Miracle-dz/UniFAR-FTUs huggingface dataset:
Biophysical characterization of cytosolic domains of three import receptors from Arabidopsis thaliana

Eukaryotic cells are characterized by the presence of several organelles that are surrounded by membranes. The majority of proteins destined to these organelles are nuclear encoded, synthesized in the cytosol and translocated across the membrane aided by specific receptors, into destined locations in the organelles. The receptors involved in protein translocation can be classified into two categories: 1) those that recognize precursor proteins through interaction with their specific presequences and 2) those that recognize cytosolic transporters (chaperones) which are involved in the delivery of precursor proteins to the import machinery for the specific organelle to which they are targeted. The projects aim to biophysically characterize the cytosolic domains of three import receptors from Arabidopsis thaliana and identifying their interactions with their binding partners. The first part of the study focuses on the cytosolic domain of Metaxin, an outer mitochondrial membrane protein. To date literature is not available delineating the exact domain boundaries of the cytosolic region of the protein. Mutational studies aid in identifying the region that can be expressed as a soluble dimer however time and concentration dependent aggregation prohibits further characterization. The second part of the project involves biophysical characterization of the cytosolic TPR domain of Toc64, a receptor on the outer membrane of the chloroplast. Previous studies with the human homologues of the chaperones suggested that this domain interacts with Hsp70/90 chaperones, with a preference for Hsp90. Using isothermal calorimetry and computational approaches, the energetics and the important residues involved in the interaction is analysed. These studies suggest that the TPR domain recognizes both chaperones with equimolar affinity contradicting previous findings. Om64, a homologue of Toc64, is TPR containing protein found in the outer mitochondrial membrane and implicated in protein import into the mitochondrion. The cytosolic TPR domain of this protein is shown to interact with the C-terminal region of Hsp90. In the third part of the project, a comparative analysis of the inter-residue interactions between TPR domains of Toc64 and Om64 with the C-terminal regions of Hsp70/Hsp90 is performed using simulation studies. Furthermore, the binding energies of the interactions are calculated. Our results suggest that Toc64 exhibits higher affinity towards Hsp70 than Hsp90, however Om64 interacts with Hsp70 and Hsp90 with similar affinity. Our findings provide an explanation for the absence of mistargeting of chloroplast precursors into mitochondria. In summary, this study reveals that the cytosolic receptor domain of Metaxin may require additional components for its stability in vitro. Furthermore, this study gives insights into the specificity of chaperone-receptor interaction and thus protein targeting to specific organelles such as mitochondria and chloroplast at the molecular level.
THE ABILITY TO DECOLORIZE DIFFERENT SYNTHETIC DYES DUE TO LACCASE PRODUCED BY TRAMETES VERSICOLOR AND FOMES FOMENTARIUS

The textile industry, by far the most frequent user of synthetic dyes, is in need of ecologically efficient solutions for its colored wastewaters. White-rot basidiomycetes are among the most potent organisms to biodegrade and detoxify a wide range of pollutants and synthetic dyes, enabled by ligninolytic enzymes, namely, laccases. Present study was undertaken to explore white-rot fungi Trametes versicolor and Fomes fomentarius for their laccase production and potential in dye decolorization. The laccase production was induced by 0.5 mM copper sulphate and their effectity in decolorization of five types of synthetic textile dyes (N-heterocyclic, azo, triphenylmethane and triarylmethane) was studied. The most effective laccase decolorization was observed for the dyes Malachite Green and Bromothymol Blue using 0.5 mM copper as inducer for both fungi.
Evaluation of soil water storage in native forest and eucalyptus areas.

