Miracle-dz/UniFAR-FTUs huggingface dataset:
THE ECOLOGICAL GENETICS OF FOREST TREES

Among the numerous writings on communities and ecosystems, this book is rather unique for several reasons. It does not have lengthy descriptions of ecosystem structure in terms of species diversity or vegetation analyses and does not relate function to the flowcharts of energy and nutrients; instead it emphasizes the ecological genetic and detailed population studies for describing the adaptations and genetic systems of different species in a community. The Preface and Introductory Remarks attempt to defend this approach, viz. "forest ecosystems under varying degrees of management, and man-made forests are also a rich source of information on ecological genetics . the published evidence of this fact has not yet significantly penetrated the botanical literature"; and the authors argue that, in contrast to agriculture, forest genetics has advanced less in breeding work but more in the study of natural populations, adaptive strategies, ecosystem management and conservation. The holistic and dialectical approach of communities as 'organisms' is repeatedly attacked and the analytical and experimental approaches are emphasized. Both authors, specially Stern, are renowned for their important and longstanding contributions to the population biology of forest trees in Europe and indeed the book reflects their strength as much as biases that most of us naturally show and therefore, should not be judged too harshly. For what it covers, the title could well have been 'The Ecological Genetics of Forest Trees'; but why it is concluded that "most of the well-founded knowledge in forest ecological genetics is based on the methods of the Drosophila mythologians" (p. 90) escapes me. There are six chapters in the book: The Ecological Niche, Adaptations, Genetics Systems, Adaptive Strategies, Forest Ecosystems, and How Man Affects Forest Ecosystems. Chapter 1 begins with the definition of niches (Hutchinson) in terms of a n-dimensional space and notations of set theory which might unfortunately "turn off" many readers but the discussion of "main characteristics of ecological niches" (p. 10-13) offers some good points. It is argued that phenotype and niche are exchangeable notions but niches
The bacterial composition of ventilation filter dust in Norwegian pre-school nurseries

The microbial content of dust collected from intake and exhaust air filters in six Norwegian nurseries was determined using 16S rRNA pyrosequencing and plate count analyses. The concentration of endotoxins was also estimated. About 96% of the sequences were classified as Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. At the genus level, about 30% of sequences from the exhaust filter were classified as bacteria of probable human origin, such as Streptococcus and Corynebacterium species. These were close to absent in intake dust samples (<1%). This suggests that occupancy shapes the indoor microbiota, creating an environment relatively rich in genera of potential health significance. There were significantly greater counts of culturable bacteria and fungi in exhaust samples, indicating that passage of air through the nursery causes deterioration in the general air quality. Although there was more endotoxin in exhaust dust, the endotoxin levels per colony forming unit were similar in both samples. This study explores, for the first time, the bacterial composition of ventilation filter dust in Norwegian nurseries, and is important as it reveals what types of microorganisms nursery users are exposed to. In addition to possible direct health issues, the nature of our early exposure to microbes may be significant in the development of immunological conditions.
Relating the midbrain dopaminergic system to hippocampal cell assembly dynamics associated with spatial memory function

