Can the combination of electrochemical regeneration of NAD+, selectivity of L‐α‐amino‐acid dehydrogenase,and reductive amination of α‐keto‐acid be applied to the inversion of configuration of a L‐α‐amino‐acid?

The inversion of configuration of L‐alanine can be carried out by combining its selective oxidation in the presence of NAD⁺ and L‐alanine dehydrogenase, electrochemical regeneration of the NAD⁺ at a carbon felt anode, and reductive amination of pyruvate, i.e., reduction of its imino derivative at a mercury cathode, the reaction mixture being buffered with concentrated ammonium/ammonia (1.28M / 1.28M). The dehydrogenase exhibits astonishing activity and stability under such extreme conditions of pH and ionic strength. The main drawback of the process is its slowness. At best, the complete inversion of a 10 mM solution of L‐alanine requires 140 h. A careful and detailed quantitative analysis of each of the key steps involved shows that the enzyme catalyzed oxidation is so thermodynamically uphill that it can be driven efficiently to completion only when both the coenzyme regeneration and the pyruvate reduction are very effective. The first condition is easily fulfilled. Under the best conditions, it is the rate of the chemical reaction producing the imine which controls the whole process kinetically. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 64: 101–107, 1999.     

Why does the magnitude of genotype‐by‐environment interaction vary?

Genotype‐by‐environment interaction (G × E), that is, genetic variation in phenotypic plasticity, is a central concept in ecology and evolutionary biology. G×E has wide‐ranging implications for trait development and for understanding how organisms will respond to environmental change. Although G × E has been extensively documented, its presence and magnitude vary dramatically across populations and traits. Despite this, we still know little about why G × E is so evident in some traits and populations, but minimal or absent in others. To encourage synthetic research in this area, we review diverse hypotheses for the underlying biological causes of variation in G × E. We extract common themes from these hypotheses to develop a more synthetic understanding of variation in G × E and suggest some important next steps.     

Bottom‐up control in the benthos of ocean‐exposed sandy beaches?

Bottom‐up control is a fundamental structuring force in food webs. Food webs of ocean‐exposed sandy beaches are predicted to be bottom‐up controlled systems, underpinned by imported organic matter rather than in situ primary production. This ecological model of resource‐based regulation of biological assemblages is juxtaposed against a prevailing paradigm built around a dominance of physical drivers in sandy beach ecosystems. Surprisingly, given the apparently ubiquitous energetic subsidies of beach food webs, the central premise of bottom‐up control has not been tested. Here we experimentally manipulated in situ nutrient levels on a sandy beach to test food web responses at the levels of primary producers (benthic microalgae) and their grazers (meiofauna). The meiofauna community as a whole appeared most strongly influenced by the local physical environment, particularly changes in sediment grain size – this supports the traditional ‘environmental control paradigm’. We also detected a significant, positive response of two consumer groups of the meiofauna (nematodes, ostracods) to nutrient enrichment that supports a model of biological, bottom‐up control. Although the predicted response of elevated producer biomass following nutrient enrichment was not detected, intense grazing pressure on new, stimulated production may have masked positive responses by the primary producers. Multichannel regulation of food webs is likely for many exposed sandy beaches, albeit an often lower importance of in situ bottom‐up forces compared with stronger environmental control.     

The hemolymph proteome of the honeybee: Gel‐based or gel‐free?

The honeybee has an invaluable economic impact and is a model for studying immunity, development and social behavior. The recent sequencing and annotation of the honeybee genome facilitates the study of its hemolymph, which reflects the physiological condition and mediates immune responses. We aimed at making a proteomic reference map of honeybee hemolymph and compared gel‐free and gel‐based techniques. One hundered and four 2‐DE spots corresponding to 62 different proteins were identified. Eight identical 2‐DLC experiments resulted in the identification of 32 unique proteins. One repeat was clearly not representative for the potential of the given 2‐DLC setup. Only 27% of the identified hemolymph proteins were found by both techniques. In addition, we found proteins of three different viruses which creates possibilities for biomarker design. Future hemolymph studies will benefit from this work.     

How do reaction conditions affect the enantiopure synthesis of 2‐substituted‐1,4‐benzodioxane derivatives?

Several biologically active compounds structurally include the enantiopure 2‐substituted‐1,4‐benzodioxane scaffold. The straightforward racemization that affects reactions involving most of the common chemical reactives is thus a crucial issue. The developing of a completely stereo‐controlled synthetic route that does not affect the enantiomeric excess is consequently mandatory. It is also important to set up a reliable chiral HPLC method, able to follow the reaction, and to improve the synthetic performances. Here, we report the chiral investigation of two different synthons, we specifically evaluated the synthetic pathways that could be run in order to afford them, avoiding the racemization processes, which could normally occur in basic conditions. In addition, we developed peculiar chiral HPLC methods in order to resolve the enantiomers, define the enantiomeric excess, and fully characterize these compounds.     

