potential control strategy
type: item
type: AcademicArticle
description: Reynoutria japonica (Japanese knotweed) is a problematic invasive plant found in many areas of Europe and North America. Notably, in the UK, the species can cause issues with mortgage acquisition. Control of R. japonica is complicated by its ability to regenerate from small fragments of plant material; however, there remains uncertainty about how much (in terms of mass) rhizome is required for successful regeneration. This study investigated the ability of crowns and rhizomes with different numbers of nodes to regenerate successfully from three sites in the north of England, UK. Two of the sites had been subject to herbicide treatment for two years prior to sampling and the third site had no history of herbicide treatment. No significant differences were observed in regenerated stem diameter, maximum height of stem and maximum growth increments among crowns. All traits measured from the planted crowns were significantly greater than those of the planted rhizome fragments and at least one node was necessary for successful regeneration of rhizomes. The smallest initial fragment weight to regenerate and survive the experiment was 0.5 g. Subjecting all plant material to desiccation for 38 days resulted in no regrowth (emergence or regeneration) after replanting. These findings suggest that desiccation could be a valuable management strategy for small to medium scale infestations common in urban settings.
format: application/pdf
format: text/html
creator: Jacob W. Lawson
creator: Mark Fennell
creator: Mark W. Smith
creator: Karen L. Bacon
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.11783
publisher: PeerJ Inc.
rights: © 2021 Lawson et al.
abstract: Reynoutria japonica (Japanese knotweed) is a problematic invasive plant found in many areas of Europe and North America. Notably, in the UK, the species can cause issues with mortgage acquisition. Control of R. japonica is complicated by its ability to regenerate from small fragments of plant material; however, there remains uncertainty about how much (in terms of mass) rhizome is required for successful regeneration. This study investigated the ability of crowns and rhizomes with different numbers of nodes to regenerate successfully from three sites in the north of England, UK. Two of the sites had been subject to herbicide treatment for two years prior to sampling and the third site had no history of herbicide treatment. No significant differences were observed in regenerated stem diameter, maximum height of stem and maximum growth increments among crowns. All traits measured from the planted crowns were significantly greater than those of the planted rhizome fragments and at least one node was necessary for successful regeneration of rhizomes. The smallest initial fragment weight to regenerate and survive the experiment was 0.5 g. Subjecting all plant material to desiccation for 38 days resulted in no regrowth (emergence or regeneration) after replanting. These findings suggest that desiccation could be a valuable management strategy for small to medium scale infestations common in urban settings.
bibliographic citation: Lawson et al. (2021) Regeneration and growth in crowns and rhizome fragments of Japanese knotweed (Reynoutria japonica) and desiccation as a potential control strategy. PeerJ 9:e11783 https://doi.org/10.7717/peerj.11783
date submitted: 2020-10-27
date accepted: 2021-06-24
issued: 2021-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lawson
  given name: Jacob W.
author list: Agent
  family name: Fennell
  given name: Mark
author list: Agent
  family name: Smith
  given name: Mark W.
author list: Agent
  family name: Bacon
  given name: Karen L.
doi: 10.7717/peerj.11783
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-12
copyright: ©2021 Lawson et al.
attribution name: Lawson et al.

Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk
type: item
type: AcademicArticle
description: Contagious bovine mastitis caused by Mycoplasma bovis and other Mycoplasma species including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma canadense is an economical obstacle affecting many dairy herds throughout California and elsewhere. Routine bacteriological culture-based assays for the pathogens are slow and subject to false-positive results due to the presence of the related, non-pathogenic species Acholeplasma laidlawii. To address the need for rapid and accurate detection methods, a new TaqMan multiplex, quantitative real-time PCR (qPCR) assay was developed that targets the 16S rRNA gene of Mycoplasma, rpoB gene of M. bovis, and the 16S to 23S rRNA intergenic transcribed spacer (ITS) region of A. laidlawii. qPCR amplification efficiency and range of detection were similar for individual assays in multiplex as when performed separately. The multiplex assay was able to distinguish between M. bovis and A. laidlawii as well as detect Mycoplasma spp. collectively, including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma canadense, Mycoplasma arginini and Mycoplasma alkalescens. In milk, the lower limit of detection of M. bovis, M. californicum, and A. laidlawii with the multiplex assay was between 120 to 250 colony forming units (CFU) per mL. The assay was also able to simultaneously detect both M. bovis and A. laidlawii in milk when present in moderate (103 to 104 CFU/mL) to high (106 to 107 CFU/mL) quantities. Compared to laboratory culture-based methods, the multiplex qPCR diagnostic specificity (Sp) was 100% (95% CI [86.8–100]; n = 26) and diagnostic sensitivity (Se) was 92.3% (95% CI [74.9–99.1]; n = 26) for Mycoplasma species in milk samples collected from California dairy farms. Similarly, the Sp was 100% (95% CI [90.5–100]; n = 37) and Se was 93.3% (95% CI [68.1–99.8]; n = 15) for M. bovis. Our assay can detect and distinguish among M. bovis, other prevalent Mycoplasma spp.,…
format: application/pdf
format: text/html
creator: Kanika Chauhan
creator: Sharif S. Aly
creator: Terry W. Lehenbauer
creator: Karen H. Tonooka
creator: Kathy Glenn
creator: Paul Rossitto
creator: Maria L. Marco
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.11881
publisher: PeerJ Inc.
rights: © 2021 Chauhan et al.
abstract: Contagious bovine mastitis caused by Mycoplasma bovis and other Mycoplasma species including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma canadense is an economical obstacle affecting many dairy herds throughout California and elsewhere. Routine bacteriological culture-based assays for the pathogens are slow and subject to false-positive results due to the presence of the related, non-pathogenic species Acholeplasma laidlawii. To address the need for rapid and accurate detection methods, a new TaqMan multiplex, quantitative real-time PCR (qPCR) assay was developed that targets the 16S rRNA gene of Mycoplasma, rpoB gene of M. bovis, and the 16S to 23S rRNA intergenic transcribed spacer (ITS) region of A. laidlawii. qPCR amplification efficiency and range of detection were similar for individual assays in multiplex as when performed separately. The multiplex assay was able to distinguish between M. bovis and A. laidlawii as well as detect Mycoplasma spp. collectively, including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma canadense, Mycoplasma arginini and Mycoplasma alkalescens. In milk, the lower limit of detection of M. bovis, M. californicum, and A. laidlawii with the multiplex assay was between 120 to 250 colony forming units (CFU) per mL. The assay was also able to simultaneously detect both M. bovis and A. laidlawii in milk when present in moderate (103 to 104 CFU/mL) to high (106 to 107 CFU/mL) quantities. Compared to laboratory culture-based methods, the multiplex qPCR diagnostic specificity (Sp) was 100% (95% CI [86.8–100]; n = 26) and diagnostic sensitivity (Se) was 92.3% (95% CI [74.9–99.1]; n = 26) for Mycoplasma species in milk samples collected from California dairy farms. Similarly, the Sp was 100% (95% CI [90.5–100]; n = 37) and Se was 93.3% (95% CI [68.1–99.8]; n = 15) for M. bovis. Our assay can detect and distinguish among M. bovis, other prevalent Mycoplasma spp.,…
bibliographic citation: Chauhan et al. (2021) Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk. PeerJ 9:e11881 https://doi.org/10.7717/peerj.11881
date submitted: 2021-03-22
date accepted: 2021-07-07
issued: 2021-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chauhan
  given name: Kanika
author list: Agent
  family name: Aly
  given name: Sharif S.
author list: Agent
  family name: Lehenbauer
  given name: Terry W.
author list: Agent
  family name: Tonooka
  given name: Karen H.
author list: Agent
  family name: Glenn
  given name: Kathy
author list: Agent
  family name: Rossitto
  given name: Paul
author list: Agent
  family name: Marco
  given name: Maria L.
doi: 10.7717/peerj.11881
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-12
copyright: © 2021 Chauhan et al.
attribution name: Chauhan et al.

