Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and characterization of cutE, a gene involved in copper transport in Escherichia coli

The copper-sensitive/temperature-sensitive phenotype of the Escherichia coli cutE mutant has been complemented by cloning wild-type genomic DNA into the plasmid vector pACYC184 and selecting transformants on medium containing 4 mM copper sulfate and chloramphenicol. One of these complementing clones, designated pCUT1, contained a 5.6-kb BamHI fragment. This recombinant plasmid transformed cutE, allowing wild-type growth of transformants on medium containing copper sulfate. Complementation of copper sensitivity was assessed by comparing both cell survival at increased copper levels and the results of 64Cu accumulation assays. An EcoRI subclone, 2.3 kb in size, was also shown to complement cutE when cloned in both medium- and high-copy-number vectors and was completely sequenced. This clone was mapped on the E. coli physical map at 705.70 to 707.80 kb. A series of subclones was constructed from pCUT1 and used to show that the large open reading frame of the translated sequence was essential for complementation. This open reading frame has a potential upstream promoter region, ribosome-binding site, and transcriptional terminator and encodes a putative protein of 512 amino acids that contains a region showing some homology to a putative copper-binding site.
Chondroitin sulfate disrupts axon pathfinding in the optic tract and alters growth cone dynamics.

Little is known about the cues that guide retinal axons across the diencephalon en route to their midbrain target, the optic tectum. Here we show that chondroitin sulfate proteoglycans are differentially expressed within the diencephalon at a time when retinal axons are growing within the optic tract. Using exposed brain preparations, we show that the addition of exogenous chondroitin sulfate results in retinal pathfinding errors. Retinal axons disperse widely from their normal trajectory within the optic tract and extend aberrantly into inappropriate regions of the forebrain. Time-lapse analysis of retinal growth cone dynamics in vivo shows that addition of exogenous chondroitin sulfate causes intermittent stalling and increases growth cone complexity. These results suggest that chondroitin sulfate may modulate the guidance of retinal axons as they grow through the diencephalon towards the optic tectum.
Prevention and Induction of Autoimmune Exocrinopathy Is Dependent on Pathogenic Autoantigen Cleavage in Murine Sjögren’s Syndrome1

The in vivo role of autoantigen cleavage during apoptosis in autoimmune diseases remains unclear. Previously, we found a cleavage product of 120-kDa α-fodrin as an important autoantigen in the pathogenesis of primary Sjögren’s syndrome (SS). In the murine primary SS model, tissue-infiltrating CD4+ T cells purified from the salivary glands bear a large proportion of Fas ligand, and the salivary gland duct cells constitutively possess Fas. Infiltrating CD4+ T cells, but not CD8+ T cells, identified significant 51Cr release against mouse salivary gland cells. In vitro studies demonstrated that apoptotic mouse salivary gland cells result in a specific α-fodrin cleavage into 120 kDa and that preincubation with caspase inhibitor peptides blocked α-fodrin cleavage. In vivo treatment with caspase inhibitors N-benzyloxycarbonyl-Val-Ala-Asp fluoromethyl ketone and N-acetyl-Asp-Glu-Val-Asp-al-CHO into the murine model results in dramatic inhibitory effects on the development of autoimmune lesions and in restoration of sicca syndrome. Furthermore, we found that immunization with recombinant α-fodrin protein identical with an autoantigen into normal recipients induced autoimmune lesions similar to SS. These data indicate that prevention and induction of autoimmune exocrinopathy is dependent on autoantigen cleavage via caspase cascade and that caspase inhibitors might provide a new therapeutic option directed at reducing tissue damage in the murine model for SS.
The complexity of outsourced services and the role of international business travel

We hypothesize that face-to-face communication between international business partners is a valuable mechanism for reducing transaction costs, even in contexts where electronic communication is pervasive. Specifically, we examine whether face-to-face interactions (as measured by international business travel) have greater impacts where transaction costs are higher, e.g., where services with greater complexity are outsourced offshore. Matching data from the Survey of International Air Travelers with Bureau of Economic Analysis data on U.S. service outsourcing, we find that international business travel leads to more outsourcing of more complex services. We further provide evidence on the differential role of international business travel by showing that: (i) business travel by managers leads to relatively more outsourcing of more complex services and (ii) business travel by non-diaspora members leads to relatively more outsourcing of more complex services.
RACK1 Recruits STAT3 Specifically to Insulin and Insulin-Like Growth Factor 1 Receptors for Activation, Which Is Important for Regulating Anchorage-Independent Growth