What is the function of neuronal AP‐3?

Neurotransmission requires the proper organization and rapid recycling of synaptic vesicles. Rapid retrieval has been suggested to occur either by kiss-and-stay or kiss-and-run mechanisms, whereas classical recycling is mediated by clathrin-dependent endocytosis. Molecular coats are key components in the selection of cargos, AP-2 (adaptor protein 2) playing a prominent role in synaptic vesicle endocytosis. Another coat protein, AP-3, has been implicated in synaptic vesicle biogenesis and in the generation of secretory and lysosomal-related organelles. In the present review, we will particularly focus on the recent data concerning the recycling of synaptic vesicles and the function of AP-3 and the v-SNARE (vesicular soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) TI-VAMP (tetanus neurotoxin-insensitive vesicle-associated membrane protein) in these processes. We propose that AP-3 plays an important regulatory role in neurons which contributes to the basal and stimulated exocytosis of synaptic vesicles.     

Anomalies of the forebrain with radial limb defects: Garcia‐Lurie‐Steinfeld syndrome?

BACKGROUND: Severe anomalies of the forebrain together with radial limb anomalies have been reported in Steinfeld syndrome, XK aprosencephaly, and partial monosomy 13q. Steinfeld syndrome is an extremely variable autosomal dominant condition that, in severe cases, is characterized by holoprosencephaly, radial limb defects, and renal and/or cardiac defects. In mild cases there may be only thumb hypoplasia, ocular coloboma, or oral clefts. XK aprosencephaly, also called Garcia-Lurie syndrome (GLS), is a usually sporadic disorder with radial limb defects and aprosencephaly/atelencephaly. Based on two atypical sibships, autosomal recessive inheritance has been suggested. Two patients with variations of monosomy 13q have been described with atelencephaly but, generally, Steinfeld and XK aprosencephaly patients are chromosomally normal. Holoprosencephaly in 13q deletion patients appears to be due to ZIC2 mutations, but ZIC2 has not been previously tested in Steinfeld syndrome or GLS patients. CASES: We report three sporadic cases with clinical features intermediate between Steinfeld and GLS, including severe forebrain malformations and radial limb defects. All had normal karyotypes, and mutations in ZIC2 were absent in the two cases tested. CONCLUSIONS: In our cases and in the literature there is significant clinical overlap between Steinfeld syndrome and GLS. We propose these conditions may not be nosologically or etiologically distinct. The spectrum of severe forebrain anomalies in these conditions is broader than previously thought and may include some neural tube defects. Mild cases are difficult to identify and the full range of expression remains unknown. Autosomal dominant inheritance with incomplete penetrance and frequent new mutations is postulated. Thorough clinical evaluation is recommended for children with severe forebrain and radial limb defects.     

Split‐root systems applied to the study of the legume‐rhizobial symbiosis: What have we learned?

Split‐root system (SRS) approaches allow the differential treatment of separate and independent root systems, while sharing a common aerial part. As such, SRS is a useful tool for the discrimination of systemic (shoot origin) versus local (root/nodule origin) regulation mechanisms. This type of approach is particularly useful when studying the complex regulatory mechanisms governing the symbiosis established between legumes and Rhizobium bacteria. The current work provides an overview of the main insights gained from the application of SRS approaches to understand how nodule number (nodulation autoregulation) and nitrogen fixation are controlled both under non‐stressful conditions and in response to a variety of stresses. Nodule number appears to be mainly controlled at the systemic level through a signal which is produced by nodule/root tissue, translocated to the shoot, and transmitted back to the root system, involving shoot Leu‐rich repeat receptor‐like kinases. In contrast, both local and systemic mechanisms have been shown to operate for the regulation of nitrogenase activity in nodules. Under drought and heavy metal stress, the regulation is mostly local, whereas the application of exogenous nitrogen seems to exert a regulation of nitrogen fixation both at the local and systemic levels.     

Classifying the fire‐response traits of plants: How reliable are species‐level classifications?

