Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissection of protonation sites for antibacterial recognition and transport in QacA, a multi-drug efflux transporter

QacA is a drug:H+ antiporter (DHA2) with 14 transmembrane helices, that renders antibacterial resistance to methicillin-resistant Staphylococcus aureus (MRSA) strains, with homologues in other pathogenic organisms. It is a highly promiscuous antiporter, capable of H+- driven efflux of a wide array of cationic antibacterial compounds and dyes. Our study, using a homology model of QacA, reveals a group of six protonatable residues in its vestibule. Systematic mutagenesis resulted in identification of D34 (TM1), and a cluster of acidic residues in TM13 including E407 and D411 and D323 in TM10, as being crucial for substrate recognition and transport of monovalent and divalent cationic antibacterial compounds. The transport and binding properties of QacA and its mutants were explored using whole cells, inside-out vesicles, substrate-induced H+ release and microscale thermophoresis. We identify two sites, D34 and D411 as vital players in substrate recognition while E407 facilitates substrate efflux as a protonation site. We also observe that E407 plays a moonlighting role as a substrate recognition site for dequalinium transport. These observations rationalize the promiscuity of QacA for diverse substrates. The study unravels the role of acidic residues in QacA with implications for substrate recognition, promiscuity and processive transport in multidrug efflux transporters, related to QacA. Highlights A homology model of QacA with 14 TM helices was used to test the importance of acidic residues within the vestibule. Mono and Divalent cationic substrate recognition requires two sites D34 (TM1) and D411 (TM13). E407 (TM13) is important for protonation driven efflux. Substrate recognition of a divalent substrate, dequalinium occurs at E407 instead of D411 providing glimpses into the promiscuity of substrate recognition in QacA.
The morphology of euphausiid mandibles used to assess selective predation by blue whales in the southern sector of the California Current System

We describe the mandibular morphology of the eight most abundant euphausiid species in the California Current and report regression relationships between mandible size and body total length. We applied these species-specific characters to the mandibles recovered from fecal samples of 18 blue whales ( Balaenoptera musculus (Linnaeus, 1758)) collected between 1998 to 2015 off Southern California to test for selective feeding on the euphausiid assemblage. The diets of blue whales were consistently and overwhelmingly dominated by the large neritic euphausiid Thysanoessa spinifera Holmes, 1900, even when other species were present or dominant in closely collected net samples. More than 99% of the ingested euphausiids were longer than 10 mm, indicating that blue whales in this region are highly selective by prey species and size class, and dependent upon aggregations of juveniles or adults of a limited number of coastally associated euphausiid species.
The physiological and genetic differences between flycatchers (Ficedula albicollis vs. Ficedula hypoleuca)

Abstract The paper studies interspecies physiological and genetic differences between the white-collared flycatcher and the pied flycatcher of the genus Ficedula. The fact that the flycatchers are capable of interspecies hybridization is one more reason for particular interest to these species. Using our own-developed method of taking venous blood from the eye’s sinus, we took blood samples from birds in the protected area of Homilshanski Forests, Kharkiv, Ukraine, to study their leukogram patterns. The bird feathers were also collected for genetic analysis -- to identify interspecies differences with application of the ISSR technique. It was revealed that the percentage of heterophiles in the nestlings of the pied flycatcher was lower than in the nestlings of the white-collared flycatcher. The micronucleus test did not reveal any significant difference in the interspecies groups. The spectra of amplification products obtained with the primer (AGC)6 G showed that the white-collared flycatchers had a more heterogeneous structure. The study of the leukogram, micronucleus test, and the ISSR analysis can be especially effective in the study of intra-species genetic differentiation.
Anticancer Effects of Soybean Bioactive Components and Anti-inflammatory Activities of the Soybean Peptide Lunasin