ABSTRACT Current understanding of the activation of STATs is through binding between the SH2 domain of STATs and phosphotyrosine of tyrosine kinases. Here we demonstrate a novel role of RACK1 as an adaptor for insulin and insulin-like growth factor 1 receptor (IGF-1R)-mediated STAT3 activation specifically. Intracellular association of RACK1 via its N-terminal WD domains 1 to 4 (WD1-4) with insulin receptor (IR)/IGF-1R is augmented upon respective ligand stimulation, whereas association with STAT3 is constitutive. Purified RACK1 or RACK1 WD1-4 associates directly with purified IR, IGF-1R, and STAT3 in vitro. Insulin induces multiprotein complex formation of RACK1, IR, and STAT3. Overexpression or downregulation of RACK1 greatly enhances or decreases, respectively, IR/IGF-1R-mediated activation of STAT3 and its target gene expression. Site-specific mutants of IR and IGF-1R impaired in RACK1 binding are ineffective in mediating recruitment and activation of STAT3 as well as in insulin- or IGF-1-induced protection of cells from anoikis. RACK1-mediated STAT3 activation is important for insulin and IGF-1-induced anchorage-independent growth in certain ovarian cancer cells. We conclude that RACK1 mediates recruitment of STAT3 to IR and IGF-1R specifically for activation, suggesting a general paradigm for the need of an adaptor in mediating activation of STATs by receptor protein tyrosine kinases.
Protein folding mechanisms and the multidimensional folding funnel

An important idea that emerges from the energy landscape theory of protein folding is that subtle global features of the protein landscape can profoundly affect the apparent mechanism of folding. The relationship between various characteristic temperatures in the phase diagrams and landmarks in the folding funnel at fixed temperatures can be used to classify different folding behaviors. The one‐dimensional picture of a folding funnel classifies folding kinetics into four basic scenarios, depending on the relative location of the thermodynamic barrier and the glass transition as a function of a single‐order parameter. However, the folding mechanism may not always be quantitatively described by a single‐order parameter. Several other order parameters, such as degree of secondary structure formation, collapse and topological order, are needed to establish the connection between minimalist models and proteins in the laboratory. In this article we describe a simple multidimensional funnel based on two‐order parameters that measure the degree of collapse and topological order. The appearance of several different “mechanisms” is illustrated by analyzing lattice models with different potentials and sequences with different degrees of design. In most cases, the two‐dimensional analysis leads to a classification of mechanisms totally in keeping with the one‐dimensional scheme, but a topologically distinct scenario of fast folding with traps also emerges. The nature of traps depends on the relative location of the glass transition surface and the thermodynamic barrier in the multidimensional funnel. Proteins 32:136–158, 1998. © 1998 Wiley‐Liss, Inc.
Control of neuronal synapse specification by a highly dedicated alternative splicing program

Synapse identity through specific splicing What are the mechanisms that create different, highly specific types of synapses? Traunmüller et al. found that the RNA-binding protein SLM2 regulated a very small number of alternative splicing decisions in mouse hippocampal neurons. Disrupting this splicing program resulted in specific defects in transsynaptic protein complexes. Glutamatergic transmission and synaptic plasticity were impaired. Genetically restoring one single alternative splicing event was enough to recover synaptic plasticity. SLM2 thus activates a highly specific alternative splicing program that controls the properties of glutamatergic synapses. Science, this issue p. 982 The RNA binding protein SLM2 directs the splice isoform identity of synaptic recognition receptors. Alternative RNA splicing represents a central mechanism for expanding the coding power of genomes. Individual RNA-binding proteins can control alternative splicing choices in hundreds of RNA transcripts, thereby tuning amounts and functions of large numbers of cellular proteins. We found that the RNA-binding protein SLM2 is essential for functional specification of glutamatergic synapses in the mouse hippocampus. Genome-wide mapping revealed a markedly selective SLM2-dependent splicing program primarily consisting of only a few target messenger RNAs that encode synaptic proteins. Genetic correction of a single SLM2-dependent target exon in the synaptic recognition molecule neurexin-1 was sufficient to rescue synaptic plasticity and behavioral defects in Slm2 knockout mice. These findings uncover a highly selective alternative splicing program that specifies synaptic properties in the central nervous system.
GTP hydrolysis by ADP-ribosylation factor is dependent on both an ADP-ribosylation factor GTPase-activating protein and acid phospholipids.

