The dual probiotic and antibiotic nature of Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus is a predatory bacterium which attacks and consumes other bacterial strains, including the well known pathogens E. coli O157 : H7, Salmonella typhimurium and Helicobacter pylori. This remarkable activity has been the focus of research for nearly five decades, with exciting practical applications to medical, agriculture and farming practices recently being published. This article reviews many of the exciting steps research into this bacterium, and similar bacteria, has taken, focusing primarily on their use as both an antibiotic to remove harmful and pathogenic bacteria and as a probiotic to help curb and control the bacterial populations within the intestinal tract. Owing to the unique and dual nature of this bacterium, this review proposes the use of "amphibiotic" to describe these bacteria and their activities.     

Determination of biotic aetiology of tapping panel dryness (TPD) syndrome of rubber tree (Hevea brasiliensis) by return-polyacrylamide gel electrophoresis (R-PAGE) technique

Tapping panel dryness (TPD) syndrome affecting rubber tree (Hevea brasiliensis) is known to reduce natural latex production. Its aetiology remains ambiguous despite long years of research. A low molecular weight RNA similar to viroid RNA was isolated from TPD-affected samples of rubber trees. In the present study, a modified return-polyacrylamide gel electrophoresis procedure was standardised. The viroid-like low molecular weight (LMW) RNA was found associated with leaf, bark and root tissues and rubber seedlings. The technique was employed to detect LMW RNA in different clones of rubber planted in different locations and in bud-grafted plants. The LMW RNA isolated from TPD-affected trees was found infectious on seedlings of tomato cv Pusa Ruby. The LMW RNA was reisolated from symptomatic tomato leaves but not from control plants. This is for the first time that a biotic agent, a viroid RNA, is found consistently associated with the syndrome. The technology developed can be useful to demonstrate the onset of TPD in untapped trees in the absence of other methods such as nucleic acid hybridisation.     

Inhibition of LuxS by S-ribosylhomocysteine analogues containing a [4-aza]ribose ring

LuxS (S-ribosylhomocysteinase) catalyzes the cleavage of the thioether linkage of S-ribosylhomocysteine (SRH) to produce homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor to a small signaling molecule that mediates interspecies bacterial communication called autoinducer 2 (AI-2). Inhibitors of LuxS should interfere with bacterial interspecies communication and potentially provide a novel class of antibacterial agents. In this work, SRH analogues containing substitution of a nitrogen atom for the endocyclic oxygen as well as various deoxyriboses were synthesized and evaluated for LuxS inhibition. Two of the [4-aza]SRH analogues showed modest competitive inhibition (K(I) ～40 μM), while most of the others were inactive. One compound that contains a hemiaminal moiety exhibited time-dependent inhibition, consistent with enzyme-catalyzed ring opening and conversion into a more potent species (K(I)(?)=3.5 μM). The structure-activity relationship of the designed inhibitors highlights the importance of both the homocysteine and ribose moieties for high-affinity binding to LuxS active site.     

Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases

M24B peptidases cleaving Xaa-Pro bond in dipeptides are prolidases whereas those cleaving this bond in longer peptides are aminopeptidases-P. Bacteria have small aminopeptidases-P (36-39 kDa), which are diverged from canonical aminopeptidase-P of Escherichia coli (50 kDa). Structure-function studies of small aminopeptidases-P are lacking. We report crystal structures of small aminopeptidases-P from E. coli and Deinococcus radiodurans, and report substrate-specificities of these proteins and their ortholog from Mycobacterium tuberculosis. These are aminopeptidases-P, structurally close to small prolidases except for absence of dipeptide-selectivity loop. We noticed absence of this loop and conserved arginine in canonical archaeal prolidase (Maher et al., Biochemistry. 43, 2004, 2771-2783) and questioned its classification. Our enzymatic assays show that this enzyme is an aminopeptidase-P. Further, our mutagenesis studies illuminate importance of DXRY sequence motif in bacterial small aminopeptidases-P and suggest common evolutionary origin with human XPNPEP1/XPNPEP2. Our analyses reveal sequence/structural features distinguishing small aminopeptidases-P from other M24B peptidases.     

