Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural studies of the human polymeric immunoglobulin receptor

The human polymeric immunoglobulin receptor, pIgR, is a glycosylated type I transmembrane protein expressed on the basolateral surface of secretory epithelial cells. pIgR plays a key role in mucosal immunity and, together with bound immunoglobulins (Igs), provides a first line of specific defense against pathogens and their toxins. pIgR binds dimeric IgA (dIgA) and pentameric IgM (pIgM) produced by local plasma cells and transports these polymeric Igs to the apical surface of the cell where the complexes are cleaved from the membrane and deposited into mucosal secretions. The Fc portion of dIgA initially interacts non-covalently with the N-terminal domain (D1) of pIgR, followed by a covalent interaction with D5. In order to gain insight into the molecular details of the initial interaction, we solved the 1.9 A resolution crystal structure of D1 of pIgR. The structure reveals a folding topology similar to variable Ig domains with differences in the complementarity determining regions (CDRs). CDR1, the primary determinant in dimeric IgA binding, contains a single helical turn. CDR2, the main determinant in binding to pIgM is very short and contains a potentially critical glutamic acid involved in pIgM binding. CDR3 points away from the other CDRs, preventing dimerization of D1 analogous to the variable heavy and light chains in antibodies. Surface plasmon resonance studies showed that D1, regardless of its glycosylation state, binds dIgA with an equilibrium dissociation constant of 300 nM in the absence of other pIgR domains, but does not bind to monomeric IgAl-Fca. The structure of D1 allows interpretation of previous mutagenesis studies and structure-based comparisons with other IgA and IgM receptors. To further characterize the interaction between intact pIgR and dIgA, we have also initiated structural studies of the other extracellular domains of pIgR, both alone and in complex with the Fc portion of dIgA. Finally, we have also undertaken structural studies of pIgR in complex with the choline-binding protein A, CbpA, a protein found on the surface of Streptococcus pneumoniae, a pathogen that uses pIgR as a receptor to invade the human mucosal epithelium. Thesis Supervisors: Peter S. Kim, Professor of Biology, Massachusetts Institute of Technology; President, Merck Research Laboratories Pamela J. Bjorkman, Professor of Biology and Investigator, HHMI, California Institute of Technology
Comparison of Modulation Schemes for Implementing Battery Deposit Service in LTE-A

- In this paper, a detailed comparison of modulation techniques is done for improving the quality of service of BDS, which is a technique based on cooperative device-to-device communication. Battery Deposit Service scheme allows users with higher battery level to carry traffic of users with lower battery level, thereby reducing the chances of user running out of battery early. This system can be realized in the form of a proximity service (ProSe) which will utilize device-to-device (D2D) communication architecture underlaying Long Term Evolution (LTE) technology. With the help of comparison of modulation techniques, it has been shown that 8-QAM serves to fulfill all the requirements of BDS system in an effective manner.
A Role for Histone Modification in the Mechanism of Action of Antidepressant and Stimulant Drugs: a Dissertation

