MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms

The genome‐wide association studies (GWASs) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of the model and nonmodel organisms. For this research question, the GWAS replication testing different parameters and models to validate the results'' reproducibility is common. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software packages, two designed for polyploid data (GWASpoly and SHEsis) and two designed for diploid data (GAPIT and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in a graphical interface; it manages different genotype formats, including VCF. Moreover, it allows control for population structure, relatedness, and several quality control checks on genotype data. Besides, MultiGWAS can test for additive and dominant gene action models, and, through a proprietary scoring function, select the best model to report its associations. Finally, it generates several reports that facilitate identifying false associations from both the significant and the best‐ranked association Single Nucleotide Polymorphisms (SNPs) among the four software packages. We tested MultiGWAS with public tetraploid potato data for tuber shape and several simulated data under both additive and dominant models. These tests demonstrated that MultiGWAS is better at detecting reliable associations than using each of the four software packages individually. Moreover, the parallel analysis of polyploid and diploid software that only offers MultiGWAS demonstrates its utility in understanding the best genetic model behind the SNP association in tetraploid organisms. Therefore, MultiGWAS probed to be an excellent alternative for wrapping GWAS replication in diploid and tetraploid organisms in a single analysis environment.     

Inhibition of VEGFR-2 by SU5416 increases neonatally glutamate-induced neuronal damage in the cerebral motor cortex and hippocampus

Vascular endothelial growth factor (VEGF) exerts neuroprotective or proinflammatory effects, depending on what VEGF forms (A–E), receptor types (VEGFR1–3), and intracellular signaling pathways are involved. Neonatal monosodium glutamate (MSG) treatment triggers neuronal death by excitotoxicity, which is commonly involved in different neurological disorders, including neurodegenerative diseases. This study was designed to evaluate the effects of VEGFR-2 inhibition on neuronal damage triggered by excitotoxicity in the cerebral motor cortex (CMC) and hippocampus (Hp) after neonatal MSG treatment. MSG was administered at a dose of 4 g/kg of body weight (b.w.) subcutaneously on postnatal days (PD) 1, 3, 5, and 7, whereas the VEGFR-2 inhibitor SU5416 was administered at a dose of 10 mg/kg b.w. subcutaneously on PD 5 and 7, 30 min before the MSG treatment. Neuronal damage was assessed using hematoxylin and eosin staining, fluoro-Jade staining, and TUNEL assay. Additionally, western blot assays for some proteins of the VEGF-A/VEGFR-2 signaling pathway (VEGF-A, VEGFR-2, PI3K, Akt, and iNOS) were carried out. All assays were performed on PD 6, 8, 10, and 14. Inhibition of VEGFR-2 signaling by SU5416 increases the neuronal damage induced by neonatal MSG treatment in both the CMC and Hp. Moreover, neonatal MSG treatment increased the expression levels of the studied VEGF-A/VEGFR-2 signaling pathway proteins, particularly in the CMC. We conclude that VEGF-A/VEGFR-2 signaling pathway activation could be part of the neuroprotective mechanisms that attempt to compensate for neuronal damage induced by neonatal MSG treatment and possibly also in other conditions involving excitotoxicity.     

Molecular phylogeny of the spiny-surfaced species of the dinoflagellate Prorocentrum with the description of P. thermophilum sp. nov. and P. criophilum sp. nov. (Prorocentrales,Dinophyceae)

Spiny-surfaced species of Prorocentrum form harmful algal blooms, and its taxonomic identity is obscure due to the size and shape variability. Molecular phylogenies reveal two major clades: one for P. cordatum with sequences mainly retrieved as P. minimum, and the other for P. shikokuense with sequences also retrieved as P. dentatum and P. donghaiense. Several closely related clades still need to be characterized. Here, we provide nuclear SSU and LSU rRNA genes, and nuclear ITS region (ITS1-5.8S gene-ITS2) sequences of the strain CCMP3122 isolated from Florida (initially named P. donghaiense) and strains Prorocentrum sp. RCC6871–2 from the Ross Sea, Antarctica. We describe Prorocentrum thermophilum sp. nov. based on the strain CCMP3122, a species also distributed in the open waters of the Gulf of Mexico, New Zealand, and the Arabian Gulf; and Prorocentrum criophilum sp. nov. based on the strain RCC6872, which is distributed in the Antarctic Ocean and Arctic Sea. Prorocentrum thermophilum is roundish (~14 μm long, ~12 μm wide), with an inconspicuous anterior spine-like prolongation under light microscopy, valves with tiny, short knobs (5–7 per μm²), and several (<7) large trichocyst pores (~0.3 μm) in the right valve, as well as smaller pores (~0.15 μm). Prorocentrum criophilum is round in valve view (~11 μm long, 10 μm wide) and asymmetrically roundish in lateral view, the periflagellar area was not discernible under light microscopy, valves with very tiny, short knobs (6–10 per μm²), and at least 12 large pores in the right valve. Other potentially undescribed species of spiny-surfaced Prorocentrum are discussed.     

