Notre Dame of Dadiangas University

The recently completed Caenorhabditis elegans genome sequence allows application of high-throughput (HT) approaches for phenotypic analyses using RNA interference (RNAi). As large phenotypic data sets become available, "phenoclustering" strategies can be used to begin understanding the complex molecular networks involved in development and other biological processes. The current HT-RNAi resources represent a great asset for phenotypic profiling but are limited by lack of flexibility. For instance, existing resources do not take advantage of the latest improvements in RNAi technology, such as inducible hairpin RNAi. Here we show that a C. elegans ORFeome resource, generated with the Gateway cloning system, can be used as a starting point to generate alternative HT-RNAi resources with enhanced flexibility. The versatility inherent to the Gateway system suggests that additional HT-RNAi libraries can now be readily generated to perform gene knockdowns under various conditions, increasing the possibilities for phenome mapping in C. elegans.

Abstract IL-17 is a newly described, T cell-derived cytokine with ill-defined physiologic properties. As such, we examined the release of proinflammatory mediators by human macrophages in response to recombinant human (rh) IL-17. IL-1β and TNF-α expression and synthesis were up-regulated by rhIL-17 in a dose (ED50 was 50 ± 9 ng/ml)- and time-dependent fashion, with cytokine accumulation reaching a zenith after 9 h. Release of IL-6, PGE2, IL-10, IL-12, IL-1R antagonist, and stromelysin was also stimulated by rhIL-17. IL-1β and TNF-α mRNA expression levels were controlled by rhIL-17 in a complex manner with an initial 30-min inhibitory phase, and then up-regulation beginning at 1 h and reaching a plateau at about 3 h. The latter expression pattern closely mirrored the nuclear accumulation of the transcription factor nuclear factor-κB. cAMP mimetics isobutyl-1-methylxanthine (IBMX), forskolin, PGE2, and cholera toxin reversed rhIL-17-induced release of TNF-α, but had no consistent effect on induced IL-1β synthesis. Induced release of TNF-α was also inhibited by serine/threonine protein kinase inhibitors KT-5720 (protein kinase A) and Calphostin C (protein kinase C), mitogen-activated protein kinase kinase inhibitor PD098059, and a nonspecific tyrosine kinase inhibitor, genistein. Calphostin C alone abrogated the rhIL-17-induced release of IL-1β. The antiinflammatory cytokines IL-4 (p < 0.01) and IL-10 (p < 0.02) completely reversed rhIL-17-stimulated IL-1β release, while IL-13 and TGF-β2 were partially effective (59 and 43% diminution, respectively). IL-10 exerted a significant suppressive effect on IL-17-induced TNF-α release (99%, p < 0.02), while the inhibitory effects of IL-4, IL-13, and TGF-β2 on TNF-α secretion were partial (48, 10, and 23%, respectively). The data suggest a pivotal role for IL-17 in initiating and/or sustaining an inflammatory response.

Quantum dot-metal oxide junctions are an integral part of next-generation solar cells, light emitting diodes, and nanostructured electronic arrays. Here we present a comprehensive examination of electron transfer at these junctions, using a series of CdSe quantum dot donors (sizes 2.8, 3.3, 4.0, and 4.2 nm in diameter) and metal oxide nanoparticle acceptors (SnO(2), TiO(2), and ZnO). Apparent electron transfer rate constants showed strong dependence on change in system free energy, exhibiting a sharp rise at small driving forces followed by a modest rise further away from the characteristic reorganization energy. The observed trend mimics the predicted behavior of electron transfer from a single quantum state to a continuum of electron accepting states, such as those present in the conduction band of a metal oxide nanoparticle. In contrast with dye-sensitized metal oxide electron transfer studies, our systems did not exhibit unthermalized hot-electron injection due to relatively large ratios of electron cooling rate to electron transfer rate. To investigate the implications of these findings in photovoltaic cells, quantum dot-metal oxide working electrodes were constructed in an identical fashion to the films used for the electron transfer portion of the study. Interestingly, the films which exhibited the fastest electron transfer rates (SnO(2)) were not the same as those which showed the highest photocurrent (TiO(2)). These findings suggest that, in addition to electron transfer at the quantum dot-metal oxide interface, other electron transfer reactions play key roles in the determination of overall device efficiency.

As poliarquias desenvolvidas do Ocidente condensam influências de três tradições políticas distintas: a liberal, a republicana e a democrática. As tradições liberal e republicana são as responsáveis pela "accountability horizontal", um traço crucial dessas poliarquias que está ausente das novas democracias. Discute-se o significado diso, e como a accountability horizontal poderia ser criada nestas últimas.

