TECHNICAL METHODS OF CLEANING SHIPWRECKS FROM GHOST NETS

Ghost nets are fishing gear lost and left in bodies of water that continue to be fished. Most of the fishing gear that is lost is made of synthetic materials that break down very slowly or not at all in nature and continue to work long after the net is lost. A ghost net drifts in the sea until it catches on an object, most often a shipwreck. This harms both nature and people\u27s economic interests. Currently, the release of shipwrecks and other sunken objects from fragments of lost nets is mainly done by human hands, resp. divers dive to the wreck and use hand tools to free the wreck from fragments of fishing gear. There are innovative robotic systems in the world that can partially replace the work of divers.

Promocijas darbs

Elektroniskā versija nesatur pielikumusDarbā analizētas hipofīzes šūnu kultūru biomolekulārās īpašības un no hipofīzes izcelsmes šūnām brīvās DNS molekulu klātbūtne pacientu asins plazmā. Tika konstatēts, ka viena no šūnu kultūrām ir multipotentas mezinhimāli stromālās šūnas, kas visticamāk nav galvenā PitNET šūnu populācija, bet, iespējams, tai ir audzēja darbību atbalstoša loma. Otra šūnu kultūra ir hipofīzes sfēru veidojošas šūnas, kuras visticamāk, veido audzēja galveno audu masu. Tām bija kopīgas ģenētiskās iezīmes ar galveno audzēja masu. Analizējot pacientu šķidrās biopsijas, tika atklāts, ka PitNET audu paraugos atrastās somatiskās mutācijas ar dažādu jutību ir konstatējamas arī šūnu brīvajā DNS. Atslēgvārdi: hipofīzes neiroendokrīnie audzēji, neparenhimālās šūnas, multipotentas mezinhimāli stromālās šūnas, hipofīzes sfēras, šūnu brīvā DNS, cirkulējošā audzēja DNSThe thesis analyses biomolecular signatures of pituitary cell cultures and the representation of pituitary-borne cell-free DNA molecules in the patients’ blood plasma. One of the cell cultures was detected to be multipotent mesenchymal stromal cells, which are not the main PitNET cell population but likely have a tumour supportive role. The other cell culture was pituitary sphere-forming cells, which likely constitute the main tissue mass of the tumour. They shared genetic traits with the main tumour mass. Analysing patients’ liquid biopsies revealed that the somatic mutations found in PitNET tissue samples are also detectable in cell-free DNA with varying sensitivity. Keywords: pituitary neuroendocrine tumours, non-parenchymal cells, multipotent mesenchymal stromal cells, pituispheres, cell-free DNA, circulating tumour DN

Selective enrichment of heterotrophic nitrifiers Alcaligenaceae and alcanivorax spp. From industrial wastewaters

Publisher Copyright: © 2020 the Author(s),.Removal of nitrogen from wastewaters (WW) represents a global problem. The low nitrification rate during WW treatment is often caused by ecotoxicity. This problem is attributed mostly to the industrial WW. Our study was focused on the testing of industrial WW and activated sludge (AS) with the aim to reveal the abundance of nitrifiers and increase their biomass, thus, providing the additional step, i.e., bioaugmentation, within the technological process of WW treatment. Plating of AS on the selective solidified media designated for the 1st and 2nd nitrification stages, resulted in the shift in bacterial community structure with dominated Alcaligenaceae and Alcanivorax for the 1st stage, and Alcanivorax-for the 2nd stage of nitrification, respectively. Incubation of AS in the presence of real WW and selective nitrification broth resulted in a considerable increase (one or two magnitudes in the presence of the 1st and 2nd stage nitrification broth, respectively) of culturable nitrifiers after 5 days incubation under aerated conditions. The obtained data provide with evidence about a possibility to strengthen the role of heterotrophic nitrifiers in the treatment of industrial WW, where toxicity obstacles inhibited nitrification under conventional conditions.Peer reviewe

Changes in Bacterial Community Structure in Wastewaters in the presence of Saccharomyces Cerevisiae and Benzalkonium Chloride

Publisher Copyright: © Published under licence by IOP Publishing Ltd.The benefit of bioaugmentation of activated sludge (AS) with yeasts was tested using AS and wastewaters (WW) that originated from the chemical industry, as well as synthetic WW. A stimulating effect of Saccharomyces cerevisiae on microbial respiration intensity in AS was shown. The added yeast biomass maintained viability in AS, an inhibitory effect of BAC on Bacilli was found; however, the addition of yeasts to AS reduced this effect.Peer reviewe

Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori

Publisher Copyright: © 2023 Gudra et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The spread of extended-spectrum beta-lactamases (ESBLs) in nosocomial and community-acquired enterobacteria is an important challenge for clinicians due to the limited therapeutic options for infections that are caused by these organisms. Here, we developed a panel of ESBL coding genes, evaluated the abundance and prevalence of ESBL encoding genes in patients undergoing H. pylori eradication therapy, and summarized the effects of eradication therapy on functional profiles of the gut microbiome. To assess the repertoire of known beta lactamase (BL) genes, they were divided into clusters according to their evolutionary relation. Primers were designed for amplification of cluster marker regions, and the efficiency of this amplification panel was assessed in 120 fecal samples acquired from 60 patients undergoing H. pylori eradication therapy. In addition, fecal samples from an additional 30 patients were used to validate the detection efficiency of the developed ESBL panel. The presence for majority of targeted clusters was confirmed by NGS of amplification products. Metagenomic sequencing revealed that the abundance of ESBL genes within the pool of microorganisms was very low. The global relative abundances of the ESBL-coding gene clusters did not differ significantly among treatment states. However, at the level of each cluster, classical ESBL producers such as Klebsiella sp. for blaOXY (p = 0.0076), Acinetobacter sp. for blaADC (p = 0.02297) and others, differed significantly with a tendency to decrease compared to the pre- and post-eradication states. Only 13 clusters were common across all three datasets, suggesting a patient-specific distribution profile of ESBL-coding genes. The number of AMR genes detected in the post-eradication state was higher than that in the pre-eradication state, which could be attributed, at least in part, to the therapy. This study demonstrated that the ESBL screening panel was effective in targeting ESBL-coding gene clusters from bacterial DNA and that minor differences exist in the abundance and prevalence of ESBL-coding gene levels before and after eradication therapy.Peer reviewe

Whole exome sequencing reveals novel risk genes of pituitary neuroendocrine tumors

Funding Information: This research was supported by the European Regional Development Fund (ERDF), Measure 1.1.1.1 “Industry-Driven Research” project „Molecular markers of pituitary tumour development, progression and therapy response” (Project No. 1.1.1.1/16/A/066, 2017). The authors acknowledge the Latvian Biomedical Research and Study Centre and the Genome Database of the Latvian Population for providing infrastructure, biological material and data. Publisher Copyright: © 2022 Peculis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Somatic genetic alterations in pituitary neuroendocrine tumors (PitNET) tissues have been identified in several studies, but detection of overlapping somatic PitNET candidate genes is rare. We sequenced and by employing multiple data analysis methods studied the exomes of 15 PitNET patients to improve discovery of novel factors involved in PitNET development. PitNET patients were recruited to the study before PitNET removal surgery. For each patient, two samples for DNA extraction were acquired: venous blood and PitNET tissue. Exome sequencing was performed using Illumina NexSeq 500 sequencer and data analyzed using two separate workflows and variant calling algorithms: GATK and Strelka2. A combination of two data analysis pipelines discovered 144 PitNET specific somatic variants (mean = 9.6, range 0–19 per PitNET) of which all were SNVs. Also, we detected previously known GNAS PitNET mutation and identified somatic variants in 11 genes, which have contained somatic variants in previous WES and WGS studies of PitNETs. Noteworthy, this is the third study detecting somatic variants in gene RYR1 in the exomes of PitNETs. In conclusion, we have identified two novel PitNET candidate genes (AC002519.6 and AHNAK) with recurrent somatic variants in our PitNET cohort and found 13 genes overlapping from previous PitNET studies that contain somatic variants. Our study demonstrated that the use of multiple sequencing data analysis pipelines can provide more accurate identification of somatic variants in PitNETs.publishersversionPeer reviewe

Polymorphisms in MEN1 and DRD2 genes are associated with the occurrence and characteristics of pituitary adenomas

