Effect of the particle shape on flow through porous media

In order to study the performance of shaped particles flow in porous media, filtration of two different shape - spherical and rod-like – micro particles was performed through a porous bed. Filtration was investigated at a constant flow rate of 0.04 cm/s with yeast cells, diameter 5 microns, micro spheres, diameter 1 micron, and rod-like bacilli Lactobacillus bulgaricus with 6 microns average length and 0.5 micron diameter. Yeast diameter is close to the bacillus length and micro-sphere diameter is in the scale of the bacillus diameter. All particles have similar density. For the packing, the following glass beads were used: coarse particles, size 1.125 mm; fine particles, size 0.1115 mm. Experiments were carried out using a column loaded with a binary packing (volume fraction of coarse particles in the mixture 0.7) or with a monosize packing with the same amount of coarse or fine particles as used in the binary packing. The analysis of the experimental results was based on two models: pure exclusion effect and hydrodynamic separation model (HDC). Results for spheres show that the classic HDC model ( B = 1.0) fits well the data whenever the ratio of particle size to the bend scale is high (~ 1/100, as for micro spheres). However, if this ratio increases and becomes ~ 1/20, the HDC model needs to be corrected due to the effect of channel wall curvature on the exclusion effect. This assumption leads to a modified HDC equation - R = B/ (1+2λ -2.8λ²), where B ≥ 1 and λ represents the ratio of microparticle size to the pore size. The effect of pore topology plays an important role in the separation of shaped particles when the aspect ratio λ approaches 0.1 and, in the case of bacillus, separation occurs by an exclusion mechanism. For the binary packing, the rod-like particles behave differently from the spherical particles having a length or a diameter in the same scale of bacillus length and diameter. The explanation is the interference of rod-like particles with the pore topology. The exclusion model for particles was formulated in a general form as R = A/(1-λ)², where A is a coefficient proportional to the tortuosity and parameter z = 1, 2 or 3 depends mainly on the pore shape. For instance, in a parallel-plate channel flow: R ~ 1/(1-λ), for a cylindrical pore R ~ 1/(1-λ)² , and for 3-D pore R ~ 1/(1- λ)³ . Further investigation is needed to clarify the particle – pore topology interaction and its effect on particle separation

Utilisation of controlled pore topology for the separation of bioparticles in a mixed-glass beads column

To study the flow of shaped particles in porous media, elution of spherical and rod-like micro-organisms was performed through beds of spherical glass beads. A 0.04 cm/s constant flow rate was used with 5 μm yeast suspensions, 1 μm latex micro-spheres and rod-like bacilli Lactobacillus bulgaricus 6 μm long and 0.5 μm in diameter. Yeast cells’ diameter is close to the bacilli length and micro-spheres have the same diameter as bacilli. All particle types have similar density. To make the different packing beds, 1.125 mm coarse beads and 0.1115 mm fine beads were used. Experiments were carried out using a column loaded with the binary packing (volume fraction of coarse particles in the mixture 0.7) or a monosize packing with the same amount of coarse or fine particles as used in the binary packing. Analysis of experimental results was based on two models: pure exclusion effect and hydrodynamic separation model [hydrodynamic chromatography (HDC)]. Results for spheres show that the classic HDC model fits to the experimental data whenever the ratio of particle size to the pathway bend scale is high (1/100, micro-spheres). However, if this ratio increases and becomes 1/20, the HDC model needs to be corrected due to the effect of channel wall curvature on exclusion. This led to a modified HDC equation of the form R = B/(1 + 2λ − 2.8λ2), where R is the retention, λ is the aspect ratio and constant B ≥ 1. Bacillus separation follows an exclusion mechanism, since pore topology is important in the separation of shaped particles when the aspect ratio approaches λ = 0.1. In the case of a binary packing bed, rod-like particles display a different behaviour than the one exhibited by the spherical particles of the same scale as bacilli, either in length or in diameter. This may be explained by the interaction between rod-like bacilli and the bed's pore topology. A generalised exclusion model for particles was proposed to be R = A/(1 − λ)z, where A is the coefficient proportional to the tortuosity and the parameter z = 1, 2 or 3 depends mainly on pore shape. Controlled pore topology opens interesting applications for bio-separation (in porous micro-fluidic devices, deep bed filtration) and might be especially important for macromolecules and micro-organisms separation with different shapes.Fundação para a Ciência e a Tecnologia (FCT