ADP-ribosylation factor (ARF) is a 21-kDa GTP binding protein that regulates eukaryotic membrane traffic. Both the binding and hydrolysis of GTP by ARF have been shown to be necessary for this function. However, purified mammalian ARF lacks intrinsic GTPase activity (< 0.0015 min-1). We document the presence, in bovine brain extracts, of a protein with the predicted properties for an ARF GTPase-activating protein (ARF GAP). This activity was highly dependent on phospholipids. An acid phospholipid fraction from bovine brain (containing primarily phosphatidylinositol 4,5-bisphosphate (PIP2), phosphatidylinositol 4-phosphate, phosphatidylinositol, and phosphatidylserine) had no effect on intrinsic GTPase activity of purified ARF but increased the ARF GAP activity of bovine brain homogenates about 8-fold. This dependence on acid phospholipids was retained after > 100-fold purification of ARF GAP, making it, likely, an inherent property of this reaction. PIP2 alone stimulated ARF GAP activity up to 30-fold with a half-maximal effect at 100-300 microM but had no effect on the GTPase rate of ARF alone. Phosphatidylinositol 4-phosphate was also active but had only 50% of the maximal effect and twice the EC50 of PIP2. Phosphatidylserine, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, and diacylglycerol either alone or in the presence of ARF GAP do not stimulate ARF GTPase activity. ARF proteins have been identified recently as regulators of phospholipase D. The product of the phospholipase D reaction, phosphatidic acid, stimulated ARF GAP approximately 5-fold and reduced the PIP2 concentration needed for GAP stimulation about 6-fold. The substrate of phospholipase D, phosphatidylcholine, inhibited ARF GAP activity, but this inhibition seen with phosphatidylcholine was partially reversed by phosphatidic acid. A feedback loop for the coordinate regulation of phospholipase D and ARF activities is proposed.
COLONIAL AND POST-COLONIAL SECONDARY SCHOOLS: ANALYSING FACTORS ACCOUNTING FOR DIFFERENT O’ LEVEL ACADEMIC ATTAINMENT TRENDSHARARE (2005-2010)

Educational reforms introduced at Zimbabwe’s attainment of independence resulted in the emergence of two types of schools: those established prior to attainment of independence and those established after. Ever since, there has been a common trend in the results from the two types of schools. The trend has been that the learners in schools established after attainment of independence have been and are still performing poorly when compared to those in schools established prior to attainment of independence despite the fact that they were and are still controlled by the same government and responsible authorities; they follow the same curriculum; get teachers from the same institutions; and come from similar backgrounds and environments. This prompted the primary researcher, who shall herein be referred to as the researcher, to carry out an analysis of the factors accounting for the different academic attainment trends by O’ level learners in the two types of schools in high density areas of Harare including Chitungwiza. The research was based on O’ level examination results for the period between the year 2005 and 2010. The research paradigm was quantitative and the design was a survey carried out in nine schools established prior to attainment of independence and ten schools established after attainment of independence. The major research instruments were questionnaires which the researcher administered in person. Presentation of data was done in form of statistical tables, graphs and pie charts. After respondent and factor analysis, major factors accounting for the different academic attainment trends established were as follows: Form one enrolment criteria; availability or unavailability of library and laboratory facilities in the schools; streaming of learners according to ability; extra lessons and vacation school; class sizes; parental support for children’s education. The researcher then made the following recommendations: That the stakeholders of the secondary schools established after attainment of independence should make some effort to complete construction of these schools; there is need to establish whether or not primary schools are producing results good enough at Grade seven to feed into the secondary school system; each school in the high density areas of Harare should have in place a library and laboratory; there is need for the ministry responsible for secondary education to seriously consider and implement the recommendations made by the Nziramasanga commission.
Design of Depression in Alzheimer's Disease Study-2.

