Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular and Cellular Approaches Toward Understanding Dynein-Driven Motility

Active transport is integral to organelle localization and their distribution within the cell. Kinesins, myosins and dynein are the molecular motors that drive this long range transport on the actin and microtubule cytoskeleton. Although several families of kinesins and myosins have evolved, there is only one form of cytoplasmic dynein driving active retrograde transport in cells. While dynactin is an essential co-factor for most cellular functions of dynein, the mechanistic basis for this evolutionarily well conserved interaction remains unclear. Here, I use single molecule approaches with purified dynein to reconstitute processes in vitro, and implement an optogenetic tool in neurons to further dissect regulatory mechanisms of dynein-driven transport in cells. I demonstrate for the first time, at the single molecule level, that dynactin functions as a tether to enhance the initial recruitment of dynein onto microtubules but also acts as a brake to slow the motor. I then extend this work in neurons to understand regulation of the dynein motor at the cellular level. Neurons are particulary dependent on long-range transport as organelles and macromolecules must be efficiently moved over the extended length of the axon and further, have mechanisms in place for the compartment-specific regulation of trafficking in axons and dendrites. I use a light-inducible dimerization tool to recruit motor proteins or motor adaptors to organelles in real time to examine downstream effects of organelle motility and compartment-specific regulation of motors. I find that while dynein works efficiently in both axons and dendrites, kinesins are differentially regulated in a compartment-specific manner. I further demonstrate that dynein-driven motility in neurons is largely governed by microtubule orientation and requires microtubule dynamics for efficient navigation in axons and dendrites. Together, this work sheds light on the molecular and cellular mechanisms of dynein function both in vitro and in vivo using a combination of approaches. My findings converge to a model wherein dynactin enhances the recruitment of dynein onto microtubule plus ends, leading to efficient minus-end directed motility of dynein. This becomes especially critical in neuronal growth cones and dendrites owing to the large number of highly dynamic microtubules in these compartments. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Biology First Advisor Erika L. Holzbaur Subject Categories Biophysics | Cell Biology | Molecular Biology This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1595 MOLECULAR AND CELLULAR APPROACHES TOWARD UNDERSTANDING DYNEIN-DRIVEN MOTILITY
Flutuação populacional do psilídeo-da-goiabeira, Triozoida limbata (Hemiptera: Psyllidae) na região de Londrina, Pr Population dynamic of guava psyllid Triozoida limbata (Hemiptera: Psyllidae) in Londrina Parana, Brazil

The Psyllidae are sap-suckers insects, highly host and food specific, found mainly in sprouts, and are considered important guava pests. Large populations of these insects can be hazardous, since they cause plant weakness by the toxic action of the saliva injected during their feeding process. The objective of this work was to verify the population fluctuation of the psyllidae Trizoida limbata in guava trees in Londrina, Parana, Brazil. The monitoring of an adult T.limbata population was carried out in areas of wild guava trees, using 10 yellow adhesive traps, 30 m far from each other. Collection took place monthly from March 2002 to May 2003. T.limbata populations were found during every month of the year, reaching their peak in October. Average and maximum temperatures showed a significant correlation with the psyllidae population fluctuation, affecting it positively. Heavy rain periods and low temperatures were not restricting, but they caused a reduction in population
Isolation and identification of lactic acid bacteria from Brazilian Minas artisanal cheese

ABSTRACT The microbiota of lactic acid bacteria (LAB) from Minas artisanal cheese was evaluated. Samples of Minas artisanal cheese were collected at the farms in the region of Araxá, Brazil, over two seasons. Molecular approaches were used to assess the biodiversity of the isolates. The median value of the counts of LAB ranged from 6.4 to 9.5 log units in cheeses throughout the ripening period, in both seasons. The genera of Lactobacillus, Enterococcus, Pediococcus, and Lactococcus were found. L. plantarum and L. rhamnosus were the prevailing species during both seasons, suggesting they may play a role in the development of the cheese attributes. Enterococcus rivorum was identified in one sample and it was probably the first description in cheeses. This is an important report describing the varieties of LAB in this cheese and the identification of its lactic communities could be a source of strains with specific properties.
Sulforaphane production and antioxidant enzyme activity in Lepidium draba seedlings in presence of Yeast extract and silver nitrate