Comparative survival analyses among captive chimpanzees (Pan troglodytes) in America and Japan
type: item
type: AcademicArticle
description: Detailed, long-term datasets on the life histories of long-lived species such as great apes are necessary to understand their survival patterns but are relatively rare. Such information requires prolonged and consistent record-keeping over many generations, so for chimpanzees (Pan troglodytes), this equates to many decades of input. As life history variables can be altered by differences in environmental influences (whether natural or artificial), there is substantial value to being able to compare across populations. Here, we present the first comparative analysis of life history data for two ex situ chimpanzee populations residing in North America (1975–2020; n = 730) and Japan (1980–2020; n = 660). Overall, survival patterns were similar between regions, and the median life expectancy from birth is estimated at 35.7 (95% CI = [32.4–40.0]) years for females and 30.1 (27.3–34.3) years for males across both populations. Females who survive to their first birthday are estimated to survive 42.4 (40.0–46.3) years and males 35.5 (32.6–38.0) years. We found that birth type (wild-born or captive-born) did not influence survival patterns in either population, but there were differential effects of sex on longevity. In the America population, males had higher mortality rates than females, whereas in the Japan population we found no differences between the sexes. First year mortality did not differ between populations for males (18–20%), but for females it was lower in America (15%) compared to Japan (25%). Survival patterns of chimpanzees in the present study will be useful for future investigation into potential causes of regional differences and cross-species comparisons.
format: application/pdf
format: text/html
creator: Judy Che-Castaldo
creator: Kristin Havercamp
creator: Koshiro Watanuki
creator: Tetsuro Matsuzawa
creator: Satoshi Hirata
creator: Stephen R. Ross
subject: Evolutionary Studies
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.11913
publisher: PeerJ Inc.
rights: © 2021 Che-Castaldo et al.
abstract: Detailed, long-term datasets on the life histories of long-lived species such as great apes are necessary to understand their survival patterns but are relatively rare. Such information requires prolonged and consistent record-keeping over many generations, so for chimpanzees (Pan troglodytes), this equates to many decades of input. As life history variables can be altered by differences in environmental influences (whether natural or artificial), there is substantial value to being able to compare across populations. Here, we present the first comparative analysis of life history data for two ex situ chimpanzee populations residing in North America (1975–2020; n = 730) and Japan (1980–2020; n = 660). Overall, survival patterns were similar between regions, and the median life expectancy from birth is estimated at 35.7 (95% CI = [32.4–40.0]) years for females and 30.1 (27.3–34.3) years for males across both populations. Females who survive to their first birthday are estimated to survive 42.4 (40.0–46.3) years and males 35.5 (32.6–38.0) years. We found that birth type (wild-born or captive-born) did not influence survival patterns in either population, but there were differential effects of sex on longevity. In the America population, males had higher mortality rates than females, whereas in the Japan population we found no differences between the sexes. First year mortality did not differ between populations for males (18–20%), but for females it was lower in America (15%) compared to Japan (25%). Survival patterns of chimpanzees in the present study will be useful for future investigation into potential causes of regional differences and cross-species comparisons.
bibliographic citation: Che-Castaldo et al. (2021) Comparative survival analyses among captive chimpanzees (Pan troglodytes) in America and Japan. PeerJ 9:e11913 https://doi.org/10.7717/peerj.11913
date submitted: 2021-03-26
date accepted: 2021-07-14
issued: 2021-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Che-Castaldo
  given name: Judy
author list: Agent
  family name: Havercamp
  given name: Kristin
author list: Agent
  family name: Watanuki
  given name: Koshiro
author list: Agent
  family name: Matsuzawa
  given name: Tetsuro
author list: Agent
  family name: Hirata
  given name: Satoshi
author list: Agent
  family name: Ross
  given name: Stephen R.
doi: 10.7717/peerj.11913
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-12
copyright: © 2021 Che-Castaldo et al.
attribution name: Che-Castaldo et al.

