Miracle-dz/UniFAR-FTUs huggingface dataset:
Tandem Genetic Duplications in a Derivative of Phage Lambda

Gene duplication followed by independent evolution of the duplicated genes appears to be a basic feature of the genetics of higher organisms (see Bryson and Vogel, 1965). Such duplications are rare in Escherichia coli as judged by measurements of repeating DNA sequences (Britten and Kohne, 1968), although there are multiple copies of the ribosomal RNA genes in E. coli (Yankofsky and Spiegelman, 1962; Moore and McCarthy, 1967). There have been few studies of tandem duplications in phages. Duplications in the T4 r II region have been obtained by a strong selection technique (Weil et al., 1965; Parma and Ingraham, 1970). We have found that many of the spontaneous “revertants” of the deletion mutant t del 33 (Franklin, 1967) are duplication mutants, with changes at different locations on the phage chromosome. This phage has many advantages for studying the properties and mechanism of formation of duplication mutants. Some advantages which we have exploited in the present work are as follows. (1) Since the base sequence in 80- λ hy 1 DNA is nonpermuted and the phage chromosome can be extracted as a DNA molecule of definite length, a duplication mutant can be identified as such and the end points of the duplicated segment can be located by electron microscopy of DNA heteroduplexes. (2) The dependence of phage buoyant density on DNA length provides a nonspecific selection method for mutants which have longer DNA molecules. (Selection by plaque morphology is also possible in many cases.) (3) An independent method of identifying duplication mutants is based.
Serum Glucose, Lipid Profile and Oxidative Stress Markers of Salt-induced Metabolic Syndrome Rats Administered Antioxidant Rich Nutraceutical

collaboration between all Author NL designed the experiment, performed the statistical analysis and interpreted the results. Author ASI administered the diets and charge of the literature search of the first All biochemical analysis, ABSTRACT Metabolic syndrome is indeed a high risk condition involving obesity, dyslipidemia, hypertension and diabetes mellitus. The study aim to formulate an antioxidant rich nutraceutical from locally available foodstuff (onion, garlic, ginger, tomato, lemon, palm oil, water melon seeds) and investigate their effects on body weight, serum glucose, lipid profile, insulin and oxidative stress markers in salt induced metabolic syndrome rats. The rats were placed on 8% salt diet for 6 weeks and then supplementation and treatment with nutraceutical and nifedipine in the presence of salt diet for additional 4 weeks. Feeding rats with salt diet for 6 weeks increased body weight of the salt-loaded rats relative to control. Significant (P<0.001) increase in serum blood glucose and lipid profile, and decrease in high density lipoprotein-cholesterol (HDL-C) was observed in salt-loaded rats as compared with control. Supplementation with nutraceutical lowered body weight of the salt-loaded rats and significant (P<0.001) decrease in the serum blood glucose, lipid profile, malonyldialdehyde (MDA), insulin levels, insulin resistance, and increased HDL-C and antioxidant indices was observed. The study suggests that the nutraceuticals are useful in reversing most of the component of metabolic syndrome.
PCR Protocols in Molecular Toxicology

Basics of the Polymerase Chain Reaction, W.B. Mattes Analysis of Gene Expression, J.P. Vanden Heuvel Differential Display PCR, J.C. Corton Cloning by PCR, J.P. Vanden Heuvel Genotype Analysis, D.A. Bell and G. Pittman General Molecular Biology Techniques, J.P. Vanden Heuvel Appendix I: List of Suppliers Appendix II: Companies, Online Catalogs, and Internet Resources Index
Characterization and consequences of telomere replication gone awry