Plant species in fire‐prone environments possess specific traits which allow them to survive fire. Species are commonly classified according to whether they survive fire and resprout or whether they are killed by fire and regenerate from seed. However, different populations of the same species have been shown to vary in their responses. Therefore, the classification of a species into a single category based on fire‐response traits may not necessarily be representative of every population under every circumstance. This study examined the extent of within‐species variation in fire‐response traits of woody plants in south‐eastern Australia after the 2003 fires. Species were then classified using two approaches: (i) using data from a field survey of fire‐response traits, taking into account within‐species variation; and (ii) using species' fire responses listed in a pre‐existing fire‐response database compiled from a variety of primary sources. Field data showed that the majority of species in the study area resprouted after fire with around one in 10 species variable in their resprouting response. Almost half of all species varied from site to site according to whether they regenerated from seed, either solely or in addition to resprouting. The numbers of species classified as resprouters and seed regenerators varied according to the classification method used. Differences were also found between the classification method when calculating the mean proportion of resprouters and seed regenerators across sites. The fire‐response traits for some species from the database were found to differ from the observed field responses. This study demonstrated that the application of a fire‐response trait, reported in a trait database, to an entire species, may not adequately represent the actual fire responses of the populations of interest. Rather than considering the fire‐response traits of a species, accurate prediction may be better achieved by considering how different populations of plants will respond to fire.     

What is the mechanism of ParA‐mediated DNA movement?

The stable maintenance of low‐copy‐number plasmids requires active partitioning, with the most common mechanism in prokaryotes involving the ATPase ParA. ParA proteins undergo intricate spatiotemporal relocations across the nucleoid, dynamics that function to position plasmids at equally spaced intervals. This spacing naturally guarantees equal partitioning of plasmids to each daughter cell. However, the fundamental mechanism linking ParA dynamics with regular plasmid positioning has proved difficult to dissect. In this issue of Molecular Microbiology, Vecchiarelli et al. report on a time‐delay mechanism that allows a slow cycling between the nucleoid‐bound and unbound forms of ParA. The authors also propose a mechanism for plasmid movement that does not rely on ParA polymerization.     

Who Is the King? The α‐Hydroxy‐β‐oxo‐α,β‐enone Moiety or the Catechol B Ring: Relationship between the Structure of Quercetin Derivatives and Their Pro‐Oxidative Abilities

Quercetin and other flavonoids have been reported to exhibit both antioxidant and pro‐oxidant properties. Most studies about the pro‐oxidative ability were conducted in the presence of metal ions, and the essential functional moiety of quercetin responsible for the pro‐oxidative effect is still unclear. In this study, we evaluated the pro‐oxidative abilities in the absence of metal ions of two quercetin derivatives, i.e., quercetin‐3′‐O‐β‐D ‐glucoside ( 1 ) and quercetin‐3‐O‐β‐D ‐glucoside ( 2 ), by assessing DNA cleavage and HO^.‐radical production. The binding mode between these compounds and DNA was studied by fluorescence and viscometric titrations. The results showed that 1 can efficiently induce oxidative damage to plasmid DNA, while 2 shows poor activity. Both 1 and 2 bind to DNA via groove‐binding. These results proved that the α‐hydroxy‐β‐oxo‐α,β‐enone moiety contributes to the pro‐oxidative activity of quercetin.     

Discovery of the type VII ESX‐1 secretion needle?

Mycobacterium tuberculosis, the etiological agent of human tuberculosis, harbours five ESAT‐6/type VII secretion (ESX/T7S) systems. The first esx gene clusters were identified during the genome‐sequencing project of M. tuberculosis H37Rv. Follow‐up studies revealed additional genes playing important roles in ESX/T7S systems. Among the latter genes, one can find those that encode Pro‐Glu (PE) and Pro‐Pro‐Glu (PPE) proteins as well as a gene cluster that is encoded >260 kb upstream of the esx‐1 locus and encodes ESX‐1 secretion‐associated proteins EspA (Rv3616c), EspC (Rv3615c) and EspD (Rv3614c). The espACD cluster has been suggested to have an important function in ESX‐1 secretion since EspA‐EspC and EsxA–EsxB are mutually co‐dependent on each other for secretion. However, the molecular mechanism of this co‐dependence and interaction between the substrates remained unknown. In this issue of Molecular Microbiology, Lou and colleagues show that EspC forms high‐molecular weight polymerization complexes that resemble selected components of type II, III and/or IV secretion systems of Gram‐negative bacteria. Indeed, EspC‐multimeric complexes form filamentous structures that could well represent a secretion needle of ESX‐1 type VII secretion systems. This exciting observation opens new avenues for research to discover and characterize ESX/T7S components and elucidates the co‐dependence of EsxA/B secretion with EspA/C.     

Have we underestimated the importance of humans in the biogeography of free‐living terrestrial microorganisms?

The role of humans in the global dispersal of free‐living terrestrial microorganisms has received surprisingly little attention in the literature, compared with the frequent discussions of human dispersal for aquatic microbes. Here I argue that this area needs more study, using examples from the ecology of testate amoebae to illustrate the nature of the problem. The techniques of molecular ecology now make these ideas open to investigation in a way that would have been difficult in the past, and, in the case of testate amoebae, palaeoecological approaches may also be valuable.     

