PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands
items: Patchiness of forest landscape can predict species distribution better than abundance: the case of a forest-dwelling passerine, the short-toed treecreeper, in central Italy
items: Is there any effect of pneumoperitoneum pressure on coagulation and fibrinolysis during laparoscopic cholecystectomy?
items: Improved cartilage regeneration by implantation of acellular biomaterials after bone marrow stimulation: a systematic review and meta-analysis of animal studies
items: Bioavailability of D-methionine relative to L-methionine for nursery pigs using the slope-ratio assay
items: ECG is an inefficient screening-tool for left ventricular hypertrophy in normotensive African children population
items: Genome-wide identification and characterization of WRKY gene family in Salix suchowensis
items: MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense
items: Testing the link between genome size and growth rate in maize
items: Digital Accessible Knowledge and well-inventoried sites for birds in Mexico: baseline sites for measuring faunistic change

Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands
type: item
type: AcademicArticle
description: Annual Mediterranean species of the genus Brachypodium are promising model plants for energy crops since their selfing nature and short-life cycles are an advantage in breeding programs. The false brome, B. distachyon, has already been sequenced and new genomic initiatives have triggered the de-novo genome sequencing of its close relatives such as B. stacei, a species that was until recently mistaken for B. distachyon. However, the success of these initiatives hinges on detailed knowledge about the distribution of genetic variation within and among populations for the effective use of germplasm in a breeding program. Understanding population genetic diversity and genetic structure is also an important prerequisite for designing effective experimental populations for genomic wide studies. However, population genetic data are still limited in B. stacei. We therefore selected and amplified 10 nuclear microsatellite markers to depict patterns of population structure and genetic variation among 181 individuals from 19 populations of B. stacei occurring in its predominant range, the western Mediterranean area: mainland Iberian Peninsula, continental Balearic Islands and oceanic Canary Islands. Our genetic results support the occurrence of a predominant selfing system with extremely high levels of homozygosity across the analyzed populations. Despite the low level of genetic variation found, two different genetic clusters were retrieved, one clustering all SE Iberian mainland populations and the island of Minorca and another one grouping all S Iberian mainland populations, the Canary Islands and all Majorcan populations except one that clustered with the former group. These results, together with a high sharing of alleles (89%) suggest different colonization routes from the mainland Iberian Peninsula into the islands. A recent colonization scenario could explain the relatively low levels of genetic diversity and low number of alleles found in the Canary Islands populations…
format: application/pdf
format: text/html
creator: Valeriia Shiposha
creator: Pilar Catalán
creator: Marina Olonova
creator: Isabel Marques
subject: Evolutionary Studies
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.2407
publisher: PeerJ Inc.
rights: © 2016 Shiposha et al.
abstract: Annual Mediterranean species of the genus Brachypodium are promising model plants for energy crops since their selfing nature and short-life cycles are an advantage in breeding programs. The false brome, B. distachyon, has already been sequenced and new genomic initiatives have triggered the de-novo genome sequencing of its close relatives such as B. stacei, a species that was until recently mistaken for B. distachyon. However, the success of these initiatives hinges on detailed knowledge about the distribution of genetic variation within and among populations for the effective use of germplasm in a breeding program. Understanding population genetic diversity and genetic structure is also an important prerequisite for designing effective experimental populations for genomic wide studies. However, population genetic data are still limited in B. stacei. We therefore selected and amplified 10 nuclear microsatellite markers to depict patterns of population structure and genetic variation among 181 individuals from 19 populations of B. stacei occurring in its predominant range, the western Mediterranean area: mainland Iberian Peninsula, continental Balearic Islands and oceanic Canary Islands. Our genetic results support the occurrence of a predominant selfing system with extremely high levels of homozygosity across the analyzed populations. Despite the low level of genetic variation found, two different genetic clusters were retrieved, one clustering all SE Iberian mainland populations and the island of Minorca and another one grouping all S Iberian mainland populations, the Canary Islands and all Majorcan populations except one that clustered with the former group. These results, together with a high sharing of alleles (89%) suggest different colonization routes from the mainland Iberian Peninsula into the islands. A recent colonization scenario could explain the relatively low levels of genetic diversity and low number of alleles found in the Canary Islands populations…
bibliographic citation: Shiposha et al. (2016) Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands. PeerJ 4:e2407 https://doi.org/10.7717/peerj.2407
date submitted: 2016-04-11
date accepted: 2016-08-04
issued: 2016-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shiposha
  given name: Valeriia
author list: Agent
  family name: Catalán
  given name: Pilar
author list: Agent
  family name: Olonova
  given name: Marina
author list: Agent
  family name: Marques
  given name: Isabel
doi: 10.7717/peerj.2407
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-08
copyright: © 2016 Shiposha et al.
attribution name: Shiposha et al.

