601. Using multi-tracer inference to move beyond single-catchment ecohydrology : invited reviewBenjamin W. Abbott, Viktor Baranov, Clara Mendoza-Lera, Mukundh Narayanan Balasubramanian, José Gonçalves, Stefan Krause, 2016, review article Abstract: Protecting or restoring aquatic ecosystems in the face of growing anthropogenic pressures requires an understanding of hydrological and biogeochemical functioning across multiple spatial and temporal scales. Recent technological and methodological advances have vastly increased the number and diversity of hydrological, biogeochemical, and ecological tracers available, providing potentially powerful tools to improve understanding of fundamental problems in ecohydrology, notably: 1. Identifying spatially explicit flowpaths, 2. Quantifying water residence time, and 3. Quantifying and localizing biogeochemical transformation. In this review, we synthesize the history of hydrological and biogeochemical theory, summarize modern tracer methods, and discuss how improved understanding of flowpath, residence time, and biogeochemical transformation can help ecohydrology move beyond description of site-specific heterogeneity. We focus on using multiple tracers with contrasting characteristics (crossing proxies) to infer ecosystem functioning across multiple scales. Specifically, we present how crossed proxies could test recent ecohydrological theory, combining the concepts of hotspots and hot moments with the Damköhler number in what we call the HotDam framework.
Keywords: hydrological tracer, environmental hydrology, ecohydrology, aquatic ecology
Published in DiRROS: 06.08.2024; Views: 297; Downloads: 273
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602. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived productsArne Holst-Jensen, Bjørn Spilsberg, Alfred J. Arulandhu, Esther Kok, Jianxin Shi, Jana Žel, 2016, review article Abstract: The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.
Keywords: cisgene, intragene, traceability, traceability, transcriptome sequencing, transgene, unknown GMO
Published in DiRROS: 06.08.2024; Views: 235; Downloads: 175
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603. Novel therapeutic strategies to target leukemic cells that hijack compartmentalized continuous hematopoietic stem cell nichesVashendriya V. V. Hira, Cornelis J. F. van Noorden, Hetty E. Carraway, Jaroslaw P. Maciejewski, Remco J. Molenaar, 2017, review article Abstract: Acute myeloid leukemia and acute lymphoblastic leukemia cells hijack hematopoietic stem cell (HSC) niches in the bone marrow and become leukemic stem cells (LSCs) at the expense of normal HSCs. LSCs are quiescent and resistant to chemotherapy and can cause relapse of the disease. HSCs in niches are needed to generate blood cell precursors that are committed to unilineage differentiation and eventually production of mature blood cells, including red blood cells, megakaryocytes, myeloid cells and lymphocytes. Thus far, three types of HSC niches are recognized: endosteal, reticular and perivascular niches. However, we argue here that there is only one type of HSC niche, which consists of a periarteriolar compartment and a perisinusoidal compartment. In the periarteriolar compartment, hypoxia and low levels of reactive oxygen species preserve the HSC pool. In the perisinusoidal compartment, hypoxia in combination with higher levels of reactive oxygen species enables proliferation of progenitor cells and their mobilization into the circulation. Because HSC niches offer protection to LSCs against chemotherapy, we review novel therapeutic strategies to inhibit homing of LSCs in niches for the prevention of dedifferentiation of leukemic cells into LSCs and to stimulate migration of leukemic cells out of niches. These strategies enhance differentiation and proliferation and thus sensitize leukemic cells to chemotherapy. Finally, we list clinical trials of therapies that tackle LSCs in HSC niches to circumvent their protection against chemotherapy.
Keywords: hematopoietic stem cell niche, hijacking, leukemic stem cells, bone marrow, therapy resistance, leukemia
Published in DiRROS: 06.08.2024; Views: 230; Downloads: 205
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604. Proteases and cytokines as mediators of interactions between cancer and stromal cells in tumoursBarbara Breznik, Helena Motaln, Tamara Lah Turnšek, 2017, review article Abstract: Proteolytic enzymes are highly relevant in different processes of cancer progression. Their interplay with other signalling molecules such as cytokines represents important regulation of multicellular cross-talk. In this review, we discuss protease regulation mechanisms of cytokine signalling in various types of cancer. Additionally, we highlight the reverse whereby cytokines have an impact on protease expression in an autocrine and paracrine manner, representing complex feedback mechanisms among multiple members of these two protein families. The relevance of the protease-cytokine axis is illustrated in glioblastoma, where interactions between normal mesenchymal stem cells and cancer cells play an important role in this very malignant form of brain cancer.