Depression and stimulant drug addiction each result in massive losses of health, productivity and human lives every year. Despite decades of research, current treatment regimes for depression are ineffective in approximately half of all patients. Therapy available to stimulant drug addicts is largely ineffective and moreover, dedicated treatments for drug dependence (including abuse of cocaine) are non-existent. Thus, there is a pressing need to further understanding of the molecular mechanisms underlying these disorders in order to develop novel, targeted therapeutic strategies. Chromatin remodeling, including changes in histone acetylation, has been proposed to play a role in both the etiology and treatment of depression and stimulant abuse. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) regulate numerous cellular processes, including transcription, cell cycle progression and differentiation. Moreover, histone acetylation has been shown to regulate hippocampal neurogenesis, a cellular response associated with the pathogenesis and treatment of depression and stimulant abuse (Hsieh et al., 2004, Yamaguchi et al., 2004, Fischer et al., 2007). Ultimately, such basic cellular processes impact higher order function, namely cognition and emotion. Indeed, recent studies suggest that HDAC activity in selected forebrain regions, including ventral striatum and hippocampus, modulate stimulant- and antidepressantinduced behavior (Kumar et al., 2005, Tsankova et al., 2006a, Fischer et al., 2007). These reports highlight an association between chromatin remodeling and diverse behavioral changes, including changes induced by the pleiotropic HDAC inhibitor, sodium butyrate (SB), (Kumar et al., 2005, Tsankova et al., 2006a, Fischer et al., 2007). However, behavioral, brain-metabolic and molecular effects of SB treatment in the context of rodent models of depression, dopaminergic sensitization and repeated cocaine administration remained unclear. The work described in this thesis illustrates the potential for chromatin modifying drugs in mechanisms underlying the experimental pharmacology of depression and stimulant addiction. Specifically, the data presented here support the view that treatment with the short chain fatty acid, sodium butyrate enhances: (1) antidepressant-like behavioral effects of the selective serotonin reuptake inhibitor (SSRI), fluoxetine (2) locomotor sensitization induced by repeated administration of the dopamine D1/D5 receptor agonist SKF82958; and (3) brain metabolic activation upon repeated cocaine administration as evidenced by fMRI in awake rats. Furthermore, this report provides evidence that these treatment paradigms will result in chromatin modification changes associated with active transcription, in addition to increased mRNA levels of plasticity-associated genes, including brain-derived neurotrophic factor (BDNF) at key brain regions implicated in the pathogenesis of depression and stimulant addiction. To date, little is…
Genetic Diversity and Relationship of Genus Spiraea by Random Amplified Polymorphic DNA Markers

Genus Spiraea is a woody species primarily distributed throughout Asia. Many species of this genus are important plants medicinally and ecologically. I evaluated a representative sample of the sixteen taxa with random amplified polymorphic DNA (RAPD) markers to estimate genetic relationships within genus Spiraea. In addition, RAPD analysis was also conducted to estimate the genetic diversity and population structure of these species. As the typical populations of Spiraea were small, isolated, and patchily distributed for natural populations, they maintained a low level of genetic diversity for polymorphic primers. The mean H was 0.117 across species. The Korean endemic species (S. chartacea) and patchily distributed species (S. betulifolia) showed fewer alleles per locus (mean 1.240 vs. 1.297), lower percent polymorphic locus (24.0 vs. 29.7), and lower diversity (0.092 vs. 0.121) than a relatively widely spread species. An assessment of the proportion of diversity present within species, H POP /H SP , indicated that about 87.8% the total genetic diversity was among species. Thus, the majority of genetic variation (87.8%) resided within species. The phylogenic tree showed three distinct groups. One clade includes S. prunifolia for. simpliciflora, S. thunbergii, S. chamaedryfolia var. ulmifolia, S. media, and S. cantoniensis. Another clade includes S. blumei, S. pubescens, S. chartacea, and S. chinensis. The other clade is the remaining seven species.
The High Arctic Large Igneous Province Mantle Plume caused uplift of Arctic Canada