Telomeres, the ends of linear eukaryotic chromosomes, pose several unique challenges to genome stability. My thesis work is concerned with the difficulties the replication machinery encounters when attempting to replicate telomeres, and with possible consequences of defects in telomere replication. The relevance of the DNA replication machinery precipitated while characterizing fission yeast cells lacking the telomeric binding protein Taz1 (a homologue of mammalian TRF1 & 2). In the absence of Taz1, replication forks stall when encountering telomeric sequences, leading to telomere breakage and loss. This unanticipated function of the telomeric complex suggests that telomeric sequences pose an obstacle to the replication machinery. Indeed, further experiments suggested that any repeated sequence has a propensity to cause replication fork stalling, suggesting that our findings may also be applicable to other parts of the genome. Challenges to semi-conservative replication in cells lacking Taz1 are likely to be the underlying cause of another taz1Δ-specific phenomenon: telomere entanglement and loss of viability occurring specifically at cold temperatures. Screening for suppressors of this phenotype led to the identification of two additional factors involved in the etiology of dysfunctional telomeres: the post- translational modification SUMO, and the fission yeast member of the conserved RecQ helicase family, Rqh1. A novel sumoylation deficient allele of Rqh1 was able to suppress several taz1Δ-specific phenomena without dramatically affecting other genome-wide functions of Rqh1. Interestingly, genetic analysis revealed that this allele acts in a loss-of-function manner, suggesting that Rqh1 activity is detrimental for taz1Δ telomeres. Our findings underscore the significance of telomere-specific regulation, as Rqh1, and many other factors participating in telomere metabolism, are not exclusive to telomeres.
Bartonella Clarridgeiae: Invasion of Human Microvascular Endothelial Cells and Role of Flagella in Virulence

B. henselae, B. bacilliformis and B. quintana are capable of causing vasoproliferative diseases in humans by modulating apoptosis and proliferation of endothelial cells. Bartonella clarridgeiae, a close relative of the pathogenic Bartonellae, has been implicated in human disease but has not yet been isolated from a human patient. Both B. bacilliformis and B. clarridgeiae have flagella and a flagellar type 3 secretion system, while B. henselae and B. quintana do not. We created 2 non-motile mutants of B. clarridgeiae by interrupting the flagellin gene, flaA, or the flagellar motor genes, motBC. We investigated whether B. clarridgeiae could invade human endothelial cells (HMECs) and if functional flagella were important for invasion. The non-motile mutants and the wild-type strain were capable of entering HMECs in vitro. The flaA mutant was deficient in attachment, but the HMECs in culture with the flaA mutant demonstrated increased proliferation. The motBC mutant showed enhanced invasion. Differential secretion of proteins was revealed by 2-D electrophoresis and MALDI-TOF analysis of secretomes from the co-cultures compared to uninfected HMECs. HMECS infected with wild-type B. clarridgeiae secreted proteins indicative of proliferation. The flaA mutant induced the secretion of proteins involved in cytoskeletal rearrangement, cell migration, and proliferation. The motBC-infected HMECs showed signs of hypoxia. The co-chaperonin GroES was found in higher concentration in the supernatant of the hyper-invasive motBC strain/HMEC co-culture than the wild-type co-culture and was found at a very low concentration in the flaA culture supernatant. Cross-talk between secretion systems is
Peptide mimics targeting bacterial membranes

In recent years, society has been increasingly concerned with bacteria that are no longer susceptible to commercial antibiotics. Faced with a lack of tools, medical practitioners today are forced to prescribe medicines that, although effective, cause as much harm to the patient as the principal infection. The purpose of this research project is to develop novel antibacterials that remain potent against bacterial infections without being toxic to the patient.
Investigating the effects of increased levels of the translation elongation factor eEF1A within eukaryotic cells

The highly conserved eukaryotic elongation factor 1A (eEF1A) plays a canonical role in translation elongation, where it is responsible for delivering the aminoacylated tRNA to the A-site of the 80S ribosome. Further to this essential role it is reported to be involved in a plethora of moonlighting functions that are not fully characterised or understood. One of the human isoforms, eEF1A2, is known to induce cancer when expressed in non-native tissues, although the mechanism by which it promotes tumour growth is not yet known. In this study we have characterised eEF1A overexpression in yeast and provided evidence to suggest that elevated levels of eEF1A result spindle defects which lead to chromosomal abnormalities that have the potential to induce uncontrolled cell growth in human cells. Moreover, we have confirmed conservation of this chromosomal abnormality in human cell lines suggesting that the mechanism that eEF1A utilises to induce these effects are highly conserved. We have also observed that in yeast, eEF1A overexpression results in increased metabolic activity, a hallmark of cancer cells. We hypothesise that eEF1A interacts with the dynactin complex, a regulator of spindle dynamics, resulting in aberrant spindle formation. This in turn leads to chromosomal abnormalities that appear toxic to the cell. Cells appear to overcome the toxicity induced by eEF1A by suppressing plasmid copy number to the lowest levels possible. This however, brings its own problems and appears to result in synthetic effects together with eEF1A overexpression.
RNA Sequencing and Quantitation Using Targeted Amplicons

