Crystal structure of human peptidoglycan recognition protein I alpha bound to a muramyl pentapeptide from Gram-positive bacteria

Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors of the innate immune system that bind bacterial peptidoglycans (PGNs). We determined the crystal structure, to 2.1 A resolution, of the C-terminal PGN-binding domain of human PGRP-I alpha in complex with a muramyl pentapeptide (MPP) from Gram-positive bacteria containing a complete peptide stem (L-Ala-D-isoGln-L-Lys-D-Ala-D-Ala). The structure reveals important features not observed previously in the complex between PGRP-I alpha and a muramyl tripeptide lacking D-Ala at stem positions 4 and 5. Most notable are ligand-induced structural rearrangements in the PGN-binding site that are essential for entry of the C-terminal portion of the peptide stem and for locking MPP in the binding groove. We propose that similar structural rearrangements to accommodate the PGN stem likely characterize many PGRPs, both mammalian and insect.     

Extraction and characterization of biocompatible hydroxyapatite from fresh water fish scales for tissue engineering scaffold

In bone tissue engineering, porous hydroxyapatite (HAp) is used as filling material for bone defects, augmentation, artificial bone graft and scaffold material. The present paper compares the preparation and characterization of HAp from fish scale (FS) and synthetic body fluid (SBF) solution. Thermo gravimetric analysis, differential thermal analysis, Fourier transform infrared spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM) and particle size analysis of the samples have been performed. The analysis indicates that synthesized HAp consists of sub-micron HAp particle with Ca/P ratio corresponding to FS and SBF 1.62 and 1.71, respectively. MTT assay and quantitative DNA analysis show growth and proliferation of cells over the HA scaffold with the increase in time. The shape and size (morphology) of mesenchymal stem cells after 3 days show a transition from rounded shape to elongated and flattened shape expressing its spreading behavior. These results confirm that HAp bio-materials from fish scale are physico-chemically and biologically equivalent to the chemically synthesized HAp from SBF. Biological HAp, thus, possesses a great potential for conversion of industrial by-product into highly valuable compounds using simple effective and novel processes.     

Inhibition of pathogenic bacterial biofilm by biosurfactant produced by Lysinibacillus fusiformis S9

A biosurfactant producing microbe isolated from a river bank was identified as Lysinibacillus fusiformis S9. It was identified with help of biochemical tests and 16S rRNA gene phylogenetic analysis. The biosurfactant S9BS produced was purified and characterized as glycolipid. The biosurfactant showed remarkable inhibition of biofilm formation by pathogenic bacteria like Escherichia coli and Streptococcus mutans. It was interesting to note that at concentration of 40 μg ml^?1 the biosurfactant did not show any bactericidal activity but restricted the biofilm formation completely. L. fusiformis is reported for the first time to produce a glycolipid type of biosurfactant capable of inhibiting biofilm formation by pathogenic bacteria. The biosurfactant inhibited bacterial attachment and biofilm formation equally well on hydrophilic as well as hydrophobic surfaces like glass and catheter tubing. This property is significant in many biomedical applications where the molecule should help in preventing biofouling of surfaces without being toxic to biotic system.     

Enhanced expression of Plasmodium falciparum heat shock protein PFHSP70-I at higher temperatures and parasite survival

Abstract The effect of various body temperatures, encountered during malaria fever, on the synthesis of Plasmodium falciparum heat-shock protein called PFHSP70-I and parasite growth rates among five different isolates are described. The results show that after the exposure of parasites at 39°C for 30 min the amount of PFHSP70-I in all five isolates increased markedly and significantly, whereas parasite growth rates and the amount of total blood stage antigens remained almost unaffected. This indicates that the PFHSP70-I gene responds to heat-shock by producing higher amounts of PFHSP70-I protein, presumably to protect the parasite from being killed during malaria fever.     

Information transmission in microbial and fungal communication: from classical to quantum

Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication. In particular, we highlight bacterial collective behavior with classical and quantum mechanical approaches (including quantum information). Moreover, we shed a new light to introduce the concept of quantum synthetic biology and possible cellular quantum Turing test.     

Quorum sensing: a quantum perspective

Quorum sensing is the efficient mode of communication in the bacterial world. After a lot of advancements in the classical theory of quorum sensing few basic questions of quorum sensing still remain unanswered. The sufficient progresses in quantum biology demands to explain these questions from the quantum perspective as non trivial quantum effects already have manifested in various biological processes like photosynthesis, magneto-reception etc. Therefore, it’s the time to review the bacterial communications from the quantum view point. In this article we carefully accumulate the latest results and arguments to strengthen quantum biology through the addition of quorum sensing mechanism in the light of quantum mechanics.     

