Energetic rationale for an unexpected and abrupt reversal of guanidinium chloride-induced unfolding of peptide deformylase

Peptide deformylase (PDF) catalyzes the removal of formyl group from the N-terminal methionine residues of nascent proteins in prokaryotes, and this enzyme is a high priority target for antibiotic design. In pursuit of delineating the structural-functional features of Escherichia coli PDF (EcPDF), we investigated the mechanistic pathway for the guanidinium chloride (GdmCl)-induced unfolding of the enzyme by monitoring the secondary structural changes via CD spectroscopy. The experimental data revealed that EcPDF is a highly stable enzyme, and it undergoes slow denaturation in the presence of varying concentrations of GdmCl. The most interesting aspect of these studies has been the abrupt reversal of the unfolding pathway at low to moderate concentrations of the denaturant, but not at high concentration. An energetic rationale for such an unprecedented feature in protein chemistry is offered.     

Stabilization of anionic and neutral forms of a fluorophoric ligand at the active site of human carbonic anhydrase I

We synthesized a fluorogenic dansylamide derivative (JB2-48), which fills the entire (15 Å deep) active site pocket of human carbonic anhydrase I, and investigated the contributions of sulfonamide and hydrophobic regions of the ligand structure on the spectral, kinetic, and thermodynamic properties of the enzyme–ligand complex. The steady-state and fluorescence lifetime data revealed that the deprotonation of the sulfonamide moiety of the enzyme bound ligand increases the fluorescence emission intensity as well as the lifetime of the fluorophores. This is manifested via the electrostatic interaction between the active site resident Zn²⁺ cofactor and the negatively charged sulfonamide group of the ligand, and such interaction contributes to about 2.2 kcal/mol (ΔΔG°) and 0.89 kcal/mol (ΔΔG^‡) energy in stabilizing the ground and the putative transition states, respectively. We provide evidence that the anionic and neutral forms of JB2-48 are stabilized by the complementary microscopic/conformational states of the enzyme. The implication of the mechanistic studies presented herein in rationale design of carbonic anhydrase inhibitors is discussed.     

Differential modulation of the active site environment of human carbonic anhydrase XII by cationic quantum dots and polylysine

Due to prevalence of negative charges on the protein surface, opposite to the active site pocket of human carbonic anhydrase XII (hCA XII), both positively charged CdTe quantum dots (Qds⁺) and polylysine electrostatically interact with the enzyme, and such interaction does not influence the catalytic activity of the enzyme. However, both these cationic macromolecules differently modulate the active site environment of the enzyme. The steady-state kinetic data revealed that whereas polylysine exhibited no influence on dansylamide (DNSA) dependent inhibition of the enzyme, Qds⁺ overcame such an inhibitory effect, leading to almost 70% restoration of the catalytic activity of the enzyme. We provide evidence that DNSA remains bound to the enzyme upon interaction with both polylysine and Qds⁺. Arguments are presented that the above differential feature of polylysine and Qds⁺ on hCA XII is encoded in the “rigidity” versus “flexibility” of these cationic macromolecules.     

Bacterial infections of skin and soft tissues in filariasis

Adenolymphangitis is a common occurrence in filarial lymphedema. Damage to the lymphatics and lymph nodes by F. bancrofti is followed by obliteration of lymph vessels and lymph stasis. Obstruction of lymphatics prevents the bacteria penetrating skin to be evacuated with lymph stream to regional lymph nodes. Colonization of dermis, subcutis and lymphatics evokes clinical symptoms of adenolymphangitis. The question arises which strains of bacteria are responsible for the acute and chronic types of adenolymphangitis. The most probable strains responsible for this condition belong to the cocci and probably the bacillus strains.     

Delayed greening,leaf expansion,and damage to sympatric<Emphasis Type="Italic"> Shorea</Emphasis> species in a lowland rain forest

The function of delayed greening in the seedlings of canopy tree species in a lowland tropical rain forest was examined in terms of its potential defensive value against herbivory. To explore the ecological and evolutionary backgrounds for delayed greening, we chose eight sympatric congeneric (Shorea) dipterocarp species that were either normal-greening or delayed-greening species. Expansion and toughening of leaves took approximately 30 days for all species, and did not differ between the normal- and delayed-greening species. The main factors that affected leaf damage during expansion were insect herbivory and fungal infection. Levels of leaf damage were significantly lower for delayed-greening species than for normal-greening species, but proportions of heavily damaged leaves and leaf abscission during expansion did not differ. In addition, no significant difference was found in damage levels on leaves (aged 1–2 months) of naturally occurring seedlings between normal- and delayed-greening species. Therefore, delayed greening may effectively reduce the level of leaf damage in young expanding leaves, but may not necessarily reduce leaf abscission and damage to mature leaves. The existence of delayed greening could not be simply explained by the phylogenetic and ecological backgrounds of the trees. Consequently, delayed greening may have a function in reducing damage during expansion, but more information (such as knowledge of the secondary metabolites involved in this phenomenon) is needed to explain fully why these species exhibit delayed greening.     

Species-area curves, spatial aggregation, and habitat specialization in tropical forests

The relationship between species diversity and sampled area is fundamental to ecology. Traditionally, theories of the species-area relationship have been dominated by random-placement models. Such models were used to formulate the canonical theory of species-area curves and species abundances. In this paper, however, armed with a detailed data set from a moist tropical forest, we investigate the validity of random placement and suggest improved models based upon spatial aggregation. By accounting for intraspecific, small-scale aggregation, we develop a cluster model which reproduces empirical species-area curves with high fidelity. We find that inter-specific aggregation patterns, on the other hand, do not affect the species-area curves significantly. We demonstrate that the tendency for a tree species to aggregate, as well as its average clump size, is not significantly correlated with the species' abundance. In addition, we investigate hierarchical clumping and the extent to which aggregation is driven by topography. We conclude that small-scale phenomena such as dispersal and gap recruitment determine individual tree placement more than adaptation to larger-scale topography.     

