PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles
items: The impact of climate change on flow conditions and wetland ecosystems in the Lower Biebrza River (Poland)
items: Methylase-assisted subcloning for high throughput BioBrick assembly
items: ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences
items: Intergenerational implications of alcohol intake: metabolic disorders in alcohol-naïve rat offspring
items: A prediction modeling based on SNOT-22 score for endoscopic nasal septoplasty: a retrospective study
items: https://peerj.com/articles/9899
items: First report of lionfish prey from Western Florida waters as identified by DNA barcoding
items: Two new nematode species (Plectida: Leptolaimidae, Rhadinematidae) from Chatham Rise, New Zealand
items: Antimicrobial and micronutrient interventions for the management of infants under 6 months of age identified with severe malnutrition: a literature review

Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles
type: item
type: AcademicArticle
description: Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks.
format: application/pdf
format: text/html
creator: Sylvia Schäffer
creator: Stephan Koblmüller
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.9710
publisher: PeerJ Inc.
rights: © 2020 Schäffer and Koblmüller
abstract: Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks.
bibliographic citation: Schäffer et al. (2020) Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles. PeerJ 8:e9710 https://doi.org/10.7717/peerj.9710
date submitted: 2020-05-20
date accepted: 2020-07-23
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schäffer
  given name: Sylvia
author list: Agent
  family name: Koblmüller
  given name: Stephan
doi: 10.7717/peerj.9710
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: © 2020 Schäffer and Koblmüller
attribution name: Schäffer and Koblmüller

The impact of climate change on flow conditions and wetland ecosystems in the Lower Biebrza River (Poland)
type: item
type: AcademicArticle
description: Water plays a key role in the functioning of wetlands and a shortage or contamination of it leads to changes in habitat conditions and degradation of ecosystems. This article scrutinizes the impact of climate change on the hydrological characteristics of floods (maximum flow, duration, volume) in the River Biebrza wetlands (North-East Poland). We analysed the trends in duration and volume of flood and maximum discharges in the historical period 1970–2000 and predicted these for the future periods 2020–2050 and 2070–2100, respectively. Next we assessed the impact on the wetland ecosystems. The basis of our assessments consists of statistical analyses of hydrographs and calculations by the Soil and Water Assessment Tool hydrological model and considering nine bias-corrected climate models. The results indicate that both volume and duration of winter floods will keep increasing continuously under Representative Concentration Pathways 4.5 and 8.5. The reduction in peak annual floods is expected to decline slightly in both scenarios. On the other hand, the analysis of trends in mean and standard deviation revealed negligible tendencies in the datasets for summer and winter hydrological seasons within the three time frames analysed (1970–2000; 2020–2050; 2070–2100). We foresee several future implications for the floodplain ecosystems. Shifts in transversal ecosystem zonation parallel to the river will likely take place with more highly productive flood tolerant vegetation types. Nutrient availability and algal blooms during spring inundations will likely increase. Slowdown of organic matter turnover later in summer will lead to a higher peat accumulation rate. Logistical problems with summer mowing and removal of bushes in winter may enhance shrub encroachment.
format: application/pdf
format: text/html
creator: Dorota Mirosław-Świątek
creator: Paweł Marcinkowski
creator: Krzysztof Kochanek
creator: Martin J. Wassen
subject: Ecosystem Science
subject: Climate Change Biology
subject: Ecohydrology
subject: Environmental Impacts
description: doi:10.7717/peerj.9778
publisher: PeerJ Inc.
rights: © 2020 Mirosław-Świątek et al.
