PURPOSE: Neuroimaging pipelines have long been known to generate mildly differing results depending on various factors, including software version. While considered generally acceptable and within the margin of reasonable error, little is known about their effect in common research scenarios such as inter-group comparisons between healthy controls and various pathological conditions. The aim of the presented study was to explore the differences in the inferences and statistical significances in a model situation comparing volumetric parameters between healthy controls and type 1 diabetes patients using various FreeSurfer versions. METHODS: T1- and T2-weighted structural scans of healthy controls and type 1 diabetes patients were processed with FreeSurfer 5.3, FreeSurfer 5.3 HCP, FreeSurfer 6.0 and FreeSurfer 7.1, followed by inter-group statistical comparison using outputs of individual FreeSurfer versions. RESULTS: Worryingly, FreeSurfer 5.3 detected both cortical and subcortical volume differences out of the preselected regions of interest, but newer versions such as FreeSurfer 5.3 HCP and FreeSurfer 6.0 reported only subcortical differences of lower magnitude and FreeSurfer 7.1 failed to find any statistically significant inter-group differences. CONCLUSION: Since group averages of individual FreeSurfer versions closely matched, in keeping with previous literature, the main origin of this disparity seemed to lie in substantially higher within-group variability in the model pathological condition. Ergo, until validation in common research scenarios as case-control comparison studies is included into the development process of new software suites, confirmatory analyses utilising a similar software based on analogous, but not fully equivalent principles, might be considered as supplement to careful quality control.
Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope's rule (phyletic size increase), Rensch's rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length $\ge$2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 anchored hybrid enrichment markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Rensch's rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Cope's rule. Allometric analyses reject the converse, Rensch's rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve toward an optimum size (3.2-4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, and diagnosability. Spider families, as currently defined, tend to be between 37 million years old and 98 million years old, and Nephilidae is estimated at 133 Ma (97-146), thus deserving family status. We, therefore, resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous GeratonephilaPoinar and Buckley (2012), Herennia Thorell 1877, IndoetraKuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, Palaeonephila Wunderlich 2004 from Tertiary Baltic amber, and TrichonephilaDahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically ancient phenotype (over 100 Ma), as is eSSD, though their magnitudes vary by lineage.
- MeSH
- Phylogeny * MeSH
- Spiders anatomy & histology classification genetics MeSH
- Sex Characteristics * MeSH
- Body Size genetics MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
PURPOSE: To find the shortest, acceptable stabilization period before recording resting, supine ultra-short-term Ln RMSSD and heart rate (HR). METHOD: Thirty endurance-trained male athletes (age 24.1 ± 2.3 years, maximal oxygen consumption (VO2max) 64.1 ± 6.6 ml·kg-1·min-1) and 30 male students (age 23.3 ± 1.8 years, VO2max 52.8 ± 5.1 ml·kg-1·min-1) were recruited. Upon awaking at home, resting, supine RR intervals were measured continuously for 10 min using a Polar V800 HR monitor. Ultra-short-term Ln RMSSD and HR values were calculated from 1-min RR interval segments after stabilization periods from 0 to 4 min in 0.5 min increments and were compared with reference values calculated from 5-min segment after 5-min stabilization. Systematic bias and intraclass correlation coefficients (ICC) including 90% confidence intervals (CI) were calculated and magnitude based inference was conducted. RESULTS: The stabilization periods of up to 30 s for athletes and up to 60 s for students showed positive (possibly to most likely) biases for ultra-short-term Ln RMSSD compared with reference values. Stabilization periods of 60 s for athletes and 90 s for students showed trivial biases and ICCs were 0.84; 90% CI 0.72 to 0.91, and 0.88; 0.79 to 0.94, respectively. For HR, biases were trivial and ICCs were 0.93; 0.88 to 0.96, and 0.93; 0.88 to 0.96, respectively. CONCLUSION: The shortest stabilization period required to stabilize Ln RMSSD and HR was set at 60 s for endurance-trained athletes and 90 s for university students.
- MeSH
- Time Factors MeSH
- Physical Endurance physiology MeSH
- Humans MeSH
- Young Adult MeSH
- Vagus Nerve physiology MeSH
- Athletes MeSH
- Heart Rate physiology MeSH
- Students MeSH
- Universities MeSH
- Heart Rate Determination methods MeSH
- Check Tag
- Humans MeSH
- Young Adult MeSH
- Male MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Microbes can modulate ecosystem function since they harbor a vast genetic potential for biogeochemical cycling. The spatial and temporal dynamics of this genetic diversity should be acknowledged to establish a link between ecosystem function and community structure. In this study, we analyzed the genetic diversity of bacterial phosphorus utilization genes in two microbial assemblages, microbialites and bacterioplankton of Lake Alchichica, a semiclosed (i.e., endorheic) system with marked seasonality that varies in nutrient conditions, temperature, dissolved oxygen, and water column stability. We focused on dissolved organic phosphorus (DOP) utilization gene dynamics during contrasting mixing and stratification periods. Bacterial alkaline phosphatases (phoX and phoD) and alkaline beta-propeller phytases (bpp) were surveyed. DOP utilization genes showed different dynamics evidenced by a marked change within an intra-annual period and a differential circadian pattern of expression. Although Lake Alchichica is a semiclosed system, this dynamic turnover of phylotypes (from lake circulation to stratification) points to a different potential of DOP utilization by the microbial communities within periods. DOP utilization gene dynamics was different among genetic markers and among assemblages (microbialite vs. bacterioplankton). As estimated by the system's P mass balance, P inputs and outputs were similar in magnitude (difference was <10 %). A theoretical estimation of water column P monoesters was used to calculate the potential P fraction that can be remineralized on an annual basis. Overall, bacterial groups including Proteobacteria (Alpha and Gamma) and Bacteroidetes seem to be key participants in DOP utilization responses.