In the region of the Paraiba do Sul river valley in the State of Sao Paulo, Brazil, pasture areas have been replaced by eucalyptus plantations, which can modify the dynamics of water in the soils of the region. The objective of this work was to evaluate the behavior of water in a Red-Yellow Latosol in two vegetative coverings, a six-year-old eucalyptus plantation, and a native forest, in the process of regeneration which began twenty years ago. The study was developed in the Una River basin from June 2009 to April 2011. The soil water potential was measured by 96 sensors (Watermark ™) at the depths of 20, 60 and 120 cm. The Available Water Capacity (AWC) and weekly residual soil storage for each layer were calculated. It was observed that the three layers reacted to the processes of rainfall and evapotranspiration and that there was a difference between the storage of water in the soil in the eucalyptus and native forest areas. There was no water restriction in the studied period; however, the variations in native forest storage were smoother than the variations occurring for eucalyptus. In the mean of the whole period and for the three layers, the storage in the native forest and eucalyptus were 88% and 64% of Available Water Capacity (AWC = 183 mm), respectively. These results show the native forest water conservation capacity in watersheds.
Influenza vaccines and antivirals that target the conserved hemagglutinin stem

Recently, several broadly neutralizing antibodies have been characterized that bind to a highly conserved site on the viral hemagglutinin (HA) stem region. These antibodies are protective against a wide range of diverse influenza viruses, but their efficacy depends on a host immune effector response through the antibody Fc region (ADCC). Here, I investigate the protective efficacy of a protein (HB36.6) computationally designed to bind with high affinity to the same region in the HA stem. I show that intranasal delivery of HB36.6 affords protection in mice lethally challenged with diverse strains of influenza independent of Fc-mediated effector functions or a host antiviral immune response. This designed protein prevents infection when
Linkage Analysis of Plasma ApoE in Three Ethnic Groups: Multiple Genes with Context‐Dependent Effects

We performed variance component‐based linkage analysis in four samples (two of non‐Hispanic European‐Americans from Rochester, MN; African‐Americans from Jackson, MS; and Mexican‐Americans from Starr County, TX) to identify chromosomal regions containing genes influencing plasma apolipoprotein E (apoE) levels. The APOE gene region on chromosome (chr) 19 was identified with a LOD ≥ 2.00 in both samples from Rochester and the sample from Jackson. Adjustment of apoE levels for differences among means of genotypes defined by the APOE ε2/3/4 alleles reduced evidence of linkage, indicating that the APOE gene was responsible for the majority of the linkage signal. In stratified linkage analyses, there was a LOD of 1.70 in the Starr County sibships with average total cholesterol (TC) above the median level for all sibships in that population. Adjustment for APOE genotype did not remove this LOD score, suggesting a second gene in this region may influence apoE variation. Evidence of linkage (LOD= 3.32) on chr 17 was observed in the Starr County sibships with average TC below the median. Inter‐individual variation in plasma apoE level may be influenced by variations in the structural gene, and at least one other gene whose effects differ among populations and are dependent on the influence of unmeasured genetic and environmental factors indexed by correlated measures of lipid metabolism.
Effects of Fire on Litter, Forage Dry Matter Production, and Forage Quality in Steppe Vegetation of Eastern Anatolia, Turkey

The effect of fire on vegetation of semi-arid steppe has not been studied extensively. Wildfires are rare in some steppe rangelands because of high levels of large herbivore grazing. However, grazing is sometimes restricted or excluded in areas such as national parks or the areas where afforestation projects are conducted. Therefore, sometimes, wildfires occur during the dormant season when litter (the uppermost layer of organic debris on the soil surface; essentially the freshly fallen or slightly decomposed vegetal material) mass has resulted in peak levels. Our study assessed the effects of a single fire on litter mass, forage production, and forage crude protein, Neutral Detergent Fiber (NDF), and Acid Detergent Fiber (ADF) in high altitude rangelands of Eastern Anatolia. We found significant effects of treatment (fire and no fire), years, and sampling date on all variables. Following the prescribed fire in 2011, litter mass and forage production was less in treated plots compared to untreated control plots during both years. The effect of the fire on litter and forage production was more pronounced in 2012 compared to 2013. The effects of the fire on forage quality variables were also greater in 2012 than in 2013. Forage crude protein levels were consistently higher in treated plots during all 2012 sampling periods. Similarly, NDF and ADF tended to be lower in treated plots relative to the control plots during 2012. All effects we found were more pronounced in the first growing season following the fire compared to the second growing season, suggesting a relatively transient nature of fire effects in the steppe vegetation we studied.
Spore-forming parasites infecting muscles of freshwater fishes : ecology and epidemiology