The Sverdrup Basin is an east–west-trending extensional sedimentary basin underlying the northern Canadian Arctic Archipelago. The tectonic history of the basin began with Carboniferous–Early Permian rifting followed by thermal subsidence with minor tectonism. Tectonic activity rejuvenated in the Hauterivian–Aptian by renewed rifting and extension. Strata were deformed by diapiric structures that developed during episodic flow of Carboniferous evaporites during the Mesozoic and the basin contains igneous components associated with the High Arctic Large Igneous Province (HALIP). HALIP was a widespread event emplaced in multiple pulses spanning ca. 180 to 80 Ma, with igneous rocks on Svalbard, Franz Josef Island, New Siberian Islands, and also in the Sverdrup Basin on Ellef Ringnes, Axel Heiberg, and Ellesmere islands. Broadly contemporaneous igneous activity across this broad Arctic region along with a reconstructed giant radiating dyke swarm suggests that HALIP is a manifestation of large mantle plume activity probably centred near the Alpha Ridge. Significant surface uplift associated with the rise of a mantle plume is predicted to start ∼10-20 my prior to the generation of flood basalt magmatism and to vary in shape and size subsequently throughout the LIP event (1,2,3) Initial uplift is due to dynamical support associated with the top of the ascending plume reaching a depth of about 1000 km, and with continued ascent the uplift topography broadens. Additional effects (erosion of the ductile lithosphere and thermal expansion caused by longer-term heating of the mechanical lithosphere) also affect the shape of the uplift. Topographic uplift can be between 1 to 4 km depending on various factors and may be followed by subsidence as the plume head decays or become permanent due to magmatic underplating. In the High Arctic, field and geochronological data from HALIP relevant to the timing of uplift, deformation, and volcanism are few. Here we present new evidence based on stratigraphic correlation that show thinning of strata in the northeastern part of the basin. The Isachsen Formation (Valanginian or Hauterivian to late Aptian) is a sandstone unit with interbeds of mudstone, coal, volcanic, and volcaniclastic/tuffaceous rocks attributed to HALIP. Isachsen Formation has a fairly consistent thickness over most of the Sverdrup Basin, ranging from ∼120 m at basin margins to 1370 m on western Axel Heiberg Island but is generally > 400 m thick, even over the large salt domes that rose almost to the surface immediately prior to its deposition. The thickness of the formation decreases from over 400 m thick at Ellef Ringnes Island and southern Axel Heiberg Island to less than 120 m across a broad area of central Ellesmere Island. We interpret NE thinning of these strata to be the result of topographic uplift associated with initial mantle plume activity of HALIP. However, the rejuvenation of Sverdrup Basin formation (nearer the plume centre) in the Hauterivian–Aptian reflects complexities in the uplift pattern.
THE ROLE OF INTESTINAL EPITHELIAL CELLS AND THE REGULATION OF THE POLYMERIC IMMUNOGLOBULIN RECEPTOR IN HOMEOSTASIS AND INFLAMMATION

OF DISSERTATION THE ROLE OF INTESTINAL EPITHELIAL CELLS AND THE REGULATION OF THE POLYMERIC IMMUNOGLOBULIN RECEPTOR IN HOMEOSTASIS AND INFLAMMATION The mammalian intestine harbors an estimated 100 trillion microorganisms, which normally maintain a mutually beneficial relationship with the host. The intestinal epithelium consists of a single layer of intestinal epithelial cells (IECs) that provides a physical barrier as well as innate immune defense, preventing this vast community of microbes from entering host tissues. Secretory immunoglobulin A (SIgA) acts as the first line of antigen-specific immunity at the interface between the gut microbiota and the intestinal epithelium. Polymeric IgA secreted by plasma cells in the intestinal lamina propria is transported across IECs by the polymeric immunoglobulin receptor (pIgR). Defects in epithelial barrier and immune functions can lead to infections with opportunistic and pathogenic microbes and contribute to the etiology of inflammatory bowel disease (IBD). Here we investigate the ability of IEC biomarkers to define the mechanism and severity of intestinal inflammation, as well as provide insight into the function of IEC in regulating intestinal homeostasis and inflammation. Importantly, down-regulation of pIgR expression was a common feature in human IBD and mouse models of experimental colitis. One molecule of pIgR is consumed for every molecule of SIgA transported, thus high expression of pIgR is required to maintain sufficient supply of SIgA. Accordingly, we investigate the mechanisms by which IECs regulate pIgR expression in response to colonic bacteria. Cross-talk between the microbiota and IECs is mediated by pattern recognition receptors, including Toll-like receptors (TLR), leading to expression of gene products that enhance epithelial barrier function and innate immunity. The cytoplasmic adaptor protein MyD88 transduces signals from TLRs that recognize bacterial products. We show that pIgR induction by colonic bacteria is dependent on TLR4-MyD88 activation of NF-κB signaling. We examined the role of epithelialspecific MyD88 signaling in antibacterial immunity and epithelial expression of key gene products that participate in innate immunity in the gut by generating mice with an IECtargeted deletion of the Myd88 gene (MyD88). MyD88 mice display immunological and antimicrobial defects resulting in increased susceptibility to experimental colitis. We conclude that cross-talk between bacteria and IECs via MyD88dependent signaling is crucial for maintenance of gut homeostasis.
Effect of vapor gard and calcium chloride treatments on keeping quality of Navel oranges at different storage temperatures.