Novas técnicas cromatográficas

A cromatografia é um processo de separação muito especial, na medida em que permite separar compostos de misturas complexas com grande precisão. Mesmo elementos muito similares, como as proteínas que podem variar apenas num aminoácido, podem ser separados por cromatografia. Na verdade, a cromatografia pode purificar praticamente qualquer substância solúvel ou volátil, desde que a fase sólida, a fase móvel e as condições de operação empregues sejam as correctas. A cromatografia tem ainda a vantagem de poder ser utilizada para separar produtos lábeis, desde que as condições de operação aplicadas não sejam muito severas. Por estas razões a cromatografia tem uma variedade de usos no campo da biotecnologia existindo numerosas técnicas cromatográficas, como a cromatografia de exclusão molecular, de troca iónica e de afinidade, cujos fundamentos experimentais e teóricos estão bem estabelecidos. No que se refere ao fraccionamento de macromoléculas, nanopartículas, colóides e/ou microrganismos em meios porosos permanecem ainda muitas dúvidas. Neste artigo apresenta-se uma breve descrição de dois novos tipos de cromatografia que podem constituir novas e interessantes alternativas de separação: a cromatografia hidrodinâmica e a cromatografia slalom.Fundação para a Ciência e a Tecnologia (FCT

Application of binary packing for chromatographic separation

Separation of dextran and polyethylene glycol of different molecular mass was performed using a binary packed column of glass beads (size ratio ~ 10) and a binary packed column formed by kieselguhr-G (for thin layer chromatography, Merck) and glass beads as the large size particulate fraction (size ratio ~ 30). In addition, data on the separation of micro-spheres, bacillus and yeast cells using monosized and binary glass beads columns are presented. Obtained results show the advantages of using binary packed columns formed by fine and coarse particles instead of a monosize packing of fine particles. The importance of pore channels tortuosity effect on the separation of shaped microparticles using a binary packing is demonstrated

A large CRISPR-induced bystander mutation causes immune dysregulation.

A persistent concern with CRISPR-Cas9 gene editing has been the potential to generate mutations at off-target genomic sites. While CRISPR-engineering mice to delete a ~360 bp intronic enhancer, here we discovered a founder line that had marked immune dysregulation caused by a 24 kb tandem duplication of the sequence adjacent to the on-target deletion. Our results suggest unintended repair of on-target genomic cuts can cause pathogenic bystander mutations that escape detection by routine targeted genotyping assays

Mask formulas for cograssmannian Kazhdan-Lusztig polynomials

We give two contructions of sets of masks on cograssmannian permutations that can be used in Deodhar's formula for Kazhdan-Lusztig basis elements of the Iwahori-Hecke algebra. The constructions are respectively based on a formula of Lascoux-Schutzenberger and its geometric interpretation by Zelevinsky. The first construction relies on a basis of the Hecke algebra constructed from principal lower order ideals in Bruhat order and a translation of this basis into sets of masks. The second construction relies on an interpretation of masks as cells of the Bott-Samelson resolution. These constructions give distinct answers to a question of Deodhar.Comment: 43 page

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme

A new framework for advancing in Drug-Induced Liver Injury research. The Prospective European DILI Registry

