Miracle-dz/UniFAR-FTUs huggingface dataset:
Human activities trigger change in marine landscape

Mannino, A. M. : Human activities trigger change in marine landscape. — Fl. Medit. 28: 295-311. 2018. — ISSN: 1120-4052 printed, 2240-4538 online. Biodiversity is undergoing rapid and worrying changes, partially driven by anthropogenic activities. Human impacts and climate change (e.g. increasing temperature and ocean acidification), which act at different spatial scale, represent the most serious threats to biodiversity and ecosystem structure and function. In this overview, the effects of anthropogenic pressures on unique and valuable Mediterranean systems, such as Cystoseira sp. pl. forest and Posidonia oceanica meadows, are examined. These complex systems, characterized by a high associated biodiversity, are regularly exposed to natural and anthropogenic pressures. Due to the central role they have for several important ecological processes in marine ecosystems, their loss can lead dramatic consequences. Since these ecosystems are often unable to recover naturally, it is necessary to reinforce their resilience. Therefore, reintroduction by transplantation and reforestation methods have been recently proposed. Considering future increase in anthropogenic and climatic pressures, understanding how these systems respond to stressors and preserving their resilience should be an essential component of any conservation management plan.
Antimicrobial Drug Action

Introduction. Chemotherapy of microbial infections. The antimetabolites: folate metabolism as a target for antimicrobial drugs. The cell wall as a target for antimicrobial drugs. Synthesis of nucleic acids as a target for antimicrobial drugs. Protein synthesis as a target for antibiotics. Membrane-active drugs effective against bacteria and fungi. Chemotherapy of protozoal infections.
Environmental factors affecting the heat stability of the photosynthetic apparatus

Owing to greenhouse effect and severe dry periods in the agricultural fields, cultivated plants are increasingly exposed to the adverse impact of several abiotic stresses. Therefore, an increasing emphasis should be placed on how multiple stresses affect the physiological processes in plants and how plants respond to the coexistence of combined stress factors. Simultaneous environmental factors may elicit a response different from that given to a single factor, resulting in intensification, overlapping or antagonistic effects. Although the rate of photosynthesis is significantly reduced by salinity and decreased water availability, the thermotolerance of the photosynthetic apparatus may be altered by salt and drought preconditioning. In this short review, we focused on the individual effect of heat stress and the influence of dehydration and NaCl treatment on the heat tolerance of plants. According to our present knowledge, the thermostability of the photosynthetic apparatus may usually be improved by pretreatment of drought or NaCl. At the same time, several different mechanisms in the background of the higher thermostability are hypothesized. These possible droughtand salt-induced processes are also summarized by this review article.
Palinokompleks południowopolski jako długotrwały zapis różnoskalowych zmian klimatycznych we wczesno-środkowoplejstoceńskim przejściu (MIS 22-13)

The South-Polish pollen complex, being an equivalent of the South-Polish complex in relation to its pollen content, was distinguished based on pollen data coupled with palaeomagnetic and geological investigations. The complex contains the Augustovian, Domuratovian and Ferdynandovian pollen sequences with a multicycle record of vegetation changes. The record of vegetation changes allows for the reconstruction of high-amplitude climate changes of a glacial/cooling/glacial rank and low-amplitude changes such as interstadial/stadial oscillations and climate fluctuations taking place both during interglacials and cool intervals. Based on palaeomagnetic data, vegetation and climate changes, the Augustovian succession should be correlated with MIS 21–19, the Domuratovian succession – with MIS 17, and the Ferdynandovian succession – with MIS
Acute Paralysis Virus Isolates from Honeybee Colonies Infested with Varroa Jacobsoni

SummaryLarge amounts of acute paralysis virus (APV) were extracted from dead, field-collected samples of European honeybees (Apis mellifera) from Russia and German Federal Republic. Virus isolates were compared to the British type strain. Particles of the three isolates were physically indistinguishable and closely related serologically, and each produced three well-defined protein bands of apparently identical mol wt on SDS Polyacrylamide gels. In Britain APV has never been found to be associated with mortality in nature. In both Russia and Germany the occurrence of APV in dead field bees and brood was associated with infestation of the colonies by the mite Varroa jacobsoni. The possible role of the mite in APV infection of honeybees is discussed.
Population genetic diversity of roe deer (Capreolus pygargus) in Mountains of Heilongjiang Province.

