NMR surface relaxivity in a time-dependent porous system

We demonstrate an unexpected decay-recovery behaviour in the time-dependent $^{1}\mathrm{H}$ NMR relaxation times of water confined within a hydrating porous material. Our observations are rationalised by considering the combined effects of decreasing material pore size and evolving interfacial chemistry, which facilitate a transition between surface-limited and diffusion-limited relaxation regimes. Such behaviour necessitates the realisation of temporally evolving surface relaxivity, highlighting potential caveats in the classical interpretation of NMR relaxation data obtained from complex porous systems.Comment: 12 pages, 2 figure

A non-invasive study of flow dynamics in membrane distillation hollow fiber modules using low-field nuclear magnetic resonance imaging (MRI)

Low-field bench-top nuclear magnetic resonance imaging (MRI) has been applied to investigate the hydrodynamics in novel hollow fiber modules with four different configurations of randomly-packed, spacer-knitted, curly and semi-curly fibers, specifically designed for the membrane distillation (MD) process. Imaging, spatially resolved velocity maps and propagators (probability distributions of displacement/velocity) were all acquired in the modules with flow in the shell side. The MRI data were correlated with overall module performance. The results have revealed that the curly configuration exhibited more significant transverse flow and hence enhanced mixing, compared to the randomly packed configuration; this was consistent with an enhanced MD performance in terms of permeation flux. Interestingly, the velocity maps of the spacer-knitted fiber design indicated a significant flow channeling in the center of the module, despite its enhanced MD performance. Fortunately, combined with further investigations on the localized velocity images of this configuration, the acquisition of propagators provided valuable information in revealing the existence of reduced stagnant regions and significant transverse flow at varied operating conditions, which indicated a better overall mixing and hence confirmed its module performance

Imaging of membrane concentration polarization by NaCl using 23Na nuclear magnetic resonance

Forward osmosis (FO) and reverse osmosis (RO) membrane processes differ in their driving forces: osmotic pressure versus hydraulic pressure. Concentration polarization (CP) can adversely affect both performance and lifetime in such membrane systems. In order to mitigate against CP, the extent and severity of it need to be predicted more accurately through advanced online monitoring methodologies. Whilst a variety of monitoring techniques have been used to study the CP mechanism, there is still a pressing need to develop and apply non-invasive, in situ techniques able to produce quantitative, spatially resolved measurements of heterogeneous solute concentration in, and adjacent to, the membrane assembly as caused by the CP mechanism. To this end, 23Na magnetic resonance imaging (MRI) is used to image the sodium ion concentration within, and near to, both FO and RO composite membranes for the first time; this is also coupled with 1H MRI mapping of the corresponding water distribution. As such, it is possible to directly image salt accumulation due to CP processes during desalination. This was consistent with literature expectations and serves to confirm the suitability of 23Na MRI as a novel non-invasive technique for CP studies

Impact of microplastics on organic fouling of hollow fiber membranes

Given the potential hazards of microplastics (MPs), it is desirable to efficiently remove them during wastewater treatment processes. To this end, ultrafiltration (UF) membranes can significantly increase the removal of MPs, however the fouling of such membrane modules can also be impacted by the presence of MPs. Magnetic Resonance Imaging (MRI) was used here to non-invasively quantify the effect of polyethylene (PE) MPs accumulation in a 3D UF hollow fiber (HF) membrane module containing 400 fibers, via direct non-invasive velocity imaging of the flow distribution between individual fibers during module operation. The co-effect of MPs and alginate (a common organic model foulant mimicking extracellular polymeric substances (EPS)) on fouling of the HF module was then explored. Flow was initially equally distributed with fouling causing flow in particular fibers to be significantly reduced. Fouling with MPs resulted in minimal flow distribution disruption and was easily remediated hydraulically, in contrast alginate fouling required chemical cleaning in order to fully restore homogeneous flow distribution between the fibers. The presence of both MPs and alginate resulted in a more heterogeneous disruption of the fibre flow distribution due to fouling and resulted in much more effective hydraulic cleaning of the module