Is Central Asia the eastern outpost of the Neandertal range? A reassessment of the Teshik‐Tash child

Since its discovery in southeastern Uzbekistan in 1938, the Teshik-Tash child has been considered a Neandertal. Its affinity is important to studies of Late Pleistocene hominin growth and development as well as interpretations of the Central Asian Middle Paleolithic and the geographic distribution of Neandertals. A close examination of the original Russian monograph reveals the incompleteness of key morphologies associated with the cranial base and face and problems with the reconstruction of the Teshik-Tash cranium, making its Neandertal attribution less certain than previously assumed. This study reassesses the Neandertal status of Teshik-Tash 1 by comparing it to a sample of Neandertal, Middle and Upper Paleolithic modern humans, and recent human sub-adults. Separate examinations of the cranium and mandible are conducted using multinomial logistic regression and discriminant function analysis to assess group membership. Results of the cranial analysis group Teshik-Tash with Upper Paleolithic modern humans when variables are not size-standardized, while results of the mandibular analysis place the specimen with recent modern humans for both raw and size-standardized data. Although these results are influenced by limitations related to the incomplete nature of the comparative sample, they suggest that the morphology of Teshik-Tash 1 as expressed in craniometrics is equivocal. Although, further quantitative studies as well as additional sub-adult fossil finds from this region are needed to ascertain the morphological pattern of this specimen specifically, and Central Asian Middle Paleolithic hominins in general, these results challenge current characterizations of this territory as the eastern boundary of the Neandertal range during the Late Pleistocene.     

Is fungal species richness and composition related to the occurrence of the old‐growth associated wood‐decaying Amylocystis lapponica?

Amylocystis lapponica (Romell) Singer is a widely distributed wood‐decaying polypore fungus found throughout the Northern Hemisphere. Despite its huge distribution range it occurs rather patchily and seems narrowly associated with old‐growth forest stands. Notably, it has been used as an ‘indicator species’, believed to reflect the long‐term presence of dead wood, naturalness of forest stands, and indirectly, species richness and possibly composition. In this study we focused on the last issue – whether or not there is a link between the occurrence of A. lapponica and the species richness and composition of other wood‐decaying fungi. Selecting log characteristics and microclimate as similar as possible, we compared 12 logs with and 12 logs without visible fruit bodies of A. lapponica to examine: 1) if visible fruit bodies corresponded with molecular identification of the mycelia, 2) if fungal species richness and composition of the substrate were related to A. lapponica occurrence, and 3) if A. lapponica was restricted to certain parts of the log. Fungal species were recorded by inspecting visible fruit bodies and by culture isolation and ITS sequencing from wood disc samples. Laboratory and field identification of A. lapponica had 71% correspondence, and mycelia were identified in two logs without visible fruit bodies. Twice as many fungal species were detected using ITS sequencing compared to fruit body identification. Total species richness was similar between the two log categories, but number of species per log was slightly higher in A. lapponica logs. Antrodia serialis (Fr.) Donk, and possibly also Fomitopsis pinicola (Sw.:Fr.) P. Karst. and Phellinus nigrolimitatus (Romell) Bourdot & Galzin, occurred more frequently in A. lapponica logs. Mycelia of A. lapponica were restricted to less decayed parts of the wood in the centre of the middle part of the logs.     

Rejection of brood‐parasitic shiny cowbird Molothrus bonariensis nestlings by the firewood‐gatherer Anumbius annumbi?

Costs imposed by brood parasitic birds exert strong selection on their hosts to avoid parasitism. While egg rejection is a common defence, nestling rejection is rarer and less well understood. Theoretical models suggest that among non‐evicting parasites such as cowbirds nestling rejection can only evolve when levels of parasitism are high. Here we describe a possible case of early rejection of cowbird nestlings, by an infrequently parasitised host, the firewood‐gatherer Anumbius annumbi. Firewood‐gatherers accepted most shiny cowbird Molothrus bonariensis eggs despite clear differences in coloration. Cowbird eggs usually hatched 4–5 d before host eggs. All parasitic nestlings died within 48 h, and hosts continued their breeding attempts. Nestling death was most likely due to neglect since little food was found in the stomach of dead nestlings. Feeding neglect could be due to differences in visual or acoustic appearance between host and parasite hatchlings. Alternatively, hosts may refrain from feeding nestlings that hatch too early compared to their normal incubation time. At the moment our data do not allow distinction between active nestling recognition or cowbird nestling failure due to the unsuitability of the firewood‐gatherer as a host (i.e. too long incubation). Experiments are needed to tease these alternatives apart.