abstract: Water plays a key role in the functioning of wetlands and a shortage or contamination of it leads to changes in habitat conditions and degradation of ecosystems. This article scrutinizes the impact of climate change on the hydrological characteristics of floods (maximum flow, duration, volume) in the River Biebrza wetlands (North-East Poland). We analysed the trends in duration and volume of flood and maximum discharges in the historical period 1970–2000 and predicted these for the future periods 2020–2050 and 2070–2100, respectively. Next we assessed the impact on the wetland ecosystems. The basis of our assessments consists of statistical analyses of hydrographs and calculations by the Soil and Water Assessment Tool hydrological model and considering nine bias-corrected climate models. The results indicate that both volume and duration of winter floods will keep increasing continuously under Representative Concentration Pathways 4.5 and 8.5. The reduction in peak annual floods is expected to decline slightly in both scenarios. On the other hand, the analysis of trends in mean and standard deviation revealed negligible tendencies in the datasets for summer and winter hydrological seasons within the three time frames analysed (1970–2000; 2020–2050; 2070–2100). We foresee several future implications for the floodplain ecosystems. Shifts in transversal ecosystem zonation parallel to the river will likely take place with more highly productive flood tolerant vegetation types. Nutrient availability and algal blooms during spring inundations will likely increase. Slowdown of organic matter turnover later in summer will lead to a higher peat accumulation rate. Logistical problems with summer mowing and removal of bushes in winter may enhance shrub encroachment.
bibliographic citation: Mirosław-Świątek et al. (2020) The impact of climate change on flow conditions and wetland ecosystems in the Lower Biebrza River (Poland). PeerJ 8:e9778 https://doi.org/10.7717/peerj.9778
date submitted: 2020-03-03
date accepted: 2020-07-30
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mirosław-Świątek
  given name: Dorota
author list: Agent
  family name: Marcinkowski
  given name: Paweł
author list: Agent
  family name: Kochanek
  given name: Krzysztof
author list: Agent
  family name: Wassen
  given name: Martin J.
doi: 10.7717/peerj.9778
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: © 2020 Mirosław-Świątek et al.
attribution name: Mirosław-Świątek et al.

Methylase-assisted subcloning for high throughput BioBrick assembly
type: item
type: AcademicArticle
description: The BioBrick standard makes possible iterated pairwise assembly of cloned parts without any depletion of unique restriction sites. Every part that conforms to the standard is compatible with every other part, thereby fostering a worldwide user community. The assembly methods, however, are labor intensive or inefficient compared to some newer ones so the standard may be falling out of favor. An easier way to assemble BioBricks is described herein. Plasmids encoding BioBrick parts are purified from Escherichia coli cells that express a foreign site-specific DNA methyltransferase, so that each is subsequently protected in vitro from the activity of a particular restriction endonuclease. Each plasmid is double-digested and all resulting restriction fragments are ligated together without gel purification. The ligation products are subsequently double-digested with another pair of restriction endonucleases so only the desired insert-recipient vector construct retains the capacity to transform E. coli. This 4R/2M BioBrick assembly protocol is more efficient and accurate than established workflows including 3A assembly. It is also much easier than gel purification to miniaturize, automate and perform more assembly reactions in parallel. As such, it should streamline DNA assembly for the existing community of BioBrick users, and possibly encourage others to join.
format: application/pdf
format: text/html
creator: Ichiro Matsumura
subject: Bioengineering
subject: Molecular Biology
subject: Synthetic Biology
description: doi:10.7717/peerj.9841
publisher: PeerJ Inc.
rights: © 2020 Matsumura
abstract: The BioBrick standard makes possible iterated pairwise assembly of cloned parts without any depletion of unique restriction sites. Every part that conforms to the standard is compatible with every other part, thereby fostering a worldwide user community. The assembly methods, however, are labor intensive or inefficient compared to some newer ones so the standard may be falling out of favor. An easier way to assemble BioBricks is described herein. Plasmids encoding BioBrick parts are purified from Escherichia coli cells that express a foreign site-specific DNA methyltransferase, so that each is subsequently protected in vitro from the activity of a particular restriction endonuclease. Each plasmid is double-digested and all resulting restriction fragments are ligated together without gel purification. The ligation products are subsequently double-digested with another pair of restriction endonucleases so only the desired insert-recipient vector construct retains the capacity to transform E. coli. This 4R/2M BioBrick assembly protocol is more efficient and accurate than established workflows including 3A assembly. It is also much easier than gel purification to miniaturize, automate and perform more assembly reactions in parallel. As such, it should streamline DNA assembly for the existing community of BioBrick users, and possibly encourage others to join.