Patchiness of forest landscape can predict species distribution better than abundance: the case of a forest-dwelling passerine, the short-toed treecreeper, in central Italy
type: item
type: AcademicArticle
description: Environmental heterogeneity affects not only the distribution of a species but also its local abundance. High heterogeneity due to habitat alteration and fragmentation can influence the realized niche of a species, lowering habitat suitability as well as reducing local abundance. We investigate whether a relationship exists between habitat suitability and abundance and whether both are affected by fragmentation. Our aim was to assess the predictive power of such a relationship to derive advice for environmental management. As a model species we used a forest specialist, the short-toed treecreeper (Family: Certhiidae; Certhia brachydactyla Brehm, 1820), and sampled it in central Italy. Species distribution was modelled as a function of forest structure, productivity and fragmentation, while abundance was directly estimated in two central Italian forest stands. Different algorithms were implemented to model species distribution, employing 170 occurrence points provided mostly by the MITO2000 database: an artificial neural network, classification tree analysis, flexible discriminant analysis, generalized boosting models, generalized linear models, multivariate additive regression splines, maximum entropy and random forests. Abundance was estimated also considering detectability, through N-mixture models. Differences between forest stands in both abundance and habitat suitability were assessed as well as the existence of a relationship. Simpler algorithms resulted in higher goodness of fit than complex ones. Fragmentation was highly influential in determining potential distribution. Local abundance and habitat suitability differed significantly between the two forest stands, which were also significantly different in the degree of fragmentation. Regression showed that suitability has a weak significant effect in explaining increasing value of abundance. In particular, local abundances varied both at low and high suitability values. The study lends support to the concept…
format: application/pdf
format: text/html
creator: Marco Basile
creator: Francesco Valerio
creator: Rosario Balestrieri
creator: Mario Posillico
creator: Rodolfo Bucci
creator: Tiziana Altea
creator: Bruno De Cinti
creator: Giorgio Matteucci
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.2398
publisher: PeerJ Inc.
rights: © 2016 Basile et al.
abstract: Environmental heterogeneity affects not only the distribution of a species but also its local abundance. High heterogeneity due to habitat alteration and fragmentation can influence the realized niche of a species, lowering habitat suitability as well as reducing local abundance. We investigate whether a relationship exists between habitat suitability and abundance and whether both are affected by fragmentation. Our aim was to assess the predictive power of such a relationship to derive advice for environmental management. As a model species we used a forest specialist, the short-toed treecreeper (Family: Certhiidae; Certhia brachydactyla Brehm, 1820), and sampled it in central Italy. Species distribution was modelled as a function of forest structure, productivity and fragmentation, while abundance was directly estimated in two central Italian forest stands. Different algorithms were implemented to model species distribution, employing 170 occurrence points provided mostly by the MITO2000 database: an artificial neural network, classification tree analysis, flexible discriminant analysis, generalized boosting models, generalized linear models, multivariate additive regression splines, maximum entropy and random forests. Abundance was estimated also considering detectability, through N-mixture models. Differences between forest stands in both abundance and habitat suitability were assessed as well as the existence of a relationship. Simpler algorithms resulted in higher goodness of fit than complex ones. Fragmentation was highly influential in determining potential distribution. Local abundance and habitat suitability differed significantly between the two forest stands, which were also significantly different in the degree of fragmentation. Regression showed that suitability has a weak significant effect in explaining increasing value of abundance. In particular, local abundances varied both at low and high suitability values. The study lends support to the concept…
bibliographic citation: Basile et al. (2016) Patchiness of forest landscape can predict species distribution better than abundance: the case of a forest-dwelling passerine, the short-toed treecreeper, in central Italy. PeerJ 4:e2398 https://doi.org/10.7717/peerj.2398
date submitted: 2016-05-13
date accepted: 2016-08-02
issued: 2016-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Basile
  given name: Marco
author list: Agent
  family name: Valerio
  given name: Francesco
author list: Agent
  family name: Balestrieri
  given name: Rosario
author list: Agent
  family name: Posillico
  given name: Mario
author list: Agent
  family name: Bucci
  given name: Rodolfo
author list: Agent
  family name: Altea
  given name: Tiziana
author list: Agent
  family name: De Cinti
  given name: Bruno
author list: Agent
  family name: Matteucci
  given name: Giorgio
doi: 10.7717/peerj.2398
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-08
copyright: ©2016 Basile et al.
attribution name: Basile et al.