Quantifying bite force in coexisting tayassuids and feral suids: a comparison between morphometric functional proxies and in vivo measurements
type: item
type: AcademicArticle
description: Background Measuring mammals’ bite force in laboratory conditions is not a simple task, let alone on wild medium-sized mammals in the field. Thus, morphometric-proxies are usually used to infer morphofunctional properties of musculoskeletal features. For instance, the study of bite force-indexes suggests that different capacities to crack food items reduce the competition between coexistent collared and white-lipped peccaries (Pecari tajacu and Tayassu pecari). The presence of exotic feral hogs (Sus scrofa) in peccaries’ endemic areas gives rise to new ecological interactions between them. An example is the Brazilian Pantanal wetland, where ecomorphological mechanisms may play a role in their ecological relations. Taking this scenario as a case of study, we aimed to verify if the morphometric-proxies are de facto reliable tools, by comparing bite forces-indexes with the in vivo bite forces of these species. Methods We captured 21 collared and white-lipped peccaries and feral hogs in the Brazilian Pantanal to assess their bite force at first molar. The Bite Force Measuring Tube (BiTu) is a robust and simple mechanical device designed to be used in field conditions. Only 11 individuals successfully bit the BiTu before being released. Their body measurements were compared and correlated with their bite force. The in vivo bite forces were compared with bite force-indexes of two papers based on independent morphometric methods and datasets: Sicuro & Oliveira (2002) used classic morphometrics to infer the bite forces of these three species in the Brazilian Pantanal, and Hendges et al. (2019) used geometric morphometrics to compare bite forces-indexes and feeding habits of the extant peccary species. The results of all species were standardized (Z-curves) according to each method. Doing so, we obtained comparable dimensionless comparable values but maintaining the differences between them. Results The morphometric-proxies-based studies presented similar results: collared p…
format: application/pdf
format: text/html
creator: Fernando L. Sicuro
creator: Luiz Flamarion B. Oliveira
creator: Carla D. Hendges
creator: Carlos Fonseca
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.11948
publisher: PeerJ Inc.
rights: © 2021 Sicuro et al.
abstract: Background Measuring mammals’ bite force in laboratory conditions is not a simple task, let alone on wild medium-sized mammals in the field. Thus, morphometric-proxies are usually used to infer morphofunctional properties of musculoskeletal features. For instance, the study of bite force-indexes suggests that different capacities to crack food items reduce the competition between coexistent collared and white-lipped peccaries (Pecari tajacu and Tayassu pecari). The presence of exotic feral hogs (Sus scrofa) in peccaries’ endemic areas gives rise to new ecological interactions between them. An example is the Brazilian Pantanal wetland, where ecomorphological mechanisms may play a role in their ecological relations. Taking this scenario as a case of study, we aimed to verify if the morphometric-proxies are de facto reliable tools, by comparing bite forces-indexes with the in vivo bite forces of these species. Methods We captured 21 collared and white-lipped peccaries and feral hogs in the Brazilian Pantanal to assess their bite force at first molar. The Bite Force Measuring Tube (BiTu) is a robust and simple mechanical device designed to be used in field conditions. Only 11 individuals successfully bit the BiTu before being released. Their body measurements were compared and correlated with their bite force. The in vivo bite forces were compared with bite force-indexes of two papers based on independent morphometric methods and datasets: Sicuro & Oliveira (2002) used classic morphometrics to infer the bite forces of these three species in the Brazilian Pantanal, and Hendges et al. (2019) used geometric morphometrics to compare bite forces-indexes and feeding habits of the extant peccary species. The results of all species were standardized (Z-curves) according to each method. Doing so, we obtained comparable dimensionless comparable values but maintaining the differences between them. Results The morphometric-proxies-based studies presented similar results: collared p…
bibliographic citation: Sicuro et al. (2021) Quantifying bite force in coexisting tayassuids and feral suids: a comparison between morphometric functional proxies and in vivo measurements. PeerJ 9:e11948 https://doi.org/10.7717/peerj.11948
date submitted: 2021-04-20
date accepted: 2021-07-20
issued: 2021-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sicuro
  given name: Fernando L.
author list: Agent
  family name: Oliveira
  given name: Luiz Flamarion B.
author list: Agent
  family name: Hendges
  given name: Carla D.
author list: Agent
  family name: Fonseca
  given name: Carlos
doi: 10.7717/peerj.11948
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-12
copyright: ©2021 Sicuro et al.
attribution name: Sicuro et al.

