NopA is associated with cell surface appendages produced by the type III secretion system of Rhizobium sp. strain NGR234

Rhizobium sp. strain NGR234, which is capable of interacting with a large number of legumes, utilizes a variety of signaling molecules to establish nitrogen-fixing symbioses. Among these are nodulation outer proteins (Nops) that transit through a type III secretion system (TTSS). Abolition of Nop secretion affects nodulation of certain legumes. Under free-living conditions, the secretion of Nops can be induced by the addition of flavonoids. Here, we show that an in-frame deletion of nopA abolishes secretion of all other Nops and has the same impact on nodule formation as mutations that lead to a nonfunctional TTSS. This secretion-minus phenotype of the nopA mutant, as well as bioinformatics analysis of NopA itself, suggests that NopA could be an external component of the TTSS. Electron microscopy showed that NGR234 synthesizes fibrillar structures on the cell surface in a flavonoid-inducible and NopA-dependent manner. Purification of the macromolecular surface appendages revealed that NopA is a major component of these structures.     

Phenotypic screening of hepatocyte nuclear factor (HNF) 4-gamma receptor knockout mice

Using the mouse as a model organism in pharmaceutical research presents unique advantages as its physiology in many ways resembles the human physiology, it also has a relatively short generation time, low breeding and maintenance costs, and is available in a wide variety of inbred strains. The ability to genetically modify mouse embryonic stem cells to generate mouse models that better mimic human disease is another advantage. In the present study, a comprehensive phenotypic screening protocol is applied to elucidate the phenotype of a novel mouse knockout model of hepatocyte nuclear factor (HNF) 4-gamma. HNF4-gamma is expressed in the kidneys, gut, pancreas, and testis. The first level of the screen is aimed at general health, morphologic appearance, normal cage behaviour, and gross neurological functions. The second level of the screen looks at metabolic characteristics and lung function. The third level of the screen investigates behaviour more in-depth and the fourth level consists of a thorough pathological characterisation, blood chemistry, haematology, and bone marrow analysis. When compared with littermate wild-type mice (HNF4-gamma(+/+)), the HNF4-gamma knockout (HNF4-gamma(-/-)) mice had lowered energy expenditure and locomotor activity during night time that resulted in a higher body weight despite having reduced intake of food and water. HNF4-gamma(-/-) mice were less inclined to build nest and were found to spend more time in a passive state during the forced swim test.     

Kinetics of enzymatic depolymerization of guar galactomannan

A new mathematical model based on Michaelis Menten (MM) kinetics is developed to predict the changes in molecular weight distribution (MWD) during the enzymatic depolymerization of guar galactomannan. The model accounts for the effect of branching by considering the guar molecule as a substrate having three types of bonds with different MM kinetic parameters. The overall kinetics of the enzymatic reactions then can be represented in terms of composite kinetic parameters that are functions of the MM parameters for the individual bonds. The depolymerization is assumed to follow a random scission mechanism, in which an enzyme randomly attacks the substrate molecule at any one of the three types of bonds, and leaves the substrate on cleavage of the bond. Expressions for the variation in molecular weights during depolymerization are developed by applying moment generating techniques to the kinetic model. The model is evaluated against the complete MWD obtained using gel permeation chromatography. During the initial stages of depolymerization, the enzymatic reaction is in the zero-order regime of MM kinetics and the polydispersity index (PDI) increases with time. Subsequently, the PDI decreases as the depolymerization tends to follow first order kinetics. We also show that for a zero-order, random or nonrandom scission, the variation of PDI with time can exhibit a maximum. These analyses confirm that an increase in PDI during the depolymerization is not necessarily due to nonrandom scission, as previously concluded.     

Steroid 21-hydroxylase gene mutational spectrum in 50 Tunisian patients: Characterization of three novel polymorphisms

Congenital adrenal hyperplasia (CAH) is an autosomal recessive disease of steroid biosynthesis in humans. More than 90% of all CAH cases are caused by mutations of the 21-hydroxylase gene (CYP21A2), and approximately 75% of the defective CYP21A2 genes are generated through an intergenic recombination with the neighboring CYP21A1P pseudogene. In this study, the CYP21A2 gene was genotyped in 50 patients in Tunisia with the clinical diagnosis of 21-hydroxylase deficiency. CYP21A2 mutations were identified in 87% of the alleles. The most common point mutation in our population was the pseudogene specific variant p.Q318X (26%). Three novel single nucleotide polymorphism (SNP) loci were identified in the CYP21A2 gene which seems to be specific for the Tunisian population. The overall concordance between genotype and phenotype was 98%. With this study the molecular basis of CAH has been characterized, providing useful results for clinicians in terms of prediction of disease severity, genetic and prenatal counseling.     

Paenibacillus hemolyticus, the first hemolytic Paenibacillus with growth-promoting activities discovered

Paenibacillus spp. are Gram-positive, facultatively aerobic, bacilli-shaped endospore-forming bacteria. They have been detected in a variety of environments, such as soil, water, forage, insect larvae, and even clinical samples. The strain 139SI (GenBank accession No.: JF825470.1) from three strains of Paenibacillus isolates investigated here was chosen as the type strain of the proposed novel species. The other two similar strain isolates investigated were 140SI (JF825471.1) and 141SI (JQ734548.1). These strains were identified as members of the genus Paenibacillus on the basis of phenotypic characteristics, phylogenetic analysis and 16S rRNA G+C content. Surprisingly, these strains exhibited a strong hemolytic activity on 5% sheep blood agar. Their crude extracts also showed positive growth-promoting activities in colon cancer and Vero cell lines. To our knowledge, this is the first Paenibacillus with hemolytic and growth-promoting activities reported, and the name Paenibacillus hemolyticus for this novel species is proposed. The capability of this novel species in hemolytic and cell growth activities suggests its potential in both clinical and pharmacological implications.     