Is there any effect of pneumoperitoneum pressure on coagulation and fibrinolysis during laparoscopic cholecystectomy?
type: item
type: AcademicArticle
description: Background Laparoscopic cholecystectomies (LC) are generally performed in a 12 mmHg-pressured pneumoperitoneum in a slight sitting position. Considerable thromboembolism risk arises in this operation due to pneumoperitoneum, operation position and risk factors of patients. We aim to investigate the effect of pneumoperitoneum pressure on coagulation and fibrinolysis under general anesthesia. Material and Methods Fifty American Society of Anesthesiologist (ASA) I–III patients who underwent elective LC without thromboprophlaxis were enrolled in this prospective study. The patients were randomly divided into two groups according to the pneumoperitoneum pressure during LC: the 10 mmHg group (n = 25) and the 14 mmHg group. Prothrombin time (PT), thrombin time (TT), International Normalized Ratio (INR), activated partial thromboplastin time (aPTT) and blood levels of d-dimer and fibrinogen were measured preoperatively (pre), one hour (post1) and 24 h (post24) after the surgery. Moreover, alanine amino transferase, aspartate amino transferase and lactate dehydrogenase were measured before and after the surgery. These parameters were compared between and within the groups. Results PT, TT, aPTT, INR, and D-dimer and fibrinogen levels significantly increased after the surgery in both of the groups. D-dimer level was significantly higher in 14-mmHg group at post24. Conclusion Both the 10-mmHg and 14-mmHg pressure of pneumoperitoneum may lead to affect coagulation tests and fibrinogen and D-dimer levels without any occurrence of deep vein thrombosis, but 14-mmHg pressure of pneumoperitoneum has a greater effect on D-dimer. However, lower pneumoperitoneum pressure may be useful for the prevention of deep vein thrombosis.
format: application/pdf
format: text/html
creator: Turgut Donmez
creator: Sinan Uzman
creator: Dogan Yildirim
creator: Adnan Hut
creator: Huseyin Imam Avaroglu
creator: Duygu Ayfer Erdem
creator: Erdinc Cekic
creator: Fazilet Erozgen
subject: Anesthesiology and Pain Management
subject: Gastroenterology and Hepatology
subject: Hematology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.2375
publisher: PeerJ Inc.
rights: © 2016 Donmez et al.
abstract: Background Laparoscopic cholecystectomies (LC) are generally performed in a 12 mmHg-pressured pneumoperitoneum in a slight sitting position. Considerable thromboembolism risk arises in this operation due to pneumoperitoneum, operation position and risk factors of patients. We aim to investigate the effect of pneumoperitoneum pressure on coagulation and fibrinolysis under general anesthesia. Material and Methods Fifty American Society of Anesthesiologist (ASA) I–III patients who underwent elective LC without thromboprophlaxis were enrolled in this prospective study. The patients were randomly divided into two groups according to the pneumoperitoneum pressure during LC: the 10 mmHg group (n = 25) and the 14 mmHg group. Prothrombin time (PT), thrombin time (TT), International Normalized Ratio (INR), activated partial thromboplastin time (aPTT) and blood levels of d-dimer and fibrinogen were measured preoperatively (pre), one hour (post1) and 24 h (post24) after the surgery. Moreover, alanine amino transferase, aspartate amino transferase and lactate dehydrogenase were measured before and after the surgery. These parameters were compared between and within the groups. Results PT, TT, aPTT, INR, and D-dimer and fibrinogen levels significantly increased after the surgery in both of the groups. D-dimer level was significantly higher in 14-mmHg group at post24. Conclusion Both the 10-mmHg and 14-mmHg pressure of pneumoperitoneum may lead to affect coagulation tests and fibrinogen and D-dimer levels without any occurrence of deep vein thrombosis, but 14-mmHg pressure of pneumoperitoneum has a greater effect on D-dimer. However, lower pneumoperitoneum pressure may be useful for the prevention of deep vein thrombosis.
bibliographic citation: Donmez et al. (2016) Is there any effect of pneumoperitoneum pressure on coagulation and fibrinolysis during laparoscopic cholecystectomy?. PeerJ 4:e2375 https://doi.org/10.7717/peerj.2375
date submitted: 2016-03-29
date accepted: 2016-07-28
issued: 2016-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Donmez
  given name: Turgut
author list: Agent
  family name: Uzman
  given name: Sinan
author list: Agent
  family name: Yildirim
  given name: Dogan
author list: Agent
  family name: Hut
  given name: Adnan
author list: Agent
  family name: Avaroglu
  given name: Huseyin Imam
author list: Agent
  family name: Erdem
  given name: Duygu Ayfer
author list: Agent
  family name: Cekic
  given name: Erdinc
author list: Agent
  family name: Erozgen
  given name: Fazilet
doi: 10.7717/peerj.2375
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-08
copyright: ©2016 Donmez et al.
attribution name: Donmez et al.

