Primer length dependence of binding of DNA polymerase I Klenow fragment to template-primer complexes containing site-specific bulky lesions.

The binding of the benzo[a]pyrene metabolite anti-BPDE (r7, t8-dihydroxy-t9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene) to the N(2) group of 2'-deoxyguanosine residues (dG) is known to adversely affect the Michaelis-Menten primer extension kinetics catalyzed by DNA Pol I and other polymerases. In this work, the impact of site-specific, anti-BPDE-modified DNA template strands on the formation of Pol I (Klenow fragment, KF)/template-primer complexes has been investigated. The 23-mer template strand 5'-d(AAC GC-(1) T(-)(2) ACC ATC CGA ATT CGC CC), I (dG = (+)-trans- and (-)-trans-anti-BPDE-N(2)-dG), was annealed with primer strands 18, 19, or 20 bases long. Complex formation of these template-primer strands with KF(-) (exonuclease-free) at different enzyme concentrations was determined using polyacrylamide gel mobility shift assays in the absence of dNTPs. The lesion dG causes an increase in the dissociation constants, K(d), of the monomeric, 1:1 KF(-)/DNA template-primer complexes by factors of 10-15 when the 3'-end base of the primer strand is positioned either opposite dG, or opposite dC(-)(1) in I, and the shapes of the binding isotherms are sigmoidal. The sigmoidal shapes are attributed to the formation of dimeric 2:1 KF(-)/DNA template-primer complexes. In contrast, when the 3'-end of the primer strand extends only to dT(-)(2) in I, the K(d) of 1:1 complexes is increased by factors of only 2-3, the shapes of the binding isotherms are hyperbolic and nonsigmoidal and are similar to those observed with the unmodified control, and monomeric KF(-)/DNA complexes are dominant. The impact of bulky lesions on polymerase/DNA complex formation in polymerase-catalyzed primer extension reactions needs to be taken into account in interpreting the site-specific Michaelis-Menten kinetics of these reactions.     

Use of Placket–Burman Statistical Design to Study Effect of Formulation Variables on the Release of Drug from Hot Melt Sustained Release Extrudates

The present paper was focused on exploiting Plackett–Burman design to screen the effect of nine factors—poly (ethylene oxide) molecular weight (X ₁), poly (ethylene oxide) amount (X ₂), ethylcellulose amount (X ₄), drug solubility (X ₅), drug amount (X ₆), sodium chloride amount (X ₇), citric acid amount (X ₈), polyethylene glycol amount (X ₉), and glycerin amount (X ₁₁) on the release of drugs from the extended release extrudates, i.e., release rate and release mechanism. The experiments were carried out according to a nine-factor 12-run statistical model and subjected to an 8-h dissolution study in phosphate buffer pH 6.8. The significance of the model was indicated by the ANOVA and the residual analysis. Poly (ethylene oxide) amount, ethylcellulose amount and drug solubility had significant effect on the T90 values whereas poly (ethylene oxide) amount and ethylcellulose amount had significant effect on the n value.     

Metformin inhibits mTOR–HIF-1α axis and profibrogenic and inflammatory biomarkers in thioacetamide-induced hepatic tissue alterations

