An angle-variable three-dimensional pulsed field gel electrophoresis system

A three-dimensional pulsed field electrophoretic method based on the simultaneous application of fixed and cyclically alternating polarity fields at a right angle is described. Requiring only minimal electronic hardware it provides highly homogeneous field conditions over a large gel area and the versatility to vary the pulse vector angle. The electrophoretic parameters critical to achieve fast high resolution separation over a wide range of molecular sizes have been optimized and applied to megabase-size chromosomal DNA molecules. The empirical relationships between pulse time, field strength conditions, and resolution limits derived allow selection of coordinated experimental conditions for the separation of specific DNA size ranges.     

Intronic Variants in the NFKB1 Gene May Influence Hearing Forecast in Patients with Unilateral Sensorineural Hearing Loss in Meniere's Disease

Meniere''s disease is an episodic vestibular syndrome associated with sensorineural hearing loss (SNHL) and tinnitus. Patients with MD have an elevated prevalence of several autoimmune diseases (rheumatoid arthritis, systemic lupus erythematosus, ankylosing spondylitis and psoriasis), which suggests a shared autoimmune background. Functional variants of several genes involved in the NF-κB pathway, such as REL, TNFAIP3, NFKB1 and TNIP1, have been associated with two or more immune-mediated diseases and allelic variations in the TLR10 gene may influence bilateral affectation and clinical course in MD. We have genotyped 716 cases of MD and 1628 controls by using the ImmunoChip, a high-density genotyping array containing 186 autoimmune loci, to explore the association of immune system related-loci with sporadic MD. Although no single nucleotide polymorphism (SNP) reached a genome-wide significant association (p<10⁻⁸), we selected allelic variants in the NF-kB pathway for further analyses to evaluate the impact of these SNPs in the clinical outcome of MD in our cohort. None of the selected SNPs increased susceptibility for MD in patients with uni or bilateral SNHL. However, two potential regulatory variants in the NFKB1 gene (rs3774937 and rs4648011) were associated with a faster hearing loss progression in patients with unilateral SNHL. So, individuals with unilateral MD carrying the C allele in rs3774937 or G allele in rs4648011 had a shorter mean time to reach hearing stage 3 (>40 dB HL) (log-rank test, corrected p values were p = 0.009 for rs3774937 and p = 0.003 for rs4648011, respectively). No variants influenced hearing in bilateral MD. Our data support that the allelic variants rs3774937 and rs4648011 can modify hearing outcome in patients with MD and unilateral SNHL.     

The interplay between event and background sedimentation and the origin of fossil‐rich carbonate concretions: a case study in Permian rocks of the Paraná Basin,Brazil

The Permian Serra Alta Formation was generated under transgressive conditions within a large, calm epeiric sea. A monotonous succession of ‘barren’, massive mudstones deposited under oxygen‐deficient conditions (mainly below storm wave base) is the main lithofacies of this unit. Fossils are generally rare and diluted in the matrix, but certain intervals contain shell‐rich concentrations with well‐preserved, closed articulated bivalves, mixed with shells and comminuted debris with variable quality of preservation, all encased in carbonate concretions. Two main scenarios may account for the origin of these bivalve‐rich concretions (i.e. unique events in sea‐water chemistry or unique burial‐starvation couplets). Sedimentological and taphonomic information indicates that the final deposition of the original shell‐rich mudstone intervals was probably tied to episodic influx of fine‐grained sediments in distal settings. Moderate bioturbation is also recorded suggesting low rates of sedimentation prior to early diagenesis. Hence, the fossil concentrations in concretions were formed due to the interplay of event and background sedimentation. These are internally simple concentrations with complex depositional histories. The concretion‐bearing beds are not randomly distributed in the Serra Alta Formation. Rather, they are found in the sparsely fossiliferous offshore deposits of the basal to intermediate portions of the unit. Thus, the concretionary mudstone beds and associated deposits are preserved in particular intervals and can be tracked for kilometres. This indicates that the conditions essential for concretion development existed only at particular stratigraphical intervals. Finally, our study strongly corroborates the idea that concretions are critical sources of sedimentological, taphonomic and stratigraphical information.