Development and validation of a novel survival model for acute myeloid leukemia based on autophagy-related genes
type: item
type: AcademicArticle
description: Background Acute myeloid leukemia (AML) is one of the most common blood cancers, and is characterized by impaired hematopoietic function and bone marrow (BM) failure. Under normal circumstances, autophagy may suppress tumorigenesis, however under the stressful conditions of late stage tumor growth autophagy actually protects tumor cells, so inhibiting autophagy in these cases also inhibits tumor growth and promotes tumor cell death. Methods AML gene expression profile data and corresponding clinical data were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, from which prognostic-related genes were screened to construct a risk score model through LASSO and univariate and multivariate Cox analyses. Then the model was verified in the TCGA cohort and GEO cohorts. In addition, we also analyzed the relationship between autophagy genes and immune infiltrating cells and therapeutic drugs. Results We built a model containing 10 autophagy-related genes to predict the survival of AML patients by dividing them into high- or low-risk subgroups. The high-risk subgroup was prone to a poorer prognosis in both the training TCGA-LAML cohort and the validation GSE37642 cohort. Univariate and multivariate Cox analysis revealed that the risk score of the autophagy model can be used as an independent prognostic factor. The high-risk subgroup had not only higher fractions of CD4 naïve T cell, NK cell activated, and resting mast cells but also higher expression of immune checkpoint genes CTLA4 and CD274. Last, we screened drug sensitivity between high- and low-risk subgroups. Conclusion The risk score model based on 10 autophagy-related genes can serve as an effective prognostic predictor for AML patients and may guide for patient stratification for immunotherapies and drugs.
format: application/pdf
format: text/html
creator: Li Huang
creator: Lier Lin
creator: Xiangjun Fu
creator: Can Meng
subject: Bioinformatics
subject: Hematology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.11968
publisher: PeerJ Inc.
rights: © 2021 Huang et al.
abstract: Background Acute myeloid leukemia (AML) is one of the most common blood cancers, and is characterized by impaired hematopoietic function and bone marrow (BM) failure. Under normal circumstances, autophagy may suppress tumorigenesis, however under the stressful conditions of late stage tumor growth autophagy actually protects tumor cells, so inhibiting autophagy in these cases also inhibits tumor growth and promotes tumor cell death. Methods AML gene expression profile data and corresponding clinical data were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, from which prognostic-related genes were screened to construct a risk score model through LASSO and univariate and multivariate Cox analyses. Then the model was verified in the TCGA cohort and GEO cohorts. In addition, we also analyzed the relationship between autophagy genes and immune infiltrating cells and therapeutic drugs. Results We built a model containing 10 autophagy-related genes to predict the survival of AML patients by dividing them into high- or low-risk subgroups. The high-risk subgroup was prone to a poorer prognosis in both the training TCGA-LAML cohort and the validation GSE37642 cohort. Univariate and multivariate Cox analysis revealed that the risk score of the autophagy model can be used as an independent prognostic factor. The high-risk subgroup had not only higher fractions of CD4 naïve T cell, NK cell activated, and resting mast cells but also higher expression of immune checkpoint genes CTLA4 and CD274. Last, we screened drug sensitivity between high- and low-risk subgroups. Conclusion The risk score model based on 10 autophagy-related genes can serve as an effective prognostic predictor for AML patients and may guide for patient stratification for immunotherapies and drugs.
bibliographic citation: Huang et al. (2021) Development and validation of a novel survival model for acute myeloid leukemia based on autophagy-related genes. PeerJ 9:e11968 https://doi.org/10.7717/peerj.11968
date submitted: 2021-04-19
date accepted: 2021-07-23
issued: 2021-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Li
author list: Agent
  family name: Lin
  given name: Lier
author list: Agent
  family name: Fu
  given name: Xiangjun
author list: Agent
  family name: Meng
  given name: Can
doi: 10.7717/peerj.11968
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-12
copyright: ©2021 Huang et al.
attribution name: Huang et al.

Muvi schmallenbergi gen. nov., sp. nov. (Crustacea, Tanaidacea) from the southeast Australian coast, with comments on the distribution and habitat preferences of Chondropodinae
type: item
type: AcademicArticle
description: Based on material collected from the shelf off southeast Australia (offshore of Portland), a new genus and new species, Muvi schmallenbergi gen. nov., sp. nov., of the tanaidacean family Metapseudidae, is described. Muvi is distinguishable from other genera within the subfamily Chondropodinae by having equally long antennular flagella. It also differs from other Chondropodinae by a combination of characters such as eyelobes with a group of visual elements, rostrum with smooth lateral edges, pereonites with lateral processes and pleotelson lacking lateral process, antennule article-1 with a single apophysis, maxillule inner lobe well-developed, labial palp bearing three distal setae, cheliped exopod well-developed and setose, pereopod-1 coxa with distinct apophysis, pleopods in five pairs, and uropod basis without apophysis. The genus Deidamiapseudes Sganga & Roccatagliata, 2016 is moved from Chondropodinae (Metapseudidae) to Apseudoidea incertae sedis. An identification key for the genera within Chondropodinae is given, and their distribution is discussed.