Abstract This study analyzes the relation between chief executive officer (CEO) personal risk-taking, corporate risk-taking, and total firm risk. We find evidence that CEOs who possess private pilot licenses (our proxy for personal risk-taking) are associated with riskier firms. Firms led by pilot CEOs have higher equity return volatility, beyond the amount explained by compensation components that financially reward risk-taking. We trace the source of the elevated firm risk to specific corporate policies, including leverage and acquisition activity. Our results suggest that nonpecuniary risk preferences revealed outside the scope of the firm have implications for project selection and various corporate policies.

A dual nature of the excited state of CH ₃ NH ₃ PbI ₃ perovskites is discovered, which fully identifies the spectral features in transient spectroscopy.

Griggs, D., M. Stafford Smith, J. Rockström, M. C. Öhman, O. Gaffney, G. Glaser, N. Kanie, I. Noble, W. Steffen, and P. Shyamsundar. 2014. An integrated framework for sustainable development goals. Ecology and Society 19(4): 49. https://doi.org/10.5751/ES-07082-190449

We studied the polygraphic sleep recordings of 30 infants who eventually died of sudden infant death syndrome (SIDS) and those of 60 matched control infants. All records were extracted from 20,750 sleep studies collected prospectively in 10 sleep laboratories. Of the 30 future SIDS victims, 5 were siblings of SIDS victims and 9 were studied after an apparent life-threatening event. For each SIDS victim, two normal control infants were matched for sex, gestational age, postnatal age and weight at birth. The future SIDS infants were reported to have more frequent episodes of regurgitations after feeding (p = 0.01) and profuse sweating during sleep (p = 0.01) than the control subjects. Only two polysomnographic variables characterized the future SIDS infants. Compared to control subjects, the SIDS infants moved less during sleep (p = 0.04) and had significantly more frequent obstructed breathing events. Obstructive and mixed apneas were seen in 23 of 30 future SIDS victims, but in only 9 of 60 control subjects (p = 0.01). The obstructed and mixed apneas lasted longer in the SIDS than in the control infants (p = 0.01) but did not exceed 15 seconds. The obstructed breaths occurred mainly in rapid eye movement sleep (78% of the events) and were accompanied by drops in heart rates to 68 beats per minute and in SaO2 levels to 75%. The present report adds further indirect evidence for a possible sleep-related impairment of respiratory control in some infants who eventually died of SIDS.

The advent of systems biology necessitates the cloning of nearly entire sets of protein-encoding open reading frames (ORFs), or ORFeomes, to allow functional studies of the corresponding proteomes. Here, we describe the generation of a first version of the human ORFeome using a newly improved Gateway recombinational cloning approach. Using the Mammalian Gene Collection (MGC) resource as a starting point, we report the successful cloning of 8076 human ORFs, representing at least 7263 human genes, as mini-pools of PCR-amplified products. These were assembled into the human ORFeome version 1.1 (hORFeome v1.1) collection. After assessing the overall quality of this version, we describe the use of hORFeome v1.1 for heterologous protein expression in two different expression systems at proteome scale. The hORFeome v1.1 represents a central resource for the cloning of large sets of human ORFs in various settings for functional proteomics of many types, and will serve as the foundation for subsequent improved versions of the human ORFeome.

Biotin/(strept)avidin self-assembly is a powerful platform for nanoscale fabrication and capture with many different applications in science, medicine, and nanotechnology. However, biotin/(strept)avidin self-assembly has several well-recognized drawbacks that limit performance in certain technical areas and there is a need for synthetic mimics that can either become superior replacements or operational partners with bio-orthogonal recognition properties. The goal of this tutorial review is to describe the recent progress in making high affinity synthetic association partners that operate in water or biological media. The review starts with a background summary of biotin/(strept)avidin self-assembly and the current design rules for creating synthetic mimics. A series of case studies are presented that describe recent success using synthetic derivatives of cyclodextrins, cucurbiturils, and various organic cyclophanes such as calixarenes, deep cavitands, pillararenes, and tetralactams. In some cases, two complementary partners associate to produce a nanoscale complex and in other cases a ditopic host molecule is used to link two partners. The article concludes with a short discussion of future directions and likely challenges.