Enzymatic depolymerization of alginate by two novel thermostable alginate lyases from Rhodothermus marinus

Alginate (alginic acid) is a linear polysaccharide, wherein (1→4)-linked β-D-mannuronic acid and its C5 epimer, α-L-guluronic acid, are arranged in varying sequences. Alginate lyases catalyze the depolymerization of alginate, thereby cleaving the (1→4) glycosidic linkages between the monomers by a β-elimination mechanism, to yield unsaturated 4-deoxy-L-erythro-hex-4-enopyranosyluronic acid (Δ) at the non-reducing end of resulting oligosaccharides (α-L-erythro configuration) or, depending on the enzyme, the unsaturated monosaccharide itself. In solution, the released free unsaturated monomer product is further hydrated in a spontaneous (keto-enol tautomerization) process to form two cyclic stereoisomers. In this study, two alginate lyase genes, designated alyRm3 and alyRm4, from the marine thermophilic bacterium Rhodothermus marinus (strain MAT378), were cloned and expressed in Escherichia coli. The recombinant enzymes were characterized, and their substrate specificity and product structures determined. AlyRm3 (PL39) and AlyRm4 (PL17) are among the most thermophilic and thermostable alginate lyases described to date with temperature optimum of activity at ∼75 and 81°C, respectively. The pH optimum of activity of AlyRm3 is ∼5.5 and AlyRm4 at pH 6.5. Detailed NMR analysis of the incubation products demonstrated that AlyRm3 is an endolytic lyase, while AlyRm4 is an exolytic lyase, cleaving monomers from the non-reducing end of oligo/poly-alginates

Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing

BACKGROUND: Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon (Salmo salar) derived from across the species' North Atlantic range, was selectively amplified with a novel combination of standard PCR and pyro-sequencing in a single run using 454 Titanium FLX technology (Roche, 454 Life Sciences). A unique combination of barcoded primers and a partitioned sequencing plate was employed to designate each sequence read to its original sample. The sequence reads were aligned according to the S. salar mitochondrial reference sequence (NC_001960.1), with the objective of identifying single nucleotide polymorphisms (SNPs). They were validated if they met with the following three stringent criteria: (i) sequence reads were produced from both DNA strands; (ii) SNPs were confirmed in a minimum of 90% of replicate sequence reads; and (iii) SNPs occurred in more than one individual. RESULTS: Pyrosequencing generated a total of 179,826,884 bp of data, and 10,765 of the total 10,920 S. salar sequences (98.6%) were assigned back to their original samples. The approach taken resulted in a total of 216 SNPs and 2 indels, which were validated and mapped onto the S. salar mitochondrial genome, including 107 SNPs and one indel not previously reported. An average of 27.3 sequence reads with a standard deviation of 11.7 supported each SNP per individual. CONCLUSION: The study generated a mitochondrial SNP panel from a large sample group across a broad geographical area, reducing the potential for ascertainment bias, which has hampered previous studies. The SNPs identified here validate those identified in previous studies, and also contribute additional potentially informative loci for the future study of phylogeography and evolution in the Atlantic salmon. The overall success experienced with this novel application of HT sequencing of targeted regions suggests that the same approach could be successfully applied for SNP mining in other species

Differences and similarities in enzymes from the neopullulanase subfamily isolated from thermophilic species

