Search

SUMMARY Salmonella enterica serovar Enteritidis and Campylobacter jejuni are 2 major foodborne pathogens transmitted through poultry products. These pathogens colonize the chicken cecum, leading to contamination of carcasses during slaughter and subsequent processing operations. We investigated the antimicrobial efficacy of 4 GRAS (generally recognized as safe) status plant-derived molecules, namely, trans-cinnamaldehyde, eugenol, carvacrol, and thymol, against Salmonella Enteritidis and C. jejuni in chicken cecal contents in vitro. The plant molecules were added at different concentrations (ranging from 10 to 75 mM for Salmonella Enteritidis and 10 to 30 mM for C. jejuni) to autoclaved chicken cecal contents inoculated with approximately 7.0 log10 cfu/mL of Salmonella Enteritidis or approximately 5.0 log10 cfu/mL of C. jejuni. The pathogen populations in the cecal contents after 15 s, 8 h, and 24 h of incubation at 40°C were determined. Duplicate samples of treatments and the control were included, and the study was replicated 3 times. Campylobacter jejuni was more sensitive to all the molecules than Salmonella Enteritidis (P ≤ 0.05). All molecules were highly bactericidal, with the lowest concentration of trans-cinnamaldehyde (10 mM) reducing (P ≤ 0.05) Salmonella Enteritidis populations by approximately 6.0 log10 cfu/mL after 8 h and >8.0 log10 cfu/mL after 24 h of incubation. Trans-cinnamaldehyde at 25 mM eliminated detectable (P ≤ 0.05) Salmonella Enteritidis counts by 8 h of incubation. In addition, trans-cinnamaldehyde at all tested concentrations (10, 20, and 30 mM) reduced C. jejuni counts to

Previous attempts to resolve relationships among the primary lineages of Campanulidae (e.g. Apiales, Asterales, Dipsacales) have mostly been unconvincing, and the placement of a number of smaller groups (e.g. Bruniaceae, Columelliaceae, Escalloniaceae) remains uncertain. Here we build on a recent analysis of an incomplete data set that was assembled from the literature for a set of 50 campanulid taxa. To this data set we first added newly generated DNA sequence data for the same set of genes and taxa. Second, we sequenced three additional cpDNA coding regions (ca. 8,000 bp) for the same set of 50 campanulid taxa. Finally, we assembled the most comprehensive sample of campanulid diversity to date, including ca. 17,000 bp of cpDNA for 122 campanulid taxa and five outgroups. Simply filling in missing data in the 50-taxon data set (rendering it 94% complete) resulted in a topology that was similar to earlier studies, but with little additional resolution or confidence. In contrast, the addition of the ca. 8,000 bp of sequence data provided resolution and support for a number of relationships. With the addition of many more campanulid taxa we recovered a well-resolved phylogeny for Campanulidae where, with the exception of the placement of Escalloniaceae, support was high for all major clades. In addition, we were able to confidently place a number of enigmatic taxa, some whose relationships were previously unresolved and some never before included. In light of these results, we briefly expand the discussion of floral symmetry and provide a phylogenetic classification of Campanulidae with phylogenetic definitions for all well-supported major clades.

A framework for exploring regional-scale trade-offs among ecosystem services and biodiversity protection has been established for some time, and it is clear that optimizing these trade-offs provides a strategy to address targets for a reduced rate of biodiversity loss. Recent trade-off studies have highlighted the need for better biodiversity measures, to complement measures of ecosystem services. Biodiversity typically has been linked in this context to existence and other non-use values. We argue that biodiversity will have a stronger role in such trade-off analyses if measures of biodiversity better reflect additional current and future services. These ‘evosystem services’ have been, and, if we are careful, can continue to be provided by the evolutionary process. Some services have been provided through evolution operating in the past, and a phylogenetic diversity measure can help us to quantify these current and potential future benefits derived from the tree of life. Furthermore, a variety of evosystem services are delivered through ongoing contemporary evolution, and value should therefore be placed on the maintenance of healthy evosystems. We argue that the concept of evosystem services could be useful as a complement to the traditional concept of ecosystem services. Together, these reflect a fuller range of the services supported by biodiversity, and thereby provide a sounder basis for conservation planning and decision-making.

