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.     

Genomic‐scale comparison of sequence‐ and structure‐based methods of function prediction: Does structure provide additional insight?

A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone.     

The theoretical basis of cancer‐stem‐cell‐based therapeutics of cancer: can it be put into practice?

In spite of the advances in our knowledge of cancer biology, most cancers remain not curable with present therapies. Current treatments consider cancer as resulting from uncontrolled proliferation and are non-specific. Although they can reduce tumour burden, relapse occurs in most cases. This was long attributed to incomplete tumour elimination, but recent developments indicate that different types of cells contribute to the tumour structure, and that the tumour's cellular organization would be analogous to that of a normal tissue, with a main mass of differentiating cells sensitive to anti proliferative agents, together with a small percentage of quiescent, resistant stem cells responsible for replenishing the tumour: the Cancer Stem Cells (CSCs). Anti-CSCs targeted therapeutic agents would prevent tumour regeneration. New mouse models tailored to exploit this novel concept will be critical to develop CSC-based anti-cancer therapies. Here we review the biological basis and the therapeutic implications of the stem-cell model of cancer.     

Do some deep‐sea,sediment‐dwelling species of harpacticoid copepods have 1000‐km‐scale range sizes?

The range sizes of sediment‐dwelling deep‐sea species are largely unknown. Such knowledge is important because a deep sea composed in large part of species with 100‐km‐scale ranges would be very different from one composed predominantly of species with 1000‐km‐scale ranges. For example, the total species richness would be much greater in the first case than in the second. As a step towards the determination of the distribution of species’ range sizes in the deep sea, we asked whether harpacticoid copepods (Crustacea) on the continental rise in the northeastern Pacific had 1000‐km‐scale range sizes. We chose harpacticoids because they occur widely in deep‐sea sediments and thus are a typical deep‐sea taxon. In addition, they have no pelagic stage in their life history, so they allow a conservative test of hypotheses about species’ range sizes. We used morphology and gene‐sequence data to assign individuals to species. At least 13.3% of the species we studied had 1000‐km‐scale ranges, raising the question of how these species maintain genetic continuity.     

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.     

Phylogeography of a high‐dispersal New Zealand sea‐star: does upwelling block gene‐flow?

New Zealand's (NZ) geographical isolation, extensive coastline and well-characterized oceanography offer a valuable system for marine biogeographical research. Here we use mtDNA control region sequences in the abundant endemic sea-star Patiriella regularis to test the following literature-based predictions: that coastal upwelling disrupts north-south gene flow and promotes population differentiation (hypothesis 1); and that an invasive Tasmanian population of the species was introduced anthropogenically from southern New Zealand (hypothesis 2). We sequenced 114 samples from 22 geographical locations, including nine sites from North Island, nine from South Island, one from Stewart Island and three from Tasmania. Our analysis of these sequences revealed an abundance of shallow phylogenetic lineages within P. regularis (68 haplotypes, mean divergence 0.9%). We detected significant genetic heterogeneity between pooled samples from northern vs. southern New Zealand (FST = 0.072; P = 0.0002), consistent with the hypothesis that upwelling disrupts gene flow between these regions (hypothesis 1). However, we are currently unable to rule out the alternative hypothesis that Cook Strait represents a barrier to dispersal (North Island vs. South Island; FST = 0.031; P = 0.0467). The detection of significant spatial structure in NZ samples is consistent with restricted gene flow, and the strong structure evident in northern NZ may be facilitated by distinct ocean current systems. Four shared haplotypes and nonsignificant differentiation (FST = 0.025; P = 0.2525) between southern New Zealand and Tasmanian samples is consistent with an anthropogenic origin for the latter population (hypothesis 2).     

Proteasomal dysfunction induced by 4‐hydroxy‐2,3‐trans‐nonenal,an end‐product of lipid peroxidation: a mechanism contributing to neurodegeneration?

