Inadmissible Class of Boolean Functions under Stuck-at Faults

Many underlying structural and functional factors that determine the fault behavior of a combinational network, are not yet fully understood. In this paper, we show that there exists a large class of Boolean functions, called root functions, which can never appear as faulty response in irredundant two-level circuits even when any arbitrary multiple stuck-at faults are injected. Conversely, we show that any other Boolean function can appear as a faulty response from an irredundant realization of some root function under certain stuck-at faults. We characterize this new class of functions and show that for n variables, their number is exactly equal to the number of independent dominating sets (Harary and Livingston, Appl. Math. Lett., 1993) in a Boolean n-cube. We report some bounds and enumerate the total number of root functions up to 6 variables. Finally, we point out several open problems and possible applications of root functions in logic design and testing

Long Noncoding RNAs are Frontier Breakthrough of RNA World and RNAi-based Gene Regulation

General complexities in versatile animals are not always proportional to their genome size. A notable example is that the salamander genome size is 15-fold larger than that of human, which mostly contains unfolded “junk DNA.” A vast portion of this non-protein-coding unfolded DNA undergoes transcriptional regulation and produces a large number of long noncoding RNAs (lncRNAs). LncRNAs play key roles in gene expression and therapies of different human diseases. Recently, novel lncRNAs and their function on the silencing or activation of a particular gene(s) are regularly being discovered. Another important component of gene regulation is high packing of chromatin, which is composed of mainly repetitive sequences with negligible coding potential. In particular, an epigenetic marker determines the state of the gene associated with it, whether the gene will be expressed or silenced. Here, we elaborately discuss the biogenesis pathway of lncRNAs as well as their mechanism of action and role in gene silencing and regulation, including RNA interference. Moreover, several lncRNAs are the common precursors of small regulatory RNAs. It is thus becoming increasingly clear that lncRNAs can function via numerous paradigms as key regulatory molecules in different organisms

A Potent Malaria Transmission Blocking Vaccine Based on Codon Harmonized Full Length Pfs48/45 Expressed in Escherichia coli

Malaria caused by Plasmodium falciparum is responsible for nearly 1 million deaths annually. Although much progress has been made in the recent past, the development of a safe, effective and affordable malaria vaccine has remained a challenge. A vaccine targeting sexual stages of the parasite will not only reduce malaria transmission by female Anopheles mosquitoes, but also reduce the spread of parasites able to evade immunity elicited by vaccines targeting pre-erythrocytic and erythrocytic asexual stages. We focused our studies on Pfs48/45, a protein expressed in the sexual stages developing within an infected person and one of the most promising transmission-blocking vaccine targets. Functional immunogenicity of Pfs48/45 protein requires proper disulfide bond formation, consequently evaluation of the immunogenicity of recombinant full-length Pfs48/45 has been hampered by difficulties in expressing properly folded protein to date. Here we present a strategy involving harmonization of codons for successful recombinant expression of full length Pfs48/45 in Escherichia coli. The purified protein, designated CH-rPfs48/45, was recognized by monoclonal antibodies directed against reduction-sensitive conformational epitopes in the native protein. Immunogenicity evaluation in mice revealed potent transmission blocking activity in membrane feeding assays of antisera elicited by CH-rPfs48/45 formulated in three different adjuvants, i.e. Alum, Montanide ISA-51 and complete Freund's adjuvant. More importantly, CH-rPfs48/45 formulated with Montanide ISA-51 when administered to nonhuman primates (Olive baboons, Papio anubis) resulted in uniformly high antibody responses (ELISA titers >2 million) in all five animals. Sera from these animals displayed greater than 93% blocking activity in membrane feeding assays after a single immunization, reaching nearly complete blocking after a booster dose of the vaccine. The relative ease of expression and induction of potent transmission blocking antibodies in mice and nonhuman primates provide a compelling rationale and basis for development of a CH-rPfs48/45 based malaria transmission blocking vaccine

Improved Upper Bound on Independent Domination Number for Hypercubes

We revisit the problem of determining the independent domination number in hypercubes for which the known upper bound is still not tight for general dimensions. We present here a constructive method to build an independent dominating set $S_n$ for the $n$-dimensional hypercube $Q_n$, where $n=2p+1$, $p$ being a positive integer $\ge 1$, provided an independent dominating set $S_p$ for the $p$-dimensional hypercube $Q_p$, is known. The procedure also computes the minimum independent dominating set for all $n=2^k-1$, $k>1$. Finally, we establish that the independent domination number $\alpha_n\leq 3 \times 2^{n-k-2}$ for $7\times 2^{k-2}-1\leq n1$. This is an improved upper bound for this range as compared to earlier work.Comment: 10 pages, 1 figure, and 3 table

Recognition of native Pfs48/45 in <i>P. falciparum</i> gametocyte extract.