Publisher Copyright: © 2016 European Society of Endocrinology Published by Bioscientifica Ltd. Copyright: Copyright 2017 Elsevier B.V., All rights reserved.Objective: Although pituitary adenomas (PAs) affect a significant proportion of the population, only a fraction have the potential to become clinically relevant during an individual's lifetime, causing hormonal imbalance or complications due to mass effect. The overwhelming majority of cases are sporadic and without a clear familial history, and the genotype-phenotype correlation in PA patients is poorly understood. Our aim was to investigate the involvement of genes known for their role in familial cases on drug response and tumor suppression in the development and pathology of PAs in a patient group from Latvia. Design: The study included 143 cases and 354 controls, we investigated the role of single-nucleotide polymorphisms (SNPs) in seven genes (SSTR2, SSTR5, DRD2, MEN1, AIP, GNAS, and PRKAR1A) associated with pituitary tumor occurrence, phenotype, and clinical symptoms. Methods: Genotyping of 96 tag and nonsynonymous SNPs was performed in the genomic regions of interest. Results: We discovered a significant association (OR = 17.8, CI 0.95 = 2.18-145.5, P = 0.0002) between a rare MEN1 mutation (rs2959656) and clinically active adenoma in our patients. Additionally, rs7131056 at DRD2 was associated with a higher occurrence of extrasellar growth in patients with prolactinoma and somatotropinoma (OR = 2.79, CI 0.95 = 1.58-4.95, P = 0.0004). Conclusions: rs2959656, a nonsynonymous variant in MEN1, is associated with the development of clinically active PA. Furthermore, rs7131056 in DRD2 contributes to either faster growth of the adenoma or reduced symptomatic presentation, allowing PAs to become larger before detection.publishersversionPeer reviewe

Evaluation of the Possibility to Detect Circulating Tumor DNA From Pituitary Adenoma

Funding Information: The authors acknowledge the Latvian Biomedical Research and Study Center and the Genome Database of the Latvian Population for providing infrastructure, biological material, and data. Funding. This research was supported by the European Regional Development Fund (ERDF), Measure 1.1.1.1 Industry-Driven Research project Molecular markers of pituitary tumor development, progression and therapy response (Project No. 1.1.1.1/16/A/066, 2017), and Roche Academy project Immunohistochemical analysis of pituitary adenoma tissue. Publisher Copyright: © Copyright © 2019 Megnis, Peculis, Rovite, Laksa, Niedra, Balcere, Caune, Breiksa, Nazarovs, Stukens, Konrade, Pirags and Klovins.Objective: Circulating free DNA (cfDNA) in general and circulating tumor DNA (ctDNA) in particular is becoming an increasingly used form of liquid biopsy biomarkers. In this study, we are investigating the ability to detect ctDNA from the plasma of pituitary adenoma (PA) patients. Design: Tumor tissue samples were obtained from planed PA resections, before which blood plasma samples were taken. Somatic variants found in PA tissue samples were evaluated in related cfDNA, isolated from plasma samples. Methods: Sanger sequencing, as well as previously obtained whole-exome sequencing data, were used to evaluate somatic variants composition in tumor tissue samples. cfDNA was isolated from the same PA patients and competitive allele-specific TaqMan PCR and amplicon-based next-generation sequencing (NGS) approach were used for targeted detection of variants found in corresponding tumor tissue samples. Results: Using NGS-based analysis, we detected five out of 17 somatic variants in 40 to 60% of total reads, three variants in 0.50–5.00% of total read count, including GNAS c.601C>T, which was detected using ultra-deep NGS (1.78 million X) in 0.77% of amplicons reads. Nine variants were not detected. We also detected We were not able to detect variant found in PA tissue in cfDNA using cast-PCR, indicating that the portion of variant-containing ctDNA in total isolated cfDNA is too small to be detected with this method. Conclusions: For the first time, we demonstrate the possibility to detect somatic variants of PA in cfDNA isolated from patients' blood plasma. Whether the source of variant detected in cfDNA is PA should be further tested.publishersversionPeer reviewe

Genome wide analysis of circulating miRNAs in growth hormone secreting pituitary neuroendocrine tumor patients’ plasma