The roe deer is an animal of economic importance in China and a primary food source of the Amur tiger. Understanding the morphological and molecular variation of geographically isolated roe deer populations is therefore important in establishing conservation strategies. Thirty two samples from three differences geographic regions were sequenced and the populations analysed. Twenty seven haplotypes were identified from 32 sequences of the 460 bp D-loop of mtDNA genome. Fifty sites were found to be polymorphic. The population genetic diversity of roe deer was of higher level as indicated by the following parameters: mean value of haplotype diversity (h =0.9780) and mean value of nucleotide diversity (π = 0.02260). Neither the estimate of Tajima’s D nor that of Fu & Li's D deviated significantly from the neutral selection hypothesis (P>0.1) for the three populations. The result suggests no evidence of strong selective sweeps or balancing selection. Of the three populations, the Great Khinghan Mountains geographic region was shown to have the most nucleotide diversity. To ensure conservation of genetic diversity within this population, we propose a high priority conservation classification.
Computational genomics of hyperthermophiles

With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational analyses on (hyper)thermophilic archaeal and bacterial genomes with a particular emphasis on carbohydrate metabolic pathways and their regulation. These analyses were integrated with wet-lab functional genomics data and results from classical molecular biology and microbial physiology experiments. The research was conducted on the archaea Sulfolobus solfataricus, Pyrococcus furiosus, T. kodakaraensis and the hydrogen producing bacterium Caldicellulosiruptor saccharolyticus. The reconstruction of the central carbohydrate metabolism in the thermo-acidophile S. solfataricus was carried out by a combination of genome sequence, whole transcriptome and proteome analyses. Only slight differences in the mRNA and the protein expression levels were shown when S. solfataricus was grown on peptides vs. glucose. However, the breakdown of D-arabinose vs. D-glucose revealed a complete novel pathway in the domain of Archaea. Similar catabolic pathways were identified in other prokaryotes and therefore a comprehensive genomic reconstruction was carried out on the pentose utilizing pathways in Archaea and, additionally, the results were compared to Bacteria and Eukarya. A computational promoter analysis of the glycolytic genes in the anaerobic species of the order Thermococcales (P. furiosus and T. kodakaraensis) indicated a clear cis-regulatory element that putatively controls all the genes of the glucose and starch degrading pathways. A comparative genomic analysis of the hyperthermophilic Thermococcales species led to the discovery of a putative transcriptional regulator that is probably involved in regulation of the entire regulon. The complete genome sequence of the extremely thermophilic Caldicellulosiruptor saccharolyticus revealed a circular genome of 2,970,275 base pairs that encodes 2679 putative proteins. The central carbohydrate pathways of C. saccharolyticus were studied in detail and the pathways for producing biohydrogen from plant cell wall material were unraveled. Subsequently, a whole transcriptome analysis of C. saccharolyticus grown on different monosaccharides showed a tight transcriptional regulation of these pathways, without glucose-based catabolite repression. C. saccharolyticus is therefore a good candidate to produce molecular hydrogen from biomass feedstock. The new insights into how prokaryotic genomes, genes and their encoded proteins function, as described in this thesis, can be applied on hyperthermophilic proteins and strains for use in and improvement of industrial processes.
Bodyweight and body length of foetus in endothelial dys- function model pregnant mus musculus as preeclampsia induction which was given mild regular exercise

