Search Results (8)

This study investigates the Enzyme Biofilm Method (EBM), a biological wastewater treatment technology previously developed by the authors. EBM employs microbial-derived hydrolytic enzyme groups in the initial treatment stage to break down high-molecular-weight organic matter—such as starch, proteins, and fats—into low-molecular-weight compounds. These compounds enhance the growth of native microorganisms, promoting biofilm formation on carriers and improving treatment efficiency. Over the past decade, EBM has been practically applied in food factory wastewater facilities handling high organic loads. The enzyme groups used in EBM are derived from cultures of Bacillus mojavensis, Saccharomyces cariocanus, and Lacticaseibacillus paracasei. To clarify the system’s mechanism and ensure its practical viability, this study focused on starch—a prevalent and recalcitrant component of food wastewater—using two evaluation approaches. Verification 1: Field testing at a starch factory showed that adding enzyme groups to the equalization tank effectively reduced biological oxygen demand (BOD) through starch degradation. Verification 2: Laboratory experiments confirmed that the enzyme groups possess both amylase and maltase activities, sequentially breaking down starch into glucose. The resulting glucose supports microbial growth, facilitating biofilm formation and BOD reduction. These findings confirm EBM’s potential as a sustainable and effective solution for treating high-strength food industry wastewater. Full article

The model haloarchaeon Haloferax volcanii is polyploid with about 20 copies of its major chromosome. Recently it has been described that highly efficient intermolecular gene conversion operates in H. volcanii to equalize the chromosomal copies. In the current study, 24 genes were selected that encode proteins with orthologs involved in gene conversion or homologous recombination in archaea, bacteria, or eukaryotes. Single gene deletion strains of 22 genes and a control gene were constructed in two parent strains for a gene conversion assay; only radA and radB were shown to be essential. Protoplast fusions were used to generate strains that were heterozygous for the gene HVO_2528, encoding an enzyme for carotinoid biosynthesis. It was revealed that a lack of six of the proteins did not influence the efficiency of gene conversion, while sixteen mutants had severe gene conversion defects. Notably, lack of paralogous proteins of gene families had very different effects, e.g., mutant Δrad25b had no phenotype, while mutants Δrad25a, Δrad25c, and Δrad25d were highly compromised. Generation of a quadruple rad25 and a triple sph deletion strain also indicated that the paralogs have different functions, in contrast to sph2 and sph4, which cannot be deleted simultaneously. There was no correlation between the severity of the phenotypes and the respective transcript levels under non-stressed conditions, indicating that gene expression has to be induced at the onset of gene conversion. Phylogenetic trees of the protein families Rad3/25, MutL/S, and Sph/SMC/Rad50 were generated to unravel the history of the paralogous proteins of H. volcanii. Taken together, unselected intermolecular gene conversion in H. volcanii involves at least 16 different proteins, the molecular roles of which can be studied in detail in future projects. Full article

Background: Although zinc oxide has been banned at therapeutic doses in the EU, its use is still legal in most countries with industrial pig farming. This compound has been shown to be very effective in preventing E. coli-related diseases. However, another strategy used to control this pathogen is vaccination, administered parenterally or orally. Oral vaccines contain live strains, with F4 and F18 binding factors. Since zinc oxide prevents E. coli adhesion, it is hypothesised that its presence at therapeutic doses (2500 ppm) may alter the immune response and the protection of intestinal integrity derived from the vaccination of animals. Methods: A group of piglets were orally vaccinated at weaning and divided into two subgroups; one group was fed a feed containing 2500 ppm zinc oxide (V + ZnO) for the first 15 days post-vaccination (dpv) and the other was not (V). Faeces were sampled from the animals at 6, 8, 11, 13, and 15 dpv. Unvaccinated animals without ZnO in their feed (Neg) were sampled simultaneously and, on day 15 post-vaccination, were also compared with a group of unvaccinated animals with ZnO in their feed (ZnO). Results: Differences were found in E. coli excretion, with less quantification in the V + ZnO group, and a significant increase in secretory IgA in the V group at 8 dpv, which later equalised with that of the V + ZnO group. There was also some difference in IFNα, IFNγ, IL1α, ILβ, and TNFα gene expression when comparing both vaccinated groups (p < 0.05). However, there was no difference in gene expression for the tight junction (TJ) proteins responsible for intestinal integrity. Conclusions: Although some differences in the excretion of the vaccine strain were found when comparing both vaccinated groups, there are no remarkable differences in immune stimulation or soluble IgA production when comparing animals orally vaccinated against E. coli in combination with the presence or absence of ZnO in their feed. We can conclude that the immune response produced is very similar in both groups. Full article

Protein crystallization is the bottleneck in macromolecular crystallography, and crystal recognition is a very important step in the experiment. To improve the recognition accuracy by image classification algorithms further, the Mask R-CNN model is introduced for the detection of protein crystals in this paper. Because the protein crystal image is greatly affected by backlight and precipitate, the contrast limit adaptive histogram equalization (CLAHE) is applied with Mask R-CNN. Meanwhile, the Transfer Learning method is used to optimize the parameters in Mask R-CNN. Through the comparison experiments between this combined algorithm and the original algorithm, it shows that the improved algorithm can effectively improve the accuracy of segmentation. Full article