Sulforaphane is produced through a hydrolytic reaction catalyzed by myrosinase from glucoraphanin. It has recently attracted researcher's interest due to its anticancer activities. The present study was conducted to evaluate the effects of various concentrations of yeast extract (YE) and silver ion (Ag + ) on sulforaphane production level in Lepidium draba seedlings. Our results revealed that the sulforaphane content is increased in seedlings that treated with the both elicitors, but more significantly by Ag + . All elicitor influences are depend on the elicitor dose and time of elicitation and maximized with YE at 1 mg/mL for 8 hours and with Ag + at 50 µM for 4 hours treatment. It seems that the promotion of sulforaphane content results in induction of glucoraphanin biosynthesis pathway which in turn is mediated by H 2 O 2 , as revealed by a significant increase in the activity of H 2 O 2 scavenger enzymes.
Understanding the Role of Transmembrane and Juxtamembrane Domains in Plexin and Neuropilin Signaling

Plexins (plxns) are transmembrane (TM) receptors involved in the guidance of vascular, lymphatic vessel, and neuron growth as well as cancer metastasis. Plxn signaling results in cytosolic GTPase-activating protein activity, and previous research implicates dimerization as important for activation of plxn signaling. Purified, soluble plxn extracellular and cytosolic domains exhibit only weak homomeric interactions, suggesting a role for the plxn TM and juxtamembrane regions in homooligomerization. In this study, we consider a heptad repeat in the Danio rerio PlxnA3 cytosolic juxtamembrane domain (JM) for its ability to influence PlxnA3 homooligomerization in TM-domain containing constructs. Site-directed mutagenesis in conjunction with the AraTM assay and bioluminescent energy transfer (BRET) suggest an interface involving a JM heptad repeat, in particular residue M1281, regulates PlxnA3 homomeric interactions when examined in constructs containing an ectodomain, TM and JM domain. In the presence of a neuropilin-2a co-receptor and semaphorin 3F ligand, disruption to PlxnA3 homodimerization caused by an M1281F mutation is eliminated, suggesting destabilization of the PlxnA3 homodimer in the JM is not sufficient to disrupt co-receptor complex formation. In
Avian hosts, prevalence and larval life history of the ectoparasitic fly Passeromyia longicornis (Diptera : Muscidae) in south-eastern Tasmania

Abstract. Blood-sucking fly larvae are widespread parasites of nestling birds, but in many systems we lack knowledge of their basic biology. This study reports the first observation of an endemic Tasmanian fly species, Passeromyia longicornis (Diptera : Muscidae), parasitising the forty-spotted pardalote (Pardalotus quadragintus), another Tasmanian endemic. Because the forty-spotted pardalote is an endangered and declining songbird, P. longicornis is a species of interest to conservation biologists. Its larval form is an obligate, subcutaneous parasite of nestling birds, but before this study, there were just two published records of the species infesting avian hosts, and little known about its ecology or life cycle. This study documented hosts, prevalence, and larval life history of P. longicornis by locating and monitoring nests and ectoparasites of the forest bird community in south-eastern Tasmania. I also reared P. longicornis larvae in captivity to determine the length of the pupal stage in relationship to ambient temperature. Hosts of P. longicornis included forty-spotted pardalotes (87% prevalence across nests), striated pardalotes (Pardalotus striatus) (88% prevalence), and New Holland honeyeaters (Phylidonyris novaehollandiae) (11% prevalence). Both pardalote species were new host records. P. longicornis larvae burrowed under the skin of nestlings where they developed for 4–7 days, feeding on nestling blood. When fully grown, larvae dropped into the surrounding nest material and formed pupae. Length of the pupal stage was 14–21 days, and declined with increasing ambient temperature. Median parasite abundance was 15 larvae in infested forty-spotted pardalote nests and 11 larvae in infested striated pardalote nests. Nestling mortality was frequently associated with ectoparasite presence. This study provides the first survey of P. longicornis hosts, prevalence and life cycle, and shows that this species is likely a major player in the ecology of pardalotes, and possibly other forest bird species in Tasmania.
Genetic control of fruit yield and quality characters in tomato genotypes possessing hp-1, ogc, dg, Aft and rin genes