Improved cartilage regeneration by implantation of acellular biomaterials after bone marrow stimulation: a systematic review and meta-analysis of animal studies
type: item
type: AcademicArticle
description: Microfracture surgery may be applied to treat cartilage defects. During the procedure the subchondral bone is penetrated, allowing bone marrow-derived mesenchymal stem cells to migrate towards the defect site and form new cartilage tissue. Microfracture surgery generally results in the formation of mechanically inferior fibrocartilage. As a result, this technique offers only temporary clinical improvement. Tissue engineering and regenerative medicine may improve the outcome of microfracture surgery. Filling the subchondral defect with a biomaterial may provide a template for the formation of new hyaline cartilage tissue. In this study, a systematic review and meta-analysis were performed to assess the current evidence for the efficacy of cartilage regeneration in preclinical models using acellular biomaterials implanted after marrow stimulating techniques (microfracturing and subchondral drilling) compared to the natural healing response of defects. The review aims to provide new insights into the most effective biomaterials, to provide an overview of currently existing knowledge, and to identify potential lacunae in current studies to direct future research. A comprehensive search was systematically performed in PubMed and EMBASE (via OvidSP) using search terms related to tissue engineering, cartilage and animals. Primary studies in which acellular biomaterials were implanted in osteochondral defects in the knee or ankle joint in healthy animals were included and study characteristics tabulated (283 studies out of 6,688 studies found). For studies comparing non-treated empty defects to defects containing implanted biomaterials and using semi-quantitative histology as outcome measure, the risk of bias (135 studies) was assessed and outcome data were collected for meta-analysis (151 studies). Random-effects meta-analyses were performed, using cartilage regeneration as outcome measure on an absolute 0–100% scale. Implantation of acellular biomaterials significantly im…
format: application/pdf
format: text/html
creator: Michiel W. Pot
creator: Veronica K. Gonzales
creator: Pieter Buma
creator: Joanna IntHout
creator: Toin H. van Kuppevelt
creator: Rob B.M. de Vries
creator: Willeke F. Daamen
subject: Bioengineering
subject: Orthopedics
subject: Rheumatology
subject: Translational Medicine
description: doi:10.7717/peerj.2243
publisher: PeerJ Inc.
rights: © 2016 Pot et al.
abstract: Microfracture surgery may be applied to treat cartilage defects. During the procedure the subchondral bone is penetrated, allowing bone marrow-derived mesenchymal stem cells to migrate towards the defect site and form new cartilage tissue. Microfracture surgery generally results in the formation of mechanically inferior fibrocartilage. As a result, this technique offers only temporary clinical improvement. Tissue engineering and regenerative medicine may improve the outcome of microfracture surgery. Filling the subchondral defect with a biomaterial may provide a template for the formation of new hyaline cartilage tissue. In this study, a systematic review and meta-analysis were performed to assess the current evidence for the efficacy of cartilage regeneration in preclinical models using acellular biomaterials implanted after marrow stimulating techniques (microfracturing and subchondral drilling) compared to the natural healing response of defects. The review aims to provide new insights into the most effective biomaterials, to provide an overview of currently existing knowledge, and to identify potential lacunae in current studies to direct future research. A comprehensive search was systematically performed in PubMed and EMBASE (via OvidSP) using search terms related to tissue engineering, cartilage and animals. Primary studies in which acellular biomaterials were implanted in osteochondral defects in the knee or ankle joint in healthy animals were included and study characteristics tabulated (283 studies out of 6,688 studies found). For studies comparing non-treated empty defects to defects containing implanted biomaterials and using semi-quantitative histology as outcome measure, the risk of bias (135 studies) was assessed and outcome data were collected for meta-analysis (151 studies). Random-effects meta-analyses were performed, using cartilage regeneration as outcome measure on an absolute 0–100% scale. Implantation of acellular biomaterials significantly im…
bibliographic citation: Pot et al. (2016) Improved cartilage regeneration by implantation of acellular biomaterials after bone marrow stimulation: a systematic review and meta-analysis of animal studies. PeerJ 4:e2243 https://doi.org/10.7717/peerj.2243
date submitted: 2016-02-26
date accepted: 2016-06-21
issued: 2016-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pot
  given name: Michiel W.
author list: Agent
  family name: Gonzales
  given name: Veronica K.
author list: Agent
  family name: Buma
  given name: Pieter
author list: Agent
  family name: IntHout
  given name: Joanna
author list: Agent
  family name: van Kuppevelt
  given name: Toin H.
author list: Agent
  family name: de Vries
  given name: Rob B.M.
author list: Agent
  family name: Daamen
  given name: Willeke F.
doi: 10.7717/peerj.2243
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-08
copyright: ©2016 Pot et al.
attribution name: Pot et al.