IV Acknowledgements . VI Tables of contents . VII List of figures . IX List of tables . X List of abbreviations . XI CHAPTER 1.General introduction. 1 1. General context . 2 2. Objective and outline of the thesis . 11 3. References . 13 CHAPTER 2. Synergistic anticancer effect of bioactive components from soybean in mda-mb-231 and mcf-7 human breast cancer cells in vitro . 21 1. Abstract. 23 2. Introduction . 24 3. Materials and methods . 25 4. Results and discussion . 28 5. Conclusion . 48 6. Reference . 48 CHAPTER 3. Anti-inflammatory Activity of Natural Lunasin from soybean and Recombinant Lunasin from Pichia Pastoris in LPS-stimulated RAW264.7 Cells . 51 1. Abstract. 53 2. Introduction . 54 3. Materials and methods . 55 4. Results and discussion . 58
Structurally distinct endocytic pathways for B cell receptors in B lymphocytes

B lymphocytes play a critical role in adaptive immunity. Upon antigen binding, B cell receptors (BCR) cluster on the plasma membrane and are internalized by endocytosis. In this process, B cells capture diverse antigens in various contexts and concentrations. However, it is unclear whether the mechanism of BCR endocytosis changes in response to these factors. Here, we studied the mechanism of soluble antigen-induced BCR clustering and internalization in a cultured human B cell line using correlative super resolution fluorescence and platinum replica electron microscopy. First, by visualizing nanoscale BCR clusters, we provide direct evidence that BCR cluster size increases with F(ab’)2 concentration. Next, we show that the physical mechanism of internalization switches in response to BCR cluster size. At low concentrations of antigen, B cells internalize small BCR clusters by classical clathrin-mediated endocytosis. At high antigen concentrations, when clusters size increases beyond the size of a single clathrin coated pit, B cells retrieve receptor clusters using large invaginations of the plasma membrane capped with clathrin. At these sites, we observed early and sustained recruitment of actin and an actin polymerizing protein FCHSD2. We further show that actin recruitment is required for the efficient generation of these novel endocytic carriers and for their capture into the cytosol. We propose that in B cells, the mechanism of endocytosis switches to accommodate large receptor clusters formed when cells encounter high concentrations of soluble antigen. This mechanism is regulated by the organization and dynamics of the cortical actin cytoskeleton.
Zen Buddhism, Japanese Therapies, and the Self : Philosophical and Psychiatric Concepts of Madness and Mental Health in Modern Japan

In my paper, I propose to investigate the philosophical underpinnings of representative indigenous Japanese psychotherapeutic approaches, particularly that of Morita and Naikan therapies, that have, at their foundations, distinctly Buddhist psychological tenets, and that offer to deal with mental health issues in a manifestly different way compared with their western counterparts. I offer a comprehensive account of how the characterizations of madness and mental illness have been shifting over the last two hundred years in Japanese society and culture, and how this has affected mental health care in Japan. Finally, the ways in which modern day thinkers, such as Daisetz Teitaro Suzuki and Keiji Nishitani have been re-shaping the concepts of the self in Japanese religion and philosophy while, at the same time, taking care to remain faithful to the original East Asian sensibilities will also be expounded and connected to the themes of mental health and mental illness.
Methylation status of Vitamin D receptor gene promoter in adrenocortical carcinoma

Context: Previous data of my research group showed a decreased expression of vitamin D receptor (VDR) mRNA/protein in a small group of adrenocortical carcinoma (ACC) tissues, suggesting the loss of a protective role of VDR against malignant cell growth in this type of cancer. Downregulation of VDR gene expression may result from epigenetic events, that is, methylation of cytosine nucleotide of CpG islands in VDR gene promoter. Objective: To analyse methylation of CpG sites in the VDR gene promoter in a series of ACC tissue specimens, comparing malignant adrenocortical tumour samples with those from various benign forms and normal adrenals. Methods: Methylation of CpG-rich 5′ regions was assessed by bisulfite sequencing PCR using bisulfite-treated DNA from archival microdissected paraffin-embedded adrenocortical tissues. Three normal adrenals and twenty-three various adrenocortical tumour samples including eight carcinomas and fifteen adenomas were studied. Results: Methylation in the promoter region of VDR gene was found in three of eight ACCs, while no VDR gene methylation was observed in normal adrenals and adrenocortical adenomas. VDR mRNA and protein levels were lower in ACCs than in benign tumours. VDR immunostaining was weak or negative in ACCs, including all three methylated tissue samples. Conclusion: The association between VDR gene promoter methylation and reduced VDR gene expression is not a rare event in ACC, suggesting that VDR epigenetic inactivation may have a role in adrenocortical carcinogenesis. Other epigenetic mechanisms in the upstream signalling pathway involved in silencing VDR gene expression in ACC should be investigated.
Uncoupled Evolution of Male and Female Cone Sizes in an Ancient Conifer Lineage