Five inbred lines of tomato possessing one each of the specific genes viz., hp-1, ogc, dg, Aft and rin were crossed in a half diallel fashion to determine the combining ability and gene action of fruit yield/plant, fruit weight and eight important fruit quality characters. Additive genetic component was predominant for TSS, ascorbic acid and anthocyanin contents; both additive and non-additive components was important for fruit yield/plant, fruit weight and lycopene content, and non-additive gene action was overwhelmingly important for pericarp thickness and total sugar content while estimates of both the genetic components was zero for titrable acidity and β-carotene content of fruit. General combining ability effects of the parents corresponded well to their per se performance. Homozygous recessive condition of the genes, hp-1, ogc, dg governed enhanced lycopene content in the fruits. Homozygous Aft/Aft plant had higher anthocyanin content in the fruit than the heterozygous plant indicating additivity of the Aft gene in expressing the character. The hybrid of two widely divergent parent BCT-115 dg/dg x Alisa Craig Aft/Aft emerged as outstanding for both fruit yield and quality which also opened up the possibility of developing tomato hybrid rich in both lycopene and anthocyanin contents. The hybrid BCT-115 dg/dg x BCT-111 rin/rin was also promising for commercial utilization.
Bioaugmentation and correlating anaerobic digester microbial community to process function

BIOAUGMENTATION AND CORRELATING ANAEROBIC DIGESTER MICROBIAL COMMUNITY TO PROCESS FUNCTION Kaushik Venkiteshwaran Marquette University, 2016 This dissertation describes two research projects on anaerobic digestion (AD) that investigated the relationship between microbial community structure and digester function. Both archaeal and bacterial communities were characterized using highthroughput (Illumina) sequencing technology with universal 16S rRNA gene primers. In the first project, bioaugmentation using a methanogenic, aerotolerant propionate enrichment culture was investigated as a possible method to increase digester methane production. Nine anaerobic digesters, seeded with different biomass, were operated identically and their quasi steady state function was compared. Before bioaugmentation, different seed biomass resulted in different quasi steady state function, with digesters clustering into high, medium or low methane (CH4) production groups. High CH4 production correlated with neutral pH and high Methanosarcina abundance, whereas low CH4 production correlated to low pH and high Methanobacterium and DHVEG-6 family abundance. After bioaugmentation, CH4 production from the high CH4producing digesters transiently increased by 11±3% relative to non-bioaugmented controls (p <0.05, n=3), whereas no functional changes were observed for medium and low CH4 producing digesters. The CH4 production increase after bioaugmentation was correlated to increased relative abundance of Methanosaeta and Methanospirillum originating from the bioaugment culture. In conclusion, different anaerobic digester seed biomass can result in different quasi steady state function. The bioaugmentation employed can result in a period of increased methane production. In the second project, a quantitative structure activity relationship (QSAR) between anaerobic microorganism relative abundance values and digester methane production rate was developed using 150 lab-scale anaerobic digesters seeded with 50 biomass samples obtained from 49 US states. Although all digesters were operated identically for a minimum of 5 retention cycles, their quasi steady-state performance varied significantly, with the average daily methane production rate ranging from 0.09±0.004 to 0.98±0.05 L-CH4/LR-day (average ± standard deviation). Analysis of over 4.1 million-sequence reads revealed approximately 1300 operation taxonomical units (OTUs) at the genus level across all digesters, with each digester having 158±27 OTUs (mean ± standard deviation). Using Spearman’s rank correlation, 10 OTUs, which included one archaeal OTU, were found to correlate significantly to digester methane production rate. The relative abundance values of the 10 OTUs were used as descriptors to develop a multiple linear regression (MLR) equation, with good statistical prediction of the digester methane production rates. The results are encouraging and provide an initial step for further research to develop more robust QSAR models to predict the function of anaerobic and other bioprocesses using microbial community descriptors.
Bevacizumab or standard chemotherapy in previously treated patients with metastatic colorectal cancer — a systematic review