Ahonen, Hanna Susanna Spore-forming parasites infecting muscles of freshwater fishes – ecology and epidemiology Jyväskylä: University of Jyväskylä, 2017, 36 p. (Jyväskylä Studies in Biological and Environmental Science ISSN 1456-9701; 332) ISBN 978-951-39-7108-3 (print) ISBN 978-951-39-7109-0 (pdf) Yhteenveto: Kalan lihasta infektoivat itiöloiset – ekologia ja esiintyminen Fish parasites may potentially harm fisheries and aquaculture. Infected fish are unusable, even though they would not pose a direct risk to human health. The aim of this thesis was to investigate the ecology and epidemiology of three previously unknown or poorly known spore-forming parasites infecting muscles of economically important fish species. The first novel microsporidian species, here described as Microsporidium luciopercae, was found from pikeperch (Sander lucioperca) and European perch (Perca fluviatilis) and formed opaque-looking patches in the muscles. The second novel microsporidian species, Myosporidium spraguei, was found from pike-perch and burbot (Lota lota) and occurred within xenomas in the musculature. The third muscle-dwelling parasite, Henneguya zschokkei (Cnidaria), formed white plasmodia in the muscle of whitefish (Coregonus lavaretus). Among the six study lakes, the prevalence of M. luciopercae in wild pike-perch and perch varied from 0 to 1 %, while M. spraguei was more common (prevalence of 5–26 % in pike-perch and 65 % in burbot). M. spraguei was strongly aggregated and most abundant in the middlesized (37–45 cm) pike-perch and in larger burbot (> 35 cm), but the infection was not related to host sex, sampling season or host condition. In the case of H. zschokkei, in two inland fish farms, one year-old whitefish were virtually uninfected, but the prevalence of infection was higher in 2 and 3 year old fish (up to 36 % of 3 year old fish were infected). New infections appeared seasonally in July-August. Neither the size of plasmodia nor the proportion of different plasmodium types changed from 2 to 3 year old fish, suggesting slow development of H. zschokkei in whitefish. However, the proportion of infected fish with melanised plasmodia increased with fish age, suggesting an agedependent host response against this strongly aggregated parasite.
Pathogenesis of Cerebral Malaria: Inflammation, Cytoadherence And Recent Experimental Data For Humans

This study establishes that HRPII is a Plasmodium falciparum virulence factor that triggers an innate immune inflammatory response in vascular endothelium and contributes to cerebral malaria by compromising the integrity of the blood-brain barrier. Human malaria is caused by five species of Plasmodium. Of these, P. falciparum is the deadliest and is the only species that causes cerebral malaria (CM). CM is a disease of the vascular endothelium considered by parasite sequestration, increased inflammatory cytokine production, vascular leakage and leukocyte infiltration. A distinguishing feature of P. falciparum infection is the parasite’s production and secretion of histidine-rich protein II (HRPII). HRPII accumulates to high concentrations (up to 100 g/ml) in serum, which correlates with disease severity. Using a cellular model of the blood-brain barrier, it demonstrate that HRPII activates the innate immune system in human cerebral microvascular endothelial cells, resulting in redistribution of tight junction proteins and compromise of barrier integrity. Intravenous infusion of HRPII induced vascular leakage in the cerebellum and cortex of mice and increased early mortality in a P. berghei ANKA experimental cerebral malaria model. Analogously, transgenic P. berghei expressing falciparum HRPII produced more severe disease than wild-type or control P. berghei. HRPII induced endothelial expression of adhesion receptors used by plasmodium parasites, suggesting that this protein also contributes to pathogenesis by enhancing parasite cytoadherence and thereby avoiding splenic destruction.
AFLATOXINS CONTAMINATION IN FEED AND PRODUCTS OF ALABIO DUCK (Anas platyrinchos borneo) COLLECTED FROM SOUTH KALIMANTAN, INDONESIA