bibliographic citation: Matsumura (2020) Methylase-assisted subcloning for high throughput BioBrick assembly. PeerJ 8:e9841 https://doi.org/10.7717/peerj.9841
date submitted: 2020-04-27
date accepted: 2020-08-10
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matsumura
  given name: Ichiro
doi: 10.7717/peerj.9841
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: ©2020 Matsumura
attribution name: Matsumura

ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences
type: item
type: AcademicArticle
description: Biominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpet Lottia gigantea.
format: application/pdf
format: text/html
creator: Alastair W. Skeffington
creator: Andreas Donath
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.9852
publisher: PeerJ Inc.
rights: © 2020 Skeffington and Donath
abstract: Biominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpet Lottia gigantea.
bibliographic citation: Skeffington et al. (2020) ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences. PeerJ 8:e9852 https://doi.org/10.7717/peerj.9852
date submitted: 2020-04-14
date accepted: 2020-08-11
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Skeffington
  given name: Alastair W.
author list: Agent
  family name: Donath
  given name: Andreas
doi: 10.7717/peerj.9852
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: ©2020 Skeffington and Donath
attribution name: Skeffington and Donath

Intergenerational implications of alcohol intake: metabolic disorders in alcohol-naïve rat offspring
type: item
type: AcademicArticle
description: Alcohol drinking may be associated with an increased risk of various metabolic diseases. Rat lines selectively bred for alcohol preference and alcohol avoidance constitute an interesting model to study inherited factors related to alcohol drinking and metabolic disorders. The aim of the present study was to compare the levels of selected laboratory biomarkers of metabolic disorders in blood samples from naïve offspring of Warsaw alcohol high-preferring (WHP), Warsaw alcohol low-preferring (WLP), and wild Wistar rats. Blood samples were collected from 3-month old (300–350 g) alcohol-naïve, male offspring of WHP (n = 8) and WLP rats (n = 8), as well as alcohol-naïve, male, wild Wistar rats. Markers of metabolic, hepatic, and pancreatic disorders were analysed (levels of homocysteine, glucose, total cholesterol, triglycerides and γ-glutamyl transferase (GGT), aspartate (AST), alanine aminotransferase (ALT), and amylase serum activities). Alcohol-naïve offspring of WHP, WLP, and wild Wistar rats differed significantly in the levels of triglycerides, total cholesterol, homocysteine, as well as in the activity of GGT, ALT, AST, and amylase enzymes. Most markers in the alcohol-naïve offspring of WHP rats were altered even thought they were never exposed to alcohol pre- or postnatally. This may suggest that parental alcohol abuse can have a detrimental influence on offspring vulnerability to metabolic disorders.
format: application/pdf
format: text/html
creator: Pawel Mierzejewski
creator: Alicja Zakrzewska
creator: Julita Kuczyńska
creator: Edyta Wyszogrodzka
creator: Monika Dominiak
subject: Biochemistry
subject: Genetics
subject: Psychiatry and Psychology
subject: Metabolic Sciences
description: doi:10.7717/peerj.9886
publisher: PeerJ Inc.
rights: © 2020 Mierzejewski et al.