New technical concept for alternating tangential flow filtration in biotechnological cell separation processes

Robust cell retention devices are key to successful cell culture perfusion. Currently, tangential flow filtration (TFF) and alternating tangential flow filtration (ATF) are most commonly used for this purpose. TFF, however, suffers from poor fouling mitigation, which leads to high filtration resistance and product retention, and ATF suffers from long residence times and cell accumulation. In this work, we propose a filtration system for alternating tangential flow filtration, which takes full advantage of the fouling mitigation effects of alternating flow and reduces cell accumulation. We have tested this novel setup in direct comparison with the XCell ATF® as well as TFF with a model feed comprising yeast cells and bovine serum albumin as protein at harsh permeate to feed flow conditions. We found that by avoiding the dead-end design of a diaphragm pump, the proposed filtration system exhibited a reduced filtration resistance by approximately 20% to 30% (depending on feed rate and permeate flow rate). A further improvement of the novel setup was reached by optimization of phase durations and flow control, which resulted in a fourfold extension of process duration until hollow fiber flow channel blockage occurred. Thus, the proposed concept appears to be superior to current cell retention devices in perfusion technology.     

Differential expression of the components of the two alkane hydroxylases from Pseudomonas aeruginosa

Oxidation of n-alkanes in bacteria is normally initiated by an enzyme system formed by a membrane-bound alkane hydroxylase and two soluble proteins, rubredoxin and rubredoxin reductase. Pseudomonas aeruginosa strains PAO1 and RR1 contain genes encoding two alkane hydroxylases (alkB1 and alkB2), two rubredoxins (alkG1 and alkG2), and a rubredoxin reductase (alkT). We have localized the promoters for these genes and analyzed their expression under different conditions. The alkB1 and alkB2 genes were preferentially expressed at different moments of the growth phase; expression of alkB2 was highest during the early exponential phase, while alkB1 was induced at the late exponential phase, when the growth rate decreased. Both genes were induced by C(10) to C(22)/C(24) alkanes but not by their oxidation derivatives. However, the alkG1, alkG2, and alkT genes were expressed at constant levels in both the absence and presence of alkanes.     

Surgical Management of Tibial Bone Loss in Revision Total Knee Arthroplasty: Clinical Outcomes and Radiographic Analysis of Tantalum Cones,Titanium Cones and Titanium Sleeves

BackgroundThe use of metaphyseal cones and sleeves has improved the ability to manage tibial bone loss in revision total knee arthroplasty (TKA). The purpose of this study was to compare the outcomes of three systems used for tibial metaphyseal reconstruction in revision TKA.MethodsWe performed a retrospective review of a consecutive series of 723 revision TKAs, including 145 (20%) knee revisions using tibial cones or sleeves. We compared porous tantalum (TM) cones, titanium (Ti) cones and titanium sleeves. The mean follow-up was 2.5 years.ResultsThe rate of revision for any reason was similar among all groups. Revision-free survival rates were similar among all systems studied at a mean follow-up of 2.5 years (TM cones 93%, Ti cones 94%, titanium sleeves 89%). Ti cones had a lower complication rate (6%) compared to TM cones (24%) and sleeves (29%). TM cones (15%) and titanium sleeves (13%) had higher reoperation rates (for any cause) than Ti cones (2%). Radiographic loosening was higher for sleeves (11%) than TM and Ti cones (2%).ConclusionMetaphyseal reconstruction for tibial bone loss in revision TKA using tantalum cones, titanium cones and titanium sleeves showed successful and comparable early clinical outcomes at a mean follow-up of 2.5 years with higher rates of radiographic loosening for titanium sleeves. Level of Evidence: III     

Interactions in solution of cobalt(II) and nickel(II) with nicotinamide adenine dinucleotide: a potentiometric and calorimetric study

The equilibrium constants and the thermodynamic parameters enthalpy and entropy of the interaction between Ni(II) and Co(II) with NAD(+) in aqueous solution were determined by calorimetry and potentiometry methods (ionic strength adjusted to 0.1 with sodium nitrate at 25 degrees C). The macrochelation of the systems was also studied. All the data, including the protonation enthalpy data of NAD(+) (very similar to the protonation enthalpy of 5'-AMP) suggest a less restrictive model for the NAD(+) "folded" conformation without intramolecular stacking between the bases, in agreement both with recent theoretical calculations and with the X-ray structure of trimethylene-bisadeninium or the free acid form of NAD(+).     

Collagen peptides modulate the metabolism of extracellular matrix by human dermal fibroblasts derived from sun‐protected and sun‐exposed body sites

Clinical data published in recent years have demonstrated positive effects of collagen hydrolysate (CH) on skin aging clinical signs. CH use as food supplement has a long history; however, few studies have addressed the underlying purpose of CH on the cellular and molecular biology of skin cells that could elucidate clinical improvement findings. Wide diversity of characteristics has been reported for dermal fibroblasts derived from different body sites and it is unknown whether collagen peptides could modulate differently cells from chronological aged and photoaged skin areas. This study investigated the influence of CH on the extracellular matrix metabolism and proliferation of human dermal fibroblasts (HDFs) derived from chronological aged (sun‐protected) and photoaged (sun‐exposed) body sites. CH treatment did not affect cellular proliferation of either cell cultures, but notably modulated cell metabolism in monolayer model, increasing the content of dermal matrix precursor and main protein, procollagen I and collagen I, respectively. These effects were confirmed in the human dermal equivalent model. The increase in collagen content in the cultures was attributed to stimulation of biosynthesis and decreased collagen I metabolism through inhibition of metalloproteinase activity (MMP) 1 and 2. Modulation of CH in dermal metabolism did not differ between cells derived from sun‐protected and sun‐exposed areas, although lower concentrations of CH seemed to be enough to stimulate sun‐exposed‐derived HDFs, suggesting more pronounced effect in these cells. This study contributes to understanding the biological effects of CH on skin cells and viability of its use as a functional ingredient in food supplements.