Endophytic fungal communities in woody perennials of three tropical forest types of the Western Ghats, southern India

Fungal endophytes of tropical trees are expected to be exceptionally species rich as a consequence of high tree diversity in the tropics and the purported host restriction among the endophytes. Based on this premise, endophytes have been regarded as a focal group for estimating fungal numbers because their possible hyperdiverse nature would reflect significantly global fungal diversity. We present our consolidated ten-year work on 75 dicotyledonous tree hosts belonging to 33 families and growing in three different types of tropical forests of the NBR in the Western Ghats, southern India. We conclude that endophyte diversity in these forests is limited due to loose host affiliations among endophytes. Some endophytes have a wide host range and colonize taxonomically disparate hosts suggesting adaptations in them to counter a variety of defense chemicals in their hosts. Furthermore, such polyphagous endophytes dominate the endophyte assemblages of different tree hosts. Individual leaves may be densely colonized but only by a few endophyte species. It appears that the environment (the type of forest in this case) has a larger role in determining the endophyte assemblage of a plant host than the taxonomy of the host plant. Thus, different tropical plant communities have to be studied for their endophyte diversity to test the generalization that endophytes are hyperdiverse in the tropics, estimate their true species richness, and use them as a predictor group for more accurate assessment of global fungal diversity.

Evaluation of relative growth limitation due to depletion of glucose and oxygen during fungal growth on a spherical solid particle

A mathematical model for glucose and oxygen consumption, and cell growth during fungal growth on a single solid particle is developed. A moving biofilm is assumed to be present on the surface of the solid particle. Initially only glucose is assumed to be growth limiting and later oxygen transferred from the gas phase on to the biofilm is also assumed to be growth limiting. Glucose is found to be severely growth limiting when assumed to be the only growth limiting factor and its limiting levels far less severe when oxygen limitation is also included. The objective of the model is to gain a better understanding of the mass transfer and relative growth limiting characteristics of glucose and oxygen in fungal growth systems. The results obtained from the model proposed here will be the subject of future work.

Survival of the fittest and zero sum games

Competition for available resources is natural amongst coexisting species, and the fittest contenders dominate over the rest in evolution. The. dynamics of this selection is studied using a simple linear model. It has similarities to features of quantum computation, in particular conservation laws leading to destructive interference. Compared to an altruistic scenario, competition introduces instability and eliminates the weaker species in a finite time.

A Transcript Cleavage Factor of Mycobacterium tuberculosis Important for Its Survival

After initiation of transcription, a number of proteins participate during elongation and termination modifying the properties of the RNA polymerase (RNAP). Gre factors are one such group conserved across bacteria. They regulate transcription by projecting their N-terminal coiled-coil domain into the active center of RNAP through the secondary channel and stimulating hydrolysis of the newly synthesized RNA in backtracked elongation complexes. Rv1080c is a putative gre factor (MtbGre) in the genome of Mycobacterium tuberculosis. The protein enhanced the efficiency of promoter clearance by lowering abortive transcription and also rescued arrested and paused elongation complexes on the GC rich mycobacterial template. Although MtbGre is similar in domain organization and shares key residues for catalysis and RNAP interaction with the Gre factors of Escherichia coli, it could not complement an E. coli gre deficient strain. Moreover, MtbGre failed to rescue E. coli RNAP stalled elongation complexes, indicating the importance of specific protein-protein interactions for transcript cleavage. Decrease in the level of MtbGre reduced the bacterial survival by several fold indicating its essential role in mycobacteria. Another Gre homolog, Rv3788 was not functional in transcript cleavage activity indicating that a single Gre is sufficient for efficient transcription of the M. tuberculosis genome.

Large rapidity gaps survival probabilities at LHC

We calculate the probability of large rapidity gaps in high energy hadronic collisions using a model based on QCD mini-jets and soft gluon emission down into the infrared region. Comparing with other models we find a remarkable agreement among most predictions.