In the present study, we evaluated four small molecule affinity-based probes based on agarose-immobilized benzamidine (ABA), O-Phospho-L-Tyrosine (pTYR), 8-Amino-hexyl-cAMP (cAMP), or 8-Amino-hexyl-ATP (ATP) for their ability to remove high-abundant proteins such as serum albumin from plasma samples thereby enabling the detection of medium-to-low abundant proteins in plasma samples by mass spectrometry-based proteomics. We compared their performance with the most commonly used immunodepletion method, the Multi Affinity Removal System Human 14 (MARS14) targeting the top 14 most abundant plasma proteins and also the ProteoMiner protein equalization method by label-free quantitative liquid chromatography tandem mass spectrometry (LC-MSMS) analysis. The affinity-based probes demonstrated a high reproducibility for low-abundant plasma proteins, down to picomol per mL levels, compared to the Multi Affinity Removal System (MARS) 14 and the Proteominer methods, and also demonstrated superior removal of the majority of the high-abundant plasma proteins. The ABA-based affinity probe and the Proteominer protein equalization method performed better compared to all other methods in terms of the number of analyzed proteins. All the tested methods were highly reproducible for both high-abundant plasma proteins and low-abundant proteins as measured by correlation analyses of six replicate experiments. In conclusion, our results demonstrated that small-molecule based affinity-based probes are excellent alternatives to the commonly used immune-depletion methods for proteomic biomarker discovery studies in plasma. Data are available via ProteomeXchange with identifier PXD020727. Full article

Information content of a polymeric macromolecule can be calculated in bits, by multiplying the number of building blocks that encompasses the entire length of the macromolecule with the Shannon’s entropy of each building block, which could be determined through the degree of variation (in the number) of those building blocks. DNA and the proteins that are encoded by genes, which are certain protein-coding regions of the DNA, are also polymeric macromolecules that are comprised of such building blocks, named residues. However, there is seemingly lower residue-based information amount in the protein if the mentioned approach is applied to a protein of specific size and the DNA that would be encoding the same length of a protein. Accordingly, this work initially presents the attempt to eliminate the decrease in the information amount of the protein by implementation of a new parameter in the calculation with the assumption that the information is not lost (or gained) during the protein translation process. An important additional biological significance of the work is revealed during latter calculations for the equalization of the information amounts in the protein and DNA molecules, which is the resolution of the problem of the presence of immense variation in the sizes of the proteins by accounting for the presence of introns in the eukaryotic genome. Full article

Skeletal muscle is a complex tissue that is dominated by the presence of a few abundant proteins. This wide dynamic range can mask the presence of lower abundance proteins, which can be a confounding factor in large-scale proteomic experiments. In this study, we have investigated a number of pre-fractionation methods, at both the protein and peptide level, for the characterization of the skeletal muscle proteome. The analyses revealed that the use of OFFGEL isoelectric focusing yielded the largest number of protein identifications (>750) compared to alternative gel-based and protein equalization strategies. Further, OFFGEL led to a substantial enrichment of a different sub-population of the proteome. Filter-aided sample preparation (FASP), coupled to peptide-level OFFGEL provided more confidence in the results due to a substantial increase in the number of peptides assigned to each protein. The findings presented here support the use of a multiplexed approach to proteome characterization of skeletal muscle, which has a recognized imbalance in the dynamic range of its protein complement. Full article