Preeclampsia is condition with high diastol blood pressure ≥ 90 mmHg and proteinuria in ≥ 20 weeks of gestation. Preeclampsia was the second cause of maternal mortality in Indonesia. Preeclampsia is signed by endothelial dysfunction. Prevention of preeclampsia had not been developed yet. Exercise is activity which can induce endogen anti inflammation and antioxidant. So, it can be used to prevent the same process in preeclampsia. The goal of this research was analyzing the difference of bodyweight and body length in endothelial dysfunction pregnant Mus musculus which was given mild regular exercise and whithout exercise. This research used experimental with post test only with control group design, consited of 2 steps. Step 1 to know the dose of anti QA2, and step 2 to know the effect of mild regular exercise to bodyweight and length of foetus. Step 2 consisted of 4 groups (K1 for normal pregnant, K2 for endothelial dysfunction model pregnant, K3 for endothelial dysfunction model pregnant with mild regular exercise since early pregnant, K4 for endothelial dysfunction model pregnant with mild regular exercise since 1 week before pregnant). The number of Mus musculus were 6/group based on Federer formula. Determination of anti QA2 dose to induce endothelial dysfunction was done by using some doses and examining vasoconstriction of vessel in uterus by HE examanation. The dose that caused optimal vasoconstriction was 50 ng. The result was there was no significant differences of bodyweight and body length in endothelial dysfunction pregnant Mus musculus as preeclampsia induction which was given mild regular exercise and whithout exercise. Keywords: Bodyweight, Body length, Endothelial Dysfunction, Exercise
Characterisation of SHIP-1 as a regulator of T lymphocyte function

PI3Ks have been shown to have many important functions in T cells, including in cell growth and survival, chemotaxis and differentiation; however, the role of SHIP-1 as a negative regulator of PI3K signalling has not been so thoroughly investigated. The use of knockout mouse models has given an insight into the role of SHIP-1 in murine T cells, but these are compromised by loss of function during development which impinges upon mature T cell function. In addition, some work has been undertaken to investigate the role of SHIP-1 in human leukaemic T cell lines, but it is not clear how these findings might translate to SHIP1’ s function in normal cells. Therefore the work in this thesis was undertaken to investigate the role of SHIP-1 in primary human T lymphocytes. Initial experiments demonstrated that SHIP-1 was active both in unstimulated cells and in response to a variety of stimuli. Using a lentiviral method to deliver shRNA against SHIP-1 and a constitutively active form of SHIP-1 it was found that whilst constitutive activation of SHIP-1 led to cell death, silencing of SHIP-1 expression resulted in viable cells which failed to proliferate. Furthermore, silencing of SHIP-1 revealed its crucial role in the regulation of basal PI3K signalling, actin polymerisation, cell morphology and basal motility. Interestingly, there was no additional defect in chemotaxis, in agreement with findings that SHIP-1 and TAPP PH domain probes did not localise to specific regions of the cell membrane during chemotaxis. In addition, silencing of SHIP-1 caused an abnormal profile of cytokine production and in particular, CD4+ T cells were skewed towards becoming Tregs. The observations in this study suggest that whilst the role of SHIP-1 in primary human T cells has some similarities to its role in both murine T cells and leukaemic cell lines, there are also significant differences which it will be crucial to take into account when designing drugs to target SHIP-1. The final results section comprises work completed for Novartis, the sponsor of this PhD. In this section it was found that knockout of PI3Kγ in mice resulted in elevated production of IL17A and IL-17F along with abberant expression of IL-17 receptors and loss of PI3K signalling in response to IL-17A. These findings are of particular relevance for PI3Kγ inhibitors that are in clinical trials for inflammation and autoimmune diseases.
Phylogeography of the genus Dasiphora (Rosaceae) in the Qinghai-Tibetan Plateau: divergence blurred by expansion

Plateau uprisings and climatic oscillations are considered to have caused extensive allopatric divergences that account for the rich species diversity of the Qinghai-Tibetan Plateau (QTP). However, secondary contact during range shifts in the Quaternary glacial cycles or inter-uplift stages may have restored the gene flow between species and so counteracted these divergences, particularly in rapidly-adapting dominant elements. We tested this hypothesis by determining the phylogeographical history of Dasiphora (Rosaceae), a genus of two species that are widely distributed on the QTP and co-exist in numerous localities. We sequenced two chloroplast DNA fragments (rbcL, trnT-L) for 559 individuals from 87 populations. Bayesian methods were used to identify phylogenetic relationships and to estimate divergence times. Demographic histories were inferred using neutrality tests, mismatch distribution analysis, and coalescent simulation. A total of 112 haplotypes that clustered into three major groups were identified. The formation of these groups and their subgroups was dated to between the Pliocene and the late Pleistocene. In addition, we found that some groups underwent multiple extensive expansions. Species-specific haplotypes were identified for each species, although these haplotypes phylogenetically intermixed. These results suggest that recent plateau uplifts and climatic oscillations might have caused the deep divergences observed within this genus. However, later range expansions probably blurred these divergences and possible species boundaries. Our results shed new light on the complex evolutionary history of the QTP alpine plants. (c) 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 777-788.
Identifying the mechanism of action of valproic acid on phosphoinositide signalling