Premise of research. Sexual functions in gymnosperms are mostly performed by separate reproductive structures, which largely reduces sexual interference and sets the scene for morphological and functional sexual specialization. The evolutionary trajectories followed by traits related to the male and female functions are therefore expected to be uncoupled. Studies on the fossil record of the conifer family Araucariaceae revealed important morphological changes occurring in reproductive cones. Here, we explored the pattern of evolution of male and female cone sizes in Araucariaceae, with a special focus on Araucaria—the most variable and widespread genus in the family. Methodology. We gathered data on male and female cone sizes from fossils and extant Araucariaceae species. Focusing on Araucaria, we analyzed whether cone sizes are phylogenetically structured. Furthermore, we compared the evolutionary trajectories of male and female cone sizes by evaluating the goodness of fit of different evolutionary models. Finally, we evaluated whether different selective regimes across the phylogeny could have shaped cone morphology. Pivotal results. Size changes in Araucariaceae occurred in both male and female cones, with the largest cones appearing in extant Araucaria. In this genus, different evolutionary models best described cone size changes, with male cone evolution best described by a model not influenced by phylogeny and female cone evolution by a stabilizing selection model with two optima. This resulted in contrasting phylogenetic signals, with female cone size being more phylogenetically structured than male cone size. Conclusions. Changes in cone size in Araucariaceae occurred in both male and female cones. The largest male and female cones appeared in Araucaria through uncoupled evolutionary pathways, both involving a natural selection component as a driver of evolutionary change. A contrasting pattern of phylogenetic signal in male and female cone size reflected the uncoupled evolutionary trajectories followed by these sexual structures.
A Short Bout of High-intensity Exercise Alters Ipsilesional Motor Cortical Excitability Post-stroke

Background Acute exercise can increase motor cortical excitability and enhance motor learning in healthy individuals, an effect known as exercise priming. Whether it has the same effects in people with stroke is unclear. Objectives The objective of this study was to investigate whether a short, clinically-feasible high-intensity exercise protocol can increase motor cortical excitability in non-exercised muscles of chronic stroke survivors. Methods Thirteen participants with chronic, unilateral stroke participated in two sessions, at least one week apart, in a crossover design. In each session, they underwent either high-intensity lower extremity exercise or quiet rest. Motor cortical excitability of the extensor carpi radialis muscles was measured bilaterally with transcranial magnetic stimulation before and immediately after either exercise or rest. Motor cortical excitability changes (post-exercise or rest measures normalized to pre-test measures) were compared between exercise vs. rest conditions. Results All participants were able to reach the target high-intensity exercise level. Blood lactate levels increased significantly after exercise (p < 0.001, d = 2.85). Resting motor evoked potentials from the lesioned hemisphere increased after exercise compared to the rest condition (p = 0.046, d = 2.76), but this was not the case for the non-lesioned hemisphere (p = 0.406, d = 0.25). Conclusions High-intensity exercise can increase lesioned hemisphere motor cortical excitability in a non-exercised muscle post-stroke. Our short and clinically-feasible exercise protocol shows promise as a potential priming method in stroke rehabilitation.
Comparison of Cytokine Expression and Bacterial Growth During Periparturient and Mid Lactation Mastitis in a Mouse Model