abstract: Alcohol drinking may be associated with an increased risk of various metabolic diseases. Rat lines selectively bred for alcohol preference and alcohol avoidance constitute an interesting model to study inherited factors related to alcohol drinking and metabolic disorders. The aim of the present study was to compare the levels of selected laboratory biomarkers of metabolic disorders in blood samples from naïve offspring of Warsaw alcohol high-preferring (WHP), Warsaw alcohol low-preferring (WLP), and wild Wistar rats. Blood samples were collected from 3-month old (300–350 g) alcohol-naïve, male offspring of WHP (n = 8) and WLP rats (n = 8), as well as alcohol-naïve, male, wild Wistar rats. Markers of metabolic, hepatic, and pancreatic disorders were analysed (levels of homocysteine, glucose, total cholesterol, triglycerides and γ-glutamyl transferase (GGT), aspartate (AST), alanine aminotransferase (ALT), and amylase serum activities). Alcohol-naïve offspring of WHP, WLP, and wild Wistar rats differed significantly in the levels of triglycerides, total cholesterol, homocysteine, as well as in the activity of GGT, ALT, AST, and amylase enzymes. Most markers in the alcohol-naïve offspring of WHP rats were altered even thought they were never exposed to alcohol pre- or postnatally. This may suggest that parental alcohol abuse can have a detrimental influence on offspring vulnerability to metabolic disorders.
bibliographic citation: Mierzejewski et al. (2020) Intergenerational implications of alcohol intake: metabolic disorders in alcohol-naïve rat offspring. PeerJ 8:e9886 https://doi.org/10.7717/peerj.9886
date submitted: 2020-03-13
date accepted: 2020-08-16
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mierzejewski
  given name: Pawel
author list: Agent
  family name: Zakrzewska
  given name: Alicja
author list: Agent
  family name: Kuczyńska
  given name: Julita
author list: Agent
  family name: Wyszogrodzka
  given name: Edyta
author list: Agent
  family name: Dominiak
  given name: Monika
doi: 10.7717/peerj.9886
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: ©2020 Mierzejewski et al.
attribution name: Mierzejewski et al.

A prediction modeling based on SNOT-22 score for endoscopic nasal septoplasty: a retrospective study
type: item
type: AcademicArticle
description: Background To create a nomogram prediction model for the efficacy of endoscopic nasal septoplasty, and the likelihood of patient benefiting from the operation. Methods A retrospective analysis of 155 patients with nasal septum deviation (NSD) was performed to develop a predictive model for the efficacy of endoscopic nasal septoplasty. Quality of life (QoL) data was collected before and after surgery using Sinonasal Outcome Test-22 (SNOT-22) scores to evaluate the surgical outcome. An effective surgical outcome was defined as a SNOT-22 score change ≥ 9 points after surgery. Multivariate logistic regression analysis was then used to establish a predictive model for the NSD treatment. The predictive quality and clinical utility of the predictive model were assessed by C-index, calibration plots, and decision curve analysis. Results The identified risk factors for inclusion in the predictive model were included. The model had a good predictive power, with a AUC of 0.920 in the training group and a C index of 0.911 in the overall sample. Decision curve analysis revealed that the prediction model had a good clinical applicability. Conclusions Our prediction model is efficient in predicting the efficacy of endoscopic surgery for NSD through evaluation of factors including: history of nasal surgery, preoperative SNOT-22 score, sinusitis, middle turbinate plasty, BMI, smoking, follow-up time, seasonal allergies, and advanced age. Therefore, it can be cost-effective for individualized preoperative assessment.
format: application/pdf
format: text/html
creator: Xue-ran Kang
creator: Bin Chen
creator: Yi-sheng Chen
creator: Bin Yi
creator: Xiaojun Yan
creator: Chenyan Jiang
creator: Shulun Wang
creator: Lixing Lu
creator: Runjie Shi
subject: Otorhinolaryngology
subject: Public Health
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.9890
publisher: PeerJ Inc.
rights: © 2020 Kang et al.