format: application/pdf
format: text/html
creator: Piotr Jóźwiak
creator: Magdalena Błażewicz
subject: Biodiversity
subject: Ecology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11607
publisher: PeerJ Inc.
rights: © 2021 Jóźwiak and Błażewicz
abstract: Based on material collected from the shelf off southeast Australia (offshore of Portland), a new genus and new species, Muvi schmallenbergi gen. nov., sp. nov., of the tanaidacean family Metapseudidae, is described. Muvi is distinguishable from other genera within the subfamily Chondropodinae by having equally long antennular flagella. It also differs from other Chondropodinae by a combination of characters such as eyelobes with a group of visual elements, rostrum with smooth lateral edges, pereonites with lateral processes and pleotelson lacking lateral process, antennule article-1 with a single apophysis, maxillule inner lobe well-developed, labial palp bearing three distal setae, cheliped exopod well-developed and setose, pereopod-1 coxa with distinct apophysis, pleopods in five pairs, and uropod basis without apophysis. The genus Deidamiapseudes Sganga & Roccatagliata, 2016 is moved from Chondropodinae (Metapseudidae) to Apseudoidea incertae sedis. An identification key for the genera within Chondropodinae is given, and their distribution is discussed.
bibliographic citation: Jóźwiak et al. (2021) Muvi schmallenbergi gen. nov., sp. nov. (Crustacea, Tanaidacea) from the southeast Australian coast, with comments on the distribution and habitat preferences of Chondropodinae. PeerJ 9:e11607 https://doi.org/10.7717/peerj.11607
date submitted: 2020-02-19
date accepted: 2021-05-23
issued: 2021-08-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jóźwiak
  given name: Piotr
author list: Agent
  family name: Błażewicz
  given name: Magdalena
doi: 10.7717/peerj.11607
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-11
copyright: © 2021 Jóźwiak and Błażewicz
attribution name: Jóźwiak and Błażewicz

Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species
type: item
type: AcademicArticle
description: Background Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. Methods Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a–e, II a and II b). Results The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.
format: application/pdf
format: text/html
creator: Jun Xu
creator: Ping Hu
creator: Ye Tao
creator: Puwen Song
creator: Huanting Gao
creator: Yuanyuan Guan
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11811
publisher: PeerJ Inc.
rights: © 2021 Xu et al.
abstract: Background Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. Methods Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a–e, II a and II b). Results The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.
bibliographic citation: Xu et al. (2021) Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species. PeerJ 9:e11811 https://doi.org/10.7717/peerj.11811
date submitted: 2020-12-26
date accepted: 2021-06-27
issued: 2021-08-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Jun
author list: Agent
  family name: Hu
  given name: Ping
author list: Agent
  family name: Tao
  given name: Ye
author list: Agent
  family name: Song
  given name: Puwen
author list: Agent
  family name: Gao
  given name: Huanting
author list: Agent
  family name: Guan
  given name: Yuanyuan
doi: 10.7717/peerj.11811
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-11
copyright: ©2021 Xu et al.
attribution name: Xu et al.

Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India
type: item
type: AcademicArticle
description: To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.
format: application/pdf
format: text/html
creator: Vikas Vohra
creator: Narendra Pratap Singh
creator: Supriya Chhotaray
creator: Varinder Singh Raina
creator: Alka Chopra
creator: Ranjit Singh Kataria
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.11846
publisher: PeerJ Inc.
rights: © 2021 Vohra et al.
abstract: To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.
bibliographic citation: Vohra et al. (2021) Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India. PeerJ 9:e11846 https://doi.org/10.7717/peerj.11846
date submitted: 2021-04-09
date accepted: 2021-07-01
issued: 2021-08-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vohra
  given name: Vikas
author list: Agent
  family name: Singh
  given name: Narendra Pratap
author list: Agent
  family name: Chhotaray
  given name: Supriya
author list: Agent
  family name: Raina
  given name: Varinder Singh
author list: Agent
  family name: Chopra
  given name: Alka
author list: Agent
  family name: Kataria
  given name: Ranjit Singh
doi: 10.7717/peerj.11846
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-11
copyright: © 2021 Vohra et al.
attribution name: Vohra et al.