Keywords: cellular cross-talk, glioblastoma, invasion, mesenchymal stem cells, protease-cytokine signalling
Published in DiRROS: 06.08.2024; Views: 224; Downloads: 156
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605. The hypoxic peri-arteriolar glioma stem cell niche, an integrated concept of five types of niches in human glioblastomaDiana A. Aderetti, Vashendriya V. V. Hira, Remco J. Molenaar, Cornelis J. F. van Noorden, 2018, review article Abstract: Glioblastoma is the most lethal primary brain tumor and poor survival of glioblastoma patients is attributed to the presence of glioma stem cells (GSCs). These therapy-resistant, quiescent and pluripotent cells reside in GSC niches, which are specific microenvironments that protect GSCs against radiotherapy and chemotherapy. We previously showed the existence of hypoxic peri-arteriolar GSC niches in glioblastoma tumor samples. However, other studies have described peri-vascular niches, peri-hypoxic niches, peri-immune niches and extracellular matrix niches of GSCs. The aim of this review was to critically evaluate the literature on these five different types of GSC niches. In the present review, we describe that the five niche types are not distinct from one another, but should be considered to be parts of one integral GSC niche model, the hypoxic peri-arteriolar GSC niche. Moreover, hypoxic peri-arteriolar GSC niches are structural and functional look-alikes of hematopoietic stem cell (HSC) niches in the bone marrow. GSCs are maintained in peri-arteriolar niches by the same receptor-ligand interactions as HSCs in bone marrow. Our concept should be rigidly tested in the near future and applied to develop therapies to expel and keep GSCs out of their protective niches to render them more vulnerable to standard therapies.
Keywords: glioblastoma, glioma stem cells, niches, blood vessels, extracellular matrix, tumor microenvironment, hypoxia, therapy resistance, vasculature
Published in DiRROS: 06.08.2024; Views: 335; Downloads: 198
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606. The role of plasmalemma vesicle-associated protein in pathological breakdown of blood-brain and blood-retinal barriers : potential novel therapeutic target for cerebral edema and diabetic macular edemaEsmeralda K. Bosma, Cornelis J. F. van Noorden, Reinier O. Schlingemann, Ingeborg Klaassen, 2018, review article Abstract: Breakdown of the blood–brain barrier (BBB) or inner blood–retinal barrier (BRB), induced by pathologically elevated levels of vascular endothelial growth factor (VEGF) or other mediators, can lead to vasogenic edema and significant clinical problems such as neuronal morbidity and mortality, or vision loss. Restoration of the barrier function with corticosteroids in the brain, or by blocking VEGF in the eye are currently the predominant treatment options for brain edema and diabetic macular edema, respectively. However, corticosteroids have side effects, and VEGF has important neuroprotective, vascular protective and wound healing functions, implying that long-term anti-VEGF therapy may also induce adverse effects. We postulate that targeting downstream effector proteins of VEGF and other mediators that are directly involved in the regulation of BBB and BRB integrity provide more attractive and safer treatment options for vasogenic cerebral edema and diabetic macular edema. The endothelial cell-specific protein plasmalemma vesicle-associated protein (PLVAP), a protein associated with trans-endothelial transport, emerges as candidate for this approach. PLVAP is expressed in a subset of endothelial cells throughout the body where it forms the diaphragms of caveolae, fenestrae and trans-endothelial channels. However, PLVAP expression in brain and eye barrier endothelia only occurs in pathological conditions associated with a compromised barrier function such as cancer, ischemic stroke and diabetic retinopathy. Here, we discuss the current understanding of PLVAP as a structural component of endothelial cells and regulator of vascular permeability in health and central nervous system disease. Besides providing a perspective on PLVAP identification, structure and function, and the regulatory processes involved, we also explore its potential as a novel therapeutic target for vasogenic cerebral edema and retinal macular edema.
Keywords: plasmalemma vesicle-associated protein, blood-brain barrier, blood-retinal barrier, cerebral edema, diabetic macular edema
Published in DiRROS: 06.08.2024; Views: 233; Downloads: 187
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607. The genus Wallemia - from contamination of food to health threatJanja Zajc, Nina Gunde-Cimerman, 2018, review article Abstract: The fungal genus Wallemia of the order Wallemiales (Wallemiomycotina, Basidiomycota) comprises the most xerotolerant, xerophilic and also halophilic species worldwide. Wallemia spp. are found in various osmotically challenged environments, such as dry, salted, or highly sugared foods, dry feed, hypersaline waters of solar salterns, salt crystals, indoor and outdoor air, and agriculture aerosols. Recently, eight species were recognized for the genus Wallemia, among which four are commonly associated with foods: W. sebi, W. mellicola, W. muriae and W. ichthyophaga. To date, only strains of W. sebi, W. mellicola and W. muriae have been reported to be related to human health problems, as either allergological conditions (e.g., farmer’s lung disease) or rare subcutaneous/cutaneous infections. Therefore, this allergological and infective potential, together with the toxins that the majority of Wallemia spp. produce even under saline conditions, defines these fungi as filamentous food-borne pathogenic fungi.