Funding Information: The financial support given by NSFC with Grant No. 11874034, Taishan Scholar Program of Shandong No. ts201712054, and Shandong Science and Technology Enterprise Innovation Capacity Enhancement Project (2021TSGC1036) are highly appreciated for this research. Publisher Copyright: Copyright © 2022 Niedra, Peculis, Litvina, Megnis, Madrika, Balcere, Romanovs, Steina, Stukens, Breiksa, Nazarovs, Sokolovska, Liutkeviciene, Vilkevicute, Konrade and Rovite.Background: Circulating plasma miRNAs have been increasingly studied in the field of pituitary neuroendocrine tumor (PitNET) research. Our aim was to discover circulating plasma miRNAs species associated with growth hormone (GH) secreting PitNETs versus assess how the plasma levels of discovered miRNA candidates are impacted by SSA therapy and whether there is a difference in their levels between GH secreting PitNETs versus other PitNET types and healthy individuals. Design: We compared plasma miRNA content and levels before and after surgery focusing on GH secreting PitNET patients. Selected miRNA candidates from our data and literature were then tested in a longitudinal manner in somatostatin analogues (SSA) treatment group. Additionally, we validated selected targets in an independent GH secreting PitNET group. Methods: miRNA candidates were discovered using the whole miRNA sequencing approach and differential expression analysis. Selected miRNAs were then analyzed using real-time polymerase chain reaction (qPCR). Results: Whole miRNA sequencing discovered a total of 16 differentially expressed miRNAs (DEMs) in GH secreting PitNET patients’ plasma 24 hours after surgery and 19 DEMs between GH secreting PitNET patients’ plasma and non-functioning (NF) PitNET patients’ plasma. Seven miRNAs were selected for further testing of which miR-625-5p, miR-503-5p miR-181a-2-3p and miR-130b-3p showed a significant downregulation in plasma after 1 month of SSA treatment. mir-625-5p was found to be significantly downregulated in plasma of GH secreting PitNET patients vs. NF PitNET patients. miR-625-5p alongside miR-130b-3p were also found to be downregulated in GH PitNETs compared to healthy individuals. Conclusions: Our study suggests that expression of plasma miRNAs miR-625-5p, miR-503-5p miR-181a-2-3p and miR-130b-3p in GH secreting PitNETs is affected by SSA treatment. Additionally, miR-625-5p can distinguish GH secreting PitNETs from other PitNET types and healthy controls warranting further research on these miRNAs for treatment efficacy.publishersversionPeer reviewe

Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue

Funding Information: The authors acknowledge the Latvian Biomedical Research and Study Centre and the Genome Database of the Latvian Population for providing the infrastructure, biological material, and data. Publisher Copyright: © Copyright © 2021 Saksis, Silamikelis, Laksa, Megnis, Peculis, Mandrika, Rogoza, Petrovska, Balcere, Konrade, Steina, Stukens, Breiksa, Nazarovs, Sokolovska, Pirags, Klovins and Rovite.Acromegaly is a disease mainly caused by pituitary neuroendocrine tumor (PitNET) overproducing growth hormone. First-line medication for this condition is the use of somatostatin analogs (SSAs), that decrease tumor mass and induce antiproliferative effects on PitNET cells. Dopamine agonists (DAs) can also be used if SSA treatment is not effective. This study aimed to determine differences in transcriptome signatures induced by SSA/DA therapy in PitNET tissue. We selected tumor tissue from twelve patients with somatotropinomas, with half of the patients receiving SSA/DA treatment before surgery and the other half treatment naive. Transcriptome sequencing was then carried out to identify differentially expressed genes (DEGs) and their protein–protein interactions, using pathway analyses. We found 34 upregulated and six downregulated DEGs in patients with SSA/DA treatment. Three tumor development promoting factors MUC16, MACC1, and GRHL2, were significantly downregulated in therapy administered PitNET tissue; this finding was supported by functional studies in GH3 cells. Protein–protein interactions and pathway analyses revealed extracellular matrix involvement in the antiproliferative effects of this type of the drug treatment, with pronounced alterations in collagen regulation. Here, we have demonstrated that somatotropinomas can be distinguished based on their transcriptional profiles following SSA/DA therapy, and SSA/DA treatment does indeed cause changes in gene expression. Treatment with SSA/DA significantly downregulated several factors involved in tumorigenesis, including MUC16, MACC1, and GRHL2. Genes that were upregulated, however, did not have a direct influence on antiproliferative function in the PitNET cells. These findings suggested that SSA/DA treatment acted in a tumor suppressive manner and furthermore, collagen related interactions and pathways were enriched, implicating extracellular matrix involvement in this anti-tumor effect of drug treatment.publishersversionPeer reviewe