Glucose deprivation induced upregulation of phosphoenolpyruvate carboxykinase modulates virulence in Leishmania donovani

Various physiological stimuli trigger the conversion of noninfective Leishmania donovani promastigotes to the infective form. Here, we present the first evidence of the effect of glucose starvation, on virulence and survival of these parasites. Glucose starvation resulted in a decrease in metabolically active parasites and their proliferation. However, this was reversed by supplementation of gluconeogenic amino acids. Glucose starvation induced metacyclogenesis and enhanced virulence through protein kinase A regulatory subunit (LdPKAR1) mediated autophagy. Glucose starvation driven oxidative stress upregulated the antioxidant machinery, culminating in increased infectivity and greater parasitic load in primary macrophages. Interestingly, phosphoenolpyruvate carboxykinase (LdPEPCK), a gluconeogenic enzyme, exhibited the highest activity under glucose starvation to regulate growth of L. donovani by alternatively utilising amino acids. Deletion of LdPEPCK (Δpepck) decreased virulent traits and parasitic load in primary macrophages but increased autophagosome formation in the mutant parasites. Furthermore, Δpepck parasites failed to activate the Pentose Phosphate Pathway shunt, abrogating NADPH/NADP⁺ homoeostasis, conferring increased susceptibility towards oxidants following glucose starvation. In conclusion, this study showed that L. donovani undertakes metabolic rearrangements via gluconeogenesis under glucose starvation for acquiring virulence and its survival in the hostile environment.     

Pareto-based multi-objective optimization for classification in data mining

This paper explores the possibility of classification based on Pareto multi-objective optimization. The efforts on solving optimization problems using the Pareto-based MOO methodology have gained increasing impetus on comparison of selected constraints. Moreover we have different types of classification problem based on optimization model like single objective optimization, MOO, Pareto optimization and convex optimization. All above techniques fail to generate distinguished class/subclass from existing class based on sensitive data. However, in this regard Pareto-based MOO approach is more powerful and effective in addressing various data mining tasks such as clustering, feature selection, classification, and knowledge extraction. The primary contribution of this paper is to solve such noble classification problem. Our work provides an overview of the existing research on MOO and contribution of Pareto based MOO focusing on classification. Particularly, the entire work deals with association of sub-features for noble classification. Moreover potentially interesting sub-features in MOO for classification are used to strengthen the concept of Pareto based MOO. Experiment has been carried out to validate the theory with different real world data sets which are more sensitive in nature. Finally, experimental results provide effectiveness of the proposed method using sensitive data.     

The response of a natural phytoplankton community from the Godavari River Estuary to increasing CO2 concentration during the pre-monsoon period

This paper reports for the first time upon the effects of increasing CO₂ concentrations on a natural phytoplankton assemblage in a tropical estuary (the Godavari River Estuary in India). Two short-term (5-day) bottle experiments were conducted (with and without nutrient addition) during the pre-monsoon season when the partial pressure of CO₂ in the surface water is quite low. The results reveal that the concentrations of total chlorophyll, the phytoplankton growth rate, the concentrations of particulate organic matter, the photosynthetic oxygen evolution rates, and the total bacterial count were higher under elevated CO₂ treatments, as compared to ambient conditions (control). δ¹³C of particulate organic matter (POM) varied inversely with respect to CO₂, indicating a clear signature of higher CO₂ influx under the elevated CO₂ levels. Whereas, δ¹³C_POM in the controls indicated the existence of an active bicarbonate transport system under limited CO₂ supply. A considerable change in phytoplankton community structure was noticed, with marker pigment analysis by HPLC revealing that cyanobacteria were dominant over diatoms as CO₂ concentrations increased. A mass balance calculation indicated that insufficient nutrients (N, P and Si) might have inhibited diatom growth compared to cyanobacteria, regardless of increased CO₂ supply. The present study suggests that CO₂ concentration and nutrient supply could have significant effects on phytoplankton physiology and community composition for natural phytoplankton communities in this region. However, this work was conducted during a non-discharge period (nutrient-limited conditions) and the responses of phytoplankton to increasing CO₂ might not necessarily be the same during other seasons with high physicochemical variability. Further investigation is therefore needed.     

Enzyme activities in Pennisetum seedlings germinated in the presence of abscisic and gibberellic acids

Effects of abscisic acid (ABA) and gibberellic acid (GA₃), alone and in combination, on growth and activity of alanine aminotransferase (GPT), aspartate aminotransferase (GOT), and glutamate dehydrogenase (GLDH) were studied in aerial parts of Pennisetum typhoides seedlings. ABA inhibited growth and activity of GLDH, but stimulated the activity of GPT and weakly that of GOT. GA₃, on the other hand, did not affect the activity of any of the enzymes tested, but in combination with ABA tended to antagonise the efrect of the latter.