abstract: Background To create a nomogram prediction model for the efficacy of endoscopic nasal septoplasty, and the likelihood of patient benefiting from the operation. Methods A retrospective analysis of 155 patients with nasal septum deviation (NSD) was performed to develop a predictive model for the efficacy of endoscopic nasal septoplasty. Quality of life (QoL) data was collected before and after surgery using Sinonasal Outcome Test-22 (SNOT-22) scores to evaluate the surgical outcome. An effective surgical outcome was defined as a SNOT-22 score change ≥ 9 points after surgery. Multivariate logistic regression analysis was then used to establish a predictive model for the NSD treatment. The predictive quality and clinical utility of the predictive model were assessed by C-index, calibration plots, and decision curve analysis. Results The identified risk factors for inclusion in the predictive model were included. The model had a good predictive power, with a AUC of 0.920 in the training group and a C index of 0.911 in the overall sample. Decision curve analysis revealed that the prediction model had a good clinical applicability. Conclusions Our prediction model is efficient in predicting the efficacy of endoscopic surgery for NSD through evaluation of factors including: history of nasal surgery, preoperative SNOT-22 score, sinusitis, middle turbinate plasty, BMI, smoking, follow-up time, seasonal allergies, and advanced age. Therefore, it can be cost-effective for individualized preoperative assessment.
bibliographic citation: Kang et al. (2020) A prediction modeling based on SNOT-22 score for endoscopic nasal septoplasty: a retrospective study. PeerJ 8:e9890 https://doi.org/10.7717/peerj.9890
date submitted: 2020-04-06
date accepted: 2020-08-17
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kang
  given name: Xue-ran
author list: Agent
  family name: Chen
  given name: Bin
author list: Agent
  family name: Chen
  given name: Yi-sheng
author list: Agent
  family name: Yi
  given name: Bin
author list: Agent
  family name: Yan
  given name: Xiaojun
author list: Agent
  family name: Jiang
  given name: Chenyan
author list: Agent
  family name: Wang
  given name: Shulun
author list: Agent
  family name: Lu
  given name: Lixing
author list: Agent
  family name: Shi
  given name: Runjie
doi: 10.7717/peerj.9890
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: ©2020 Kang et al.
attribution name: Kang et al.

https://peerj.com/articles/9899
type: item
type: AcademicArticle
title: Nepenthes maximoides (Nepenthaceae) a new, critically endangered (possibly extinct) species in Sect. Alatae from Luzon, Philippines showing striking pitcher convergence with N. maxima (Sect. Regiae) of Indonesia
description: Nepenthes maximoides sp. nov. (Sect. Alatae) is described and assessed as Critically Endangered (Possibly Extinct) from Luzon, Philippines and appears unrecorded in 110 years. The spectacular, large, narrowly funnel-shaped upper pitchers, lids with recurved basal and filiform apical appendages, unlike any other species in the Philippines, closely resemble those of N. maxima (Sect. Regiae) of Sulawesi–New Guinea, likely due to convergent evolution. Following recent phylogenomic analysis, sect. Alatae is divided into two, Sect. Alatae sensu stricto of Luzon to Sibuyan (including N. maximoides), and Sect. Micramphorae, expanded and recircumscribed to encompass those species of the southern Visayas, and Mindanao. A key is provided to the six species now recognised in the newly narrowly recircumscribed Sect. Alatae. The number of Nepenthes species recorded from Luzon has increased from two in 2001, to eight in 2020, all but one of which are endemic to that island, and four of which appear to be point endemics.
format: application/pdf
format: text/html
creator: Charles King
creator: Martin Cheek
subject: Biodiversity
subject: Conservation Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.9899
publisher: PeerJ Inc.
rights: © 2020 King and Cheek
abstract: Nepenthes maximoides sp. nov. (Sect. Alatae) is described and assessed as Critically Endangered (Possibly Extinct) from Luzon, Philippines and appears unrecorded in 110 years. The spectacular, large, narrowly funnel-shaped upper pitchers, lids with recurved basal and filiform apical appendages, unlike any other species in the Philippines, closely resemble those of N. maxima (Sect. Regiae) of Sulawesi–New Guinea, likely due to convergent evolution. Following recent phylogenomic analysis, sect. Alatae is divided into two, Sect. Alatae sensu stricto of Luzon to Sibuyan (including N. maximoides), and Sect. Micramphorae, expanded and recircumscribed to encompass those species of the southern Visayas, and Mindanao. A key is provided to the six species now recognised in the newly narrowly recircumscribed Sect. Alatae. The number of Nepenthes species recorded from Luzon has increased from two in 2001, to eight in 2020, all but one of which are endemic to that island, and four of which appear to be point endemics.
