Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial populations and their potential in forensic investigations

Technological advancements have increased the importance of scientific evidence in criminal investigations. The use of DNA in biological traces is a well-known example of this and various life forms can provide valuable information in forensic investigations. Microorganisms are one of the most ubiquitous life forms on earth, live in almost any habitat and often coexist in large and diverse populations, which composition is defined by the habitat. This diversity creates potential for their use in a variety of criminal cases. This thesis explores the potential of some forensically relevant microbial populations in establishing links between item(s) and crime scene(s)/donor and in cell type identification. Bacterial terminal restriction fragment length polymorphism (t-RFLP), next generation sequencing and microarray analysis were used to characterise the microbial populations in soil and in samples from forensically relevant body sites or excrements. The chapters cover the development and validation of a t-RFLP and microarray methods to characterise and compare the populations in soil and in faeces, respectively, to determine a possible common origin of questioned samples. Decision models to evaluate the similarity between the resulting profiles were developed based on pairwise comparisons. For cell type identification microarray profiles of human-associated microbial populations were generated and clustering and classification models were constructed for data analysis. In addition to the development of these methods, three criminal cases are described illustrating the high potential of microbial population analysis in forensic investigations.
Mikroorganismen auf der Spur - Es geht auch ohne Kultivierung : PCR-basierende Methoden zur kultivierungsunabhängigen Erforschung der Vielfalt und Aktivität mikrobieller Gemeinschaften

welt zu gewinnen, ist dabei prinzipiell gleich. Zunächst müssen aus den Umweltproben (Boden, Sediment, Grundwasser, Darmmaterial, .) Nukleinsäuren extrahiert und für die PCR gereinigt werden[2]. Mithilfe von Primern, die an phylogenetisch konservierte Regionen binden, werden dann aus den Nukleinsäuren gezielt DNA-Abschnitte vermehrt. Gene für die ribosomale RNA sind aufgrund ihres ubiquitären Vorkommens und ihrer phylogenetischen Konserviertheit besonders gut geeignet. Dank der heute in öffentlichen Datenbanken verfügbaren Sequenzinformationen über rRNA-Gene, mit Neue Vielfalt dank PCR
Some Biofertilizers Relieved the Stressful Drawbacks of Calcareous Soil upon Black Seed (Nigella sativa L.) Through Inhibiting Stress Markers and Antioxidant Enzymes with Enhancing Plant Growth

Calcareous soils have stressful properties to plant growth; they represent about 25-30% of the Egyptian total area. To improve soil characteristics, and hence plant growth, a number of biofertilizers (diatomaceous earth, Nostoc, sewage effluent and yeast) in addition to Hoagland medium were applied at successively increasing concentrations. Growth of Nigella sativa (black seed), a folk medicinal plant famous for its oils, was enhanced by all the applied treatments. Enhancement in plant biomass showed highest levels at a certain concentration of each treatment; sewage (20%) followed by diatomaceous earth (6g/5Kg), Nostoc (1mg/5 Kg), yeast (4*1012 cell/L) and Hoagland (1/4x). The applied treatments variably altered carbohydrates, proteins and amino acid proportions in plant biomass. Stress marker (malondialdehyde and proline) contents and antioxidant enzymes activity (superoxide oxidase, catalase and ascorbate peroxidase) have been all significantly reduced in shoots and roots of the treated plants, compared with those of the control plants grown on calcareous soil alone. Subsequently, it could be inferred that calcareous soil triggered oxidative stress and the applied biofertilizers extinguished it and overcame the stressful drawbacks of calcareous soil in terms of enhanced plant growth. Energy and carbon skeletons that are usually leaked into defense molecules (MDA, proline and antioxidant enzymes), have been saved for growth upon amendment of the stressful calcareous soil.
The distribution of phytoplankton in the Baltic Sea assessed by a prokaryotic 16S rRNA gene primer system