Background & AimsNo multi-national prospective study of drug-induced liver injury (DILI) has originated from Europe. The design of a prospective European DILI registry, clinical features and short-term outcomes of the cases and controls is reported.MethodsPatients with suspected DILI were prospectively enrolled in the United Kingdom, Spain, Germany, Switzerland, Portugal, and Iceland, 2016-2021. DILI cases or non-DILI acute liver injury controls following causality assessment were enrolled.ResultsOf 446 adjudicated patients, 246 DILI patients and 100 had acute liver injury due to other etiologies, mostly autoimmune hepatitis (n=42) and viral hepatitis (n=34). DILI patients (mean age 56?years), 57% women, 60% with jaundice and 3.6% pre-existing liver disease. DILI cases and non-DILI controls had similar demographics, clinical features, and outcomes. A single agent was implicated in 199 (81%) DILI cases. Amoxicillin-clavulanate, flucloxacillin, atorvastatin, nivolumab/ipilimumab, infliximab and nitrofurantoin were the most commonly implicated drugs. Multiple medications were implicated in 37 (15%) and 18 cases were caused by herbal and dietary supplements. Most common causative drug classes were antibacterials (40%) and antineoplastic/immunomodulating agents (27%). Overall, 13 (5.3%) had drug-induced autoimmune-like hepatitis due to nitrofurantoin, methyldopa, infliximab, methylprednisolone, and minocycline. Only six (2.4%) DILI patients died: 50% had liver-related death and another six received a liver transplantation.ConclusionsIn this first multi-national European prospective DILI Registry study antibacterials were the most commonly implicated medications, whereas antineoplastic and immunomodulating agents accounted for higher proportion of DILI than previously described. This European initiative provides an important opportunity to advance the study on DILI

Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance

Background & Aims: Serum microRNA (miRNA) levels are known to change in non-alcoholic fatty liver disease (NAFLD) and may serve as useful biomarkers. This study aimed to profile miRNAs comprehensively at all NAFLD stages. Methods: We profiled 2,083 serum miRNAs in a discovery cohort (183 cases with NAFLD representing the complete NAFLD spectrum and 10 population controls). miRNA libraries generated by HTG EdgeSeq were sequenced by Illumina NextSeq. Selected serum miRNAs were profiled in 372 additional cases with NAFLD and 15 population controls by quantitative reverse transcriptase PCR. Results: Levels of 275 miRNAs differed between cases and population controls. Fewer differences were seen within individual NAFLD stages, but miR-193a-5p consistently showed increased levels in all comparisons. Relative to NAFL/non-alcoholic steatohepatitis (NASH) with mild fibrosis (stage 0/1), 3 miRNAs (miR-193a-5p, miR-378d, and miR378d) were increased in cases with NASH and clinically significant fibrosis (stages 2–4), 7 (miR193a-5p, miR-378d, miR-378e, miR-320b, miR-320c, miR-320d, and miR-320e) increased in cases with NAFLD activity score (NAS) 5–8 compared with lower NAS, and 3 (miR-193a-5p, miR-378d, and miR-378e) increased but 1 (miR-19b-3p) decreased in steatosis, activity, and fibrosis (SAF) activity score 2–4 compared with lower SAF activity. The significant findings for miR-193a-5p were replicated in the additional cohort with NAFLD. Studies in Hep G2 cells showed that following palmitic acid treatment, miR-193a-5p expression decreased significantly. Gene targets for miR-193a-5p were investigated in liver RNAseq data for a case subgroup (n = 80); liver GPX8 levels correlated positively with serum miR-193a-5p. Conclusions: Serum miR-193a-5p levels correlate strongly with NAFLD activity grade and fibrosis stage. MiR-193a-5p may have a role in the hepatic response to oxidative stress and is a potential clinically tractable circulating biomarker for progressive NAFLD. Lay summary: MicroRNAs (miRNAs) are small pieces of nucleic acid that may turn expression of genes on or off. These molecules can be detected in the blood circulation, and their levels in blood may change in liver disease including non-alcoholic fatty liver disease (NAFLD). To see if we could detect specific miRNA associated with advanced stages of NAFLD, we carried out miRNA sequencing in a group of 183 patients with NAFLD of varying severity together with 10 population controls. We found that a number of miRNAs showed changes, mainly increases, in serum levels but that 1 particular miRNA miR-193a-5p consistently increased. We confirmed this increase in a second group of cases with NAFLD. Measuring this miRNA in a blood sample may be a useful way to determine whether a patient has advanced NAFLD without an invasive liver biopsy