The potential inhibitory effect of the antidiabetic and anti-inflammatory drug, metformin on thioacetamide (TAA)-induced hepatotoxicity associated with the inhibition of mammalian target of rapamycin (mTOR)–hypoxia-inducible factor-1α (HIF-1α) axis has not been investigated before. Therefore, we tested whether metformin can protect against liver injuries including fibrosis induced by TAA possibly via the downregulation of mTOR–HIF-1α axis and profibrogenic and inflammatory biomarkers. Rats either injected with TAA (200 mg/kg; twice a week for 8 weeks) before being killed after 10 weeks (model group) or were pretreated with metformin (200 mg/kg) daily for 2 weeks before TAA injections and continued receiving both agents until the end of the experiment, at Week 10 (protective group). Using light and electron microscopy examinations, we observed in the model group substantial damage to the hepatocytes and liver tissue such as collagen deposition, infiltration of inflammatory cells, and degenerative cellular changes with ballooned mitochondria that were substantially ameliorated by metformin. Metformin also significantly ( p < 0.05) inhibited TAA-induced HIF-1α, mTOR, the profibrogenic biomarker α-smooth muscle actin, tissue inhibitor of metalloproteinases-1, tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), alanine aminotransferase (ALT) and aspartate aminotransferase in harvested liver homogenates and blood samples. In addition, a significant ( p < 0.01) positive correlation between hypoxia scoring (HIF-1α) and the serum levels of TNF-α ( r = 0.797), IL-6 ( r = 0.859), and ALT ( r = 0.760) was observed. We conclude that metformin protects against TAA-induced hepatic injuries in rats, which is associated with the inhibition of mTOR–HIF-1α axis and profibrogenic and inflammatory biomarkers; thus, may offer therapeutic potential in humans.     

Wide hybridization between oat and pearl millet belonging to different subfamilies of Poaceae

Oat (Avena sativa L.) and pearl millet (Pennisetum glaucum L.) belong to different subfamilies of Poaceae. When emasculated oat was pollinated by millet, fertilization took place and all seven millet chromosomes were retained along the complete haploid oat complement during early stages of embryogenesis. Fourteen days after pollination, we cultured 170 embryos onto rescue medium, of which 99 were attached with endosperm tissue. Twenty-one embryos germinated and showed shoot growth. One of them also developed roots. The shoots of the rootless embryos elongated, but rolled to the scutellum side and eventually died in light conditions. Chromosome observations and marker analyses indicated that the seedling plants were true hybrids that retained all of the oat and millet chromosomes. One exceptional embryo with shoot and root grew under light conditions. This was a haploid of oat and developed to a fertile adult plant. One embryo generated a callus after 6 months cultivation, and it was found to harbor four out of the seven millet chromosomes corresponding to linkage groups 2, 4, 6, and 7. The callus grew vigorously but did not develop shoots or roots.     

Force Generation in Lamellipodia Is a Probabilistic Process with Fast Growth and Retraction Events

Polymerization of actin filaments is the primary source of motility in lamellipodia and it is controlled by a variety of regulatory proteins. The underlying molecular mechanisms are only partially understood and a precise determination of dynamical properties of force generation is necessary. Using optical tweezers, we have measured with millisecond (ms) temporal resolution and picoNewton (pN) sensitivity the force-velocity (Fv) relationship and the power dissipated by lamellipodia of dorsal root ganglia neurons. When force and velocity are averaged over 3-5 s, the Fv relationships can be flat. On a finer timescale, random occurrence of fast growth and subsecond retractions become predominant. The maximal power dissipated by lamellipodia over a silica bead with a diameter of 1 μm is 10⁻¹⁶ W. Our results clarify the dynamical properties of force generation: i), force generation is a probabilistic process; ii), underlying biological events have a bandwidth up to at least 10 Hz; and iii), fast growth of lamellipodia leading edge alternates with local retractions.     

Distribution of Virulence Factors and Molecular Fingerprinting of Aeromonas Species Isolates from Water and Clinical Samples: Suggestive Evidence of Water-to-Human Transmission