Enhanced Survival of Probiotic Lactobacillus acidophilus by Encapsulation with Nanostructured Polyelectrolyte Layers through Layer-by-Layer Approach

The encapsulation of probiotic Lactobacillus acidophilus through layer-by-layer self-assembly of polyelectrolytes (PE) chitosan (CHI) and carboxymethyl cellulose (CMC) has been investigated,to enhance its survival m adverse conditions encountered in the GI tract The survival of encapsulated cells in simulated gastric (SGF) and intestinal fluids (SIF) is significant when compared to nonencapsulated cells On sequential exposure to SGF and SIF fox 120 nun, almost complete death of free cells is observed However, for cells coated with three nanolayers of PEs (CHI/CMC/CHI) about 33 log % of the cells (6 log cfu/500 mg) survived under the same conditions The enhanced survival rate of encapsulated L acidophilus can be attributed to the impermeability of polyelectrolyte nanolayers to large enzyme molecules like pepsin, and pancreatin that cause proteolysis and to the stability of the polyelectrolyte nanolayers in gastric and intestinal pH The PE coating also serves to reduce viability losses during freezing and freeze- drying About 73 and 92 log % of uncoated and coated cells survived after freeze:drying, and the losses occurring between freezing and freeze-drying were found to be lower for coated cells

Biosorption of heavy metal ions from aqueous and cyanide solutions using fungal biomass

A waste fungal biomass containing killed cells of Aspergillus niger was efficiently used in the removal of toxic metal ions such as nickel, calcium, iron and chromium from aqueous solutions. The role of different parameters such as initial metal ion concentration, solution pH and biomass concentration on biosorption capacity was established. The maximum metal uptake was found to be dependent on solution pH and increased with biomass loading upto 10g/L. The adsorption densities for various metal ions could be arranged as Ca>Cr (III)>Ni>Fe>Cr (VI). The effect of the presence of various metal ions in binary, ternary and quaternary combinations on biosorption was also assessed. Ni uptake was significantly affected, while that of Cr (VI) the least, in the presence of other metal ions. Uptake of base metals from an industrial cyanide effluent was studied using different species of fungi such as Aspergillus niger, Aspergillus terreus and Penicillium funiculosum and yeast such as Saccharomyces cerevisiae which were isolated from a gold mine. Traces of gold present in the cyanide effluent could be efficiently recovered. Among the four base metal contaminants present in the cyanide effluent, zinc was found to be most efficiently biosorbed, followed by iron, copper and lead. The role of both living and dead biomass on biosorption was distinguished and probable mechanisms illustrated.

Rodent seed predation: effects on seed survival, recruitment, abundance, and dispersion of bird-dispersed tropical trees

Tropical tree species vary widely in their pattern of spatial dispersion. We focus on how seed predation may modify seed deposition patterns and affect the abundance and dispersion of adult trees in a tropical forest in India. Using plots across a range of seed densities, we examined whether seed predation levels by terrestrial rodents varied across six large-seeded, bird-dispersed tree species. Since inter-specific variation in density-dependent seed mortality may have downstream effects on recruitment and adult tree stages, we determined recruitment patterns close to and away from parent trees, along with adult tree abundance and dispersion patterns. Four species (Canarium resiniferum, Dysoxylum binectariferum, Horsfieldia kingii, and Prunus ceylanica) showed high predation levels (78.5-98.7%) and increased mortality with increasing seed density, while two species, Chisocheton cumingianus and Polyalthia simiarum, showed significantly lower seed predation levels and weak density-dependent mortality. The latter two species also had the highest recruitment near parent trees, with most abundant and aggregated adults. The four species that had high seed mortality had low recruitment under parent trees, were rare, and had more spaced adult tree dispersion. Biotic dispersal may be vital for species that suffer density-dependent mortality factors under parent trees. In tropical forests where large vertebrate seed dispersers but not seed predators are hunted, differences in seed vulnerability to rodent seed predation and density-dependent mortality can affect forest structure and composition.