Central to the understanding of memory is a detailed understanding of the processes contributing to how some information is retained as memories, yet other information is not. Relevant to this is the question, does value and saliency information coded by dopaminergic neurons of the ventral tegmental area (VTA) affect hippocampal memory function and how might this arise? In order to address this question, I performed large scale extracellular recordings combined with optogenetic activation of dopaminergic neurons in mice. Tetrodes were located in the VTA and pyramidal cell layer of the CA1 subfield of the dorsal hippocampus. Midbrain dopaminergic neurons were made to express a chimeric protein formed of the light activated ion channel channelrhodopsin-2 and enhanced yellow florescent protein (ChR2-eYFP) through injection of a Cre activated viral construct in the VTA of DAT-IRES-Cre+/- mice. Mice explored familiar and novel open fields in the presence or absence of photostimulation. Periods of sleep and rest were recorded before and after each exploration in order to calculate the reactivation strength of hippocampal waking firing activity during subsequent sleep; a process thought to aid the stabilisation of representations enhancing their retention as memories. ChR2-eYFP expressing axons were present in the dorsal hippocampus demonstrating a direct dopaminergic projection from the midbrain to the hippocampus. Units isolated from midbrain tetrodes showed a sustained increase in mean firing rate during exploration of a novel over a familiar environment, indicating they have the potential to drive sustained dopamine release in target structures in response to such a sustained novelty cue. Hippocampal reactivation strength after exploration of a novel environment was higher than that seen after exploration of a familiar environment and this was further enhanced by burst mode photoactivation of dopaminergic neurons at their cell bodies in the VTA or at the afferent dopaminergic fibres in the dorsal CA1. A second group of mice performed a spatial learning task on a maze dubbed the 'crossword maze'. Photostimulation during learning trials did not increase the rate of learning but it did increase performance in a probe test held one hour after the end of the learning trials. Additionally, there was enhanced reinstatement of the hippocampal spatial representation during the probe test and it was preceded by enhanced reactivation of the newly formed representation in the intervening rest period. These findings reveal that midbrain dopaminergic neurons, encoding salient information about an environment, promote hippocampal network dynamics associated with memory persistence, thus modulating hippocampal memory function according to the value of the information to be remembered.
Microarchitectural alterations in arthritic subchondral bone

PUBLICATIONS ARISING FROM THIS THESIS CONFERENCE PRESENTATIONS AND ADWARDS CHAPTER 1 Subchondral bone in osteoarthritis: insight into risk factors and microstructural changes CHAPTER 2 Rationale, hypothesis and aims CHAPTER 3 Influence of age and gender on microarchitecture and bone remodeling in subchondral bone of the osteoarthritic femoral head CHAPTER 4 Subchondral bone plate integrity is closely associated with subchondral trabecular bone homeostasis in osteoarthritis CHAPTER 5 Subchondral bone deterioration in femoral heads from patients with osteoarthritis secondary to hip dysplasia CHAPTER 6 Identical subchondral bone microarchitecture pattern with increased bone resorption in rheumatoid arthritis as compared to osteoarthritis CHAPTER 7 Discussion and future directions 7.1 General discussion 7.2 Future directions CHAPTER 8 References ---------------------------------------------------------------1 ----------------------------------------------------------------2 ------------------------------------------------------------------------------3 -----------------------------------6 ------------------------------7 ------------------------------------------------------------------10 -----------------------------------------26 ------------------30 ----------------------------42 ------------------------------------------77
Emotional intimacy with nature and life & intellectual interest in life of pre-service biology teachers for environmental education

Abstract We investigated emotional intimacy with nature and life, and intellectual interest in life among South Korean pre-service teachers (N = 114) training in biology education, analysing the differences between these two constructs as well as their relationship to environmental behaviour and sensitivity. In addition, differences in the respondents’ experiences of nature, concerns about environmental problems and willingness to perform environmental education were explored. Four groups of pre-service biology teachers, categorised by the two investigated personal variables, showed different responses for the environment-related characteristics and other variables. Our results suggest that biology teachers should have higher emotional and intellectual interest in nature and life, and a balance between emotional intimacy with nature and life, and intellectual interest in life is needed to prepare them.
Evaluation of dietary fat sources on growth performance, excreta microbiology and noxious gas emissions in Ross broilers