bibliographic citation: King et al. (2020) Nepenthes maximoides (Nepenthaceae) a new, critically endangered (possibly extinct) species in Sect. Alatae from Luzon, Philippines showing striking pitcher convergence with N. maxima (Sect. Regiae) of Indonesia. PeerJ 8:e9899 https://doi.org/10.7717/peerj.9899
date submitted: 2020-07-16
date accepted: 2020-08-17
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: King
  given name: Charles
author list: Agent
  family name: Cheek
  given name: Martin
doi: 10.7717/peerj.9899
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: © 2020 King and Cheek
attribution name: King and Cheek

First report of lionfish prey from Western Florida waters as identified by DNA barcoding
type: item
type: AcademicArticle
description: DNA barcoding was used to identify prey fragments recovered from the stomachs of lionfish harvested during the 2016 Sarasota Lionfish Derby. A total of 305 prey fragments were recovered from 50 stomachs (mean = 4.6 per stomach), of which 184 (60.3%) fragments could be identified to either species or genus when Cytochrome Oxidase I (COI) sequences were queried against the Barcode of Life Database. We identified 21 fish prey species which represented fourteen families and accounted for 95.7% of genetically identifiable prey items. The remaining prey items identified corresponded to six crustacean species. The four most common prey taxa in lionfish stomachs were Ptereleotris calliura (24.3%), an unidentified Microgobius species (20.4%), Diplectum formosum (14.3%), and Apogon aurolineatus (12.2%). The most frequently observed crustacean species, Metapenaeopsis goodei, was found in only three stomachs (6.1%). We also report eleven taxa as putative novel lionfish prey species, most of which are common in Florida waters. Sixteen prey items were identified as lionfish (P. volitans); however, it was not definitive whether these detections were due to cross contamination or cannibalization. This represents the first report of lionfish diets from Florida waters in the Eastern Gulf of Mexico based on barcoding efforts. Our results are largely congruent with previous COI barcoding based studies of lionfish diets, indicating these predators to be generalists exhibiting preferences for specific prey traits but with regional differences in their diets.
format: application/pdf
format: text/html
creator: Carlos A. Santamaria
creator: James Locascio
creator: Taylor M. Greenan
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.9922
publisher: PeerJ Inc.
rights: © 2020 Santamaria et al.
abstract: DNA barcoding was used to identify prey fragments recovered from the stomachs of lionfish harvested during the 2016 Sarasota Lionfish Derby. A total of 305 prey fragments were recovered from 50 stomachs (mean = 4.6 per stomach), of which 184 (60.3%) fragments could be identified to either species or genus when Cytochrome Oxidase I (COI) sequences were queried against the Barcode of Life Database. We identified 21 fish prey species which represented fourteen families and accounted for 95.7% of genetically identifiable prey items. The remaining prey items identified corresponded to six crustacean species. The four most common prey taxa in lionfish stomachs were Ptereleotris calliura (24.3%), an unidentified Microgobius species (20.4%), Diplectum formosum (14.3%), and Apogon aurolineatus (12.2%). The most frequently observed crustacean species, Metapenaeopsis goodei, was found in only three stomachs (6.1%). We also report eleven taxa as putative novel lionfish prey species, most of which are common in Florida waters. Sixteen prey items were identified as lionfish (P. volitans); however, it was not definitive whether these detections were due to cross contamination or cannibalization. This represents the first report of lionfish diets from Florida waters in the Eastern Gulf of Mexico based on barcoding efforts. Our results are largely congruent with previous COI barcoding based studies of lionfish diets, indicating these predators to be generalists exhibiting preferences for specific prey traits but with regional differences in their diets.
bibliographic citation: Santamaria et al. (2020) First report of lionfish prey from Western Florida waters as identified by DNA barcoding. PeerJ 8:e9922 https://doi.org/10.7717/peerj.9922
date submitted: 2020-06-19
date accepted: 2020-08-21
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santamaria
  given name: Carlos A.
author list: Agent
  family name: Locascio
  given name: James
author list: Agent
  family name: Greenan
  given name: Taylor M.
doi: 10.7717/peerj.9922
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: © 2020 Santamaria et al.
attribution name: Santamaria et al.