The experiments were conducted in two successive seasons (2004 2005) on Washington Navel orange fruits to study the effect of cold storage conditions on reducing postharvest losses and improving keeping quality for the export market.Fruit samples were obtained from El–Fayoum governorate, Egypt and treated with vapor gard (VG) 2%, calcium chloride (CaCl2) 4% or vapor gard 2% + calcium chloride 4%. Fruits were stored at 2 or 8 oC for 60 days and the last group was stored at 2 oC for 30 days and transferred to be stored at 8oC for another 30 days at R.H. 8590%. The results revealed that during storage fruits treated with Vapor gard (2%) alone or with calcium chloride (4%) + Vapor gard (2%) had been in good quality as well as it caused a pronounced increase in peel color and fruit firmness, while fruit weight loss and juice percentage were decreased. In addition, it caused a significant increase in ascorbic acid, total sugar and calcium concentration, but there is no significant effect in T.S. S. / acid ratio. While, free amino acid, total soluble phenols and free proline concentrations were decreased. Furthermore, the fruits storaged at 2o + 8oC caused a pronounced increase in fruit firmness, while fruit weight losses, juice percentage and peel color were decreased. Also, it caused a pronounced decrease in T.S. S. / acid ratio, total sugar, total free amino acid, total soluble phenols and free proline concentrations, but there is no significant effect on calcium concentration. In addition, there is an increase in ascorbic acid concentration. Generally, the results revealed that Vapor gard either alone or combired with calcium chloride dipping treatments and stored at 2o + 8oC had better results in improving fruit quality and decreasing total fruit losses compared with control or calcium chloride treatment alone at other storage temperatures and this was also accompanied by changes in various metabolic and physiological processes of orange fruits.
Network-biased Technical Change: How Modern Digital Collaboration Tools Overcome Some Biases but Exacerbate Others

Using three years’ data from more than 1,000 employees at a large professional services firm, we find that adopting an expertise search tool improves employee work performance in billable revenue, which results from improvements in network connections and information diversity. More importantly, we also find that adoption does not benefit all employees equally. Two types of employees benefit more from adoption of digital collaboration tools than others. First, junior employees and women benefit more from the adoption of digital collaboration tools than do senior employees and men, respectively. These tools help employees overcome the institutional barriers to resource access faced by these employees in their searches for expertise. Second, employees with greater social capital at the time of adoption also benefit more than others. The tools eliminate natural barriers associated with traditional offline interpersonal networks, enabling employees to network even more strategically than before. We explore the mechanisms for these differential benefits. Digital collaboration tools increase the volume of communication more for junior employees and women, indicating greater access to knowledge and expertise than they had before adoption. The tools also decrease the volume of communication for people with greater social capital, indicating more efficient access to knowledge and expertise. An important implication of our findings is that digital collaboration tools have the potential to overcome some of the demographic institutional biases that organizations have long sought to change. It does so, however, at the expense of potentially creating new biases toward network-based features—a characteristic we call “network-biased technical change. ”
Mycoplasma pneumoniae terminal organelle development and gliding motility