Bioavailability of D-methionine relative to L-methionine for nursery pigs using the slope-ratio assay
type: item
type: AcademicArticle
description: This experiment was conducted to determine the bioavailability of D-methionine (Met) relative to L-Met for nursery pigs using the slope-ratio assay. A total of 50 crossbred barrows with an initial BW of 13.5 kg (SD = 1.0) were used in an N balance study. A Met-deficient basal diet (BD) was formulated to contain an adequate amount of all amino acids (AA) for 10–20 kg pigs except for Met. The two reference diets were prepared by supplementing the BD with 0.4 or 0.8 g L-Met/kg at the expense of corn starch, and an equivalent concentration of D-Met was added to the BD for the two test diets. The pigs were adapted to the experimental diets for 5 d and then total but separated collection of feces and urine was conducted for 4 d according to the marker-to-marker procedure. Nitrogen intakes were similar across the treatments. Fecal N output was not affected by Met supplementation regardless of source and consequently apparent N digestibility did not change. Conversely, there was a negative linear response (P < 0.01) to Met supplementation with both Met isomers in urinary N output, which resulted in increased retained N (g/4 d) and N retention (% of intake). No quadratic response was observed in any of the N balance criteria. The estimated bioavailability of D-Met relative to L-Met from urinary N output (g/4 d) and N retention (% of intake) as dependent variables using supplemental Met intake (g/4 d) as an independent variable were 87.6% and 89.6%, respectively; however, approximately 95% of the fiducial limits for the relative bioavailability estimates included 100%. In conclusion, with an absence of statistical significance, the present study indicated that the mean relative bioequivalence of D- to L-Met was 87.6% based on urinary N output or 89.6% based on N retention.
format: application/pdf
format: text/html
creator: Changsu Kong
creator: Jong Young Ahn
creator: Beob G. Kim
subject: Agricultural Science
subject: Animal Behavior
subject: Veterinary Medicine
subject: Zoology
subject: Nutrition
description: doi:10.7717/peerj.2368
publisher: PeerJ Inc.
rights: © 2016 Kong et al.
abstract: This experiment was conducted to determine the bioavailability of D-methionine (Met) relative to L-Met for nursery pigs using the slope-ratio assay. A total of 50 crossbred barrows with an initial BW of 13.5 kg (SD = 1.0) were used in an N balance study. A Met-deficient basal diet (BD) was formulated to contain an adequate amount of all amino acids (AA) for 10–20 kg pigs except for Met. The two reference diets were prepared by supplementing the BD with 0.4 or 0.8 g L-Met/kg at the expense of corn starch, and an equivalent concentration of D-Met was added to the BD for the two test diets. The pigs were adapted to the experimental diets for 5 d and then total but separated collection of feces and urine was conducted for 4 d according to the marker-to-marker procedure. Nitrogen intakes were similar across the treatments. Fecal N output was not affected by Met supplementation regardless of source and consequently apparent N digestibility did not change. Conversely, there was a negative linear response (P < 0.01) to Met supplementation with both Met isomers in urinary N output, which resulted in increased retained N (g/4 d) and N retention (% of intake). No quadratic response was observed in any of the N balance criteria. The estimated bioavailability of D-Met relative to L-Met from urinary N output (g/4 d) and N retention (% of intake) as dependent variables using supplemental Met intake (g/4 d) as an independent variable were 87.6% and 89.6%, respectively; however, approximately 95% of the fiducial limits for the relative bioavailability estimates included 100%. In conclusion, with an absence of statistical significance, the present study indicated that the mean relative bioequivalence of D- to L-Met was 87.6% based on urinary N output or 89.6% based on N retention.
bibliographic citation: Kong et al. (2016) Bioavailability of D-methionine relative to L-methionine for nursery pigs using the slope-ratio assay. PeerJ 4:e2368 https://doi.org/10.7717/peerj.2368
date submitted: 2016-03-02
date accepted: 2016-07-25
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Changsu
author list: Agent
  family name: Ahn
  given name: Jong Young
author list: Agent
  family name: Kim
  given name: Beob G.
doi: 10.7717/peerj.2368
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: © 2016 Kong et al.
attribution name: Kong et al.

ECG is an inefficient screening-tool for left ventricular hypertrophy in normotensive African children population
type: item
type: AcademicArticle
description: Background Left ventricular hypertrophy (LVH) is a marker of pediatric hypertension and predicts development of cardiovascular events. Electrocardiography (ECG) screening is used in pediatrics to detect LVH thanks to major accessibility, reproducibility and easy to use compared to transthoracic echocardiography (TTE), that remains the standard technique. Several diseases were previously investigated, but no data exists regarding our study population. The aim of our study was to evaluate the relationship between electrocardiographic and echocardiographic criteria of LVH in normotensive African children. Methods We studied 313 children (mean age 7,8 ± 3 yo), in north-Madagascar. They underwent ECG and TTE. Sokolow-Lyon index was calculated to identify ECG-LVH (>35 mm). Left ventricle mass (LVM) with TTE was calculated and indexed by height2.7 (LVMI2.7) and weight (LVMIw). We report the prevalence of TTE-LVH using three methods: (1) calculating percentiles age- and sex- specific with values >95th percentile identifying LVH; (2) LVMI2.7 >51 g/m2.7; (3) LVMIw >3.4 g/weight. Results 40 (13%) children showed LVMI values >95th percentile, 24 children (8%) an LVMI2.7 >51 g/m2.7 while 19 children (6%) an LVMIw >3.4 g/kg. LVH-ECG by Sokolow-Lyon index was present in five, three and three children respectively, with poor values of sensitivity (ranging from 13 to 16%), positive predictive value (from 11 to 18%) and high values of specificity (up to 92%). The effects of anthropometrics parameters on Sokolow-Lyon were analyzed and showed poor correlation. Conclusion ECG is a poor screening test for detecting LVH in children. In clinical practice, TTE remains the only tool to be used to exclude LVH.