A limited survey was conducted to determine aflatoxins contaminations in feed and products of Alabio duck. A total of 271 feed samples, 48 liver sample, 42 meat samples, and 38 egg samples were analyzed for determination of aflatoxin B1 (AFB1) and aflatoxin M1 (AFM1) using Enzyme-Linked Immuno-Sorbent Assay (ELISA) tests. Results showed high prevalence of AFB1 contamination in feed sample, especially in feed concentrate, dried fish, and rice hulls (100%). AFB1 concentrations were higher than tolerable limit for AFB1 in feed for laying duck according to Indonesia National Standard (SNI), being 20 ppb, except for sago pit. This survey also showed high prevalence and levels of aflatoxin residues in the products of Alabio duck. AFB1 was found in all liver samples, with concentrations ranging from 4 to 12 ppb (average: 7 ppb). AFM1 was found in all of liver, meat, and egg samples. The highest level of AMF1 was found in liver which was ranging from 105 to 1,215 ppt (average: 304 ppt). High level of AFM1 was also found in meat, namely between 71 to 128 ppt (averaged: 91 ppt). Although found at low level, AFM1 was detected in egg, which was ranging from 10 to 36 ppt (average: 19 ppt). This survey showed high contaminations of aflatoxins in the liver, meat and egg of Alabio duck collected from the area of survey and their concentrations of aflatoxins were harmful for the consumer.
Profiling evolutionary landscapes underlying drug resistance

Bacteria have existed on earth for 3.5 million years and their ability to evolve has allowed for their survival in almost all global niches. Bacteria evolve and adapt easily due to their short generation times, plastic genomes, acquisition (external) DNA and their ability to form protective bacterial communities i.e. biofilms or dormant metabolic states. Antibiotic drugs are currently our best medicine to treat (against) bacterial pathogens due to antibiotics unique properties of being small molecules that are soluble and act systemically. These qualities allow for many modern medical procedures to occur due to antibiotics preventative/ prophylactic and therapeutic qualities. Despite bacterial antibiotic resistance mechanisms always being present in nature, the overuse and misuse of antibiotics by humans are accelerating the rise and dissemination of bacterial antibiotic resistance. Bacterial antibiotic resistance is global threat to public health; especially because of lack of new drugs. It has been highlighted that understanding antibiotic resistance by further elucidating mechanisms of evolution, molecular mechanisms of action and reservoirs of resistance are essential Therefore, the work involved in this PhD thesis, examines the evolution of antibiotic resistance in bacterial populations. Two main studies were performed: the first to elucidate the molecular mechanisms of collateral sensitive drug pairs and collateral resistance drug pairs in adaptation of Escherichia coli populations; and the second exploring mutant variant dynamics in cystic fibrosis lung, by analyzing sputum samples from chronic carriers of Pseudomonas aeruginosa undergoing antibiotic treatment. Both studies explore the trajectories of antibiotic resistance within bacterial populations: the first study by exploring antibiotic resistance loci, and the in the second by whole-gene sequencing. The desired outcome from both studies is to find methods to use antibiotic therapy more rationally to treat infection efficiently and effectively whilst reducing the evolution of antibiotic resistance.
Population genomics of bank vole populations reveals associations between immune related genes and the epidemiology of Puumala hantavirus in Sweden

Infectious pathogens are major selective forces acting on individuals. The recent advent of high-throughput sequencing technologies now enables to investigate the genetic bases of resistance/susceptibility to infections in non-model organisms. From an evolutionary perspective, the analysis of the genetic diversity observed at these genes in natural populations provides insight into the mechanisms maintaining polymorphism and their epidemiological consequences. We explored these questions in the context of the interactions between Puumala hantavirus (PUUV) and its reservoir host, the bank vole Myodes glareolus. Despite the continuous spatial distribution of M. glareolus in Europe, PUUV distribution is strongly heterogeneous. Different defence strategies might have evolved in bank voles as a result of co-adaptation with PUUV, which may in turn reinforce spatial heterogeneity in PUUV distribution. We performed a genome scan study of six bank vole populations sampled along a North/South transect in Sweden, including PUUV endemic and non-endemic areas. We combined candidate gene analyses (Tlr4, Tlr7, Mx2 genes) and high throughput sequencing of RAD (Restriction-site Associated DNA) markers. We found evidence for outlier loci showing high levels of genetic differentiation. Ten outliers among the 52 that matched to mouse protein-coding genes corresponded to immune related genes and were detected using ecological associations with variations in PUUV prevalence. One third of the enriched pathways concerned immune processes, including platelet activation and TLR pathway. In the future, functional experimentations should enable to confirm the role of these these immune related genes with regard to the interactions between M. glareolus and PUUV.
How will sea-level rise affect threats to nesting success for Seaside Sparrows?