Due to the evolutionary relationship between cyanobacteria and chloroplasts of all oxygenic eukaryotic photoautotrophs, both can be amplified by prokaryotic 16S rRNA gene primers. In marine water samples, chloroplast sequences often make up as much as 50% of a 16S rRNA gene library, yet because of the comparatively low phylogenetic resolution within limited chloroplast databases, they are usually removed from further analyses. However, chloroplast 16S rRNA gene databases are constantly improving and our aim was to test if the combined 16S rRNA gene sequences of phototrophic prokaryotes and eukaryotes generated by a prokaryotic primer set could be used to characterize their distribution. Using the phytoREF database, in situ 16S rRNA gene distribution characterization was performed for samples throughout the Baltic Sea (cells >0.2 μm) and compared to microscopic (cells >20 μm) as well as flow-cytometric (cells <7 μm) data. Generally, microscopic and molecular methods revealed similar distribution patterns of diatoms, chlorophytes and filamentous cyanobacteria. Although not directly comparable, flow cytometry delivered semi-quantitative patterns, on a very broad classification level, to the molecular approach. In conclusion, the combination of molecular and non-molecular analyses provided an improved overview of the phototrophic community, demonstrating its usefulness as a tool in monitoring strategies.
Artificially applied vanillic acid changed soil microbial communities in the rhizosphere of cucumber (Cucumis sativus L.)

Zhou, X. and Wu, F. 2013. Artificially applied vanillic acid changed soil microbial communities in the rhizosphere of cucumber (Cucumis sativus L.). Can. J. Soil Sci. 93: 13-21. Phenolic acids (PAs) have been implicated as autotoxins of cucumber (Cucumis sativus L.), but doubts about the importance of these compounds also exist due to their low concentrations in the field. The physiological alterations caused by PAs are concentration dependent, and the range of bioactivity is between 0.1 and 1 mM. Here, vanillic acid (VA) (0.02, 0.05, 0.1, 0.2 µmol g-1 soil) was applied into the soil every other day for five times. The effects of VA on C. sativus seedling growth and rhizosphere soil microbial communities were evaluated. Soil bacterial and fungal community structures and sizes were analyzed with polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and real-time PCR methods, respectively. Vanillic acid significantly inhibited C. sativus seedling growth at concentrations ≥ 0.05 µmol g-1 soil, and stimulated soil dehydrogenase activity, soil microbial biomass carbon content, and soil bacterial and fungal community sizes at all concentrations tested. Vanillic acid also caused shifts in rhizosphere soil bacterial and fungal community structures. Overall, VA could change rhizosphere soil microbial communities even when the VA concentration was lower than the level that produced a significant phytotoxic effect in cucumber.
Cardiovascular regulation by Kvβ1.1 subunit

ix Chapter One: Introduction . 1 Significance.1 Background . 3 Voltage-Gated Potassium Channels . 3 Kvβ Subunits . 4 Trafficking and Assembly of Kv Channels and the Kvβ Subunits . 8 Cardiac Action Potential . 11 Kvβ1 in Cardiovascular System . 12 Tables and Figures . 15 Chapter Two: Characterization of Kvβ1. 1 knockout mouse model and its cardiovascular implications: Electrical changes in both male and female however cardiac hypertrophy online in female: Role of Kvβ1. 1 subunit . 17 Introduction . 17 Materials and Methods . 19 Ethical Approval of Animals . 19 Cell culture (H9C2) and siRNA . 19 Histochemistry . 20 Echocardiography . 20 Electrocardiography (ECG) . 21 Blood Pressure Measurements . 21 Monophasic Action Potentials . 21 Quantitative real-time PCR (qRT-PCR) . 22 Western Blotting . 22 Pull-down Assay . 23 Pathway Analysis . 23 Statistical Analysis . 24 Results . 24
Serum Level and Genetic Polymorphism of Secretary Phospholipase A2-IIA in Alzheimer’s Disease. Med Chem (Los Angeles) 6:670-673.