format: application/pdf
format: text/html
creator: Giuseppe Di Gioia
creator: Antonio Creta
creator: Cosimo Marco Campanale
creator: Mario Fittipaldi
creator: Riccardo Giorgino
creator: Fabio Quintarelli
creator: Umberto Satriano
creator: Alessandro Cruciani
creator: Vincenzo Antinolfi
creator: Stefano Di Berardino
creator: Davide Costanzo
creator: Ranieri Bettini
creator: Giuseppe Mangiameli
creator: Marco Caricato
creator: Giovanni Mottini
subject: Cardiology
subject: Epidemiology
subject: Pediatrics
description: doi:10.7717/peerj.2439
publisher: PeerJ Inc.
rights: © 2016 Di Gioia et al.
abstract: Background Left ventricular hypertrophy (LVH) is a marker of pediatric hypertension and predicts development of cardiovascular events. Electrocardiography (ECG) screening is used in pediatrics to detect LVH thanks to major accessibility, reproducibility and easy to use compared to transthoracic echocardiography (TTE), that remains the standard technique. Several diseases were previously investigated, but no data exists regarding our study population. The aim of our study was to evaluate the relationship between electrocardiographic and echocardiographic criteria of LVH in normotensive African children. Methods We studied 313 children (mean age 7,8 ± 3 yo), in north-Madagascar. They underwent ECG and TTE. Sokolow-Lyon index was calculated to identify ECG-LVH (>35 mm). Left ventricle mass (LVM) with TTE was calculated and indexed by height2.7 (LVMI2.7) and weight (LVMIw). We report the prevalence of TTE-LVH using three methods: (1) calculating percentiles age- and sex- specific with values >95th percentile identifying LVH; (2) LVMI2.7 >51 g/m2.7; (3) LVMIw >3.4 g/weight. Results 40 (13%) children showed LVMI values >95th percentile, 24 children (8%) an LVMI2.7 >51 g/m2.7 while 19 children (6%) an LVMIw >3.4 g/kg. LVH-ECG by Sokolow-Lyon index was present in five, three and three children respectively, with poor values of sensitivity (ranging from 13 to 16%), positive predictive value (from 11 to 18%) and high values of specificity (up to 92%). The effects of anthropometrics parameters on Sokolow-Lyon were analyzed and showed poor correlation. Conclusion ECG is a poor screening test for detecting LVH in children. In clinical practice, TTE remains the only tool to be used to exclude LVH.
bibliographic citation: Di Gioia et al. (2016) ECG is an inefficient screening-tool for left ventricular hypertrophy in normotensive African children population. PeerJ 4:e2439 https://doi.org/10.7717/peerj.2439
date submitted: 2016-05-02
date accepted: 2016-08-13
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Di Gioia
  given name: Giuseppe
author list: Agent
  family name: Creta
  given name: Antonio
author list: Agent
  family name: Campanale
  given name: Cosimo Marco
author list: Agent
  family name: Fittipaldi
  given name: Mario
author list: Agent
  family name: Giorgino
  given name: Riccardo
author list: Agent
  family name: Quintarelli
  given name: Fabio
author list: Agent
  family name: Satriano
  given name: Umberto
author list: Agent
  family name: Cruciani
  given name: Alessandro
author list: Agent
  family name: Antinolfi
  given name: Vincenzo
author list: Agent
  family name: Di Berardino
  given name: Stefano
author list: Agent
  family name: Costanzo
  given name: Davide
author list: Agent
  family name: Bettini
  given name: Ranieri
author list: Agent
  family name: Mangiameli
  given name: Giuseppe
author list: Agent
  family name: Caricato
  given name: Marco
author list: Agent
  family name: Mottini
  given name: Giovanni
doi: 10.7717/peerj.2439
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: ©2016 Di Gioia et al.
attribution name: Di Gioia et al.

Genome-wide identification and characterization of WRKY gene family in Salix suchowensis
type: item
type: AcademicArticle
description: WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing of Salix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I–III), with five subgroups (IIa–IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon–intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events (SDs) played a more prominent role in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of thi…
format: application/pdf
format: text/html
creator: Changwei Bi
creator: Yiqing Xu
creator: Qiaolin Ye
creator: Tongming Yin
creator: Ning Ye
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.2437
publisher: PeerJ Inc.
rights: © 2016 Bi et al.
abstract: WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing of Salix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I–III), with five subgroups (IIa–IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon–intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events (SDs) played a more prominent role in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of thi…
bibliographic citation: Bi et al. (2016) Genome-wide identification and characterization of WRKY gene family in Salix suchowensis. PeerJ 4:e2437 https://doi.org/10.7717/peerj.2437
date submitted: 2016-06-24
date accepted: 2016-08-13
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bi
  given name: Changwei
author list: Agent
  family name: Xu
  given name: Yiqing
author list: Agent
  family name: Ye
  given name: Qiaolin
author list: Agent
  family name: Yin
  given name: Tongming
author list: Agent
  family name: Ye
  given name: Ning
doi: 10.7717/peerj.2437
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: © 2016 Bi et al.
attribution name: Bi et al.

MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense
type: item
type: AcademicArticle
description: Many methylotrophs, microorganisms that consume carbon compounds lacking carbon–carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. The MxaFI methanol dehydrogenase (MDH) contains calcium in its active site, while the XoxF enzyme contains a lanthanide in its active site. The genes encoding the MDH enzymes are differentially regulated by the presence of lanthanides. In this study, we found that the histidine kinase MxaY controls the lanthanide-mediated switch in Methylomicrobium buryatense 5GB1C. MxaY controls the transcription of genes encoding MxaFI and XoxF at least partially by controlling the transcript levels of the orphan response regulator MxaB. We identify a constitutively active version of MxaY, and identify the mutated residue that may be involved in lanthanide sensing. Lastly, we find evidence to suggest that tight control of active MDH production is required for wild-type growth rates.
format: application/pdf
format: text/html
creator: Frances Chu
creator: David A.C. Beck
creator: Mary E. Lidstrom
subject: Genetics
subject: Microbiology
description: doi:10.7717/peerj.2435
publisher: PeerJ Inc.
rights: © 2016 Chu et al.
abstract: Many methylotrophs, microorganisms that consume carbon compounds lacking carbon–carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. The MxaFI methanol dehydrogenase (MDH) contains calcium in its active site, while the XoxF enzyme contains a lanthanide in its active site. The genes encoding the MDH enzymes are differentially regulated by the presence of lanthanides. In this study, we found that the histidine kinase MxaY controls the lanthanide-mediated switch in Methylomicrobium buryatense 5GB1C. MxaY controls the transcription of genes encoding MxaFI and XoxF at least partially by controlling the transcript levels of the orphan response regulator MxaB. We identify a constitutively active version of MxaY, and identify the mutated residue that may be involved in lanthanide sensing. Lastly, we find evidence to suggest that tight control of active MDH production is required for wild-type growth rates.
bibliographic citation: Chu et al. (2016) MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense. PeerJ 4:e2435 https://doi.org/10.7717/peerj.2435
date submitted: 2016-05-25
date accepted: 2016-08-12
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chu
  given name: Frances
author list: Agent
  family name: Beck
  given name: David A.C.
author list: Agent
  family name: Lidstrom
  given name: Mary E.
doi: 10.7717/peerj.2435
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: ©2016 Chu et al.
attribution name: Chu et al.

Testing the link between genome size and growth rate in maize
type: item
type: AcademicArticle
description: Little is known about the factors driving within species Genome Size (GS) variation. GS may be shaped indirectly by natural selection on development and adaptative traits. Because GS variation is particularly pronounced in maize, we have sampled 83 maize inbred lines from three well described genetic groups adapted to contrasted climate conditions: inbreds of tropical origin, Flint inbreds grown in temperate climates, and Dent inbreds distributed in the Corn Belt. As a proxy for growth rate, we measured the Leaf Elongation Rate maximum during nighttime (LERmax) as well as GS in all inbred lines. In addition we combined available and new nucleotide polymorphism data at 29,090 sites to characterize the genetic structure of our panel. We found significant variation for both LERmax and GS among groups defined by our genetic structuring. Tropicals displayed larger GS than Flints while Dents exhibited intermediate values. LERmax followed the opposite trend with greater growth rate in Flints than in Tropicals. In other words, LERmax and GS exhibited a significantly negative correlation (r = − 0.27). However, this correlation was driven by among-group variation rather than within-group variation—it was no longer significant after controlling for structure and kinship among inbreds. Our results indicate that selection on GS may have accompanied ancient maize diffusion from its center of origin, with large DNA content excluded from temperate areas. Whether GS has been targeted by more intense selection during modern breeding within groups remains an open question.
format: application/pdf
format: text/html
creator: Maud I. Tenaillon
creator: Domenica Manicacci
creator: Stéphane D. Nicolas
creator: Francois Tardieu
creator: Claude Welcker
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.2408
publisher: PeerJ Inc.
rights: © 2016 Tenaillon et al.