The valence effective Hamiltonian technique is applied to a series of polymers to compute ionization potentials, bandwidths, and band gaps. The polymers considered represent systems of interest to the conducting polymers area and include various derivatives of polyacetylene and polyphenylene, polydiacetylene, polyacene, polybenzyl, and polyyne. The theoretical results for relative ionization potentials are in excellent agreement with available experimental estimates, as well as with the observed behavior of the electrical conductivity of these systems on exposure to weak (I2) versus strong (AsF5) electron acceptors. The bandwidths of the highest occupied band show a qualitative correlation to the conductivities achieved with acceptor doping. Band gaps for the planar systems considered are also in good agreement with experiment.

Surface acoustic waves (SAWs), are electro-mechanical waves that form on the surface of piezoelectric crystals. Because they are easy to construct and operate, SAW devices have proven to be versatile and powerful platforms for either direct chemical sensing or for upstream microfluidic processing and sample preparation. This review summarizes recent advances in the development of SAW devices for chemical sensing and analysis. The use of SAW techniques for chemical detection in both gaseous and liquid media is discussed, as well as recent fabrication advances that are pointing the way for the next generation of SAW sensors. Similarly, applications and progress in using SAW devices as microfluidic platforms are covered, ranging from atomization and mixing to new approaches to lysing and cell adhesion studies. Finally, potential new directions and perspectives on the field as it moves forward are offered, with a specific focus on potential strategies for making SAW technologies for bioanalytical applications.

Reelin is a large extracellular protein that controls cortical development. It binds to lipoprotein receptors very-low-density lipoprotein receptor and apolipoprotein-E receptor type 2, thereby inducing phosphorylation of the adapter Dab1. In vivo, Reelin is cleaved into three fragments, but their respective function is unknown. Here we show the following: (1) the central fragment is necessary and sufficient for receptor binding in vitro and for Dab1 phosphorylation in neuronal cultures; (2) Reelin does not bind the protocadherin cadherin-related neuronal receptor (CNR1) as reported previously; (3) Reelin and its central fragment are equally able to rescue the reeler phenotype in a slice culture assay; and (4) anti-receptor antibodies can induce Dab1 phosphorylation but do not correct the reeler phenotype in slices. These observations show that the function of Reelin is critically dependent on the central fragment generated by processing but primarily independent of interactions with CNR1 and on the N-terminal region. They also indicate that events acting in parallel to Dab1 phosphorylation might be required for full activity.

There has been increasing evidence that micro and messenger RNA derived from exosomes play important roles in pancreatic and other cancers. In this work, a microfluidics-based approach to the analysis of exosomal RNA is presented based on surface acoustic wave (SAW) exosome lysis and ion-exchange nanomembrane RNA sensing performed in conjunction on two separate chips. Using microRNA hsa-miR-550 as a model target and raw cell media from pancreatic cancer cell lines as a biological sample, SAW-based exosome lysis is shown to have a lysis rate of 38%, and an ion-exchange nanomembrane sensor is shown to have a limit of detection of 2 pM, with two decades of linear dynamic range. A universal calibration curve was derived for the membrane sensor and used to detect the target at a concentration of 13 pM in a SAW-lysed sample, which translates to 14 target miRNA per exosome from the raw cell media. At a total analysis time of ~1.5 h, this approach is a significant improvement over existing methods that require two overnight steps and 13 h of processing time. The platform also requires much smaller sample volumes than existing technology (~100 μL as opposed to ~mL) and operates with minimal sample loss, a distinct advantage for studies involving mouse models or other situations where the working fluid is scarce.

Transient absorption microscopy was employed to image charge carrier dynamics in epitaxial multilayer graphene. The carrier cooling exhibited a biexponential decay that showed a significant dependence on carrier density. The fast and slow relaxation times were assigned to coupling between electrons and optical phonon modes and the hot phonon effect, respectively. The limiting value of the slow relaxation time at high pump intensity reflects the lifetime of the optical phonons. Significant spatial heterogeneity in the dynamics was observed due to differences in coupling between graphene layers and the substrate.

Hydrogels comprise a class of soft materials which are extremely useful in a number of contexts, for example as matrix-mimetic biomaterials for applications in regenerative medicine and drug delivery. One particular subclass of hydrogels consists of materials prepared through non-covalent physical crosslinking afforded by supramolecular recognition motifs. The dynamic, reversible, and equilibrium-governed features of these molecular-scale motifs often transcend length-scales to endow the resulting hydrogels with these same properties on the bulk scale. In efforts to engineer hydrogels of all types with more precise or application-specific uses, inclusion of stimuli-responsive sol-gel transformations has been broadly explored. In the context of biomedical uses, temperature is an interesting stimulus which has been the focus of numerous hydrogel designs, supramolecular or otherwise. Most supramolecular motifs are inherently temperature-sensitive, with elevated temperatures commonly disfavoring motif formation and/or accelerating its dissociation. In addition, supramolecular motifs have also been incorporated for physical crosslinking in conjunction with polymeric or macromeric building blocks which themselves exhibit temperature-responsive changes to their properties. Through molecular-scale engineering of supramolecular recognition, and selection of a particular motif or polymeric/macromeric backbone, it is thus possible to devise a number of supramolecular hydrogel materials to empower a variety of future biomedical applications.