As Next Generation Sequencing matures, it is quickly moving into translational research applications where it has promise to be a useful tool for diagnosing and treating in a clinical setting. RNA profiling using NGS (RNA-seq) is one of the applications where this potential is currently being realized. RNA-seq experiments have traditionally started with a whole-transcriptome library preparation that produces a sequencing template from all RNA species in a sample. However, in many cases, only a handful of the genes present are necessary to make a clinically relevant diagnosis. We have demonstrated new technology that allows for RNA-seq from a panel of directed amplicons using an AmpliSeq™ approach with Ion Torrent semiconductor sequencing. This approach offers many advantages over microarray or qPCR such as faster turnaround and data analysis, sample multiplexing, lower RNA inputs, and ability to use degraded or FFPE-derived samples. In addition, the technique simultaneously provides quantitative gene expression information and gene sequence at the single nucleotide level. We have compiled three gene panels for testing the method including a cancer panel, apoptosis panel, and a panel derived from the Micro Array Quality Control (MAQC) consortium. Starting with 10ng of total RNA, cDNA is made, followed by amplification using primers designed for targeted genes. Resulting amplicons are prepared for sequencing using the AmpliSeqTM technology and sequenced on the Ion Torrent PGM. We demonstrate that the technique produces results that are technically reproducible, quantitative, and have excellent correlation with qPCR using TaqMan® assays. Employing barcodes, we have also tested multiple samples on a single chip thereby increasing the cost-effectiveness of the tool for clinical and research use.
Effectiveness of Reality Therapy in the Treatment of Bullying among Adolescents in Owerri North, Imo State, Nigeria

Aims: This study aimed at treating bullying behaviours among adolescents using reality therapy. It also investigated age as a factor in treatment outcome. Considering the prevalence of bullying among adolescents and the link between bullying in adolescence and violent behaviours like rape in adulthood this study was conducted. Study Design: It adopted a pre-test and post-test repeated measures design. Place and Duration of Study: The study participants were selected from junior and senior Secondary sections of Comprehensive Secondary School Amakohia, in Uratta, Owerri, Imo State, Nigeria. The study lasted for two (2) months of two counselling sessions per week. Original Research Article Madukwe et al.; BJESBS, 15(4): 1-8, 2016; Article no.BJESBS. 26093 2 Methodology: Thirty (30) participants (15males and 15 females) within the age bracket of 13-17 years, mean age of 15.03 and standard deviation (SD) of 1.30 were selected for the study using purposive sampling technique. Two hypotheses were stated and tested. Questionnaire was shared to selected students to assess the nature and frequency of their bullying behaviour (pre-test), after which sixteen (16) sessions of reality therapy were conducted before the post-test using the same questionnaire. Results: At the significant level of P < . 001 a clear difference was noticed in the rate of bullying between pre-test (m = 31.63) and post-test (m = 11.47) of bullies as shown in the result (t (29) = 31.09, P < . 001). The mean scores of age groups did not differ significantly at the pretest (Age >= 15, M = 31.53; Age < 15, M = 31.82) and post-test (Age >= 15, M = 11.26; Age < 15, M = 11.82) no significant difference was found in treatment outcome as shown in the result (t (28) = -. 39, P > . 05). Conclusion: This study concluded that reality therapy should be adopted in the management of bullying behaviour among young and old adolescents.
Interaction between diatoms and bacteria in the biofilm of the River Danube