A total of 227 isolates of Aeromonas obtained from different geographical locations in the United States and different parts of the world, including 28 reference strains, were analyzed to determine the presence of various virulence factors. These isolates were also fingerprinted using biochemical identification and pulse-field gel electrophoresis (PFGE). Of these 227 isolates, 199 that were collected from water and clinical samples belonged to three major groups or complexes, namely, the A. hydrophila group, the A. caviae-A. media group, and the A. veronii-A. sobria group, based on biochemical profiles, and they had various pulsotypes. When virulence factor activities were examined, Aeromonas isolates obtained from clinical sources had higher cytotoxic activities than isolates obtained from water sources for all three Aeromonas species groups. Likewise, the production of quorum-sensing signaling molecules, such as N-acyl homoserine lactone, was greater in clinical isolates than in isolates from water for the A. caviae-A. media and A. hydrophila groups. Based on colony blot DNA hybridization, the heat-labile cytotonic enterotoxin gene and the DNA adenosine methyltransferase gene were more prevalent in clinical isolates than in water isolates for all three Aeromonas groups. Using colony blot DNA hybridization and PFGE, we obtained three sets of water and clinical isolates that had the same virulence signature and had indistinguishable PFGE patterns. In addition, all of these isolates belonged to the A. caviae-A. media group. The findings of the present study provide the first suggestive evidence of successful colonization and infection by particular strains of certain Aeromonas species after transmission from water to humans.Aeromonas species cause both intestinal and extraintestinal infections (25, 33, 78), and the latter include septicemia, cellulitis, wound infections, urinary tract infections, hepatobiliary tract infections, soft tissue infections, and, occasionally, meningitis and peritonitis (25, 30, 78). In immunocompromised children, these pathogens can cause even more severe forms of infections, such as hemolytic-uremic syndrome (HUS) and necrotizing fasciitis (3, 23), although detailed studies are needed to establish such associations. Worldwide, the rate of isolation of Aeromonas from diarrheic stools has been reported to be as high as 10.8%, compared to 2.1% for healthy controls (25, 37, 78). An increased rate of isolation of Aeromonas species was reported in flood water samples during Hurricane Katrina in New Orleans (58), and skin and soft tissue infections caused by Aeromonas species were among the most common infections in the survivors of the 2004 tsunami in southern Thailand (28). In particular, Aeromonas salmonicida causes fish infections that result in huge economical losses in the fishing industry (6, 22). The ability of aeromonads, as well as other bacteria, to survive in chlorinated water when they are in biofilms and their resistance to multiple antibiotics are major public health concerns (46).Aeromonas-related gastroenteritis remains somewhat controversial (24, 36). There have been a number of well-described cases and a few documented outbreaks, but whether all aeromonad fecal isolates from symptomatic persons are the actual causes of diarrheal disease is still questionable. One theory for this conundrum was posed in 2000 by two of us, who suggested that only specific subsets of Aeromonas strains within and between species are actually pathogenic for humans (38). This highlights the importance of developing accurate biotyping, molecular fingerprinting, and virulence factor analysis methods for differentiating environmental and clinical aeromonads from one another and for comparing them (38).Of the 19 currently recognized Aeromonas species, A. hydrophila, A. caviae, and A. veronii biovar sobria are the most common species known to cause the majority of human infections, and they account for more than 85% of all clinical isolates (34). The pathogenesis of Aeromonas infections is multifactorial, as aeromonads produce a wide variety of virulence factors, including hemolysins, cytotonic and cytotoxic enterotoxins, proteases, lipases, leucocidins, endotoxin, adhesions, and an S layer, that act in concert to cause disease in the host (12-14, 50, 51). The cytotoxic enterotoxin Act, which has some similarities to aerolysin (31), is one of the most significant virulence factors in diarrheal isolate SSU of A. hydrophila and was first characterized in our laboratory (12). Act is secreted by the type II secretion system (T2SS) and has hemolytic, cytotoxic, and enterotoxic activities (12). In addition, our laboratory recently sequenced and characterized two other secretion systems, T3SS and T6SS, that were found to contribute to the virulence of A. hydrophila SSU (66, 67, 72). We recently characterized an effector of the T3SS, which was designated AexU, and found