Background: Alzheimer’s disease (AD) is a neurodegenerative disease and is the most common because of late life dementia. Alteration of Secretary Phospholipase A2-IIA (sPLA2-IIA) may have an important role in membrane phospholipids metabolism and the pathogenesis of AD. The aim of our study was to determine serum levels and genetic variant of sPLA2-IIA in Alzheimer’s disease and compare to controls. Methods: This study included 40 healthy unrelated individuals and 40 patients with AD. Serum levels and the polymorphisms of sPLA2-IIA enzyme were determined. Results: In Alzheimer patients¸ the CC genotype and C allele frequencies of enzyme were significantly lower while the CG and GG genotypes and G allele frequencies of enzyme were significantly higher than controls. The mean concentration and mean rank of enzyme for CC genotype significantly were lower while the CG and GG genotypes of enzyme were significantly higher than controls. Conclusion: The effect of different gene polymorphisms for the incident of AD is still unclear. We determined gene polymorphisms of sPLA2-IIA which may relate to AD. It can be suggest that a single or combination of gene polymorphisms have possible effect for development of AD. Further studies are needed to research the functional roles of sPLA2-IIA in the context of AD.
The effect of citrus flavanones on the redox homeostasis in cells exposed to oxidative stress – studies in vitro

Introduction: Flavanones (an important group of antioxidants in citrus fruits) are beneficial for health, which is connected with their anti-inflammatory, anti-atherogenic and anti-carcinogenic properties. The present study was undertaken to investigate whether – and in what way – the presence of flavanones influences the redox homeostasis of fibroblasts and alleviates the effects of oxidative stress. Material and methods: The study was conducted on murine fibroblast cell cultures with the addition of flavanones (hesperidin, hesperetin, naringin, naringenin), exposed to oxidative stress (Fe/Asc). In cell homogenates, the activity of superoxide dismutase (SOD) and glutathione peroxidase (GPx) was measured; in the medium, the concentration of nitric oxide was measured. Results and conclusion: Our results demonstrate that the addition of naringenin, hesperetin, naringin and hesperidin has a protective effect on cells subjected to oxidative stress The changes observed are particularly visible in the case of aglycone forms of both compounds. Despite the protective properties against oxidative stress which flavanones display, we determined distrubances in redox homeostasis in comparison to the control culture.
A novel method for quantifying overdispersion in count data and its application to farmland birds

The statistical modelling of count data permeates the discipline of ecology. Such data often exhibit overdispersion compared to a standard Poisson distribution, so that the variance of the counts is greater than that of the mean. Whilst modelling to reveal the effects of explanatory variables on the mean is commonplace, overdispersion is generally regarded as a nuisance parameter to be accounted for and subsequently ignored. Instead we propose a method that models the overdispersion as a biologically interesting property of a dataset and show how novel inference is provided as a result. We adapted the double hierarchical generalized linear model approach to create an easily extendible model structure that quantifies the influence of explanatory variables on the overdispersion of count data, and apply it to farmland birds. These data were from a study within Irish agricultural ecosystems, in which total bird species abundance and the abundance of farmland indicator species were compared on dairy and non-dairy farms in the winter and breeding seasons. In general, overdispersion in bird counts was greatest on dairy farms compared with non-dairy farms, and for total bird numbers, overdispersion was greatest on dairy farms in winter. Our code is fitted using the Bayesian package Rstan, and we make all code and data available in a GitHub repository. Within a Bayesian framework, this approach facilitates a meaningful quantification of the effects of categorical explanatory variables on any response variable with a tendency to overdispersion that has a meaningful biological or ecological explanation. This article is protected by copyright. All rights reserved.
EM as a tool to study structure and function to guide inhibitor design

Rational drug design is underpinned by structural biology, in particular X-ray crystallography. This work aimed to explore a simple question; can electron microscopy (EM) play a useful role in the drug discovery process? To this end, two biological systems, the V-ATPase and Imidazoleglycerol-phosphate dehydratase (IGPD), were studied via EM. A modest (~1 nm) structure of the V-ATPase was solved via cryo-EM, permitting existing high resolution crystal structures to be accurately fitted in the context of the whole 1 MDa complex. This allowed new mechanistic insights to be uncovered. The dissociated V1 domain was studied to see if the mechanism of ATP silencing, used as a regulatory control, could provide new inhibitor targets to be identified. Although the specific mechanism could not be identified the resulting structures have shown a much more complicated regulatory mechanism than previously thought. The ubiquitous nature of the V ATPase makes selectivity a significant challenge. To address this the binding mode of the selective V-ATPase inhibitor, Pea Albumin 1 subunit b (PA1b), was studied at low resolution using negative stain EM. Combined with biochemical analysis this has successfully identified the subunits responsible for binding PA1b. Furthermore, IGPD was used as a model system for high resolution cryo EM studies to directly visualise inhibitor binding. A 3.1 A reconstruction was obtained which allowed the de novo building of the atomic model and the identification of a small molecule inhibitor within the EM map. This work shows the potential of EM to provide valuable information for drug design at a wide range of resolutions, from rapid low resolution binding studies to direct visualisation of inhibitors at ~3 A.
Bee visitation rates to cultivated sunflowers increase with the amount and accessibility of nectar sugars