Transport of biodeposits and benthic footprint around an oyster farm, Damariscotta Estuary, Maine
type: item
type: AcademicArticle
description: The benthic impact of aquaculture waste depends on the area and extent of waste accumulation on the sediment surface below and around the farm. In this study we investigated the effect of flow on biodeposit transport and initial deposition by calculating a rough aquaculture “footprint” around an oyster aquaculture farm in the Damariscotta River, ME. We also compared a site under the farm to a downstream “away” site calculated to be within the footprint of the farm. We found similar sediment biogeochemical fluxes, geochemical properties and macrofaunal communities at the site under the farm and the away site, as well as low organic enrichment at both sites, indicating that biodeposition in this environment likely does not have a major influence on the benthos. To predict accumulation of biodeposits, we measured sediment erodibility under a range of shear stresses and found slightly higher erosion rates at the farm than at the away site. A microalgal mat was observed at the sediment surface in many sediment cores. Partial failure of the microalgal mat was observed at high shear velocity, suggesting that the mat may fail and surface sediment erode at shear velocities comparable to or greater than those calculated fromin situ flow measurements. However, this study took place during neap tide, and it is likely that peak bottom velocities during spring tides are high enough to periodically “clear” under-farm sediment of recent deposits.
format: application/pdf
format: text/html
creator: Kara Gadeken
creator: William C. Clemo
creator: Will Ballentine
creator: Steven L. Dykstra
creator: Mai Fung
creator: Alexis Hagemeyer
creator: Kelly M. Dorgan
creator: Brian Dzwonkowski
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Biogeochemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.11862
publisher: PeerJ Inc.
rights: © 2021 Gadeken et al.
abstract: The benthic impact of aquaculture waste depends on the area and extent of waste accumulation on the sediment surface below and around the farm. In this study we investigated the effect of flow on biodeposit transport and initial deposition by calculating a rough aquaculture “footprint” around an oyster aquaculture farm in the Damariscotta River, ME. We also compared a site under the farm to a downstream “away” site calculated to be within the footprint of the farm. We found similar sediment biogeochemical fluxes, geochemical properties and macrofaunal communities at the site under the farm and the away site, as well as low organic enrichment at both sites, indicating that biodeposition in this environment likely does not have a major influence on the benthos. To predict accumulation of biodeposits, we measured sediment erodibility under a range of shear stresses and found slightly higher erosion rates at the farm than at the away site. A microalgal mat was observed at the sediment surface in many sediment cores. Partial failure of the microalgal mat was observed at high shear velocity, suggesting that the mat may fail and surface sediment erode at shear velocities comparable to or greater than those calculated fromin situ flow measurements. However, this study took place during neap tide, and it is likely that peak bottom velocities during spring tides are high enough to periodically “clear” under-farm sediment of recent deposits.
bibliographic citation: Gadeken et al. (2021) Transport of biodeposits and benthic footprint around an oyster farm, Damariscotta Estuary, Maine. PeerJ 9:e11862 https://doi.org/10.7717/peerj.11862
date submitted: 2021-01-26
date accepted: 2021-07-05
issued: 2021-08-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gadeken
  given name: Kara
author list: Agent
  family name: Clemo
  given name: William C.
author list: Agent
  family name: Ballentine
  given name: Will
author list: Agent
  family name: Dykstra
  given name: Steven L.
author list: Agent
  family name: Fung
  given name: Mai
author list: Agent
  family name: Hagemeyer
  given name: Alexis
author list: Agent
  family name: Dorgan
  given name: Kelly M.
author list: Agent
  family name: Dzwonkowski
  given name: Brian
doi: 10.7717/peerj.11862
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-11
copyright: ©2021 Gadeken et al.
attribution name: Gadeken et al.

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