that it was associated with ADP ribosylation of host cell proteins, a rounded phenotype in HeLa cells, inhibition of phagocytosis, induction of apoptosis, and mouse mortality (66, 67). In recent studies, we also investigated the role of two T6SS-associated effectors, the valine-glycine repeat G (VgrG) family of proteins and hemolysin-coregulated protein (Hcp), in the virulence of A. hydrophila (71, 72). We demonstrated that VgrG1 of A. hydrophila had actin-ADP ribosylation activity that induced host cell cytotoxicity (71). Based on the model for T6SS, the VgrG1 protein must assemble with the highly homologous VgrG2 and VgrG3 proteins to form a cell-puncturing device to deliver effector proteins into the host cells (59). We also obtained evidence that expression of the hcp gene in HeLa cells led to their apoptosis, and animals immunized with recombinant Hcp were protected from subsequent challenge with a lethal dose of wild-type A. hydrophila SSU (72).In addition, cytotonic enterotoxins (e.g., Alt [heat labile] and Ast [heat stable]) were identified in a diarrheal A. hydrophila SSU isolate (14, 63) that induced fluid secretion in the ligated small intestinal loops of animals (47). More recently, we identified some additional virulence factor-encoding and regulatory genes, such as the enolase, hlyA (hemolysin), gidA (glucose-inhibited division A), vacB (virulence-associated protein B), dam (DNA adenine methyltransferase), and tagA (ToxR-regulated lipoprotein) genes, which modulated the virulence of A. hydrophila SSU (19-21, 57, 62, 64). The production of such a wide array of virulence factors by Aeromonas species is indicative of their potential to cause severe diseases in humans. These virulence factor-encoding genes might be differentially expressed in Aeromonas species depending on the environmental conditions, such as water or the human host.A cell-to-cell signaling system, known as quorum sensing (QS), might play an important role in sensing physiological conditions and helping bacteria express the virulence genes at an appropriate time under the appropriate conditions. Thus far, at least three QS circuits have been identified in Gram-negative bacteria, and they were designated LuxRI (autoinducer 1 [AI-1]), LuxS (AI-2), and AI-3 (epinephrine/norepinephrine). All of these QS systems were detected in our SSU clinical strain of A. hydrophila, and we recently demonstrated that N-acyl homoserine lactone (AHL) (AI-1) and AI-2-mediated QS controlled the virulence of A. hydrophila SSU (40, 43). Further, we observed decreased production of N-acyl homoserine lactones when we deleted two major virulence factor-encoding genes, the act gene and the gene encoding an outer membrane protein (aopB), an important component of the T3SS (65), from A. hydrophila SSU. Likewise, we observed that N-acyl homoserine lactone production was also modulated by regulatory genes, such as dam and gidA, in A. hydrophila SSU (18). Thus, differential expression of genes might also be an important factor in the pathogenesis of Aeromonas species.The presence of any virulence gene in strains of Aeromonas isolated from water should be carefully scrutinized, as such genes could be expressed better in a human host, which could lead to devastating outcomes. In addition, it is possible that in the environment certain Aeromonas clones may predominate and cause human diseases more frequently than other clones. Thus, it is important to determine the clonal variation of a range of Aeromonas species isolated from various sources and identify predominant clones by a polyphasic approach that includes biochemical phenotyping, virulence marker detection, and molecular fingerprinting techniques.In the present study, we compared 199 Aeromonas isolates, 146 of which were from water sources and 53 of which were from human patients with diarrhea in the Unites States. In addition, 28 reference and classical strains that were obtained from various culture collections and/or were isolated from specimens obtained in diverse geographical areas of the world, including water and clinical specimens, were also characterized. All isolates were biochemically identified to the phenospecies group level, examined for the presence of a set of 11 virulence factors by using DNA colony blot hybridization, and fingerprinted by using pulsed-field gel electrophoresis (PFGE). Some of the virulence factors selected, including T6SS effectors, were also examined by using functional assays. Our data provide the first suggestive evidence of water-to-human transmission, i.e., of successful colonization and infection by particular strains of certain Aeromonas species.     

Discovery of a series of potent,orally active α,α-disubstituted piperidine NK1 antagonists

Modification of prototype NK₁ antagonist 2 resulted in the synthesis of a series of simple amides 6 and retroamides 9. These compounds were shown to be potent and orally active NK₁ antagonists.