Stereoselectivity of the guanyl-exchangeable nucleotide-binding site of tubulin probed by guanosine 5'-O-(2-thiotriphosphate) diastereoisomers

The active site of the exchangeable nucleotide-binding site of tubulin was studied by using diastereoisomers A (Sp) and B (Rp) of guanosine 5'-O-(2-thiotriphosphate) (GTP beta S) where the phosphorus atom to which sulfur is attached is chiral. Turbidimetric measurements were used to follow kinetics, and electron microscopy was used to evaluate polymeric forms. Both isomers at 0.5 mM promoted the assembly of tubulin in buffer containing 0.1 M 2-(N-morpholino)ethanesulfonic acid, 30% glycerol, 3 mM MgCl2, and 1 mM EGTA, pH 6.6, 23-37 degrees C. GTP beta S(A) promoted assembly into microtubules, although a few bundles were also found by electron microscopy. However, GTP beta S(B) induced assembly of tubulin into bundles of sheets and microtubules. As expected, 0.5 mM GTP induced tubulin to assemble into microtubules, thin sheets, and a few bundles. Both GTP and GTP beta S(A) were hydrolyzed in the tubulin polymers. However, more than 95% of the bound GTP beta S(B) was not hydrolyzed. Higher concentrations of GTP beta S(B), i.e., 1 mM, also induced bundles of sheets and microtubules, with 86% of the thionucleotide bound as the triphosphate. The GTP beta S(B)-induced polymers were considerably more cold stable than the GTB beta S(A)-induced microtubules, which were more cold stable than GTP-induced polymers. Mg(II) (2-5 mM) had minimal effects on the structures induced by GTP beta S(A) or -(B) isomers in the tubulin assembly system. However, at 1 mM Mg(II), no assembly was found with GTP beta S(A) and tubulin.(ABSTRACT TRUNCATED AT 250 WORDS)     

Ethanol and carbon-source starvation enhance the accumulation of HSP80 in Neurospora crassa

In Neurospora crassa, heat shock results in the induction of 9 to 11 heat shock proteins (HSP), of which HSP80 is the most abundant and the first to be synthesized. The induction of HSP80 was investigated during normal growth (2% sucrose) and under sucrose starvation. Transfer of mycelium to a medium supplemented with ethanol stimulated the synthesis of HSP80, even at the normal growth temperature of 28 degrees C. It was also synthesized under carbon starvation conditions, where the medium was supplemented with 0.02% sucrose, 0.3% acetate, 0.2% lactate, or ethanol. A 30-35 kilodalton polypeptide was induced by heat shock in carbon-sufficient media, but in 0.02% sucrose and 0.3% acetate containing media it was synthesized at normal temperatures. While the overall heat shock response remained unaltered in these cultures, the abundance of HSP90 and HSP70, relative to HSP80, was greater. HSP80 appears to be controlled by carbon-catabolite repression as well as heat shock. Another high molecular mass protein (tentatively designated alc'80') was observed to be induced by heat shock, provided carbon starvation conditions prevailed concurrently.     

Short Communication: Leaching of Chromite overburden with various native bacterial strains

Four heterotrophic bacterial strains were isolated from soil and water samples from a chromite mine in Sukinda valley in Orissa. They were identified as Lactobacillus acidophilus, Staphylococcus lactis, Lactobacillus sp. and Propionibacterium acnes. Each strain was used for leaching of metals from chromite overburden of Sukinda. Comparatively, Lactobacillus sp. showed maximum capability for metal solubilization. It leached a maximum of 5.98% of nickel in 35 days of contact time.     

Classification of pathogenic microbes using a minimal set of single nucleotide polymorphisms derived from whole genome sequences

In a context specific manner, Intra-species genomic variation plays an important role in phenotypic diversity observed among pathogenic microbes. Efficient classification of these pathogens is important for diagnosis and treatment of several infectious diseases. NGS technologies have provided access to wealth of data that can be utilized to discover important markers for pathogen classification. In this paper, we described three different approaches (Jensen-Shannon divergence, random forest and Shewhart control chart) for identification of a minimal set of SNPs that can be used for classification of organisms. These methods are generic and can be implemented for analysis of any organism. We have shown usefulness of these approaches for analysis of Mycobacterium tuberculosis and Escherichia coli isolates. We were able to identify a minimal set of 18 SNPs that can be used as molecular markers for phylogroup based classification and 8 SNPs for pathogroup based classification of E. coli.