The biofilms were investigated on surfaces of artificial substrata (glass microscope slides) submerged into the River Danube at the NE part of Szentendre Island. The collected biofilm samples were plated on two different diatom media. Diatoms were isolated and identified by scanning electron microscope from biofilm samples. Bacterial strains were isolated from surfaces of cultivated diatoms. The laboratory cultures and original gravel samples of the River Danube were similary examined by scanning electron microscope in order to determine the characteristic partner sin diatombacterial interactions. The studies have shown that bacteria with extracellular fibers attached to each pther and to the diatoms. Specific (molecular level) interactions between bacteria and diatoms were also investigated.
Financial Inclusion and Income Inequality: A Case Study of Selected Countries in Sub-Saharan Africa

This paper looks at the impact of financial inclusion on income inequality in subSaharan Africa. Very few studies exist on this theme for African countries. The empirical testing is done using data for a select number of sub-Saharan African countries. Data on financial inclusion are disaggregated into formal and informal financial inclusion. The hypothesis is that in Africa, it is improvements in formal financial inclusion that are likely to have a wholesome impact on inequality reduction. The methodology used to test the hypothesis is the calculation of the Concentration Index using Convenient Covariance and Convenient Regression. This methodology which was originally developed in a World Bank study on health equity is being applied for the first time to analyse the relationship between financial inclusion and income inequality.
Entanglement transition from variable-strength weak measurements

We show that weak measurements can induce a quantum phase transition of interacting many-body systems from an ergodic thermal phase with a large entropy to a nonergodic localized phase with a small entropy, but only if the measurement strength exceeds a critical value. We demonstrate this effect for a one-dimensional quantum circuit evolving under random unitary transformations and generic positive operator-valued measurements of variable strength. As opposed to projective measurements describing a restricted class of open systems, the measuring device is modeled as a continuous Gaussian probe, capturing a large class of environments. By employing data collapse and studying the enhanced fluctuations at the transition, we obtain a consistent phase boundary in the space of the measurement strength and the measurement probability, clearly demonstrating a critical value of the measurement strength below which the system is always ergodic, irrespective of the measurement probability. These findings provide guidance for quantum engineering of many-body systems by controlling their environment.
Do troublesome pupils impact teacher perception of the behaviour of their classmates?

Abstract The widely supported wish for more inclusive education places ever greater expectations on teachers’ abilities to teach all children, including those with special needs and challenging behaviours. The present study aimed at the question whether teachers judge pupil behaviour more negatively if there are more children with difficult behaviour in class. The teachers of 184 classes in 31 regular primary schools were asked to complete the Strength and Difficulties Questionnaire (SDQ-L) for 3649 pupils. Six linear mixed models were carried out with as independent variable the number of pupils that teachers perceived to have ‘abnormal behaviour’, and the class mean without these pupils as the dependent variable. For all SDQ-L subscales – emotional problems, behavioural problems, problems with hyperactivity, problems with peers, poor prosocial behaviour and total problems – the number of pupils perceived as problematic was associated with less favourable teacher perceptions of the rest of the class. The results of this study are a plea for a contextual perspective on pupil behaviour in class, both where teachers are asked to report on individual pupils, as well as where interventions are done on emotional and behavioural problems in class.
Enantioselective synthesis of vicinal (R,R)-diols by yeast butanediol dehydrogenase

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Enantioselective synthesis of vicinal (R,R)-diols by yeast butanediol dehydrogenase Eduard Calam, Eva González-Roca, M Rosario Fernández, Sylvie Dequin, Xavier Parés, Albert Virgili, Josep A Biosca
From Reductive to Robust: Seeking the Core of Complex Adaptive Systems Theory