Toll-like receptor 2 and Toll-like receptor 4 polymorphisms and susceptibility to asthma and allergic rhinitis: a case-control analysis

The aim of the study was to investigate whether polymorphisms in genes encoding Toll-like receptors (TLR2 and TLR4) may modify relative risk for development of asthma or allergic rhinitis. The results showed that the genotype and allele frequencies of the TLR2 Arg753Gln and TLR4 Asp299Gly polymorphisms were not significantly different between asthmatic children or allergic rhinitis when compared to controls (p>0.05 for each) or even when compared further with IgE level. However, it was shown that the mutant allele of TLR2 or TLR4 polymorphisms were significantly associated with the moderate-severe group compared to the mild group in both atopic asthmatics and allergic rhinitis group (p>0.001 for each). In conclusion, our study demonstrates a lack of association of TLR2 and TLR4 polymorphisms with asthma and allergic rhinitis but suggests significant association between these genetic variants and the disease severity.     

Correlation between trochlear groove depth and patellar position during open and closed kinetic chain exercises in subjects with anterior knee pain

The purpose of this study was to correlate the trochlear shape and patellar tilt angle and lateral patellar displacement at rest and maximal voluntary isometric contraction (MVIC) exercises during open (OKC) and closed kinetic chain (CKC) in subjects with and without anterior knee pain. Subjects were all women, 20 who were clinically healthy and 19 diagnosed with anterior knee pain. All subjects were evaluated and subjected to magnetic resonance exams during OKC and CKC exercise with the knee placed at 15, 30, and 45 degrees of flexion. The parameters evaluated were sulcus angle, patellar tilt angle and patellar displacement using bisect offset. Pearson's r coefficient was used, with p < .05. Our results revealed in knee pain group during CKC and OKC at 15 degrees that the increase in the sulcus angle is associated with a tilt increase and patellar lateral displacement. Comparing sulcus angle, patellar tilt angle and bisect offset values between MVIC in OKC and CKC in the knee pain group, it was observed that patellar tilt angle increased in OKC only with the knee flexed at 30 degrees. Based on our results, we conclude that reduced trochlear depth is correlated with increased lateral patellar tilt and displacement during OKC and CKC at 15 degrees of flexion in people with anterior knee pain. By contrast, 30 degrees of knee flexion in CKC is more recommended in rehabilitation protocols because the patella was more stable than in other positions.     

Withaferin A Induces Proteasome Inhibition,Endoplasmic Reticulum Stress,the Heat Shock Response and Acquisition of Thermotolerance

In the present study, withaferin A (WA), a steroidal lactone with anti-inflammatory and anti-tumor properties, inhibited proteasome activity and induced endoplasmic reticulum (ER) and cytoplasmic HSP accumulation in Xenopus laevis A6 kidney epithelial cells. Proteasomal inhibition by WA was indicated by an accumulation of ubiquitinated protein and a decrease in chymotrypsin-like activity. Additionally, immunoblot analysis revealed that treatment of cells with WA induced the accumulation of HSPs including ER chaperones, BiP and GRP94, as well as cytoplasmic/nuclear HSPs, HSP70 and HSP30. Furthermore, WA-induced an increase in the relative levels of the protein kinase, Akt, while the levels of actin were unchanged compared to control. Northern blot experiments determined that WA induced an accumulation in bip, hsp70 and hsp30 mRNA but not eIF-1α mRNA. Interestingly, WA acted synergistically with mild heat shock to enhance HSP70 and HSP30 accumulation to a greater extent than the sum of both stressors individually. This latter phenomenon was not observed with BiP or GRP94. Immunocytochemical analysis indicated that WA-induced BiP accumulation occurred mainly in the perinuclear region in a punctate pattern, while HSP30 accumulation occurred primarily in a granular pattern in the cytoplasm with some staining in the nucleus. Prolonged exposure to WA resulted in disorganization of the F-actin cytoskeleton as well as the production of relatively large HSP30 staining structures that co-localized with F-actin. Finally, prior exposure of cells to WA treatment, which induced the accumulation of HSPs conferred a state of thermal protection since it protected the F-actin cytoskeleton against a subsequent cytotoxic thermal challenge.     

Crossing over...Markov meets Mendel

Chromosomal crossover is a biological mechanism to combine parental traits. It is perhaps the first mechanism ever taught in any introductory biology class. The formulation of crossover, and resulting recombination, came about 100 years after Mendel's famous experiments. To a great extent, this formulation is consistent with the basic genetic findings of Mendel. More importantly, it provides a mathematical insight for his two laws (and corrects them). From a mathematical perspective, and while it retains similarities, genetic recombination guarantees diversity so that we do not rapidly converge to the same being. It is this diversity that made the study of biology possible. In particular, the problem of genetic mapping and linkage-one of the first efforts towards a computational approach to biology-relies heavily on the mathematical foundation of crossover and recombination. Nevertheless, as students we often overlook the mathematics of these phenomena. Emphasizing the mathematical aspect of Mendel's laws through crossover and recombination will prepare the students to make an early realization that biology, in addition to being experimental, IS a computational science. This can serve as a first step towards a broader curricular transformation in teaching biological sciences. I will show that a simple and modern treatment of Mendel's laws using a Markov chain will make this step possible, and it will only require basic college-level probability and calculus. My personal teaching experience confirms that students WANT to know Markov chains because they hear about them from bioinformaticists all the time. This entire exposition is based on three homework problems that I designed for a course in computational biology. A typical reader is, therefore, an instructional staff member or a student in a computational field (e.g., computer science, mathematics, statistics, computational biology, bioinformatics). However, other students may easily follow by omitting the mathematically more elaborate parts. I kept those as separate sections in the exposition.