Until noninvasive neuroradiological examinations were put into practice, the study of the septum pellucidum was only of interest to embryologists and anatomists. The septum pellucidum appears around the 10th–12th embryonic week and deepens around the 16th, forming the cavum septi pellucidi which radiology objectifies frequently and without correspondence with the determined clinical frame. The present study is based on a review of the literature (97 publications) and an anatomical series of 6057 cases (3396 males and 2661 females), with ages ranging from the 21st week of gestation to 95 years. All the cases come from a general hospital.To be included in the study, the individual had to be of known age and sex, and free from any clinical psychiatric syndrome. The volume of the lateral ventricles had to have been measured and the massa intermedia examined. All cases come from brains systematically autopsied in the Division of Neuropathology of the Geneva University Hospital between the years 1971 and 1976 inclusively, and all are free from affections, duly diagnosed, and come from the clinics of this same hospital. The cases used in the study fit the following criteria: (1) knowledge of age and sex; (2) knowledge of the capacity, in cc, of the two lateral ventricles; (3) notion of the presence or absence of the massa intermedia. The first stage of the septum pellucidum is made up of pluripotential stem cells which degenerate quite early, leaving a liquid between them. A number of hypotheses have been put forward to explain the origin of this liquid, without any agreement being reached. Our explanation for the appearance of this liquid is the following: as in every necrosis, the molecular concentration increases after the disintegration of the large protein molecules into amino acids; this concentration necessarily attracts liquid to equalise the oncological pressure. Cellular resorption is easier to study in the periventricular telencephalic matrix than in the resorption of the stem cells of the septum pellucidum, as it occurs a little later, and this makes the microglia, being nearer to maturity, easier to be recognised. The incidence of cavum septi pellucidi during the embryo-foetal phase is quite well-known by virtue of the various concordant results of different authors. In contrast, over the course of adult life, the results published are extraordinarily discordant; moreover, the cases presented are taken together, that is to say, globally. Our results, which take the succession of decades into account, indicate that the cavum septi pellucidi persists among adults in 1224 of the 6057 cases studied, this being an incidence of 20.2%. From 57.7% at birth, the incidence establishes itself quite early in life at around 16%, and this rate is maintained until old age.This stability from one decade to the next supports the hypothesis that the cavum septi pellucidi is resorbed at its own precise moment. 1224 cava septi pellucidi were found in men and 466 in women.This discrepancy works out to a male preponderance of around 3:2, a result which corresponds with the greater part of the literature. The rare documents that deal with hereditary speak against such an origin. The only homozygotes that carry cavum septi pellucidi are those that appear in Craig et al. (Mayo Clin Proc 1953;28:330–5). Just as for the cavum septi pellucidi, the agenesis of the massa intermedia is preponderant in males (x2 of 23,900, Morel [Acta Anatomica 1947;4:203–7]). In our series, it is approximately the same among cavum septi pellucidi carriers as it is in Morel’s series. In an anatomo-clinical and statistical study of the colloid cyst of the third ventricle, made up of 75 cases, found by Witzig (Acta Neurol Belg 1982;82:281–99) in a total of 13,389 autopsies, a very low incidence (0.46%) is noted with a clear male preponderance (62 men, 13 women, x2 of 8.99). In 40 of his cases, 7 were carriers of a cavum septi pellucidi, or 17.5%. This fact confirms the possible co-existence of these two dysgeneses near to one another, estimated by Moseley at 10%. This relation is significant, as each of the two can lead to a hydrocephalus, the origin of which is then to be determined by radiology. The terms cavum and cyst, frequently used to designate each other, are not the same on an anatomical level. The former must be reserved for an enclosed space of liquid content, whose wall does not form an epithelium. In contrast, the cyst, also an enclosed space, has its wall covered by an epithelium and its contents are not always liquid (cellular debris, mucus, squama, cholesterol, etc.). As far as the cavum septi pellucidi is concerned, if at the beginning of life it is indeed a cavum, in the course of life the immature cells bordering become modified and end up as genuine ependymocytes. Many authors have studied these cellular transformations and most of them currently acknowledge that the cavum can transform into a cyst. The seeming ability of a given cavum to expand does not relate to age but perhaps to sex (female predominance), either by genetic programming or hormonal factors. In the cases studied, the enlargement of the cavum septi pellucidi is independent of that of the lateral ventricles of the brain. The association “cavum septi pellucidi-hydrocephalus” has been recognised for a long time. In an attempt to determine this frequency, which is still approximate, we chose 42 publications of anatomo- clinical cases of cavum septi pellucidi, published separately or in small series. They supplied 91 cases. Among the extreme cases, 49 simultaneously show both cavum septi pellucidi and hydrocephalus (28 men, 21 women). When the hind portion of the cavum septi pellucidi is separated from the front by contact between trigona and the corpus callosum, it is referred to as cavum vergae. Certain authors contest its existence by assimilating it to the cavum septi pellucidi. It is, in fact, exceptional (only one case among the 7711 pneumoencephalographies of Finke and Koch [Dtsch Z Nervenheilk 1968; 193:154–7]). Our 4 cases added to the 12 found in the literature indicate a form of female predominance (11 women, 5 men). The correlation with hydrocephalus is vague. None of the 1224 cases studied displayed particular neurological or mental symptoms. In certain cases, where such symptoms exist, one can easily link them to other concomitant dysgeneses. The cavum septi pellucidi can provoke disorders if (a) it attains a certain width (generally given as 10 mm); (b) it is free of fenestration, that is to say, non-communicating; (c) it is expanding. The blocking of one or both of Monro’s holes (Sylvius’ duct in case of cavum vergae) manifests itself through a syndrome of intracranial hypertension and its accompanying symptoms.Among the latter, which are well-known, the various types of epilepsy and mental retardation are too widespread to be taken account of in this context. Moreover, following lesions to the trigona, which remain unproven, certain behavioural and emotional disorders have been linked to secondary lesions of the limbic lobes, also unproven. Singly or doubly partitioned, the septum pellucidum can be split in one or several places. These perforations, which connect the cavum septi pellucidi to the lateral ventricles, are given as fenestration. They are produced under various circumstances: (a) they often accompany the various cerebral atrophies and internal hydrocephalies; (b) they are produced as result of manipulations of the pneumoencephalography and often by certain types of cranio-cerebral traumatism, among which those brought on by boxing are well-documented. Expanding cava septi pellucidi are operated on by means of various neurosurgical operations which range from simple endoscopic fenestration to the placing of a shunt by conventional stereotaxis. Full article