A full-length bifunctional protein involved in c-di-GMP turnover is required for long-term survival under nutrient starvation in Mycobacterium smegmatis

The bacterial second messenger cyclic diguanosine monophosphate (c-di-GMP) plays an important role in a variety of cellular functions, including biofilm formation, alterations in the cell surface, host colonization and regulation of bacterial flagellar motility, which enable bacteria to survive changing environmental conditions. The cellular level of c-di-GMP is regulated by a balance between opposing activities of diguanylate cyclases (DGCs) and cognate phosphodiesterases (PDE-As). Here, we report the presence and importance of a protein, MSDGC-1 (an orthologue of Rv1354c in Mycobacterium tuberculosis), involved in c-di-GMP turnover in Mycobacterium smegmatis. MSDGC-1 is a multidomain protein, having GAF, GGDEF and EAL domains arranged in tandem, and exhibits both c-di-GMP synthesis and degradation activities. Most other proteins containing GGDEF and EAL domains have been demonstrated to have either DGC or PDE-A activity. Unlike other bacteria, which harbour several copies of the protein involved in c-di-GMP turnover, M. smegmatis has a single genomic copy, deletion of which severely affects long-term survival under conditions of nutrient starvation. Overexpression of MSDGC-1 alters the colony morphology and growth profile of M. smegmatis. In order to gain insights into the regulation of the c-di-GMP level, we cloned individual domains and tested their activities. We observed a loss of activity in the separated domains, indicating the importance of full-length MSDGC-1 for controlling bifunctionality.

Involvement of the Global Regulator H-NS in the Survival of Escherichia coli in Stationary Phase

Long-term batch cultures of Escherichia coli grown in nutrient-rich medium accumulate mutations that provide a growth advantage in the stationary phase (GASP). We have examined the survivors of prolonged stationary phase to identify loci involved in conferring a growth advantage and show that a mutation in the hns gene causing reduced activity of the global regulator H-NS confers a GASP phenotype under specific conditions. The hns-66 allele bears a point mutation within the termination codon of the H-NS open reading frame, resulting in a longer protein that is partially functional. Although isolated from a long-term stationary-phase culture of the parent carrying the rpoS819 allele that results in reduced RpoS activity, the hns-66 survivor showed a growth disadvantage in the early stationary phase (24 to 48 h) when competed against the parent. The hns-66 mutant is also unstable and reverts at a high frequency in the early stationary phase by accumulating second-site suppressor mutations within the ssrA gene involved in targeting aberrant proteins for proteolysis. The mutant was more stable and showed a moderate growth advantage in combination with the rpoS819 allele when competed against a 21-day-old parent. These studies show that H-NS is a target for mutations conferring fitness gain that depends on the genetic background as well as on the stage of the stationary phase.

Differential modulation of intracellular survival of cytosolic and vacuolar pathogens by curcumin

Curcumin, a principal component of turmeric, acts as an immunomodulator regulating the host defenses in response to a diseased condition. The role of curcumin in controlling certain infectious diseases is highly controversial. It is known to alleviate symptoms of Helicobacter pylori infection and exacerbate that of Leishmania infection. We have evaluated the role of curcumin in modulating the fate of various intracellular bacterial pathogens. We show that pretreatment of macrophages with curcumin attenuates the infections caused by Shigella flexneri (clinical isolates) and Listeria monocytogenes and aggravates those caused by Salmonella enterica serovar Typhi CT18 (a clinical isolate), Salmonella enterica serovar Typhimurium, Staphylococcus aureus, and Yersinia enterocolitica. Thus, the antimicrobial nature of curcumin is not a general phenomenon. It modulated the intracellular survival of cytosolic (S. flexneri and L. monocytogenes) and vacuolar (Salmonella spp., Y. enterocolitica, and S. aureus) bacteria in distinct ways. Through colocalization experiments, we demonstrated that curcumin prevented the active phagosomal escape of cytosolic pathogens and enhanced the active inhibition of lysosomal fusion by vacuolar pathogens. A chloroquine resistance assay confirmed that curcumin retarded the escape of the cytosolic pathogens, thus reducing their inter- and intracellular spread. We have demonstrated that the membrane-stabilizing activity of curcumin is crucial for its differential effect on the virulence of the bacteria.

