Construction of a series of vectors for high throughput cloning and expression screening of membrane proteins from Mycobacterium tuberculosis

<p>Abstract</p> <p>Background</p> <p>One of the major challenges for membrane protein structural genomics is establishing high-throughput cloning and expression screening methods to obtain enough purified protein in a homogeneous preparation for structural and functional studies. Here a series of ligation independent cloning based vectors were constructed to address this challenge.</p> <p>Results</p> <p>The feasibility of these vectors was tested with 41 putative membrane proteins from <it>Mycobacterium tuberculosis</it>. The efficiency for direct cloning of these target genes from PCR products was 95% (39/41). Over 40% of cloned genes were overexpressed in <it>Escherichia coli </it>BL21 (DE3)-RP codon plus strain in the first round of expression screening. For those proteins which showed no expression, three protein fusion partners were prepared and it was found that each of the target proteins could be overexpressed by at least one of these fusions, resulting in the overexpression of two thirds of the cloned genes.</p> <p>Conclusion</p> <p>This expression platform features high throughput cloning, high flexibility for different constructs, and high efficiency for membrane protein overexpression, and is expected to be useful in membrane protein structural and functional studies.</p

Exploring Spin AGP Ansatze for Strongly Correlated Spin Systems

The antisymmetrized geminal power (AGP), a wave function equivalent to number-projected Hartree--Fock--Bogoliubov (HFB), and number-projected Bardeen--Cooper--Schrieffer (BCS) when working in the paired (natural orbitals) basis, has proven to be an excellent reference for strong pairing interactions. Several correlation methods have also been applied on top of AGP. In this work, we show how AGP can also be applied to spin systems by simply basing its formulation on a spin $su(2)$ algebra. We here implement spin AGP and spin AGP-based correlation techniques and benchmark them on the XXZ and $\mathrm{J_1-J_2}$ Heisenberg models, both in 1 and 2 dimensions. Our results indicate that spin AGP is a promising starting point for modeling spin systems.Comment: Version

The position profiles of order cancellations in an emerging stock market

Order submission and cancellation are two constituent actions of stock trading behaviors in order-driven markets. Order submission dynamics has been extensively studied for different markets, while order cancellation dynamics is less understood. There are two positions associated with a cancellation, that is, the price level in the limit-order book (LOB) and the position in the queue at each price level. We study the profiles of these two order cancellation positions through rebuilding the limit-order book using the order flow data of 23 liquid stocks traded on the Shenzhen Stock Exchange in the year 2003. We find that the profiles of relative price levels where cancellations occur obey a log-normal distribution. After normalizing the relative price level by removing the factor of order numbers stored at the price level, we find that the profiles exhibit a power-law scaling behavior on the right tails for both buy and sell orders. When focusing on the order cancellation positions in the queue at each price level, we find that the profiles increase rapidly in the front of the queue, and then fluctuate around a constant value till the end of the queue. These profiles are similar for different stocks. In addition, the profiles of cancellation positions can be fitted by an exponent function for both buy and sell orders. These two kinds of cancellation profiles seem universal for different stocks investigated and exhibit minor asymmetry between buy and sell orders. Our empirical findings shed new light on the order cancellation dynamics and pose constraints on the construction of order-driven stock market models.Comment: 17 pages, 6 figures and 6 table

Separability and entanglement in 2x3xN composite quantum systems

The separability and entanglement of quantum mixed states in \Cb^2 \otimes \Cb^3 \otimes \Cb^N composite quantum systems are investigated. It is shown that all quantum states $\rho$ with positive partial transposes and rank $r(\rho)\leq N$ are separable.Comment: Latex, 15 page

Quantum asymmetric cryptography with symmetric keys

Based on quantum encryption, we present a new idea for quantum public-key cryptography (QPKC) and construct a whole theoretical framework of a QPKC system. We show that the quantum-mechanical nature renders it feasible and reasonable to use symmetric keys in such a scheme, which is quite different from that in conventional public-key cryptography. The security of our scheme is analyzed and some features are discussed. Furthermore, the state-estimation attack to a prior QPKC scheme is demonstrated.Comment: 8 pages, 1 figure, Revtex

Phenotypic plasticity of gut structure and function during periods of inactivity in Apostichopus japonicus.

Apostichopus japonicus is a common sea cucumber that undergoes seasonal inactivity phases and ceases feeding during the summer months. We used this sea cucumber species as a model in which to examine phenotypic plasticity of the digestive tract in response to food deprivation. We measured the body mass, gross gut morphology and digestive enzyme activities of A. japonicus before, during, and after the period of inactivity to examine the effects of food deprivation on the gut structure and function of this animal. Individuals were sampled semi-monthly from June to November (10 sampling intervals over 178 days) across temperature changes of more than 18°C. On 5 September, which represented the peak of inactivity and lack of feeding, A. japonicus decreased its body mass, gut mass and gut length by 50%, 85%, and 70%, respectively, in comparison to values for these parameters preceding the inactive period. The activities of amylase, cellulase and lipase decreased by 77%, 98%, and 35% respectively, in comparison to mean values for these enzymes in June, whereas pepsin activity increased two-fold during the inactive phase. Alginase and trypsin activities were variable and did not change significantly across the 178-day experiment. With the exception of amylase and cellulase, all body size indices and digestive enzyme activities recovered and even surpassed the mean values preceding the inactive phase during the latter part of the experiment (October-November). Principal Component Analysis (PCA) utilizing the digestive enzyme activity and body size index data divided the physiological state of this cucumber into four phases: an active stage, prophase of inactivity, peak inactivity, and a reversion phase. These phases are all consistent with previously suggested life stages for this species, but our data provide more defined characteristics of each phase. A. japonicus clearly exhibits phenotypic plasticity (or life-cycle staging) of the digestive tract during its annual inactive period

Persistent problems of access to appropriate, affordable TB services in rural China: experiences of different socio-economic groups

BACKGROUND: Large-scale Tuberculosis (TB) control programmes in China have been hailed a success. Concerns remain, however, about whether the programme is reaching all sections of the population, particularly poorer groups within rural communities, and whether there are hidden costs. This study takes a household perspective to investigate receipt of appropriate care and affordability of services for different socio-economic groups with TB symptoms in rural China. METHODS: Secondary analysis of Chinese National Household Health Survey for 2003: 40,000 rural households containing 143,991 individuals, 2,308 identified as TB suspects. Outcomes: use of services and expenditure of TB suspects, by gender and socio-economic position, indicated by household income, education, material assets, and insurance status. RESULTS: 37% of TB suspects did not seek any professional care, with low-income groups less likely to seek care than more affluent counterparts. Of those seeking care, only 35% received any of the recommended diagnostic tests. Of the 182 patients with a confirmed TB diagnosis, 104 (57%) received treatment at the recommended level, less likely if lacking health insurance or material assets. The burden of payment for services amounted to 45% of annual household income for the low-income group, 16% for the high-income group. CONCLUSION: Access to appropriate, affordable TB services is still problematic in some rural areas of China, and receipt of care and affordability declines with declining socio-economic position. These findings highlight the current shortcomings of the national TB control programme in China and the formidable challenge it faces if it is to reach all sections of the population, including the poor with the highest burden of disease