Two new nematode species (Plectida: Leptolaimidae, Rhadinematidae) from Chatham Rise, New Zealand
type: item
type: AcademicArticle
description: Two new species of the order Plectida are described from Chatham Rise, New Zealand. Leptolaimus dififtinus sp. nov. is characterised by the short body 319–420 microns long, truncate labial region slightly offset from body contour and bearing conspicuous outer labial papillae, cephalic setae 1.3–1.4 microns long, amphid located 4–9 microns from anterior end, lateral alae originating from middle of buccal cavity length, female without supplements, male with precloacal and postcloacal pairs of subventral setae, nine tubular supplements (alveolar supplements absent), tubular supplements weakly S-shaped with pointed tip, spicules arcuate 24 microns or 1.4 cloacal body diameters long and dorsal gubernacular apophyses. Lavareda iramscotti sp. nov. is characterised by adult body length 3,023–3,121 microns long, eight longitudinal rows of body pores each with short papilla, cephalic setae 4–5 microns long, tail 146–165 microns long, male with spicules 54 microns long, gubernaculum with triangular apophyses, 20 precloacal supplements with bifid distal tips arranged in 9 + 1 + 10 pattern, female with vulva at 55% of body length from anterior and cuticularisation perpendicular to vagina at level of vulva. The present study provides the first record of a Leptolaimus species from the New Zealand region and the first description of a female specimen of the genus Lavareda.
format: application/pdf
format: text/html
creator: Daniel Leduc
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9923
publisher: PeerJ Inc.
rights: © 2020 Leduc
abstract: Two new species of the order Plectida are described from Chatham Rise, New Zealand. Leptolaimus dififtinus sp. nov. is characterised by the short body 319–420 microns long, truncate labial region slightly offset from body contour and bearing conspicuous outer labial papillae, cephalic setae 1.3–1.4 microns long, amphid located 4–9 microns from anterior end, lateral alae originating from middle of buccal cavity length, female without supplements, male with precloacal and postcloacal pairs of subventral setae, nine tubular supplements (alveolar supplements absent), tubular supplements weakly S-shaped with pointed tip, spicules arcuate 24 microns or 1.4 cloacal body diameters long and dorsal gubernacular apophyses. Lavareda iramscotti sp. nov. is characterised by adult body length 3,023–3,121 microns long, eight longitudinal rows of body pores each with short papilla, cephalic setae 4–5 microns long, tail 146–165 microns long, male with spicules 54 microns long, gubernaculum with triangular apophyses, 20 precloacal supplements with bifid distal tips arranged in 9 + 1 + 10 pattern, female with vulva at 55% of body length from anterior and cuticularisation perpendicular to vagina at level of vulva. The present study provides the first record of a Leptolaimus species from the New Zealand region and the first description of a female specimen of the genus Lavareda.
