An ultraviolet resonance Raman study of dehydrogenase enzymes and their interactions with coenzymes and substrates

Ultraviolet resonance Raman (UVRR) spectra, with 260-nm excitation, are reported for oxidized and reduced nicotinamide adenine dinucleotides (NAD+ and NADH, respectively). Corresponding spectra are reported for these coenzymes when bound to the enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and liver and yeast alcohol dehydrogenases (LADH and YADH). The observed differences between the coenzyme spectra are interpreted in terms of conformation, hydrogen bonding, and general environment polarity differences between bound and free coenzymes and between coenzymes bound to different enzymes. The possibility of adenine protonation is discussed. UVRR spectra with 220-nm excitation also are reported for holo- and apo-GAPDH (GAPDH-NAD+ and GAPDH alone, respectively). In contrast with the 260-nm spectra, these show only bands due to vibrations of aromatic amino acid residues of the protein. The binding of coenzyme to GAPDH has no significant effect on the aromatic amino acid bands observed. This result is discussed in the light of the known structural change of GAPDH on binding coenzyme. Finally, UVRR spectra with 240-nm excitation are reported for GAPDH and an enzyme-substrate intermediate of GAPDH. Perturbations are reported for tyrosine and tryptophan bands on forming the acyl enzyme.     

Telemetered electromyography of peroneus longus in Varecia variegata and Eulemur rubriventer: implications for the functional significance of a large peroneal process

A foot specialized for grasping small branches with a divergent opposable hallux (hallucal grasping) represents a key adaptive complex characterizing almost all arboreal non-human euprimates. Evolution of such grasping extremities probably allowed members of a lineage leading to the common ancestor of modern primates to access resources available in a small-branch niche, including angiosperm products and insects. A better understanding of the mechanisms by which euprimates use their feet to grasp will help clarify the functional significance of morphological differences between the euprimate grasp complex and features representing specialized grasping in other distantly related groups (e.g., marsupials and carnivorans) and in closely related fossil taxa (e.g., plesiadapiforms). In particular, among specialized graspers euprimates are uniquely characterized by a large peroneal process on the base of the first metatarsal, but the functional significance of this trait is poorly understood. We tested the hypothesis that the large size of the peroneal process corresponds to the pull of the attaching peroneus longus muscle recruited to adduct the hallux during grasping. Using telemetered electromyography on three individuals of Varecia variegata and two of Eulemur rubriventer, we found that peroneus longus does not generally exhibit activity consistent with an important function in hallucal grasping. Instead, extrinsic digital flexor muscles and, sometimes, the intrinsic adductor hallucis are active in ways that indicate a function in grasping with the hallux. Peroneus longus helps evert the foot and resists its inversion. We conclude that the large peroneal tuberosity that characterizes the hallucal metatarsal of prosimian euprimates does not correlate to "powerful" grasping with a divergent hallux in general, and cannot specifically be strongly linked to vertical clinging and climbing on small-diameter supports. Thus, the functional significance of this hallmark, euprimate feature remains to be determined.     

Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes

The absorption and energy transfer properties of photosynthetic pigments are strongly influenced by their local environment or “site.” Local electrostatic fields vary in time with protein and chromophore molecular movement and thus transiently influence the excited state transition properties of individual chromophores. Site-specific information is experimentally inaccessible in many light-harvesting pigment–proteins due to multiple chromophores with overlapping spectra. Full quantum mechanical calculations of each chromophores excited state properties are too computationally demanding to efficiently calculate the changing excitation energies along a molecular dynamics trajectory in a pigment–protein complex. A simplified calculation of electrostatic interactions with each chromophores ground to excited state transition, the so-called charge density coupling (CDC) for site energy, CDC, has previously been developed to address this problem. We compared CDC to more rigorous quantum chemical calculations to determine its accuracy in computing excited state energy shifts and their fluctuations within a molecular dynamics simulation of the bacteriochlorophyll containing light-harvesting Fenna–Mathews–Olson (FMO) protein. In most cases CDC calculations differed from quantum mechanical (QM) calculations in predicting both excited state energy and its fluctuations. The discrepancies arose from the inability of CDC to account for the differing effects of charge on ground and excited state electron orbitals. Results of our study show that QM calculations are indispensible for site energy computations and the quantification of contributions from different parts of the system to the overall site energy shift. We suggest an extension of QM/MM methodology of site energy shift calculations capable of accounting for long-range electrostatic potential contributions from the whole system, including solvent and ions.     

Four Decades of Forest Persistence,Clearance and Logging on Borneo

The native forests of Borneo have been impacted by selective logging, fire, and conversion to plantations at unprecedented scales since industrial-scale extractive industries began in the early 1970s. There is no island-wide documentation of forest clearance or logging since the 1970s. This creates an information gap for conservation planning, especially with regard to selectively logged forests that maintain high conservation potential. Analysing LANDSAT images, we estimate that 75.7% (558,060 km²) of Borneo''s area (737,188 km²) was forested around 1973. Based upon a forest cover map for 2010 derived using ALOS-PALSAR and visually reviewing LANDSAT images, we estimate that the 1973 forest area had declined by 168,493 km² (30.2%) in 2010. The highest losses were recorded in Sabah and Kalimantan with 39.5% and 30.7% of their total forest area in 1973 becoming non-forest in 2010, and the lowest in Brunei and Sarawak (8.4%, and 23.1%). We estimate that the combined area planted in industrial oil palm and timber plantations in 2010 was 75,480 km², representing 10% of Borneo. We mapped 271,819 km of primary logging roads that were created between 1973 and 2010. The greatest density of logging roads was found in Sarawak, at 0.89 km km⁻², and the lowest density in Brunei, at 0.18 km km⁻². Analyzing MODIS-based tree cover maps, we estimate that logging operated within 700 m of primary logging roads. Using this distance, we estimate that 266,257 km² of 1973 forest cover has been logged. With 389,566 km² (52.8%) of the island remaining forested, of which 209,649 km² remains intact. There is still hope for biodiversity conservation in Borneo. Protecting logged forests from fire and conversion to plantations is an urgent priority for reducing rates of deforestation in Borneo.     