Keywords: food, air, pathogen, xerophile, halophile, mycotoxin, farmerʼs lung disease, subcutaneous infection
Published in DiRROS: 06.08.2024; Views: 227; Downloads: 191
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608. Effects of the green tea polyphenol epigallocatechin-3-gallate on glioma : a critical evaluation of the literatureChung T. Le, William P. J. Leenders, Remco J. Molenaar, Cornelis J. F. van Noorden, 2018, review article Abstract: The review discusses the effects of Epigallocatechin-3-gallate Gallate (EGCG) on glioma as a basis for future research on clinical application of EGCG. Epidemiological studies on the effects of green tea or EGCG on the risk of glioma is inconclusive due to the limited number of studies, the inclusion of all tea types in these studies, and the focus on caffeine rather than EGCG. In vivo experiments using EGCG monotherapy are inconclusive. Nevertheless, EGCG induces cell death, prevents cellular proliferation, and limits invasion in multiple glioma cell lines. Furthermore, EGCG enhances the efficacy of anti-glioma therapies, including irradiation, temozolomide, carmustine, cisplatin, tamoxifen, and TNF-related apoptosis-inducing ligand, but reduces the effect of bortezomib. Pro-drugs, co-treatment, and encapsulation are being investigated to enhance clinical applicability of EGCG. Mechanisms of actions of EGCG have been partly elucidated. EGCG has both anti-oxidant and oxidant properties. EGCG inhibits pro-survival proteins, such as telomerase, survivin, GRP78, PEA15, and P-gp. EGCG inhibits signaling of PDGFR, IGF-1R, and 67LR. EGCG reduces invasiveness of cancer cells by inhibiting the activities of various metalloproteinases, cytokines, and chemokines. Last, EGCG inhibits some NADPH-producing enzymes, thus disturbing redox status and metabolism of glioma cells. In conclusion, EGCG may be a suitable adjuvant to potentiate anti-glioma therapies.
Keywords: green tea, glioma
Published in DiRROS: 06.08.2024; Views: 252; Downloads: 117
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609. Critical assessment of digital PCR for the detection and quantification of genetically modified organismsTigst Demeke, David Dobnik, 2018, review article Abstract: The number of genetically modified organisms (GMOs) on the market is steadily increasing. Because of regulation of cultivation and trade of GMOs in several countries, there is pressure for their accurate detection and quantification. Today, DNA-based approaches are more popular for this purpose than protein-based methods, and real-time quantitative PCR (qPCR) is still the gold standard in GMO analytics. However, digital PCR (dPCR) offers several advantages over qPCR, making this new technique appealing also for GMO analysis. This critical review focuses on the use of dPCR for the purpose of GMO quantification and addresses parameters which are important for achieving accurate and reliable results, such as the quality and purity of DNA and reaction optimization. Three critical factors are explored and discussed in more depth: correct classification of partitions as positive, correctly determined partition volume, and dilution factor. This review could serve as a guide for all laboratories implementing dPCR. Most of the parameters discussed are applicable to fields other than purely GMO testing.
Keywords: digital PCR, droplet digital PCR, chip-based digital PCR, genetically modified organisms, quantification
Published in DiRROS: 06.08.2024; Views: 243; Downloads: 183
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610. Review of heterobranch molluscs fauna in the Boka Kotorska Bay, MontenegroMilica Jovanović, Vesna Mačić, Domen Trkov, Martina Orlando-Bonaca, Lovrenc Lipej, 2019, review article Abstract: Heterobranch molluscs fauna in Montenegro has been poorly investigated so far. The aim of the present paper is to improve the knowledge about species diversity of these marine organisms in the Boka Kotorska Bay, specific fjord-like entity in the southern Adriatic Sea. New records of seven heterobranch species were obtained by field surveys in 2017, while three new records were provided by analysing underwater photographs from previous periods. The resulted checklist summarizes the knowledge of the diversity of heterobranchs in the Boka Kotorska Bay from the oldest record in 1967 to the present day, and consists of a total of 62 heterobranch species.
Keywords: heterobranch fauna, Boka Kotorska Bay, Montenegro
Published in DiRROS: 06.08.2024; Views: 290; Downloads: 157
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