Comparison of Cytokine Expression and Bacterial Growth During Periparturient and Mid-Lactation Mastitis in a Mouse Model Rhonda Nicole Chronis Department of Microbiology and Molecular Biology, BYU Master of Science Clinical cases of bovine mastitis are most severe in the early stages of lactation. The causes of this increased propensity for severe mastitis during early lactation, compared to mid and late lactation are unclear. In order to better understand the early lactation immune response to mastitis, a murine model of mastitis was employed. Intramammary inoculation of a mastitis causing Escherichia coli strain was performed in lactating mice at various stages of lactation to model the immune response seen in cows during lactation. In our experiments, mice in the early stages of lactation exhibited altered mRNA expression of cytokines IL-1β, IL-6, IL-10, and TNFα over the course of infection when compared to mice at mid-lactation. Additionally, increased bacterial growth was observed in the mammary gland of mice infected during early lactation compared to late lactation. These results are consistent with the immune response observed in cows at early lactation. These results suggest that the mouse may provide a useful model to study differences in the immune response seen during different times in lactation.
Seeing emotions, reading emotions: behavioral and ERPs evidence of the effect of strategy and of regulation for pictures and words

Background Whilst there has been extensive study of the mechanisms underlying the effect of regulation for the emotions elicited by pictures, the ability and the mechanisms beyond the regulation of words remains to be clarified. Similarly, the effect of strategy when applying a regulatory process is still poorly explored. The present study seeks to elucidate these issues comparing the effect of regulation and of strategy to both neutral and emotional words and pictures. Methodology/Principal Findings Thirty young adults observed and took the distance from unpleasant and neutral pictures and words while their subjective ratings and ERPs were recorded. At a behavioral level, participants successfully regulated the arousal and the valence of both pictures and words. At a neural level, unpleasant pictures produced an increase in the late positive potential modulated during the regulate condition. Unpleasant linguistic stimuli elicited a posterior negativity as compared to neutral stimuli, but no effect of regulation on ERP was detectable. More importantly, the effect of strategy independently of stimulus type, produced a significant larger Stimulus Preceding Negativity. Dipole reconstruction localized this effect in the middle frontal areas of the brain. Conclusions As such, these new psychophysiological findings might help to understand how pictures and words can be regulated by distancing in daily life and clinical contexts, and the neural bases of the effect of strategy for which we suggest an integrative model.
Étude des changements de conformation du cotransporteur de Na⁺/glucose (SGLT1) à l'aide de mesures électrophysiologiques et de marqueurs fluorescents

In this thesis, we have studied the structure and mechanisms of action of the Na/glucose cotransporter SGLT1. This membrane protein drives secondary active transport of glucose by using the electrochemical Na gradient. In the introduction, recent structural and mechanistic findings in the field of membrane proteins are presented, along with a review of the scientific literature concerning SGLT1 before presenting and discussing our results, presented as four separate publications. First, the membrane topology of loop 13-14 of SGLT1 was studied using a combination of substituted cysteine accessibility method (SCAM) and fluorescent labeling. We observed that charged, thiol-reactive reagents produced effects on the activity of some site-directed, cysteine-inserted mutant forms of SGLT1 and that a fluorescent probe could be attached to some specific positions in this loop. We proposed a novel topology for this loop and hypothesized that it could indeed be the voltage sensor for this protein. Second, we have studied the roles of the 15 endogenous cysteine residues in SGLT1. We found that 12 of them play essential roles in trafficking or in the voltage-dependent reorientation of the free transporters. We identified a disulfide bridge between C255 and C511, which is the first known physical constraint in SGLT1’s 3D structure. We then studied, experimentally and theoretically, presteady state currents measured, in the presence of glucose, with mutants C255A and C511A, which lack the disulfide bridge, and in wt SGLT1. Interestingly, these two mutants exhibit presteady state currents in the presence of a saturating glucose concentration, in contrast to what is observed in normal SGLT1 as well as in the majority of other cotransporters in the presence of their substrate. We proposed a simple, five-state kinetic model which quantitatively explains these results. Finally, we used voltage-clamp fluorometry to study conformational changes, with four different fluorescent probes attached to positions C255 and C511. Our observations of changes in fluorescence under different conditions indicate that glucose binding modifies the environment of C255 and C511 and provide support for our kinetic model. vi We conclude that the C255-C511 disulfide bridge stabilizes the voltage sensor, which could include the loop 13-14, and facilitates the conformational change of the fully loaded cotransporter. This disulfide bridge is located in such a way that fluorescent dyes attached to one or the other cysteine experience conformational changes in response to membrane potential, Na and substrate.
Assessment of the Integral Role of Laboratory Facilities in the Preparation of Science Teachers for Functional Science Education