ABSTRACT Sea-level rise (SLR) threatens the nesting success of salt marsh breeding birds, including Seaside Sparrows (Ammodramus maritimus), by increasing the magnitude and frequency of extreme high tides that flood nests. However, the threat to nesting success from tidal flooding is intertwined with that of predation because the threats are connected through a trade-off along a nest height gradient. Therefore, to understand the risk to nesting success from SLR, it is necessary to consider predation threats simultaneously. I used an individual-based model of Seaside Sparrow nesting behavior, calibrated using empirical data on nest success rates and nest-site selection behaviors, to project the effects of SLR conditions on the relative importance of predation and flooding threats in affecting nesting success, and to investigate whether nest-site selection along a gradient of nest height can modulate the risk of SLR. Outputs from the model revealed that present-day levels of predation risk pose as great a risk to nesting success as tidal flooding under simulated SLR conditions with extreme flooding risks. Nest success rates could become very low under extreme SLR scenarios, especially when predation risk is very high. The risks of failure from either threat are linked through nest-site selection behaviors: In high-predation-risk seasons, failure probability from flooding is greater than it would be under lower predation risk, due to the predation avoidance behavior of nesting closer to the ground. Therefore, management actions to reduce the risk of excessive failures from predation could reduce the risk of failures from both threats—a potentially useful management strategy, given that controlling predation is more tractable than controlling increased flooding from SLR at a local level.
Population monitoring of small and declining brush-tailed rock wallaby (Petrogale penicillata) colonies at the extreme of their range using faecal DNA sampling

Obtaining much-needed information on population parameters such as abundance and genetic diversity can be difficult for small and declining populations. The brush-tailed rock-wallaby (Petrogale penicillata) is an endangered and cryptic species with many colonies in decline. The Warrumbungle National Park (NP) in New South Wales contains a declining metapopulation of P. penicillata at the western (inland) extreme of the species’ current range. Loss of these colonies would cause substantial range contraction and probable loss of regional genetic diversity in the Central Evolutionary Significance Unit (ESU). We used non-invasive genetic methods to identify individuals from faecal DNA from five colonies in the Warrumbungle NP. We identified a minimum of 21 individuals, with the largest colony containing seven individuals. The Warrumbungle NP colonies showed significant intercolony structuring and we were able to detect a single dispersal event. Comparison of genetic diversity to other Central ESU colonies shows that loss of the Warrumbungle NP population will result in loss of unique diversity from this region. The minimum number of animals and genetic diversity information obtained in this study was used to support management actions of herbivore control and translocation in the Warrumbungle NP population.
Diversity of lichen flora of Odisha, India- A review

Based on the compilation of literature on lichens of Odisha (India) and other specimens and preserved in herbaria, we estimate that 252 species of lichens, belonging to 81 genera and 35 families are known from the state. Graphidaceae with 49 species is the dominant family, followed by Arthoniaceae (21), Pyrenulaceae (19), Parmeliaceae (18), Trypetheliaceae (17), Physciaceae (15), Teloschistaceae (14), Lecanoraceae (13), Pertusariaceae (12), Ramalinaceae (11), Caliciaceae (11), Thelotremataceae (9) and Lecidiaceae (4). Among the lichen genera Graphis is dominant with 27 species, followed by Pyrenula (16), Caloplaca (14), Pertusaria (12), Lecanora (10), Parmotrema (9), Cryptothecia (9) and Pyxine (6). Accounts of lichens are only available from 13 out of 30 districts. Of these only cursory collections from 10 districts are available, whereas Mayurbhanj, Jharsuguda and Ganjam districts are well-explored for their lichen flora. The present enumeration of more than 250 species clearly indicates a rich diversity of lichens for the state. Further exploration in other unexplored districts will add more species to the lichen flora of the state.