Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands
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 while older colonization events are hypothesized to explain the high genetic diversity values found in the Majorcan populations. Our study provides widely applicable information about geographical patterns of genetic variation in B. stacei. Among others, the genetic pattern and the existence of local alleles will need to be adequately reflected in the germplasm collection of B. stacei for efficient genome wide association studies.
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
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
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 that the degree of fragmentation can contribute to alter not only the suitability of an area for a species, but also its abundance. Even if the relationship between suitability and abundance can be used as an early warning of habitat deterioration, its weak predictive power needs further research. However, we define relationships between a species and some landscape features (i.e., fragmentation, extensive rejuvenation of forests and tree plantations) which could be easily controlled by appropriate forest management planning to enhance environmental suitability, at least in an area possessing high conservation and biodiversity values.
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
Is there any effect of pneumoperitoneum pressure on coagulation and fibrinolysis during laparoscopic cholecystectomy?
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.
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
Improved cartilage regeneration by implantation of acellular biomaterials after bone marrow stimulation: a systematic review and meta-analysis of animal studies
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 improved cartilage regeneration by 15.6% compared to non-treated empty defect controls. The addition of biologics to biomaterials significantly improved cartilage regeneration by 7.6% compared to control biomaterials. No significant differences were found between biomaterials from natural or synthetic origin or between scaffolds, hydrogels and blends. No noticeable differences were found in outcome between animal models. The risk of bias assessment indicated poor reporting for the majority of studies, impeding an assessment of the actual risk of bias. In conclusion, implantation of biomaterials in osteochondral defects improves cartilage regeneration compared to natural healing, which is further improved by the incorporation of biologics.
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
Bioavailability of D-methionine relative to L-methionine for nursery pigs using the slope-ratio assay
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.
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
ECG is an inefficient screening-tool for left ventricular hypertrophy in normotensive African children population
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.
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
Genome-wide identification and characterization of WRKY gene family in Salix suchowensis
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 this gene family in flowering plants.
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
MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense
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.
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
Testing the link between genome size and growth rate in maize
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.
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
Digital Accessible Knowledge and well-inventoried sites for birds in Mexico: baseline sites for measuring faunistic change
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.
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