DNA barcodes for marine fungal identification and discovery

We employed DNA barcodes for identification of fungal species in marine sediments. Sediments were collected seasonally along the Southeast coast of India from which a culturable fungal library was constructed. All cultured species were morphologically documented using microscopical analysis. A maximum population density of 19.3 × 10³ CFU/g was recorded in monsoon and minimum of 3 × 10³ CFU/g in premonsoon season. Two-way analysis of variance suggests that the fungal community varied significantly between the seasons (F = 9.543, P < 0.001) and at various depths sampled (F = 4.655, P < 0.05). In total, 54 fungal species belonging to 13 different families were documented and all species were sequenced for internal transcribed spacer genes. Each species was represented by at least two specimens constituting a total of 171 specimens for DNA barcoding. Twelve species of a marine fungi were sequenced for the first time. Branching patterns of phylogenetic tree strongly supported the sequence variations within and between all species barcoded. Based on the pairwise distance model we suggest barcode gaps of 15 %, 21 %, 30 %, 35 % and 51 % for genera, family, order, class and phyla respectively.     

Distance- and density-dependent leaf dynamics of seedlings of a tropical rainforest tree

Parental distance and plant density dependence of seedling leaf turnover and survival was examined to investigate predictions of the Janzen–Connell hypothesis. The focal study species, Shorea macroptera is a canopy tree species in a lowland rain forest in peninsular Malaysia. We found that the peak of the distribution of plants shifted from 3–6 m to 6–9 m during the course of the change from seedling to sapling stage. The leaf demography of the seedlings was influenced by their distance from the adult tree and also by the seedling density. Although significant density- and distance dependence in leaf production was not detected, seedling leaf loss decreased with distance from the parent tree and with seedling density. Similarly, leaf damage was not found to be distance- or density-dependent, but net leaf gain of seedlings increased with distance from the parent tree. Although no significant distance- or density-dependence was evident in terms of leaf damage, significant distance dependence of the net leaf gain was found. Thus, we concluded that positive distance dependence in the leaf turnover of seedlings may gradually contribute to a shift in the distribution pattern of the progeny through reductions in growth and survivorship.     

Dynamics of the forest communities at Pasoh and Barro Colorado: comparing two 50-ha plots

Dynamics of the Pasoh forest in Peninsular Malaysia were assessed by drawing a comparison with a forest in Panama, Central America, whose dynamics have been thoroughly described. Census plots of 50 ha were established at both sites using standard methods. Tree mortality at Pasoh over an eight-year interval was 1.46% yr(-1) for all stems > or = 10 mm diameter at breast height (dbh), and 1.48% yr(-1) for stems > or = 100 mm dbh. Comparable figures at the Barro Colorado Island site in Panama (BCI) were 2.55% and 2.03%. Growth and recruitment rates were likewise considerably higher at BCI than at Pasoh. For example, in all trees 500-700 mm in dbh, mean BCI growth over the period 1985-1995 was 6 mm yr(-1), whereas mean Pasoh growth was about 3.5 mm yr(-1). Examining growth and mortality rates for individual species showed that the difference between the forests can be attributed to a few light-demanding pioneer species at BCI, which have very high growth and mortality; Pasoh is essentially lacking this guild. The bulk of the species in the two forests are shade-tolerant and have very similar mortality, growth and recruitment. The Pasoh forest is more stable than BCI's in another way as well: few of its tree populations changed much over the eight-year census interval. In contrast, at BCI, over 10% of the species had populations increasing or decreasing at a rate of >0.05 yr(-1) compared to just 2% of the species at Pasoh). The faster species turnover at BCI can probably be attributed to severe droughts that have plagued the forest periodically over the past 30 years; Pasoh has not suffered such extreme events recently. The dearth of pioneer species at Pasoh is associated with low-nutrient soil and slow litter breakdown, but the exact mechanisms behind this association remain poorly understood.     

Recent Surveys in the Forests of Ulu Segama Malua,Sabah, Malaysia,Show That Orang-utans (P. p. morio) Can Be Maintained in Slightly Logged Forests

Background

Today the majority of wild great ape populations are found outside of the network of protected areas in both Africa and Asia, therefore determining if these populations are able to survive in forests that are exploited for timber or other extractive uses and how this is managed, is paramount for their conservation.

Methodology/Principal Findings

In 2007, the “Kinabatangan Orang-utan Conservation Project” (KOCP) conducted aerial and ground surveys of orang-utan (Pongo pygmaeus morio) nests in the commercial forest reserves of Ulu Segama Malua (USM) in eastern Sabah, Malaysian Borneo. Compared with previous estimates obtained in 2002, our recent data clearly shows that orang-utan populations can be maintained in forests that have been lightly and sustainably logged. However, forests that are heavily logged or subjected to fast, successive coupes that follow conventional extraction methods, exhibit a decline in orang-utan numbers which will eventually result in localized extinction (the rapid extraction of more than 100 m³ ha⁻¹ of timber led to the crash of one of the surveyed sub-populations). Nest distribution in the forests of USM indicates that orang-utans leave areas undergoing active disturbance and take momentarily refuge in surrounding forests that are free of human activity, even if these forests are located above 500 m asl. Displaced individuals will then recolonize the old-logged areas after a period of time, depending on availability of food sources in the regenerating areas.

Conclusion/Significance

These results indicate that diligent planning prior to timber extraction and the implementation of reduced-impact logging practices can potentially be compatible with great ape conservation.