OBJECTIVE Research on the efficacy of antidepressant therapy for depressive symptoms in Alzheimer disease has been hampered by lack of systematic diagnosis, small sample sizes, and short-term follow up. To address these issues, the authors present the design of the Depression in Alzheimer's Disease Study-2 (DIADS-2), a randomized, placebo-controlled multicenter trial to evaluate the efficacy and safety of the selective serotonin reuptake inhibitor sertraline for the treatment of depression in people with Alzheimer disease. METHODS The authors present and discuss the following important aspects of the design: the inclusion of structured psychosocial therapy for the caregivers of all participants; the measurement not only of patient mood outcomes, but also of global and functional outcomes for patients and mood and burden outcomes for caregivers; the ongoing rating of multiple diagnostic criteria to allow nosologic study of depression in Alzheimer disease; the evaluation of both short-term efficacy and longer-term outcomes; the follow up of all patients regardless of whether they complete study treatment; and the unmasking of treatment assignment at the conclusion of each patient's treatment phase. CONCLUSIONS The authors believe these design elements are important features to be included in trials of depression and other neuropsychiatric disturbances in Alzheimer disease.
Pbp1 Is Involved in Ccr4- and Khd1-Mediated Regulation of Cell Growth through Association with Ribosomal Proteins Rpl12a and Rpl12b

ABSTRACT The Saccharomyces cerevisiae Pbp1 [poly(A)-binding protein (Pab1)-binding protein] is believed to be involved in RNA metabolism and regulation of translation, since Pbp1 regulates a length of poly(A) tail and is involved in stress granule (SG) formation. However, a physiological function of Pbp1 remains unclear, since the pbp1Δ mutation has no obvious effect on cell growth. In this study, we showed that PBP1 genetically interacts with CCR4 and KHD1, which encode a cytoplasmic deadenylase and an RNA-binding protein, respectively. Ccr4 and Khd1 modulate a signal from Rho1 in the cell wall integrity pathway by regulating the expression of RhoGEF and RhoGAP, and the double deletion of CCR4 and KHD1 confers a severe growth defect displaying cell lysis. We found that the pbp1Δ mutation suppressed the growth defect caused by the ccr4Δ khd1Δ mutation. The pbp1Δ mutation also suppressed the growth defect caused by double deletion of POP2, encoding another cytoplasmic deadenylase, and KHD1. Deletion of the gene encoding previously known Pbp1-interacting factor Lsm12, Pbp4, or Mkt1 did not suppress the growth defect of the ccr4Δ khd1Δ mutant, suggesting that Pbp1 acts independently of these factors in this process. We then screened novel Pbp1-interacting factors and found that Pbp1 interacts with ribosomal proteins Rpl12a and Rpl12b. Similarly to the pbp1Δ mutation, the rpl12aΔ and rpl12bΔ mutations also suppressed the growth defect caused by the ccr4Δ khd1Δ mutation. Our results suggest that Pbp1 is involved in the Ccr4- and Khd1-mediated regulation of cell growth through the association with Rpl12a and Rpl12b.
Trade openness and economic development in the UAE: an asymmetric approach

Purpose The purpose of this paper is to offer a review of the trade policy in the UAE. It also investigates the dynamic interaction between trade openness and GDP per capita in this emerging economy. Design/methodology/approach The asymmetric generalized impulse response functions and the asymmetric causality tests developed by Hatemi-J are used. Findings The results from asymmetric generalized impulse response functions indicate that a positive permanent shock in the trade openness results in a significant positive response in the cumulative sum of the positive component of the GDP per capita. Such a response is not found for the negative shocks in the trade openness. Furthermore, neither a positive nor a negative shock in the GPD per capita results in any significant response in the trade openness. These empirical findings are also supported by the implemented asymmetric causality tests. Originality/value This is the first attempt that investigates the impact of trade openness on economic performance in the UAE. Unlike previous literature on the topic, this paper allows for asymmetric impacts in the empirical model.
Introduction: Independence, global entanglement and the co-production of sovereignty