Six glycoside hydrolase (GH) family 13 members, classified under the polyspecific neopullulanase subfamily GH13_20 (also termed cyclomaltodextrinase) were analysed. They originate from thermophilic bacterial strains (Anoxybacillus flavithermus, Laceyella sacchari, and Geobacillus thermoleovorans) or from environmental DNA, collected after in situ enrichments in Icelandic hot springs. The genes were isolated following the CODEHOP consensus primer strategy, utilizing the first two of the four conserved sequence regions in GH13. The typical domain structure of GH13_20, including an N-terminal domain (classified as CBM34), the catalytic module composed of the A-and B-domains, and a C-terminal domain, was found in five of the encoded enzymes (abbreviated Amy1, 89, 92, 98 and 132). These five enzymes degraded cyclomaltodextrins (CDs) and starch, while only three, Amy92 (L. sacchari), Amy98 (A. flavithermus) and Amy132 (environmental DNA), also harboured neopullulanase activity. The L. sacchari enzyme was monomeric, but with CD as the preferred substrate, which is an unusual combination. The sixth enzyme (Amy29 from environmental DNA), was composed of the ABC-domains only. Preferred substrate for Amy29 was pullulan, which was degraded to panose, and the enzyme had no detectable activity on CDs. In addition to its different activity profile and domain composition, Amy29 also displayed a different conservation (LPKF) in the fifth conserved region (MPKL) proposed to identify the subfamily. All enzymes had apparent temperature optima in the range 50–65°C, while thermostability varied, and was highest for Amy29 with a half-life of 480 min at 80°C. Calcium dependent activity or stability was monitored in four enzymes, but could not be detected for Amy29 or 98. Tightly bound calcium can, however, not be ruled out, and putative calcium ligands were conserved in Amy98

Pore-scale analysis of formation damage in Bentheimer sandstone with in-situ NMR and micro-computed tomography experiments

We investigated fines movement through sandstone in-situ at the micrometre pore scale and studied the associated pore-scale mechanisms leading to formation damage. We used two in-situ techniques to accomplish this, namely nuclear magnetic resonance T2 relaxation time (NMR) measurements (of pore size distributions) and high resolution x-ray micro-computed tomography (μCT; at high resolutions of (0.89 μm)3 and (3.4 μm)3). The μCT images showed the precise 3D location of the fines particles in the plug and demonstrated that initially pore throats are plugged, followed by filling of adjacent pore bodies by solid particles. These measurements in combination with traditionally used (indirect) permeability and production curve measurements and ex-situ SEM imaging enabled us to propose a new mechanistic pore-scale plugging model; furthermore we demonstrated that the amount of fines trapped decayed rapidly with core depth. We conclude that it is feasible to analyse formation damage in-situ by a combination of NMR and μCT measurements

Some (bacilli) like it hot: Genomics of Geobacillus species

Copyright © 2014 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.What are Geobacillus?BBSR

MEGGASENSE – pretraživač (meta)genomski anotiranih sekvencija pomoću govornog jezika – platforma za izradu bioloških skladišta podataka

The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya. The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described. In addition to standard assembly of reads, a novel ‘functional’ assembly was developed, in which screening of reads with the HMM profiles occurs before the assembly. The AMYLOMICS database incorporates additional HMM profiles for carbohydrate-modifying enzymes and it is illustrated how the combination of HMM and BLAST analyses helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.Platforma MEGGASENSE služi za izradu relacijskih baza podataka koje sadržavaju nukleotidne ili proteinske sekvencije. Osnovna funkcionalna analiza zasniva se na primjeni 14 106 profila skrivenih Markovljevih modela (HMM), temeljenih na sekvencijama dostupnim u bazi podataka KEGG. Pomoću tražilice Solr mogu se zadati napredni upiti u sprezi s implementiranom pretragom BLAST. Osnovne funkcionalnosti platforme omogućile su izradu baze podataka SCATT, temeljene na predviđenom proteomu bakterije Streptomyces cattleya. U radu je opisana implementacija specijalizirane metagenomske baze podataka (AMYLOMICS) za „bioprospecting“ enzima koji modificiraju ugljikohidrate. Uz standardno slaganje očitanih kratkih sljedova DNA, razvijen je funkcionalni postupak pretraživanja HMM profila u očitanim slijedovima DNA prije slaganja. Baza podataka AMYLOMICS sadržava i dodatne HMM profile enzima za modifikaciju ugljikohidrata. U radu je prikazano kako se kombinacijom analiza HMM i BLAST mogu identificirati ciljani geni. Platforma MEGGASENSE upotrijebljena je za izradu raznih proteomskih i metagenomskih baza podataka