An experiment was conducted to evaluate fat sources on growth performance, excreta microbiology and noxious gas emissions in broilers. Experimental birds were reared for 5 weeks and divided into two periods: Starter (0 to 3 weeks) and finisher (4 to 5 weeks). A total of 150 one day old Ross 308 broiler chicks were randomly allocated into five treatments with five replications (six birds per replicate) following a completely randomized design. Dietary treatments included FT1 (corn-soybean meal based basal diet with soybean oil), FT2 (corn-soybean meal based basal diet with chicken fat), FT3 (corn-soybean meal based basal diet with tallow), FT4 (corn-soybean meal based basal diet with tallow and lard) and FT5 (corn-soybean meal based basal diet with pork fat/lard). Overall body weight gain and feed intake did not differ due to addition of different dietary fat sources in broiler diet; however, feed conversion ratio was better in FT1 fed group in comparison to other fat groups (P<0.10). The result of the serum immunoglobulins data indicated that, a significant elevation of serum immunoglobulin M (IgM) was observed after dietary addition of FT1, FT2 and FT5 relative to FT4 (P<0.05) Excreta pH did not differ, however, yeast and mold count was highest in FT4 and FT5 relative to FT1 and FT3 (P<0.05). Excreta noxious gas emissions (NH3, H2S and SO2) were lower in FT1 and FT2 in comparison to other fat groups (P<0.05). Overall, the results of the present study suggested that FT1 and FT2 can be prioritized in the diet of broilers with positive influence on body weight gain and feed efficiency, and substantial reduction of noxious gas emissions. Further detail study could be conducted to investigate the single and combination of different dietary fats (with different ratio) on performance and meat quality indices. Key words: Broilers, growth performance, immunity, noxious gas emissions.
Cross-talk between α-synuclein post-translational modifications in yeast as model of Parkinson’s disease

Post-translational modifications modulate several characteristics of proteins. They can regulate substrate activity, localization, stability, but also feature and structure, remarkably in disease-associated proteins. The major hallmark of Parkinson’s disease is the accumulation of proteinaceous inclusions termed Lewy bodies (LBs), which are mainly composed of α-synuclein. They lead to neuronal cell death upon different mechanisms, which are often yet unknown. α-synuclein, a presynaptic neuronal protein, plays an important role in Parkinson’s disease pathogenesis. It undergoes various post-translational modifications during pathological conditions. The cytotoxicity and aggregation of α-synuclein can be mimicked in yeast. In this study, the two major post-translational modifications of α-synuclein, sumoylation and serine-129 (S129) phosphorylation, are addressed. Heterologously expressed wild type α-synuclein and A30P mutant are sumoylated in yeast at the same major α-synuclein sumoylation residues, lysine 96 (K96) and lysine 102 (K102) as in human. Lowering the cellular pool of the ubiquitin like modifier SUMO resulted in severe growth reduction in cells expressing α-synuclein, which correlated with increased numbers of cells with inclusion formation. This suggests that sumoylation protects against α-synuclein-mediated toxicity and inclusion formation in yeast. Expression of sumoylation-deficient α-synuclein caused the same growth rate, validating the protective role of α-synuclein sumoylation in cis. Overexpression of the human kinases GRK5 and PLK2 elevated α-synuclein phosphorylation level at S129. Interestingly, α-synuclein-mediated cytotoxicity associated with sumoylation impairment was compensated by a kinase-dependent higher phosphorylation rate at S129 of α-synuclein. Phosphorylation reduced inclusion formation and improved yeast growth. In order to get more insight into the cross-talk between α-synuclein sumoylation and S129 phosphorylation, α-synuclein aggregate clearance was monitored. Promoter shut-off studies were conducted in parallel with chemical inhibition of the cellular degradation pathways. In the absence of SUMO, α-synuclein aggregates were mainly cleared via the ubiquitin proteasome system. This suggests that sumoylation supports autophagy in α-synuclein aggregate clearance. In the presence of the human kinases GRK5 or PLK2, sumoylation-deficient α-synuclein aggregates were subjected to the ubiquitin proteasome as well as the autophagy pathway in a kinase-dependent manner, which was accompanied with altering α-synuclein-ubiquitination profile. GRK5 was able to partially rescue autophagy and further promotes the proteasome system to clear sumoylation-deficient α-synuclein aggregates. Both degradation pathways contributed equally to α-synuclein aggregate clearance in the absence of SUMO when PLK2 is overexpressed. This cross-talk between α-synuclein phosphorylation and sumoylation opens novel avenues for therapeutic intervention in Parkinson’s disease and other synucleinopathies.
Brine shrimp lethality assay