Ethionamide (ETH) is an important second-line antitubercular drug used for the treatment of patients infected with multidrug-resistant Mycobacterium tuberculosis. Although ETH is a structural analogue of isoniazid, only little cross-resistance to these two drugs is observed among clinical isolates. Both isoniazid and ETH are pro-drugs that need to be activated by mycobacterial enzymes to exert their antimicrobial activity. We have recently identified two M. tuberculosis genes, Rv3854c (ethA) and Rv3855 (ethR), involved in resistance to ETH. ethA encodes a protein that belongs to the Flavin-containing monooxygenase family catalysing the activation of ETH. We show here that ethR, which encodes a repressor belonging to the TetR/CamR family of transcriptional regulators, negatively regulates the expression of ethA. By the insertion of the ethA promoter region upstream of the lacZ reporter gene, overexpression of ethR in trans was found to cause a strong inhibition of ethA expression, independently of the presence of ETH in the culture media. Electrophoretic mobility shift assays indicated that EthR interacts directly with the ethA promoter region. This interaction was confirmed by DNA footprinting analysis, which, in addition, identified the EthR-binding region. Unlike other TetR/CamR members, which typically bind 15 bp operators, EthR recognises an unusually long 55 bp region suggesting multimerization of the repressor on its operator. Identification by primer-extension of the ethA transcriptional start site indicated that it is located within the EthR-binding region. Taken together, bacterial two-hybrid experiments and gel filtration assays suggested a dimerization of EthR in the absence of its operator. In contrast, surface plasmon resonance analyses showed that eight EthR molecules bind cooperatively to the 55 bp operator, which represents a novel repression mechanism for a TetR/CamR member.

Recent observations of neutrino oscillations imply nonzero neutrino masses and lepton flavor violation (LFV), most economically explained by the seesaw mechanism. Within the context of supersymmetry, LFV among the neutrinos can be communicated to the sleptons and from there to the charged leptons. We show that LFV can appear in the couplings of the neutral Higgs bosons, an effect that is strongly enhanced at large $\mathrm{tan}\ensuremath{\beta}$. We calculate the branching fraction for $\ensuremath{\tau}\ensuremath{\rightarrow}3\ensuremath{\mu}$ and $\ensuremath{\mu}\ensuremath{\rightarrow}3e$ mediated by Higgs and find they can be as large as ${10}^{\ensuremath{-}7}$ and $5\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}14}$, respectively. These modes, along with $\ensuremath{\tau}\ensuremath{\rightarrow}\ensuremath{\mu}\ensuremath{\gamma}$ and $\ensuremath{\mu}\ensuremath{\rightarrow}e\ensuremath{\gamma}$, can provide key insights into the neutrino mass matrix.

Natural products have historically been a rich source of diverse chemical matter with numerous biological activities, and have played an important role in drug discovery in many areas including infectious disease. Synthetic and medicinal chemistry have been, and continue to be, important tools to realize the potential of natural products as therapeutics and as chemical probes. The formation of biofilms by bacteria in an infection setting is a significant factor in the recalcitrance of many bacterial infections, conferring increased tolerance to many antibiotics and to the host immune response, and as yet there are no approved therapeutics for combatting biofilm-based bacterial infections. Small molecules that interfere with the ability of bacteria to form and maintain biofilms can overcome antibiotic tolerance conferred by the biofilm phenotype, and have the potential to form combination therapies with conventional antibiotics. Many natural products with anti-biofilm activity have been identified from plants, microbes, and marine life, including: elligic acid glycosides, hamamelitannin, carolacton, skyllamycins, promysalin, phenazines, bromoageliferin, flustramine C, meridianin D, and brominated furanones. Total synthesis and medicinal chemistry programs have facilitated structure confirmation, identification of critical structural motifs, better understanding of mechanistic pathways, and the development of more potent, more accessible, or more pharmacologically favorable derivatives of anti-biofilm natural products.

Emerging trends and future prospects for nanoparticle synthesis and colloidal ink formulation, additive printing processes, and functional devices are highlighted.