<p>(a) Western blot analysis with non-reduced (left panel) or reduced (right panel) <i>P. falciparum</i> gametocyte extract against serum of individual mouse immunized with either CFA or ISA-51 or alum formulation. Stage V gametocyte extract was run either in non-reduced or reduced (10 mM 2-mercaptothanol) form in SDS-PAGE and transferred to nitrocellulose membrane. Mice sera were allowed to react at 1∶1000 dilution for 1 h at 22°C. HRP-conjugated anti-mouse IgG at 1∶10000 dilution was used as detection antibody and was developed using ECL substrate. Lane 1, mAb IIC5B10; lane 2, one representative mouse serum immunized in CFA; lane 3, one representative mouse serum immunized in Montanide ISA-51; lane 4, one representative mouse serum immunized in alum formulation. The figure is assembled from separate experiments. (b) Mouse sera (1∶1000 dilution) were tested by live immunofluorescence assays as described under <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006352#s4" target="_blank">materials and methods</a>.</p

Follow up of immune responses elicited by CH-rPfs48/45 in baboons.

<p>Analysis of anti-CH-rPfs48/45 IgG titers (open bars) and percent transmission blocking activity (closed bars) upto 7 months post second boost in baboons. Results show mean antibody titer and mean transmission blocking activity of 5 baboons +95% CI.</p

Helminth infection impairs the immunogenicity of a Plasmodium falciparum DNA vaccine, but not irradiated sporozoites, in mice

Development of an effective vaccine against malaria remains a priority. However, a significant number of individuals living in tropical areas are also likely to be co-infected with helminths, which are known to adversely affect immune responses to a number of different existing vaccines. Here we compare the response to two prototype malaria vaccines: a transmission blocking DNA vaccine based on Pfs25, and a pre-erythrocytic malaria vaccine based on irradiated sporozoites in mice infected with the intestinal nematode Heligmosomoides polygyrus. Following primary immunization with Pfs25 DNA vaccine, levels of total IgG, as well as IgG1, IgG2a, IgG2b (all P = 0.0002), and IgG3 (P = 0.03) Pfs25 antibodies were significantly lower in H. polygyrus-infected mice versus worm-free controls. Similar results were observed even after two additional boosts, while clearance of worms with anthelmintic treatment 3 weeks prior to primary immunization significantly reversed the inhibitory effect of helminth infection. In contrast, helminth infection had no inhibitory effect on immunization with irradiated sporozoites. Mean anti-CSP antibody responses were similar between H. polygyrus-infected and worm-free control mice following immunization with a single dose (65,000 sporozoites) of live radiation attenuated (irradiated) Plasmodium yoelii sporozoites (17X, non-lethal strain), and protection upon sporozoite challenge was equivalent between groups. These results indicate that helminth infection may adversely affect certain anti-malarial vaccine strategies, and highlight the importance of these interactions for malaria vaccine development. © 2010 Elsevier Ltd

Analysis of anti-Pfs48/45 antibody production by Olive baboons (<i>Papio anubis</i>).

<p>(a) Each animal was immunized with CH-rPfs48/45 (50 µg in 0.25 ml endotoxin free PBS) formulated in Montanide ISA-51 (0.25 ml) in baboons, administered intra muscularly (quadriceps, two sites). Schedules for immunization and bleeds are indicated and sera were stored at −20°C until shipped frozen from Kenya to Baltimore for ELISA and MFA. The samples were shipped under an export permit CITES # 008101. (b) Anti-Pfs48/45 whole IgG titer at various time points analyzed by ELISA. Pre-immune +3 x SD is shown by solid horizontal lines. ELISA readings with sera dilutions, 1 month post primary immunization (filled square), 1 month post first boost (filled triangle) and 1 month post second boost (filled diamond) are shown with±SD for individual baboons (Pan 3104, Pan 3140, Pan 3163, Pan 3275, Pan 3313). (c) Distribution of anti-Pfs48/45 IgG1(solid diamonds) and IgG2 (open diamonds) subtypes in 1 month post primary immunization sera (Dec 10), 1 month post 1^st boost (Jan 10), 1 month post 2^nd boost (Mar 06), and 3 months post 2^nd boost (May 05). Data are presented as mean OD₄₀₅ value±SD for individual baboon.</p

Figure 2

<p>(a) ELISA analysis of CH-rPfs48/45 immunized individual mouse sera in three different adjuvant formulations: Complete Freund's adjuvant (top panel), Montanide ISA-51 (middle panel), and Alum (bottom panel). All the results are representative of three independent experiments. Pooled pre-immune sera + 3SD are shown by broken lines. ELISA OD₄₀₅ values for individual mice are shown; mouse 1 (filled triangle), mouse 2 (open square), mouse 3 (filled square), mouse 4 (open circle), mouse 5 (filled circle). (b) Analysis of anti-Pfs48/45 IgG isotype distribution in individual mouse sera: IgG1 (filled columns), IgG2a (hatched columns), IgG2b (stippled columns), IgG3 (blank columns).</p