4-Hydroxy-2,3-trans-nonenal (HNE) is a neurotoxic unsaturated aldehyde end-product of lipid peroxidation. The addition of HNE to NT-2 and SK-N-MC cell lines induces apoptosis and we now investigated the time-course of events occurring prior to apoptosis. Treatment of both NT-2 and SK-N-MC cell lines with HNE led to HNE association with the proteasome, increased levels of protein carbonyls and ubiquitinated proteins, and decreased proteasomal function. There was also decreased metabolic activity, cytochrome c release and activation of caspase 3, followed by apoptotic changes including chromatin condensation, cell shrinkage and DNA fragmentation and laddering. Overexpression of mutant superoxide dismutase 1 proteins associated with amyotrophic lateral sclerosis decreased proteasomal activities in the absence of HNE and accelerated the apoptosis induced by HNE. By contrast, overexpression of wild-type superoxide dismutase 1 did not affect basal levels of proteasomal activity. The data suggest that accumulation of ubiquitinated proteins and impairment of proteasomal function are important events in HNE toxicity. We propose that the proteasomal system is a significant target of HNE neurotoxicity in a wide range of neurodegenerative diseases, especially if abnormal proteins are being expressed.     

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.     

Bundle‐sheath cell regulation of xylem‐mesophyll water transport via aquaporins under drought stress: a target of xylem‐borne ABA?

The hydraulic conductivity of the leaf vascular system (K_leaf) is dynamic and decreases rapidly under drought stress, possibly in response to the stress phytohormone ABA, which increases sharply in the xylem sap (ABA_xyl) during periods of drought. Vascular bundle‐sheath cells (BSCs; a layer of parenchymatous cells tightly enwrapping the entire leaf vasculature) have been hypothesized to control K_leaf via the specific activity of BSC aquaporins (AQPs). We examined this hypothesis and provide evidence for drought‐induced ABA_xyl diminishing BSC osmotic water permeability (P_f) via downregulated activity of their AQPs. ABA fed to the leaf via the xylem (petiole) both decreased K_leaf and led to stomatal closure, replicating the effect of drought. In contrast, smearing ABA on the leaf blade, while also closing stomata, did not decrease K_leaf within 2–3 h of application, demonstrating that K_leaf does not depend entirely on stomatal closure. GFP‐labeled BSCs showed decreased P_f in response to ‘drought’ and ABA treatment, and a reversible decrease with HgCl₂ (an AQP blocker). These P_f responses, absent in mesophyll cells, suggest stress‐regulated AQP activity specific to BSCs, and imply a role for these cells in decreasing K_leaf via a reduction in P_f. Our results support the above hypothesis and highlight the BSCs as hitherto overlooked vasculature sensor compartments, extending throughout the leaf and functioning as ‘stress‐regulated valves’ converting vasculature chemical signals (possibly ABA_xyl) into leaf hydraulic signals.     

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.     

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.     

An example of de‐Tai‐isation? Longue durée ethnic change in a mountainous area of southern China

Inspired by Grant Evans’ work Tai‐ization: Ethnic Change in Northern Indo‐China, this article explores aspects of historical ethnic change in the Yunkai and Yunwu Mountain Ranges, a small upland region intersected by the boundary of Guangdong and Guangxi provinces in southern China over the period 600–1700 C.E. The discussion begins with some of the early linguistic evidence for populations of Tai speakers in the region and what is known of their political and cultural systems, then moves on to consider how Chinese military conquests of the eighth century coupled with the migration of Sinitic and Mien peoples from the eleventh century onwards altered the ethnic composition and political landscape of the region. This is followed by an examination of different exonyms used in Chinese texts for populations of southern China from the fifteenth century onwards and how these might have related to linguistic groupings and identities on the ground, demonstrating that historical usage of Chinese exonyms now connected with Tai or Mien speakers is not always a reliable indicator of a corresponding presence of historical Tai or Mien‐speaking populations. Further research drawing on a number of disciplines is required on a localised level in order to determine when Tai and Mien languages were abandoned in the region and how the inhabitants of the area shifted from the status of named Others to ordinary Chinese subjects.     

Does lethal control of top‐predators release mesopredators? A re‐evaluation of three Australian case studies

Top‐predators can sometimes be important for structuring fauna assemblages in terrestrial ecosystems. Through a complex trophic cascade, the lethal control of top‐predators has been predicted to elicit positive population responses from mesopredators that may in turn increase predation pressure on prey species of concern. In support of this hypothesis, many relevant research papers, opinion pieces and literature reviews identify three particular case studies as supporting evidence for top‐predator control‐induced release of mesopredators in Australia. However, many fundamental details essential for supporting this hypothesis are missing from these case studies, which were each designed to investigate alternative aims. Here, we re‐evaluate the strength of evidence for top‐predator control‐induced mesopredator release from these three studies after comprehensive analyses of associated unpublished correlative and experimental data. Circumstantial evidence alluded to mesopredator releases of either the European Red Fox (Vulpes vulpes) or feral Cat (Felis catus) coinciding with Dingo (Canis lupus dingo) control in each case. Importantly, however, substantial limitations in predator population sampling techniques and/or experimental designs preclude strong assertions about the effect of lethal control on mesopredator populations from these studies. In all cases, multiple confounding factors and plausible alternative explanations for observed changes in predator populations exist. In accord with several critical reviews and a growing body of demonstrated experimental evidence on the subject, we conclude that there is an absence of reliable evidence for top‐predator control‐induced mesopredator release from these three case studies. Well‐designed and executed studies are critical for investigating potential top‐predator control‐induced mesopredator release.     