Introduction. The BRAF V600E mutation (BRAFmt) occurring in the metastatic colorectal cancer (mCRC) patients is associated with poorer prognosis, in comparison to the wild-type variant of the BRAF gene (BRAFwt). Aim of this work was to assess the clinical efficacy of bevacizumab (BEVA) or standard chemotherapy (ChT) in the 2nd or further lines of treatment in mCRC BRAFmt population. Material and methods. MEDLINE/PubMed, Embase and Cochrane CENTRAL databases were systematically searched. The reference lists of relevant studies were also checked. Results. 6 eligible trials were identified: MOMA (BEVA ± ChT), allowing for limited overall survival (OS) assessment, WJOG 6210G (BEVA + FOLFIRI), RAISE and 20050181 (FOLFIRI), PICCOLO and Spindler 2013 (irinotecan monotherapy). None of those trials were designed for the treatment evaluation in BRAFmt population. Available evidence was restricted to limited analyses in small subgroups (from a few to several dozens of patients), occasionally comprising RAS gene mutation (RASmt) as well. Based on the identified studies, the comparison of BEVA ± ChT vs. ChT or among different ChTs in BRAFmt population was not feasible. In case of BEVA (MOMA), OS hazard ratio (HR) for BRAFmt vs. BRAFwt was 1.52 (95% CI: 0.79–2.89) with difference in medians equal to 12.1 months (19.2 vs. 31.3 months, respectivelly), and BRAFmt or RASmt patients had median OS lower by 7.9 months and median progression free survival (PFS) by 3.0 months in WJOG 6210G trial. In case of ChT, median PFS was lower in BRAFmt by 12–67% (HRs range: 1.01–5.3), and median OS by 34–73% (HRs range: 1.05–5.00). Conclusions. Due to limited clinical evidence, assessment of further lines of treatment in BRAFmt mCRC patients is uncertain, however existing data consistently suggest lower effectiveness of BEVA ± ChT or ChT in BRAFmt, than in BRAFwt subgroup. Hopefully, combining anti-EGFR therapies with BRAF/MEK inhibitor is expected to improve prognosis of those patients.
Ageing behavior of electrical resistance in manganite NTC ceramics

Experimental results on thermally induced degradation tests, carried out at relatively low ageing temperature (170 C) in NTC thermistors based on Cu0.1Ni0. 8Co0.2Mn1. 9O4 spinel-structured ceramics, are discussed. It is shown the kinetics of the observed degradation processes is described mainly by well known DeBast–Gillard or Williams–Watts relaxation function, the deviations from this conclusion being observed only in multiphase ceramic samples. The inhibition effect in ageing of the investigated ceramics is observed at small concentration of additional NiO-enriched rock-salt phase. # 2003 Elsevier Ltd. All rights reserved.
Possible heterogeneity of Streptococcus milleri determined by DNA mol % (guanine plus cytosine) measurement and physiological characterization.

: DNA base pair ratios (mol % guanine + cytosine) were calculated, for eighteen strains of Streptococcus milleri, from measurements of DNA melting temperature (Tm). Strains of vaginal origin which were also 'atypical' physiologically had a value of 40.3. The two culture collection of 'minute' beta-haemolytic strains of Lancefield groups G and F had values of 36.8 and 38.8 mol%, respectively. Three other reference strains had a DNA guanine plus cytosine content ranging from 40.4 to 43.0 mol%, including Streptococcus sp MG which had a value of 42.0 mol%. Strain 7H of oral origin had a value of 40.9 mol%. The remaining physiologically typical strains, of medical origin, had guanine plus cytosine contents ranging from 36.6 to 42.1 mol%. It therefore seems possible that genetic heterogeneity may exist among representatives of Streptococcus milleri.
Cardiotoxic effects of enrofloxacin on electrophysiological activity, cardiac markers, oxidative stress, and haematological findings in rabbits