abstract: Little is known about the factors driving within species Genome Size (GS) variation. GS may be shaped indirectly by natural selection on development and adaptative traits. Because GS variation is particularly pronounced in maize, we have sampled 83 maize inbred lines from three well described genetic groups adapted to contrasted climate conditions: inbreds of tropical origin, Flint inbreds grown in temperate climates, and Dent inbreds distributed in the Corn Belt. As a proxy for growth rate, we measured the Leaf Elongation Rate maximum during nighttime (LERmax) as well as GS in all inbred lines. In addition we combined available and new nucleotide polymorphism data at 29,090 sites to characterize the genetic structure of our panel. We found significant variation for both LERmax and GS among groups defined by our genetic structuring. Tropicals displayed larger GS than Flints while Dents exhibited intermediate values. LERmax followed the opposite trend with greater growth rate in Flints than in Tropicals. In other words, LERmax and GS exhibited a significantly negative correlation (r = − 0.27). However, this correlation was driven by among-group variation rather than within-group variation—it was no longer significant after controlling for structure and kinship among inbreds. Our results indicate that selection on GS may have accompanied ancient maize diffusion from its center of origin, with large DNA content excluded from temperate areas. Whether GS has been targeted by more intense selection during modern breeding within groups remains an open question.
bibliographic citation: Tenaillon et al. (2016) Testing the link between genome size and growth rate in maize. PeerJ 4:e2408 https://doi.org/10.7717/peerj.2408
date submitted: 2016-05-26
date accepted: 2016-08-04
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tenaillon
  given name: Maud I.
author list: Agent
  family name: Manicacci
  given name: Domenica
author list: Agent
  family name: Nicolas
  given name: Stéphane D.
author list: Agent
  family name: Tardieu
  given name: Francois
author list: Agent
  family name: Welcker
  given name: Claude
doi: 10.7717/peerj.2408
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: ©2016 Tenaillon et al.
attribution name: Tenaillon et al.

Digital Accessible Knowledge and well-inventoried sites for birds in Mexico: baseline sites for measuring faunistic change
type: item
type: AcademicArticle
description: Background Faunal change is a basic and fundamental element in ecology, biogeography, and conservation biology, yet vanishingly few detailed studies have documented such changes rigorously over decadal time scales. This study responds to that gap in knowledge, providing a detailed analysis of Digital Accessible Knowledge of the birds of Mexico, designed to marshal DAK to identify sites that were sampled and inventoried rigorously prior to the beginning of major global climate change (1980). Methods We accumulated DAK records for Mexican birds from all relevant online biodiversity data portals. After extensive cleaning steps, we calculated completeness indices for each 0.05° pixel across the country; we also detected ‘hotspots’ of sampling, and calculated completeness indices for these broader areas as well. Sites were designated as well-sampled if they had completeness indices above 80% and >200 associated DAK records. Results We identified 100 individual pixels and 20 broader ‘hotspots’ of sampling that were demonstrably well-inventoried prior to 1980. These sites are catalogued and documented to promote and enable resurvey efforts that can document events of avifaunal change (and non-change) across the country on decadal time scales. Conclusions Development of repeated surveys for many sites across Mexico, and particularly for sites for which historical surveys document their avifaunas prior to major climate change processes, would pay rich rewards in information about distributional dynamics of Mexican birds.
format: application/pdf
format: text/html
creator: A. Townsend Peterson
creator: Adolfo G. Navarro-Sigüenza
creator: Enrique Martínez-Meyer
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.2362
publisher: PeerJ Inc.
rights: © 2016 Peterson et al.
abstract: Background Faunal change is a basic and fundamental element in ecology, biogeography, and conservation biology, yet vanishingly few detailed studies have documented such changes rigorously over decadal time scales. This study responds to that gap in knowledge, providing a detailed analysis of Digital Accessible Knowledge of the birds of Mexico, designed to marshal DAK to identify sites that were sampled and inventoried rigorously prior to the beginning of major global climate change (1980). Methods We accumulated DAK records for Mexican birds from all relevant online biodiversity data portals. After extensive cleaning steps, we calculated completeness indices for each 0.05° pixel across the country; we also detected ‘hotspots’ of sampling, and calculated completeness indices for these broader areas as well. Sites were designated as well-sampled if they had completeness indices above 80% and >200 associated DAK records. Results We identified 100 individual pixels and 20 broader ‘hotspots’ of sampling that were demonstrably well-inventoried prior to 1980. These sites are catalogued and documented to promote and enable resurvey efforts that can document events of avifaunal change (and non-change) across the country on decadal time scales. Conclusions Development of repeated surveys for many sites across Mexico, and particularly for sites for which historical surveys document their avifaunas prior to major climate change processes, would pay rich rewards in information about distributional dynamics of Mexican birds.
bibliographic citation: Peterson et al. (2016) Digital Accessible Knowledge and well-inventoried sites for birds in Mexico: baseline sites for measuring faunistic change. PeerJ 4:e2362 https://doi.org/10.7717/peerj.2362
date submitted: 2016-06-14
date accepted: 2016-07-23
issued: 2016-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peterson
  given name: A. Townsend
author list: Agent
  family name: Navarro-Sigüenza
  given name: Adolfo G.
author list: Agent
  family name: Martínez-Meyer
  given name: Enrique
doi: 10.7717/peerj.2362
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-07
copyright: ©2016 Peterson et al.
attribution name: Peterson et al.

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