This chapter seeks to identify the core of complex adaptive systems (CAS) theory. To achieve this end, this chapter introduces innovative methods for measuring and advancing the validity of a theory by understanding the structure of theory. Two studies of CAS theory are presented that show how the outer belt of atomistic and loosely connected concepts support the evolution of a theory; while, in contrast, the robust core of theory, consisting of co-causal propositions, supports the validity and testability of a theory. Each may be seen as being derived from differing epistemologies. It is hoped that the tools presented in this chapter will be used to support the purposeful evolution of theory by improving the validity of intelligent complex adaptive systems (ICAS) theory. IGI PUBLISHING This paper appears in the publication, Intelligent Complex Adaptive Systems edited by A. Yang and Y. Shan © 2008, IGI Global 701 E. Chocolate Avenue, Suite 200, Hershey PA 17033-1240, USA Tel: 717/533-8845; Fax 717/533-8661; URL-http://www.igi-global.com ITB15289
Contributions Mechanical Engineering 1-1-2016 Spaceflight Activates Lipotoxic Pathways in Mouse Liver

Spaceflight affects numerous organ systems in the body, leading to metabolic dysfunction that may have long-term consequences. Microgravity-induced alterations in liver metabolism, particularly with respect to lipids, remain largely unexplored. Here we utilize a novel systems biology approach, combining metabolomics and transcriptomics with advanced Raman microscopy, to investigate altered hepatic lipid metabolism in mice following short duration spaceflight. Mice flown aboard Space Transportation System -135, the last Shuttle mission, lose weight but redistribute lipids, particularly to the liver. Intriguingly, spaceflight mice lose retinol from lipid droplets. Both mRNA and metabolite changes suggest the retinol loss is linked to activation of PPARα-mediated pathways and potentially to hepatic stellate cell activation, both of which may be coincident with increased bile acids and early signs of liver injury. Although the 13-day flight duration is too short for frank fibrosis to develop, the retinol loss plus changes in markers of extracellular matrix remodeling raise the concern that longer duration exposure to the space environment may result in progressive liver damage, increasing the risk for nonalcoholic fatty liver disease.
) ClpP 1 and ClpP 2 Function Together in Protein Degradation and are Required for Viability \ ( in \ ) \ ( vitro \ ) and During Infection

In most bacteria, Clp protease is a conserved, non-essential serine protease that regulates the response to various stresses. Mycobacteria, including Mycobacterium tuberculosis (Mtb) and Mycobacterium smegmatis, unlike most well studied prokaryotes, encode two ClpP homologs, ClpP1 and ClpP2, in a single operon. Here we demonstrate that the two proteins form a mixed complex (ClpP1P2) in mycobacteria. Using two different approaches, promoter replacement, and a novel system of inducible protein degradation, leading to inducible expression of clpP1 and clpP2, we demonstrate that both genes are essential for growth and that a marked depletion of either one results in rapid bacterial death. ClpP1P2 protease appears important in degrading missense and prematurely terminated peptides, as partial depletion of ClpP2 reduced growth specifically in the presence of antibiotics that increase errors in translation. We further show that the ClpP1P2 protease is required for the degradation of proteins tagged with the SsrA motif, a tag co-translationally added to incomplete protein products. Using active site mutants of ClpP1 and ClpP2, we show that the activity of each subunit is required for proteolysis, for normal growth of Mtb in vitro and during infection of mice. These observations suggest that the Clp protease plays an unusual and essential role in Mtb and may serve as an ideal target for antimycobacterial therapy. Citation: Raju RM, Unnikrishnan M, Rubin DHF, Krishnamoorthy V, Kandror O, et al. (2012) Mycobacterium tuberculosis ClpP1 and ClpP2 Function Together in Protein Degradation and Are Required for Viability in vitro and During Infection. PLoS Pathog 8(2): e1002511. doi:10.1371/journal.ppat. 1002511 Editor: Sabine Ehrt, Weill Medical College of Cornell University, United States of America Received May 30, 2011; Accepted December 14, 2011; Published February 16, 2012 Copyright: 2012 Raju et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the National Institute of Allergy and Infectious Disease grant R01 AI071881 (EJR), the National Institute of General Medical Sciences grant R01 GM51923 (ALG), a Harvard Catalyst Pilot Grant, and a grant to Cornell University by the Bill and Melinda Gates Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: erubin@hsph.harvard. edu . These authors contributed equally to this work.