Brine shrimp lethality assay is an important tool for the preliminary cytotoxicity assay of plant extract and others based on the ability to kill a laboratory cultured larvae (nauplii). The nauplii were exposed to different concentrations of plant extract for 24 hours. The number of motile nauplii was calculated for the effectiveness of the extract. It is a simple, cost effective and requires small amount of test material. Video Clip of Methodology : Brine Shrimp Lethality Assay: 4 min 9 sec Full Screen Alternate
A Molecular Phylogeny of the Lythraceae and Inference of the Evolution of Heterostyly

72 Introduction.74 Methods.80 Taxon Sampling and Molecular Data.80 Ancestral Character State Reconstruction.83 Results.86 Discussion.96 Limitations of Current Models.96 Repeated Loss of Heterostyly in Lythraceae.99 Literature Cited.104
S100-RAGE signaling in the pathogenesis of Head and Neck Squamous Cell Carcinoma

An aberrant expression of RAGE (receptor for advanced glycation end products) and its ligands, especially the S100-calgranulins has been demonstrated in squamous cell carcinoma of the upper aerodigestive tract. However, while S100-RAGE signaling is commonly linked to the induction and maintenance of a cancer promoting inflammation, the question whether RAGE-signaling is causally linked with neoplastic transformation of keratinocytes in mucosal epithelia has not been addressed so far. The presence of S100-calgranulin positive infiltrating immune cells as well as S100-calgranulin expression in tumor cells was assessed in oropharyngeal squamous cell carcinoma (OPSCC) on tissue microarrays (TMAs) containing tumor biopsies from 188 human patients and compared with the amount of CD66b positive myeloid inflammatory cells on the same TMAs. To address the causal role of S100-RAGE signaling in the onset of oral carcinogenesis, the well established mouse model of 4-nitroquinoline-1-oxide (4-NQO) induced carcinogenesis was used to investigate tumor development in control and RAGE deficient (Rage-/-) mice as well as mice deficient in S100a9 (S100a9-/-). While patient tumors varied strongly with regard to the amount of S100-calgranulin and CD66b positive immune cells as well as the expression pattern of S100-calgranulins in tumor cells, these features did not correspond with clinico-pathological parameters or prognosis. In the onset of oral and esophageal cancer, driven by 4-NQO induced genotoxic stress and in the absence of an additional inflammatory stimulus, both Rage and S100a9 expression was dispensable for tumor development. In both cohorts, mice developed tumors in the esophagus and tongue with similar incidence rates and comparable multiplicity. Also a detailed analysis of tumor sections by histological and immunohistochemical staining revealed no difference in size or histological architecture of 4-NQO induced lesions, tumor cell proliferation and the number of inflammatory immune cells in the tumor microenvironment. S100a8 and S100a9 were induced upon 4-NQO treatment independent of the presence of RAGE, which may in part be explained by induced transcript and protein levels of the Toll-like receptor 4 (Tlr4) in carcinogen treated tissue, suggesting that signaling via the S100-TLR4 axis may compensate for the lack of RAGE in early stages of tumor development. In summary, these data point out that the impact of S100-RAGE signaling is critically depending on the context. While important in inflammation associated cancer, S100-RAGE signaling is dispensable in cancer caused by genotoxic stress without a promoting inflammation. With regard to therapy and prevention, this illustrates the need of a clear stratification for the presence of a driving inflammation.
Annotated zoogeography of non-marine Tardigrada. Part IV: Africa