A third of epilepsy patients are resistant to currently available medication, highlighting a need to identify new antiepileptic drugs. To identify new drugs, researchers often explore new chemical structures with a common mechanism of action, but surprisingly the direct cellular target for many drugs remains unclear. One such drug is valproic acid (VPA), commonly used in the treatment of both epilepsy and bipolar disorder (BD). Previous research using the single celled amoeba Dictyostelium discoideum identified phosphoinositide recycling as a potential therapeutic mechanism for VPA and this has been validated in animal seizure models, however, the molecular target for this mechanism is unclear. To identify this target, research in this thesis initially focuses on assessing the role of several key enzymes involved in phosphoinositide signalling as potential VPA targets. Loss of these proteins did not confer resistance to VPA in this model, suggesting that VPA may function through targeting proteins in the phosphatidylinositol (PI) salvage pathway. In this pathway three key enzymes, cytidine-diphosphate-diacylglycerol synthase (CDS), cytidine-diphosphatediacylglycerol-inositol-3-phosphatidyltransferase (CDIPT) and diacylglycerol kinase (DGK) were investigated, with phylogenetic analysis establishing evolutionary conservation. Attempts to ablate the single D. discoideum Cds (CdsA) and Cdipt encoding genes were unsuccessful, suggesting a vital role for these proteins. In contrast, overexpressing both proteins showed that cells with elevated expression of CDIPT, but not CDSA, were resistant to therapeutic VPA concentrations. Furthermore, deletion of the single D. discoideum DGK (DGKA) gene was successful, with the mutant resistant to VPA during both acute and chronic treatment, that was restored on reintroduction of DGKA. To investigate whether loss of DGKA is related to epilepsy and BD, a range of related compounds were investigated for an effect on cell development. These experiments suggest that in D. discoideum, DGKA may provide a common target for both epilepsy and BD treatments, supporting data provided from preclinical and clinical studies in both disorders. Together this work suggests that DGK may provide a new therapeutic target for the treatment of both epilepsy and BD.
Preučevanje delovanja antioksidanta epigalokatehin galata in oksidanta menadiona v celicah z metodo infrardeče spektroskopije