This study examined the roles of laboratory facilities for functional science education among science teachers in Ondo State, Nigeria. The study employed descriptive research design of survey type. A total of 51 science teachers were sampled from selected 15 public secondary schools in Ondo West Local Government Area of Ondo State. A validated questionnaire tagged Laboratory Facilities and Functional Science Education Questionnaire (LFFSEQ) was used for data collection. The data collected were analysed using mean and standard deviation. The results of the study showed that secondary school teachers perceived that science education is important in improving scientific literacy, understanding the natural world and making crucial decisions on everyday issues. Some laboratory facilities were observed to be available but not adequate for teaching and learning of science. Teachers perceived that laboratory facilities have integral roles to play in preparing science teachers for functional science education. It was recommended that laboratory facilities should be made available and adequate for teaching and learning of science. Science teachers should have access to innovative classroom and scientific equipments. In-service training of science teachers should take cognizance of teachers’ knowledge of the integral roles of laboratory facilities.
Influence of Landscape Factors on Amphibian Roadkills at the National Level

Roads exert multiple effects on wildlife, from animal mortality, habitat and population fragmentation, to modification of animal reproductive behaviour. Amphibians are the most frequently road-killed animal group. Many studies have attempted to analyse the factors driving amphibian casualties on roads, but these factors are limited to the roads themselves (e.g., traffic, type of roads, roads crossing water bodies) or to structures along them (e.g., ditches, walls). Sometimes, roadkills are related to land use along the roads. We analysed the influence of landscape factors on roadkill hotspots at the national level (Slovenia). Specifically, we aimed at: (1) identifying hotspots of roadkills, (2) analysing whether records of amphibian presence on roads are related to the distribution of water bodies and (3) analysing which factors (proximity to water bodies or human factors) explain the distribution of hotspots. Hotspots were identified by Malo’s method. Roadkills were modelled with Maxent for the first time in Slovenia. The relationships between amphibian presence and hotspots with factors were analysed with GLM. A total of 237 road sections were identified as hotspots, corresponding to 8% of road sections and containing 90% of road-killed individuals. Proximity to forests, meadows and agricultural land were the most important variables in Maxent models. The number of roadkills depended on the proximity to agricultural land, forests, water bodies and wetland areas, while the number of hotspots additionally depended on the proximity to urban settlements.
EFFECT OF BAYKAL EM-1 ON GROWTH DEVELOPMENT AND MICROBIOLOGICAL STATUS OF SUCKLING PIGS

Ivanova, S. , A. Dimitrova, T. Nikolova, S. Yordanov, R. Nedeva and K. Mateeva, 2018. Effect of Baykal EM-1 on growth development and microbiological status of suckling pigs Bulg. J. Agric. Sci., 24 (Sup. 2): 27-32 In an experiment with 15 equalized by piglet age, origin and size litters, of which 8 litters in the trial and 7 litterts in the control group, the effect of Baikal EM-1 feed additive, a multi-purpose microbiological product containing a complex of living, useful microorganisms, on the weight development and the microbiological status of the gastrointestinal tract of the pigs, was studied. The additive was included in the feed of the sows and pigs at a dosage of 10 ml / kg of feed, from the day 8th after birth to the day 35th at weaning of the pigs. On the day 21st and day 35th the body weights of the pigs were recorded, and on the day 35th, 10 rectal tampon samples (RTS) from the two groups were taken and microbiologically examined. It was found that the data on weight development, total growth and average daily gain did not show any significant differences in the benefit of the trial group, which contradicts the hitherto established for many other feed additives. Microbiological tests showed that 40% of the RTS of both groups were positive for E. coli, of which in the trial group 75% were nonpathogenic and 25% pathogenic (O139:F4) in and in the control group 75% pathogenic (O139:F4) and 25% non-pathogenic, which represents the product as a good prophylactic remedy.