In September 2014 the residents of Scotland went to the polls to decide whether they would remain a part of the United Kingdom or forge a separate course as an independent state. A year later, at the University of St. Andrews, a group of scholars, not only from Scotland but from across the world, met to engage in a broader discussion of independence.1 The idea for the workshop arose from a number observations regarding the impact of the larger national, regional and international context on the Scottish referendum campaign. The numerous comparisons generated in the global media to other independence campaigns, ranging from Quebec and Catalonia to Kosovo, Tibet, Hong Kong and Kashmir, as well as historically to the United States, Africa or Ireland, among others, were a further inspiration. The scholarly contributions raised conceptual questions about what it means to be ‘independent’ in a deeply entangled global space, comprised of multiple and intersecting legal and political regimes, as well as the political, cultural and constitutional implications of re-imagining these relationships. The wide variety of cases and theoretical approaches together demonstrated that traditional grammars of the right to self-determination are increasingly unable to either understand or respond appropriately to the challenges of state-building and state-fragmentation at the beginning of the twenty-first century. This special issue draws on a selection of papers from the interdisciplinary workshop, which related to international law and international relations. While building on broader concerns raised during the workshop, the contributions here focus more explicitly on a question of how intersecting
Laboratory security and emergency response guidance for laboratories working with select agents. Centers for Disease Control and Prevention.

In recent years, concern has increased regarding use of biologic materials as agents of terrorism, but these same agents are often necessary tools in clinical and research microbiology laboratories. Traditional biosafety guidelines for laboratories have emphasized use of optimal work practices, appropriate containment equipment, well-designed facilities, and administrative controls to minimize risk of worker injury and to ensure safeguards against laboratory contamination. The guidelines discussed in this report were first published in 1999 (U.S. Department of Health and Human Services/CDC and National Institutes of Health. Biosafety in microbiological and biomedical laboratories [BMBL]. Richmond JY, McKinney RW, eds. 4th ed. Washington, DC: US Department of Health and Human Services, 1999 [Appendix F]). In that report, physical security concerns were addressed, and efforts were focused on preventing unauthorized entry to laboratory areas and preventing unauthorized removal of dangerous biologic agents from the laboratory. Appendix F of BMBL is now being revised to include additional information regarding personnel risk assessments, and inventory controls. The guidelines contained in this report are intended for laboratories working with select agents under biosafety-level 2, 3, or 4 conditions as described in Sections II and III of BMBL. These recommendations include conducting facility risk assessments and developing comprehensive security plans to minimize the probability of misuse of select agents. Risk assessments should include systematic, site-specific reviews of 1) physical security; 2) security of data and electronic technology systems; 3) employee security; 4) access controls to laboratory and animal areas; 5) procedures for agent inventory and accountability; 6) shipping/transfer and receiving of select agents; 7) unintentional incident and injury policies; 8) emergency response plans; and 9) policies that address breaches in security. The security plan should be an integral part of daily operations. All employees should be well-trained and equipped, and the plan should be reviewed annually, at least.
A People-Centred Approach to Heritage: The Experience of the Heritage Lottery Fund 1994–2014

The strategic development of the Heritage Lottery Fund (HLF) from 1994 has demonstrated an increasing emphasis on pubic engagement and benefit. This paper uses evidence from HLF's evaluation and review work, along with my personal experience, to demonstrate how that increasing emphasis on people was achieved. It argues that it is this role of being a Lottery funder—with an imperative to deliver public benefit—that has been the most important factor in driving the organization's progression. The paper then assesses the limitations of HLF's people focussed approach, and the challenges it faces in more straitened financial times. I offer the paper, not from the standpoint of an academic, but as the personal perspective of a heritage professional employed at the Fund since 2004.