Discovery of GlyT1 inhibitors with improved pharmacokinetic properties

Glycine transporter 1 (GlyT1) represents a novel target for the treatment of schizophrenia via the potentiation of glutamatergic NMDA receptors. The discovery of 4,4-disubstituted piperidine inhibitors of GlyT1 which exhibit improved pharmacokinetic properties, including oral bioavailability, is discussed.     

Factors influencing the seed source and sink functions of a floodplain nature reserve in the Netherlands

Question: How do species traits and abiotic factors influence the extent of hydrochorous dispersal into and out of a small floodplain area along a free‐flowing river in The Netherlands? Location: The Kappersbult nature reserve (53°07′28″N, 6°37′14″E), which is a floodplain along the Dutch River Drentsche Aa. Methods: Seeds transported by the river were collected in fine mesh nets for 24 consecutive hours once or twice a week for 1 year, upstream and downstream of the studied floodplain. Data on the captured seeds were related to species traits and abiotic factors and species composition in the floodplain. Results: The floodplain functioned both as a seed source and sink. High levels of river water seemed to promote seed transport to or from the floodplain. Seeds of riverbank species occurred significantly more often in the river water than expected. Net source species had significantly higher seed production, taller stature and higher seed buoyancy, but lower site elevation than net sink species. Seed weight was significantly higher for sink species than for other species. Conclusion: Our study found that inundation, and therefore more natural river water management, is a prerequisite for seed transport to and from a floodplain. The restoration of target floodplain vegetation may be successful for common species that produce many seeds and grow in proximity to the river. Consequently, it is expected that the probability of restoring vegetation types that occur further from the river, such as wet grasslands, by hydrochorous dispersal is low.     

Transgenic resistance confers effective field level control of bacterial spot disease in tomato

We investigated whether lines of transgenic tomato (Solanum lycopersicum) expressing the Bs2 resistance gene from pepper, a close relative of tomato, demonstrate improved resistance to bacterial spot disease caused by Xanthomonas species in replicated multi-year field trials under commercial type growing conditions. We report that the presence of the Bs2 gene in the highly susceptible VF 36 background reduced disease to extremely low levels, and VF 36-Bs2 plants displayed the lowest disease severity amongst all tomato varieties tested, including commercial and breeding lines with host resistance. Yields of marketable fruit from transgenic lines were typically 2.5 times that of the non-transformed parent line, but varied between 1.5 and 11.5 fold depending on weather conditions and disease pressure. Trials were conducted without application of any copper-based bactericides, presently in wide use despite negative impacts on the environment. This is the first demonstration of effective field resistance in a transgenic genotype based on a plant R gene and provides an opportunity for control of a devastating pathogen while eliminating ineffective copper pesticides.     

Role of MAPK/ERK in Neurotrophin-4 Potentiation of Necrotic Neuronal Death

Neurotrophic factors have been proposed for the treatment of a variety of neurological diseases. However, to this point they have failed in clinical trials. One potential problem is that while neurotrophic factors attenuate apoptosis, they have the potential to enhance necrosis. In this study we show that neurotrophin-4 (NT-4) attenuated apoptotic neuronal death while potentiating necrotic neuronal death in cortical cultures. The protective effects of NT-4 were not blocked by the mitogen-activated protein kinase kinase (MEK) inhibitors PD098059 or U0126, while the injury potentiation by NT-4 was blocked by these inhibitors. NT-4 stimulated the phosphorylation of ERK1/2 and this phosphorylation was attenuated by U0126 and PD098059. The results indicate a disassociation between the pathway by which NT-4 potentiates necrosis, and that by which it attenuates apoptosis, and suggest that addition of a MEK inhibitor may enhance the beneficial effects of NT-4 in treating complex injuries such as occur in vivo.     

Dental topography indicates ecological contraction of lemur communities

Understanding the paleoecology of extinct subfossil lemurs requires reconstruction of dietary preferences. Tooth morphology is strongly correlated with diet in living primates and is appropriate for inferring dietary ecology. Recently, dental topographic analysis has shown great promise in reconstructing diet from molar tooth form. Compared with traditionally used shearing metrics, dental topography is better suited for the extraordinary diversity of tooth form among subfossil lemurs and has been shown to be less sensitive to phylogenetic sources of shape variation. Specifically, we computed orientation patch counts rotated (OPCR) and Dirichlet normal energy (DNE) of molar teeth belonging to 14 species of subfossil lemurs and compared these values to those of an extant lemur sample. The two metrics succeeded in separating species in a manner that provides insights into both food processing and diet. We used them to examine the changes in lemur community ecology in Southern and Southwestern Madagascar that accompanied the extinction of giant lemurs. We show that the poverty of Madagascar's frugivore community is a long-standing phenomenon and that extinction of large-bodied lemurs in the South and Southwest resulted not merely in a loss of guild elements but also, most likely, in changes in the ecology of extant lemurs.