With a minimal genome containing less than 700 open reading frames and a cell volume < 10% of that of model prokaryotes, Mycoplasma pneumoniae is considered among the smallest and simplest organisms capable of self-replication. And yet, this unique wall-less bacterium exhibits a remarkable level of cellular complexity with a dynamic cytoskeleton and a morphological asymmetry highlighted by a polar, membrane-bound terminal organelle containing an elaborate macromolecular core. The M. pneumoniae terminal organelle functions in distinct, and seemingly disparate cellular processes that include cytadherence, cell division, and presumably gliding motility, as individual cells translocate over surfaces with the cell pole harboring the structure engaged as the leading end. While recent years have witnessed a dramatic increase in the knowledge of protein interactions required for core stability and adhesin trafficking, the mechanism of M. pneumoniae gliding has not been defined nor have interdependencies between the various terminal organelle functions been assessed. The studies presented in the current volume describe the first genetic and molecular investigations into the location, components, architecture, and regulation of the M. pneumoniae gliding machinery. The data indicate that cytadherence and gliding motility are separable properties, and identify a subset of M. pneumoniae proteins contributing directly to the latter process. Characterizations of novel gliding-deficient mutants confirm that the terminal organelle contains the molecular gliding machinery, revealing that with the loss of a single terminal organelle cytoskeletal element, protein P41, terminal organelles detach from the cell body but retain gliding function. The current studies additionally reveal that an intricate balance of transient activation and repression of the gliding machinery is required for normal terminal organelle development and cell division. A second terminal organelle protein, P24, which is normally transcribed with the gene encoding P41, is shown to directly contribute towards this regulation in a P41-dependent manner. INDEX WORDS: mycoplasma, terminal organelle, gliding motility, cell division, cytadherence, protein trafficking MYCOPLASMA PNEUMONIAE TERMINAL ORGANELLE DEVELOPMENT AND GLIDING MOTILITY
Photosynthetic efficiency and pigment contents in alfalfa (Medicago sativa) seedlings subjected to dark and chilling conditions

The functional activities of the photosynthetic apparatus of alfalfa (Medicago sativa L.) was investigated after 24 h of dark chilling treatment at 10°C and after 48 h recovery period at 25°C and 420 μmol m -2 S-1. Dark chilling limits photosynthesis due to chilling-associated oxidative damage, which enhanced the production of active oxygen species (AOS). Dark chilling treatment resulted in a significant reduction in the CO2 assimilation rate and decreased stomatal conductance. Stomatal limitation was largely responsible for the inhibition of CO2 assimilation generated by affections in the PSII functioning and also in the Calvin cycle. Photosynthetic parameters and chlorophyll fluorescence analyses showed the same degree of inhibition during the dark chilling period. However, chlorophyll fluorescence analysis showed an increase in the process of energy dissipation in the dark chilled leaves. In addition, leaves showed a significant decrease in chlorophyll a:b ratio and higher carotenoids-to-total chlorophyll ratio providing photoprotection. Under recovery, leaves recovered photosynthetic activity thus diminishing the potential power for AOS generation.
Agrobacterium tumefaciens-mediated transformation of an elite Australian barley cultivar with virus resistance and reporter genes

Efficient transformation of barley cv. Schooner was achieved using Agrobacterium delivery, hygromycin or bialaphos selection and embryogenic callus. Using this system, transgenic plants were generated that contained either the green fluorescent protein gene, or transgenes derived from barley yellow dwarf (BYDV) and cereal yellow dwarf (CYDV) viruses. Many of these plants contained 1-3 transgene copies that were inherited in a simple Mendelian manner. Some plants containing BYDV and/or CYDV derived transgenes showed reduced virus symptoms and rates of viral replication when challenged with the appropriate virus. The ability to transform Schooner is a significant advance for the Australian barley industry, as this elite malting variety is, and has for the last 15 years been, the most widely grown barley variety in eastern Australia.
Investigation of the role of the 5’-3’ exoribonuclease pacman in Drosophila wound healing

The Drosophila gene pacman encodes a 5’-3’ exoribonuclease, which is involved in RNA degradation. pacman mutants were created by P-element excision. These mutants have phenotypes including dull and blistered wings, kinked legs and thoracic closure defects. Also, pacman mutant embryos show a dorsal closure defect. The thorax and dorsal closure phenotypes in pacman mutants closely resemble those observed in flies mutant for genes of the highly conserved JNK signalling pathway, for example hemipterous (JNKK), basket (JNK) and kayak (Dfos). These similarities suggest pacman may be involved in regulating the JNK pathway. The JNK signalling pathway is known to regulate morphological processes such as dorsal closure during Drosophila development and wound healing. The phenotypes of our pacman mutants suggest pacman may have a role in these processes possibly through interactions with the JNK signalling pathway.
Design of a low power frontend system for fetal monitoring applications

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