Pollinators make foraging decisions based on numerous floral traits, including nectar and pollen rewards, and associated visual and olfactory cues. For insect‐pollinated crops, identifying and breeding for attractive floral traits may increase yields. In this study, we examined floral trait variation within cultivated sunflowers and its effects on bee foraging behaviours. Over 2 years, we planted different sunflower inbred lines, including male‐fertile and male‐sterile lines, and measured nectar volume, nectar sugar concentration and composition, and corolla length. During bloom, we recorded visits by both managed honey bees and wild bees. We then examined consistency in relative nectar production by comparing field results to those from a greenhouse experiment. Sunflower inbred lines varied significantly in all floral traits, including the amount and composition of nectar sugars, and in corolla length. Both wild bee and honey bee visits significantly increased with nectar sugar amount and decreased with corolla length, but appeared unaffected by nectar sugar composition. While wild bees made more visits to sunflowers providing pollen (male‐fertile), honey bees preferred plants without pollen (male‐sterile). Differences in nectar quantity among greenhouse‐grown sunflower lines were similar to those measured in the field, and bumble bees preferentially visited lines with more nectar in greenhouse observations. Our results show that sunflowers with greater quantities of nectar sugar and shorter corollas receive greater pollination services from both managed and wild bees. Selecting for these traits could thus increase sunflower crop yields and provide greater floral resources for bees.
Changes in the composition and diversity of topsoil bacterial, archaeal and fungal communities after 22 years conventional and no-tillage managements in Northern China

ABSTRACT A comprehensive comparison about microbial community (bacterial, archaeal and fungal) response to different tillage managements in Northern China remain little studied, in this study we compared no-tillage (NT) versus conventional tillage (CT) management on topsoil microbial community diversity and composition in field experiment. We found that NT practice significantly increased the soil moisture content (SMC), bulk density, stocks of soil organic carbon (SOC), total nitrogen (TN), and microbial biomass carbon and nitrogen (P < 0.05). Moreover, higher levels of bacterial and archaeal alpha diversity were observed in NT relative to CT while unexpectedly, there was no significant difference found in fungal diversity between two treatments. The most pronounced shifts in the composition of the different microbial groups were found for the archaeal community, which followed by bacterial and fungal. NT practice markedly enhanced abundances of Proteobacteria (belongs to bacteria) phyla, Thaumarchaeota phyla (belongs to archaea) and Glomeromycota phyla (belongs to fungi). Redundancy analysis revealed that the factor that most closely correlated with bacterial, archaeal and fungal composition were SMC, TN and SOC, respectively. Considering NT enhanced both microbial composition and C storage in topsoil, we suggest that NT offers significant promise to improve topsoil health in this region.
Race Model for the Stop Signal Paradigm Revisited: Perfect Negative Dependence

In the stop-signal paradigm, participants perform a response time task (go task) and, occasionally, the go stimulus is followed by a stop signal after a variable delay, indicating subjects to withhold their response (stop task). The main interest is in estimating the unobservable stop-signal reaction time (SSRT), that is, the latency of the stopping process, as a characterization of the response inhibition mechanism. In the Independent Race Model the stop-signal task is represented as a race with stochastically independent GO and STOP processes. Neurophysiological studies, however, have shown that the neural correlates of the GO and STOP processes produce saccadic eye movements through a network of interacting neurons. Here we propose a Dependent Race Model that assumes perfect negative stochastic dependence between GO and STOP processes. It resolves the apparent paradox between behavioral and neural data but nonetheless retains the distribution-free properties of the Independent Race Model.
A Fournier Index upgrade as a new approach for quantitative phenological studies in plant communities