- MeSH
- Alkaline Phosphatase genetics MeSH
- Bacteria enzymology genetics metabolism MeSH
- Bacteroidetes genetics metabolism MeSH
- Genes, Bacterial genetics MeSH
- RNA, Bacterial analysis MeSH
- DNA, Bacterial analysis MeSH
- Ecosystem MeSH
- Phosphorus chemistry metabolism MeSH
- Phylogeny * MeSH
- Genetic Variation * MeSH
- Genetic Markers genetics MeSH
- Lakes microbiology MeSH
- Oxygen chemistry MeSH
- Polymerase Chain Reaction methods MeSH
- Proteobacteria genetics metabolism MeSH
- Gene Expression Regulation, Bacterial MeSH
- Seasons MeSH
- Base Sequence MeSH
- Sequence Analysis MeSH
- Phosphorus Compounds chemistry metabolism MeSH
- Water chemistry MeSH
- Aquatic Organisms genetics metabolism MeSH
- Environment MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Mexico MeSH
Bacteria represent an underexplored source of diglycosidases. Twenty-five bacterial strains from the genera Actinoplanes, Bacillus, Corynebacterium, Microbacterium, and Streptomyces were selected for their ability to grow in diglycosylated flavonoids-based media. The strains Actinoplanes missouriensis and Actinoplanes liguriae exhibited hesperidin deglycosylation activity (6-O-α-L-rhamnosyl-β-D-glucosidase activity, EC 3.2.1.168), which was 3 to 4 orders of magnitude higher than the corresponding monoglycosidase activities. The diglycosidase production was confirmed in A. missouriensis by zymographic assays and NMR analysis of the released disaccharide, rutinose. The gene encoding the 6-O-α-L-rhamnosyl-β-D-glucosidase was identified in the genome sequence of A. missouriensis 431(T) (GenBank accession number BAL86042.1) and functionally expressed in Escherichia coli. The recombinant protein hydrolyzed hesperidin and hesperidin methylchalcone, but not rutin, which indicates its specificity for 7-O-rutinosylated flavonoids. The protein was classified into the glycoside hydrolase family 55 (GH55) in contrast to the known eukaryotic diglycosidases, which belong to GH1 and GH5. These findings demonstrate that organisms other than plants and filamentous fungi can contribute to an expansion of the diglycosidase toolbox.
- MeSH
- Bacterial Proteins genetics metabolism MeSH
- beta-Glucosidase genetics metabolism MeSH
- Chalcones chemistry metabolism MeSH
- Disaccharides chemistry metabolism MeSH
- Escherichia coli genetics metabolism MeSH
- Gene Expression MeSH
- Flavonoids chemistry metabolism MeSH
- Phylogeny MeSH
- Glycosides chemistry metabolism MeSH
- Hesperidin analogs & derivatives chemistry metabolism MeSH
- Hydrolysis MeSH
- Cloning, Molecular MeSH
- Micromonosporaceae classification genetics metabolism MeSH
- Recombinant Proteins genetics metabolism MeSH
- Rhamnose chemistry metabolism MeSH
- Substrate Specificity MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Philophthalmosis is a zoonotic disease associated largely with the spread of the invasive freshwater snail Melanoides tuberculata, serving as an intermediate host. Here we examined Philophthalmus gralli focal fenced infection site reported recently as being associated with Tinamus major and M. tuberculata in Alajuela, Costa Rica. Removal of the definitive hosts allowed us to address also the long-term survival strategy of the parasite. Initially, the snail intermediate hosts displayed high prevalence of P. gralli infection across all its age cohorts. Two years following the removal of definitive hosts, the infection rate decreased by one order of magnitude, while the snails aging less than one year displayed zero infection prevalence. Additionally, phylogenetic analysis of mitochondrial (ND1) and nuclear (ITS1, ITS2) DNA loci revealed negligible intrasite DNA variability of the specimens obtained at the study site in Costa Rica (but not of those obtained earlier in Peru or New Zealand), supporting strongly the hypothesis on focal origin of the infection. The observed dynamics of infection suggests the explanation for the high variability in P. gralli prevalence in intermediate hosts experienced worldwide. We noticed that the reports claiming >20% prevalence of M. tuberculata infection by P. gralli originated exclusively from foci with known eye infection of the definitive hosts, while the P. gralli infection penetrance <2% is typically associated with sites, where the infection of definitive hosts was not observed, suggesting that the infected definitive hosts were present onsite only in the past, or were present only at a site upstream or downstream of the respective sampling site. Thus, this is the first evidence on the possible persistence of eye-trematode infection site for over two years following the last confirmed outbreak in its adult hosts.
- MeSH
- DNA, Helminth chemistry genetics MeSH
- Disease Outbreaks * MeSH
- Phylogeny MeSH
- Snails parasitology MeSH
- Trematode Infections epidemiology parasitology MeSH
- Humans MeSH
- DNA, Ribosomal Spacer chemistry genetics MeSH
- Molecular Sequence Data MeSH
- Base Sequence MeSH
- Sequence Analysis, DNA MeSH
- Fresh Water MeSH
- Trematoda genetics isolation & purification physiology MeSH
- Disease Reservoirs MeSH
- Zoonoses MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