Bi‐parental vs. cooperative breeding in a passerine: fitness‐maximizing strategies of males in response to risk of extra‐pair paternity?

In socially monogamous species, males that risk cuckoldry more than others might gain inclusive fitness by yielding paternity to relatives. We tested this prediction in the Tibetan ground tit Pseudopodoces humilis , an unusual facultative cooperative breeder wherein most helpers (87% males) join a mated pair shortly before clutch completion. Extra-pair paternity among bi-parental broods occurred less often (26% of broods, 9% of young) compared with cooperative broods (68%, 25%). In the former, most extra-pair sires (88%) were pair breeders unrelated to the cuckolded males, whereas in the latter, sires (87%) were mainly helpers related to the dominant males. Brood productivity did not differ between the bi-parental and cooperative breeders, but helpers' partitioning over group paternity reduced the realized reproductive success of helped males. After taking inclusive fitness into account, however, there was no difference in success of dominant males between the two social systems. One possible explanation for the differences in the rates of cuckoldry in the two systems was body size, because pair-bond males in bi-parental situations were significantly larger than those in cooperative ones. We propose two alternative strategies for males to maximize fitness: breed as a pair if large to avoid cuckoldry from helpers, or breed cooperatively if small but compromise some paternity to relatives. Our results provide an unusual route to the incidence of cooperative groups, based on constraints imposed by low competitive ability of breeding males rather than some external ecological or demographic factors.     

Étienne Geoffroy St.‐Hilaire: father of “evo‐devo”?

SUMMARY In the early decades of the nineteenth century, the most important disagreement among comparative anatomists was not evolution versus "special creation" but between advocates of "transcendental morphology" and those of teleological anatomy—form versus function. In France this dichotomy was represented by the 1830–1832 public debate between Geoffroy St.-Hilaire (form) and Cuvier (function). Geoffroy's aim was to establish links of homology (known to him as "analogies") between the four "embranchements" into which Cuvier had divided the animal kingdom. Despite the fanciful nature of some of his homologies, Geoffroy, who was guided by his " principe de connections ," set in motion a school of morphology, some of whose conclusions, notably the homology of the dorsal surface of segmented invertebrates with the ventral surface of vertebrates, has been corroborated by recent studies in developmental genetics.     

Non‐native conditions favor non‐native populations of invasive plant: demographic consequences of seed size variation?

Trait differences between native and non‐native populations may explain the greater abundance and impact of some organisms in their non‐native ranges than in their native ranges. Here, we conducted reciprocal common gardens in southwestern Turkey (home) and central Argentina (away) to explore the hypothesis that the greater success of the invasive ruderal Centaurea solstitialis in Argentina than Turkey is partially explained by differences between home and away populations. Unusual among common gardens, our experimental design included seed additions to explicitly evaluate population level responses, as well as disturbance and no‐disturbance treatments. We documented seed mass in native and non‐native populations, and during the experiment, we periodically measured density, plant size, and herbivory. After six months, we determined the establishment of plants for populations from both origins in both home and away common gardens. Seed mass was two times larger for Argentinean than Turkish populations. Density, plant size and final establishment were also greater for plants from Argentinean than from Turkish populations, but only in the common garden in Argentina. In Turkey, no differences between population origins were detected for these variables. Herbivory was similar for populations from both origins in both common gardens. As expected, disturbance generally increased plant performance in both regions. Our results suggest that increased seed size in non‐native populations may have demographic consequences under non‐native conditions that can contribute to the invasive success of C. solstitialis. This is the first reciprocal common garden that supports the idea that seed size variation contributes to demographic differences for an invasive species between native and non‐native distributions, but our findings further suggest that seed size effects on demography depend on the ecological context in which population processes occur.     

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.