The aim of this research was to investigate the effect of normal and high doses of enrofloxacin on basal electrocardiographic (ECG) parameters including corrected QT (QTc) values along with biochemical and haematological findings in healthy rabbits. In total 21 New Zealand rabbits were used. The animals were randomly divided into three groups including 7 rabbits in each. The normal dose (5 mg/kg) of enrofloxacin and a toxic dose (50 mg/kg) were given intravenously in group 1, and the normal dose was given for 6 weeks in group 2. The last group was designated as a negative control (group 3). ECG, serum biochemistry parameters, and total antioxidant capacity (TAC) and total oxidant status (TOS) were determined every week. At the end of the experiment, necropsy was performed and histology was evaluated. Some oxidative parameters were measured in the heart tissue. No cardiotoxic effect was observed on ECG, in biochemical or haematological findings, or macroscopic or histological findings in groups 2 and 3. The results indicated that enrofloxacin is not harmful for the heart in clinically healthy rabbits at normal and toxic doses compared with the negative control group in terms of ECG, biochemical or haematological findings, or macroscopic or histological findings.
Expression and responsiveness of cytokines and their receptors in breast cancer

Chronic inflammation is a critical component in breast cancer progression. Pro-inflammatory mediators along with growth/survival factors within the tumor microenvironment potentiate enhanced expression of pro-inflammatory cytokines (IL-1, IL-6, TNF-? ), chemotactic cytokines and their receptors (CXCR4, CXCL12, CXCL8) and angiogenic factors (VEGF) that often overcome the function of anti-inflammatory molecules (IL-4, IL-10) eradicating the host? s anti-tumor immunity. Therefore detailed knowledge of the regulatory mechanisms determining cytokine levels is essential to understand the pathogenesis of several diseases including breast cancer. Activated transcription factors such as NF-? B and HIF-1? are important players for the establishment of a pro-inflammatory and potentially oncogenic environment. HIF-1? is the key mediator of the cellular response to oxygen deprivation and induces the expression of genes involved in survival and angiogenesis within solid hypoxic tumors. The expression of these genes is often modulated by the p53 tumor suppressor protein which induces apoptosis or cell cycle arrest in neoplastic cells. Functional crosstalk between HIF-1? and p53 pathways mediated by co-regulators shared between the two transcription factors such as SRC-1 and SIRT-1 differentially regulate diverse subsets of target gene expression under variable stress conditions. In an attempt to shed light in the complex regulatory mechanisms involved in cancer related inflammation, we investigated the effect of the chemotherapeutic drug etoposide, which induces p53, on the expression of inflammatory genes (CXCR4, TNF-? , IL-10) carrying hypoxia responsive elements within the regulatory regions of their promoters in breast cancer cells under hypoxia mimicking conditions. In addition, the role of two common p53 and HIF-1? co-regulators, namely SRC-1 and SIRT-1, in the expression of the highly potent metastatic chemokine receptor CXCR4 was evaluated. Both SRC-1 and SIRT-1 overexpression in DSFX treated MCF-7 cells reduced CXCR4 cellular levels implying that both co-regulators are crucial factors in the determination of the metastatic potential of breast cancer cells.
Immunoglobulin A Antibody Responses in Patients with Primary or Secondary Dengue Infections

IgM serological diagnostic plays an important role in the dengue epidemiological surveillance. However, IgA has been identified as a possible diagnostic marker for early stage and recent infections. The aim of this study was to know the IgA response in dengue patients in relation to type of infection, serotype specificity and role as early and recent infection marker. IgA behavior in dengue patients, using a method defined as Indirect Sandwich ELISA-IgA (ELISA-IgA) and Capture IgM ELISA (MAC- ELISA) as reference assay was studied. The sensibility and specificity of the system were 91.06% and 83.73% respectively. In acute phase of illness, IgA was only detected in secondary cases with 32.3%. IgM appears later than IgA in secondary cases. No significant differences in IgA or IgM responses between primary and secondary cases were found in samples collected after day 5 of onset of symptoms. In days 41-54, the percentage of IgA was lower respect to IgM. IgA was detected until day47 inprimary and until day50 insecondary cases. An elevated cross-reactivity in IgA was observed between dengue serotypes contrary to IgM. The usefulness of IgA, as alternative early diagnostic tool, could be influenced by the absence or very low percentages of positives cases in the first four days of onset of symptoms. However, for definition of secondary infection could be important. IgA could be an alternative tool, better than IgM, as recent infection marker for dengue fever, but this requires more studies in future investigations.