V okviru magistrskega dela smo preverili vpliv in delovanje induktorja oksidativnega stresa menadiona na celice kvasovk Saccharomyces cerevisiae, kot modelnega organizma za raziskave oksidativnega stresa ter vlogo antioksidanta epigalokatein-3-galata (EGCG) pri zasciti celic pred oksidativnim stresom. Celice kvasovke smo izpostavili preucevanim snovem v razlicnih koncentracijah, in sicer antioksidantu epigalokatehin galatu v koncentraciji 0,1 g/L ter oksidantu menadionu v koncentraciji 60 mmol/L. Vpliv oksidativnega stresa na celice smo preucevali tako, da smo celice najprej izpostavili antioksidantu in nato oksidantu ali pa le oksidantu brez predhodnega tretiranja. Oksidativni stres in zascitno delovanje antioksidanta ter vplive na fiziolosko stanje celic smo preverjali s pomocjo razlicnih metod, v osnovi pa so te bile: dolocanje znotrajcelicne oksidacije, oksidativnih poskodb lipidov in celicne energijske metabolne aktivnosti, dolocanje kultivabilnosti celic ter analiza absorpcijskih spektrov s pomocjo metode ATR-FTIR. Izkazalo se je, da so znotrajcelicna oksidacija in oksidativne poskodbe lipidov v celicah, ki so bile izpostavljene EGCG in nato menadionu, nižje v primerjavi s celicami, ki so bile izpostavljene le menadionu. Celicna metabolna aktivnost je bila v celicah, ki so bile izpostavljene oksidativnemu stresu, zaradi aktivacije popravljalnih mehanizmov visja, hkrati pa je EGCG inducirajoce vplival na metabolno aktivnost. Dodatek antioksidanta ni bistveno vplival na zvisanje kultivabilnosti celic kvasovk, se je pa ta zaradi oksidativnega stresa zmanjsala. Spremembe v fizioloskem stanju celic po tretiranju smo potrdili tudi z metodo ATR-FTIR, in sicer so bile razlike med razlicno tretranimi vzorci najbolj opazne v vsebnosti lipidov in ogljikovih hidratov. Na podlagi vseh rezultatov ocenjujemo, da je ATR-FTIR primerna metoda za oceno sprememb znotrajcelicnega redoks stanja po tretiranju celic z oksidantom/antioksidantom.
Jak2 deficiency prevents mice from LPS-induced sepsis by modulating innate immunity without affecting adaptive immunity through STAT5 and STAT6 pathways (91.17)

Dendritic cells (DCs) serve as a key component of innate immunity and bridge innate and adaptive immune responses against to bacteria and other pathogens. Many immune disorders are thought to be a consequence of out-of-control of inflammatory response to bacterial toxins, such as sepsis is a result of excessive inflammation with a suppression of adaptive immunity post-sepsis. Therefore, manipulating the function of DC in innate immune response without affecting its capability to initiate adaptive immunity could be a novel therapeutic approach for treatment of sepsis. Using an inducible Jak2 deficiency model, here we have demonstrated that Jak2 could be a perfect target to solely suppress DC's capacity in innate immune response. Other than its functionality in DC development, Jak2 also plays a pivotal role in modulation of innate immune response. DCs deficient for Jak2 display an immature phenotype characterized by low expression of MHC-II and costimulatory molecules and a reduced secretion of pro-inflammatory cytokines upon stimulation. However, their capability to initiate adaptive immune response was not impaired. As a result, mice deficient for Jak2 are resistant to LPS-induced septic shock. Our studies further revealed that Jak2/SATA5 signaling is implicated in DC development, while Jak2/STAT6 signaling is responsible for the regulation of pro-inflammatory cytokine secretion in DCs.
γ-radiation-induced G2 delay, apoptosis, and p53 response as potential susceptibility markers for lung cancer

γ-Radiation results in cell cycle arrest and apoptosis in a wide variety of cells. Cell cycle arrest provides time for the cell to repair damaged DNA before entering the next phase of the cycle. If the damage is severe and cannot be repaired, the cells undergo apoptosis. However, if the damaged cells continue to grow without repair or apoptosis, then carcinogenic transformation may occur. We hypothesized that individuals with inherited disruption in cell cycle control and/or apoptosis and/or DNA repair may be susceptible to lung cancer development. The cells from susceptible individuals would have a shorter G2 period and less apoptosis compared with cells from normal individuals upon exposure to γ-radiation. To test this hypothesis, the following methods were used: (a) fluorescence-activated cell sorting method was used to measure apoptosis and G2 cell cycle delay; (b) the ELISA method was used to measure p53 protein expression levels in these cell lines; and (c) γ-radiation-induced chromatid breaks were counted as a marker for DNA damage or repair. Next, γ-radiation-induced G2 delay and apoptosis were tested in three lymphoblastoid cell lines to determine the dose response effect and optimal time points of γ-radiation. Finally, these assays were tested in lymphoblastoid cell lines from 30 lung cancer patients and 22 healthy controls. We found a dose-response relationship for γ-radiation-induced G2 delay and apoptosis. The optimal time points to detect differential G2 delay and apoptotic index were 10 h and 48 h after γ-radiation, respectively. The mean G2 delay was 22.5% ± 10.5% for the control cell lines and 14.71% ± 8.8% for case cell lines (P