bibliographic citation: Leduc (2020) Two new nematode species (Plectida: Leptolaimidae, Rhadinematidae) from Chatham Rise, New Zealand. PeerJ 8:e9923 https://doi.org/10.7717/peerj.9923
date submitted: 2020-07-17
date accepted: 2020-08-21
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leduc
  given name: Daniel
doi: 10.7717/peerj.9923
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: ©2020 Leduc
attribution name: Leduc

Antimicrobial and micronutrient interventions for the management of infants under 6 months of age identified with severe malnutrition: a literature review
type: item
type: AcademicArticle
description: Background Infants under 6 months (U6M) contribute a significant proportion of the burden and mortality of severe malnutrition globally. Evidence of underlying aetiology in this population is sparse, but it is known that the group includes ex-preterm and low birthweight (LBW) infants. They represent a unique population given their dependence on breastmilk or a safe, secure alternative. Nutrition agencies and health providers struggle to make programming decisions on which interventions should be provided to this group based upon the 2013 WHO Guidelines for the ‘Management of Severe Acute Malnutrition in Infants and Young Children’ since there are no published interventional trial data focussed on this population. Interim guidance for this group might be informed by evidence of safety and efficacy in adjacent population groups. Methodology A narrative literature review was performed of systematic reviews, meta-analyses and randomised controlled trials of antimicrobial and micronutrient interventions (antibiotics, deworming, vitamin A, vitamin D, iron, zinc, folic acid and oral rehydration solution (ORS) for malnutrition) across the population groups of low birthweight/preterm infants, infants under 6 months, infants and children over 6 months with acute malnutrition or through supplementation to breastfeeding mothers. Outcomes of interest were safety and efficacy, in terms of mortality and morbidity. Results Ninety-four articles were identified for inclusion within this review. None of these studied interventions exclusively in severely malnourished infants U6M. 64% reported on the safety of studied interventions. Significant heterogeneity was identified in definitions of study populations, interventions provided, and outcomes studied. The evidence for efficacy and safety across population groups is reviewed and presented for the interventions listed. Conclusions The direct evidence base for medical interventions for severely malnourished infants U6M is sparse. Our r…
format: application/pdf
format: text/html
creator: Timothy J. Campion-Smith
creator: Marko Kerac
creator: Marie McGrath
creator: James A. Berkley
subject: Emergency and Critical Care
subject: Global Health
subject: Nutrition
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.9175
publisher: PeerJ Inc.
rights: © 2020 Campion-Smith et al.
abstract: Background Infants under 6 months (U6M) contribute a significant proportion of the burden and mortality of severe malnutrition globally. Evidence of underlying aetiology in this population is sparse, but it is known that the group includes ex-preterm and low birthweight (LBW) infants. They represent a unique population given their dependence on breastmilk or a safe, secure alternative. Nutrition agencies and health providers struggle to make programming decisions on which interventions should be provided to this group based upon the 2013 WHO Guidelines for the ‘Management of Severe Acute Malnutrition in Infants and Young Children’ since there are no published interventional trial data focussed on this population. Interim guidance for this group might be informed by evidence of safety and efficacy in adjacent population groups. Methodology A narrative literature review was performed of systematic reviews, meta-analyses and randomised controlled trials of antimicrobial and micronutrient interventions (antibiotics, deworming, vitamin A, vitamin D, iron, zinc, folic acid and oral rehydration solution (ORS) for malnutrition) across the population groups of low birthweight/preterm infants, infants under 6 months, infants and children over 6 months with acute malnutrition or through supplementation to breastfeeding mothers. Outcomes of interest were safety and efficacy, in terms of mortality and morbidity. Results Ninety-four articles were identified for inclusion within this review. None of these studied interventions exclusively in severely malnourished infants U6M. 64% reported on the safety of studied interventions. Significant heterogeneity was identified in definitions of study populations, interventions provided, and outcomes studied. The evidence for efficacy and safety across population groups is reviewed and presented for the interventions listed. Conclusions The direct evidence base for medical interventions for severely malnourished infants U6M is sparse. Our r…
bibliographic citation: Campion-Smith et al. (2020) Antimicrobial and micronutrient interventions for the management of infants under 6 months of age identified with severe malnutrition: a literature review. PeerJ 8:e9175 https://doi.org/10.7717/peerj.9175
date submitted: 2019-10-11
date accepted: 2020-04-21
issued: 2020-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campion-Smith
  given name: Timothy J.
author list: Agent
  family name: Kerac
  given name: Marko
author list: Agent
  family name: McGrath
  given name: Marie
author list: Agent
  family name: Berkley
  given name: James A.
doi: 10.7717/peerj.9175
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-10
copyright: ©2020 Campion-Smith et al.
attribution name: Campion-Smith et al.

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