This paper is the fourth monograph in a series that describes the global records of limno-terrestrial water bears (Tardigrada). Here, we provide a comprehensive list of non-marine tardigrades recorded from Africa, providing an updated and revised taxonomy accompanied by geographic co-ordinates, habitat, and biogeographic comments. It is hoped this work will serve as a reference point and background for further zoogeographical and taxonomical studies.
Multiple trans-Beringia dispersals of the barklouse genus Trichadenotecnum (Insecta: Psocodea: Psocidae)

The causes underlying disjunct distributions are of major importance in biogeography. Arcto-Tertiary relict biotas in the temperate northern hemisphere, which typically show disjunct distributions between Asia and the Nearctic region, are widely known but often poorly understood examples of disjunct distributions. The distributional pattern of the barklouse genus Trichadenotecnum is an example of an Arcto-Tertiary relict, with centers of species diversity in Asia and Central America. We evaluated the potential causes of this disjunct distribution in Trichadenotecnum using a molecular phylogeny, divergence dating, and ancestral area reconstruction. Phylogenetic analysis identified three separate clades of New World Trichadenotecnum, whereas all other groups were distributed in the Old World. Ancestral area and dating analyses recovered three independent events of trans-Beringian dispersal in the Oligocene to Miocene (27–15 MYA). The formation of two disjunct centers of diversity can be explained by the restriction of distributional areas to temperate refugia during the Quaternary glaciations (2.5–0.02 MYA). The South American Trichadenotecnum appeared to have arisen from two independent dispersal events in the Miocene (19–9 MYA). These estimated dispersal dates is much older than the generally assumed date (Pleistocene: ca. 3 MYA) for the formation of the Isthmus of Panama. ADDITIONAL
Bacterias hidrocarburoclásticas del género Pseudomonas en la rizosfera de Samanea saman (Jacq.) Merr.

The research goal includes isolation, characterization and identification of Pseudomonas species existing in the rhizosphere of a legume present (colonizing or survivor) in a savanna soil polluted by an oil spill, in order to explain the support of the growth of this leguminous plant through the reduction of the toxicity of spilled oil (hydrocarbonoclastic effects). The site is located at Amana del Tamarindo village entrance, Monagas State, Venezuela (9 ° 38' 52 "N, 63 ° 7' 20" E, 46 masl). An area of 50 m 2 was sampled. In concordance to the descriptions, keys, and comparison with the UOJ Herbarium exsiccatae, the legume collected was identified as Samanea saman (Jacq.) Merr. , which belongs to the Fabaceae family. The results of the biochemical characterization and the production of pyocyanine and fluorescein pigments allowed identifying 10 isolates as P. fluorescens , 5 as P. putida and 5 as P. aeruginosa . Samanea saman is recommended for re-vegetation of the contaminated area.
Distinct pattern of epigenetic DNA modification in leukocytes from patients with colorectal carcinoma and individuals with precancerous conditions, benign adenoma and inflammatory bowel disease – a link to oxidative stress

A characteristic feature of malignant cells, including colorectal cancer cells, is a profound decrease in level of 5-hydroxymethylcytosine, product of 5-methylcytosine oxidation by TET enzymes. This study included four groups of subjects: healthy controls, and patients with inflammatory bowel disease (IBD), benign polyps and colorectal cancer. Patients from all groups presented with significantly lower levels of 5-methylcytosine and 5-hydroxymethylcytosine than the controls. A similar tendency was also observed for 5-hydroxymethyluracil level. Patients with IBD showed the highest levels of 5-formylcytosine and 8-oxo-7,8-dihydro-2’-deoxyguanosine of all study subjects, and individuals with colorectal cancer presented with the lowest concentrations of vitamin C and A. Expressions of TET1 and TET2 turned out to be the highest in IBD group. To the best of our knowledge, this is the first study to show that healthy subjects, individuals with precancerous conditions and colorectal cancerpatients present with distinct specific patterns of epigenetic modifications in leukocyte DNA.