[Review of] Ambrose Y.C. King and Rance P.L. Lee, eds. Social Life and Development in Hong Kong

This book is a collection of research papers on the political and social conditions of Hong Kong sponsored by the Social Research Centre of The Chinese University of Hong Kong. The collection is not a comprehensive coverage of such conditions in Hong Kong. I t is a selective report with the purpose of updating existing information. The new information will provide a better understanding of Hong Kong\u27s problems and serve as a resource in coping with these problems

Kinetic Accessibility of Buried DNA Sites in Nucleosomes

Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and reburial on the site position, which is measurable experimentally and pertinent to gene regulation. We find the dependence to be roughly described by a random walker model. Close inspection reveals a surprising physical effect of flexibility-assisted barrier crossing, which we characterize within a toy model, the "semiflexible Brownian rotor."Comment: final version as published in Phys. Rev. Let

Analytic solutions of the Rolie Poly model in time-dependent shear

We consider shear flows that comprise of step changes in the shear rate. For these flows, we derive analytic solutions of the Rolie-Poly constitutive equation. Our method involves piecing together solutions for constant rate shear in a variety of flow rate regimes. We obtain solutions for interrupted shear, recoverable strain and non-linear relaxation following cessation of flow. Whenever strong flow is present we neglect reptation, as other mechanisms dominate and for interrupted shear our solution is approximate as we neglect convective constraint release. Our analytic solutions provide new insight in several ways. These include revealing the mechanism of some experimental features of these flows; suggesting a method to extract the polymer contribution to the normal stress in the velocity gradient direction (σyy) from shear stress measurements alone; and a method to isolate the influence of convective constraint release (CCR) from damping function measurements. We also run complementary GLaMM model calculations to verify that insight from our analytic approach translates to this more detailed model

The Pleistocene geoarchaeology and geochronology of Con Moong Cave, North Vietnam: Site formation processes and hominin activity in the humid tropics

This paper presents the results of geoarchaeological and geochronological investigations at Con Moong Cave, North Vietnam. Beneath the published, terminal Pleistocene sequence, recent excavations have uncovered a ~5 m stratigraphic sequence containing flaked stone artifacts and sedimentary features that indicate extensive post-depositional change. As the effects of tropical conditions on Pleistocene cave sediments are poorly resolved, a range of complementary techniques was selected to reconstruct the nature of on-site sedimentation and occupation, while assessing the taphonomy of archaeological and palaeoecological materials. Our approach incorporates microstratigraphic, geochemical and sedimentological analyses, using optically stimulated luminescence (OSL) dating to estimate the time of sediment deposition in the cave. This case study has broad application to tropical zones worldwide. Sedimentation began in early Marine Isotope Stage (MIS) 4, while micromorphologically observed human occupation commenced before 42 thousand years ago (ka). By placing our results within the context of published, high-resolution regional records of climate, we demonstrate that on-site rhythms of Pleistocene occupation correlated with environmental changes in the region. During MIS 3, episodic abandonment of the site coincided with periods of drier conditions, while rapid climate fluctuations in MIS 2 corresponded with short-lived occupation events and a switch to predominantly geogenic deposition in the cave

Theory for polymer coils with necklaces of micelles

If many micelles adsorb onto the same polymer molecule then they are said to form a necklace. A minimal model of such a necklace is proposed and shown to be almost equivalent to a 1-dimensional fluid with nearest-neighbour interactions. The thermodynamic functions of this fluid are obtained and then used to predict the change in the critical micellar concentration of the surfactant in the presence of the polymer. If the amount of polymer is not too large there are two critical micellar concentrations, one for micelles in necklaces and one for free micelles.Comment: 12 pages, 5 figure

Development of a novel data mining tool to find cis-elements in rice gene promoter regions

<p>Abstract</p> <p>Background</p> <p>Information on more than 35 000 full-length <it>Oryza sativa </it>cDNAs, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as <it>cis</it>-regulatory elements with key roles under the various conditions.</p> <p>Results</p> <p>We have developed a novel tool that searches for <it>cis</it>-element candidates in the upstream, downstream, or coding regions of differentially regulated genes. The tool first lists <it>cis-</it>element candidates by motif searching based on the supposition that if there are <it>cis-</it>elements playing important roles in the regulation of a given set of genes, they will be statistically overrepresented and will be conserved. Then it evaluates the likelihood scores of the listed candidate motifs by association rule analysis. This strategy depends on the idea that motifs overrepresented in the promoter region could play specific roles in the regulation of expression of these genes. The tool is designed so that any biological researchers can use it easily at the publicly accessible Internet site <url>http://hpc.irri.cgiar.org/tool/nias/ces</url>. We evaluated the accuracy and utility of the tool by using a dataset of auxin-inducible genes that have well-studied <it>cis-</it>elements. The test showed the effectiveness of the tool in identifying significant relationships between <it>cis-</it>element candidates and related sets of genes.</p> <p>Conclusion</p> <p>The tool lists possible <it>cis-</it>element motifs corresponding to genes of interest, and it will contribute to the deeper understanding of gene regulatory mechanisms in plants.</p

Chloroquine and inhibition of Toll-like receptor 9 protect from sepsis-induced acute kidney injury

Mortality from sepsis has remained high despite recent advances in supportive and targeted therapies. Toll-like receptors (TLRs) sense bacterial products and stimulate pathogenic innate immune responses. Mice deficient in the common adapter protein MyD88, downstream from most TLRs, have reduced mortality and acute kidney injury (AKI) from polymicrobial sepsis. However, the identity of the TLR(s) responsible for the host response to polymicrobial sepsis is unknown. Here, we show that chloroquine, an inhibitor of endocytic TLRs (TLR3, 7, 8, 9), improves sepsis-induced mortality and acute kidney injury in a clinically relevant polymicrobial sepsis mouse model, even when administered 6h after the septic insult. Chloroquine administration attenuated the decline in renal function, splenic apoptosis, serum markers of damage to other organs, and prototypical serum pro- and anti-inflammatory cytokines TNF-alpha and IL-10. An oligodeoxynucleotide inhibitor (H154) of TLR9 and TLR9-deficient mice mirror the actions of chloroquine in all functional parameters that we tested. In addition, chloroquine decreased TLR9 protein abundance in spleen, further suggesting that TLR9 signaling may be a major target for the protective actions of chloroquine. Our findings indicate that chloroquine improves survival by inhibiting multiple pathways leading to polymicrobial sepsis, and that chloroquine and TLR9 inhibitors represent viable broad-spectrum and targeted therapeutic strategies, respectively, that are promising candidates for further clinical development

Selection of restriction endonucleases using artificial cells

We describe in this article an in vitro system for the selection of restriction endonucleases using artificial cells. The artificial cells are generated in the form of a water-in-oil emulsion by in vitro compartmentalization. Each aqueous compartment contains a reconstituted transcription/translation mix along with the dispersed DNA templates. In the compartments containing endonuclease genes, an endonuclease expressed in vitro cleaves its own DNA template adjacent to the gene, leaving a sticky end. The pooled DNA templates are then ligated to an adaptor with a compatible end. The endonuclease genes are then enriched by adaptor-specific PCR on the ligation mix. We demonstrate that the system can achieve at least 100-fold enrichment in a single round of selection. It is sensitive enough to enrich an active endonuclease gene from a 1:105 model library in 2–3 rounds of selection. Finally, we describe experiments where we selected endonuclease genes directly from a bacterial genomic DNA source in three rounds of selections: the known PstI gene from Providencia stuartii and the new TspMI gene from Thermus sp. manalii. This method provides a unique tool for cloning restriction endonuclease genes and has many other potential applications