Abstract: This paper proposes a new quantitative approach, based on the association of species basal area, as a dominance indicator, weighted by the arcsine transformation of the current Fournier Index, for studying quantitative plant phenology at the community level. Since plant basal area is strongly correlated with its height and crown volume, this upgrade enhances the ecological importance of phenodynamics at the canopy level for plant community analysis. The curves in phenograms of the original Fournier´s index of intensity and those ones produced by this new approach did not overlap in a standardized ranging scale. These differences resulted in distinct phenological patterns, in particular concerning phenophase peaks. This new approach broadens our ability to evaluate resource availability and seasonality patterns in plant communities. It provides a more adequate basis for hypothesis testing on the influence of environmental factors on plant phenodynamics, and refines the quantitative description of all phenophases when the community structure is described.
A New and Noteworthy Hybrid of Viola (Violaceae) from Iwate, Northern Japan: Viola rostrata var. japonica × V. violacea var. makinoi

with many interspecific hybrids. Species of violets generally have weak barriers to interspecific gene flow (Conesa et al. 2008) and many hybrids have been reported (e.g. Becker 1910, 1917, Brainerd 1924, Hama 1975, 2002, Marcussen & Karlsson 2010). The verification of interspecific hybrids based on molecular evidence has increased (e.g. Neuffer et al. 1999, Conesa et al. 2008, Marcussen et al. 2011, 2012). One of us (S. Takeda) found a morphological intermediate between Viola rostrata Pursh var. japonica (W. Becker et H. Boissieu) Ohwi and V. violacea Makino var. makinoi (H. Boissieu) Hiyama ex F. Maek. in a location where the two species coexist (Fig. 1). The main features of the intermediate plant are summarized in Table 1. Viola rostrata has a particularly long spur (hence the common name, long-spurred violet). It occurs in eastern North America and in the Japanese archipelago adjacent to the Sea of Japan (Harvey 1966, Hashimoto 1967). In addition to the main area of distribution in Japan, isolated occurrences have been reported from the Pacific side of the Tohoku, Kanto, and Shikoku districts (Hama 1975, 2002). The Japanese populations are classified as the endemic variety, V. rostrata var. japonica, which grows primarily in the understory or on the edge of deciduous forests (Akiyama et al. 1999). Viola rostrata is a member of sect. Viola, subsect. Rostratae Kupffer (syn. sect. Trigonocarpea Godr.; basic chromosome number, x = 10). Species in subsect. Rostratae are characteristically perennial and usually caulescent herbs with a cylindrical style (Marcussen & Karlsson 2010). Approximately 50 species are included in this subsection (van den Hof et al. 2008), 11 of which are native to Japan. In conA New and Noteworthy Hybrid of Viola (Violaceae)
Open access increases citations of papers in ecology

Open access (OA) can effectively increase the accessibility and visibility of scientific articles and thus potentially confer them with citation advantages. Such an impact may be more pronounced in developing countries where the cost for journal subscription is comparably expensive and usually unaffordable. By comparing one OA article with one non-OA article published in the same issue, we tested the impact of OA on citation advantages of articles published in 46 ecology journals indexed in the Journal Citation Reports (JCR). We compared OA to non-OA articles published in the same issue of these journals, thereby controlling for potentially confounding effects of publication requirement and period. OA articles received significantly more citations than non-OA articles, and this citation advantage of approximately one citation per year was sustained across publication years from 2009 to 2013. The OA citation advantage did not depend upon income of the country of origin of the citing scientists, and the OA citation advantage was found for citing scientists from North America, Europe, Asia, Africa, and Oceania, but not for Latin America. A total of 10 countries contributed more than 1000 citations each, and the OA citation advantage was found in all the 10 countries except Canada. Therefore, in ecology journals OA confers articles with citation advantages and such an impact accumulates with years and independent of the economic status of the countries. This information may guide decisions of scientific societies, journals, and individual authors as they weigh the relative costs and benefits of open electronic accessibility of scientific research.