Dramatic Structural Changes Resulting from the Loss of a Crucial Hydrogen Bond in the Hinge Region Involved in C-Terminal Helix Swapping in SurE: A Survival Protein from Salmonella typhimurium

Domain swapping is an interesting feature of some oligomeric proteins in which each protomer of the oligomer provides an identical surface for exclusive interaction with a segment or domain belonging to another protomer. Here we report results of mutagenesis experiments on the structure of C-terminal helix swapped dimer of a stationary phase survival protein from Salmonella typhimurium (StSurE). Wild type StSurE is a dimer in which a large helical segment at the C-terminus and a tetramerization loop comprising two beta strands are swapped between the protomers. Key residues in StSurE that might promote C-terminal helix swapping were identified by sequence and structural comparisons. Three mutants in which the helix swapping is likely to be avoided were constructed and expressed in E. coli. Three-dimensional X-ray crystal structures of the mutants H234A and D230A/H234A could be determined at 2.1 angstrom and 2.35 angstrom resolutions, respectively. Contrary to expectations, helix swapping was mostly retained in both the mutants. The loss of the crucial D230 OD2- H234 NE2 hydrogen bond (2.89 angstrom in the wild type structure) in the hinge region was compensated by new inter and intra-chain interactions. However, the two fold molecular symmetry was lost and there were large conformational changes throughout the polypeptide. In spite of these changes, the dimeric structure and an approximate tetrameric organization were retained, probably due to the interactions involving the tetramerization loop. Mutants were mostly functionally inactive, highlighting the importance of precise inter-subunit interactions for the symmetry and function of StSurE.

Inhibition of cancer cell proliferation and apoptosis-inducing activity of fungal taxol and its precursor baccatin III purified from endophytic Fusarium solani

Background: Taxol (generic name paclitaxel), a plant-derived antineoplastic agent, used widely against breast, ovarian and lung cancer, was originally isolated from the bark of the Pacific yew, Taxus brevifolia. The limited supply of the drug has prompted efforts to find alternative sources, such as chemical synthesis, tissue and cell cultures of the Taxus species both of which are expensive and yield low levels. Fermentation processes with microorganisms would be the methods of choice to lower the costs and increase yields. Previously we have reported that F. solani isolated from T. celebica produced taxol and its precursor baccatin III in liquid grown cultures J Biosci 33: 259-67, 2008. This study was performed to evaluate the inhibition of proliferation and induction of apoptosis of cancer cell lines by the fungal taxol and fungal baccatin III of F. solani isolated from T. celebica. Methods: Cell lines such as HeLa, HepG2, Jurkat, Ovcar3 and T47D were cultured individually and treated with fungal taxol, baccatin III with or without caspase inhibitors according to experimental requirements. Their efficacy on apoptotic induction was examined. Results: Both fungal taxol and baccatin III inhibited cell proliferation of a number of cancer cell lines with IC50 ranging from 0.005 to 0.2 mu M for fungal taxol and 2 to 5 mu M for fungal baccatin III. They also induced apoptosis in JR4-Jurkat cells with a possible involvement of anti-apoptotic Bcl2 and loss in mitochondrial membrane potential, and was unaffected by inhibitors of caspase-9,-2 or -3 but was prevented in presence of caspase-10 inhibitor. DNA fragmentation was also observed in cells treated with fungal taxol and baccatin III. Conclusions: The cytotoxic activity exhibited by fungal taxol and baccatin III involves the same mechanism, dependent on caspase-10 and membrane potential loss of mitochondria, with taxol having far greater cytotoxic potential.