Genetic elements determine phenotypes of organisms by interacting with environments. Despite genetic diversity within and between species being the fundamental basis of biological diversity, its contribution has been long neglected in biodiversity studies. This situation is rapidly changing as quantification of genetic diversity, from intraspecific up to the ecosystem level, has become more accessible owing to the development of next-generation sequencing technologies (NGSTs). Whole-genome sequencing techniques provide two specific approaches for accessing genetic diversity at large scales: metagenomics (environmental genomics) and EST (Expressed Sequence Tag) comparisons. The former has been applied successfully in the profiling of different microbial biomes, and it is particularly interesting in understanding their ecosystem structure and function. The latter is particularly useful in the studies of adaptation and the assessment of functional traits. Unquestionably, advances in the genomic sciences combined with a new generation of ecological and evolutionary science will boost new approaches to global and local assessments of biodiversity changes, and more importantly, will surely reframe the questions we are asking in biodiversity science.

The reconstruction of ancestors is a central aim of comparative anatomy and evolutionary developmental biology, not least in attempts to understand the relationship between developmental and organismal evolution. Inferences based on living taxa can and should be tested against the fossil record, which provides an independent and direct view onto historical character combinations. Here, we consider the nature of the last common ancestor of living ecdysozoans through a detailed analysis of palaeoscolecids, an early and extinct group of introvert-bearing worms that have been proposed to be ancestral ecdysozoans. In a review of palaeoscolecid anatomy, including newly resolved details of the internal and external cuticle structure, we identify specific characters shared with various living nematoid and scalidophoran worms, but not with panarthropods. Considered within a formal cladistic context, these characters provide most overall support for a stem-priapulid affinity, meaning that palaeoscolecids are far-removed from the ecdysozoan ancestor. We conclude that previous interpretations in which palaeoscolecids occupy a deeper position in the ecdysozoan tree lack particular morphological support and rely instead on a paucity of preserved characters. This bears out a more general point that fossil taxa may appear plesiomorphic merely because they preserve only plesiomorphies, rather than the melange of primitive and derived characters anticipated of organisms properly allocated to a position deep within animal phylogeny.

Campylobacter is a leading cause of foodborne illness in the United States, and epidemiological evidence indicates poultry products to be a significant source of human Campylobacter infections. Caprylic acid, an eight-carbon medium-chain fatty acid, reduces Campylobacter colonization in chickens. How caprylic acid reduces Campylobacter carriage may be related to changes in intestinal microflora. To evaluate this possibility, cecal microbial populations were evaluated with denaturing gradient gel electrophoresis from market-age broiler chickens fed caprylic acid. In the first trial, chicks (n = 40 per trial) were assigned to four treatment groups (n = 10 birds per treatment group): positive controls (Campylobacter, no caprylic acid), with or without a 12-h feed withdrawal before slaughter; and 0.7% caprylic acid supplemented in feed for the last 3 days of the trial, with or without a 12-h feed withdrawal before slaughter. Treatments were similar for trial 2, except caprylic acid was supplemented for the last 7 days of the trial. At age 14 days, chicks were orally challenged with Campylobacter jejuni, and on day 42, ceca were collected for denaturing gradient gel electrophoresis and Campylobacter analysis. Caprylic acid supplemented for 3 or 7 days at 0.7% reduced Campylobacter compared with the positive controls, except for the 7-day treatment with a 12-h feed withdrawal period. Denaturing gradient gel electrophoresis profiles of the cecal content showed very limited differences in microbial populations. The results of this study indicate that caprylic acid's ability to reduce Campylobacter does not appear to be due to changes in cecal microflora.

Bayesian inference provides a powerful framework for integrating different sources of information (in particular, molecules and fossils) to derive estimates of species divergence times. Indeed, it is currently the only framework that can adequately account for uncertainties in fossil calibrations. We use 2 Bayesian Markov chain Monte Carlo programs, MULTIDIVTIME and MCMCTREE, to analyze 3 empirical datasets to estimate divergence times in amphibians, actinopterygians, and felids. We evaluate the impact of various factors, including the priors on rates and times, fossil calibrations, substitution model, the violation of the molecular clock and the rate-drift model, and the exact and approximate likelihood calculation. Assuming the molecular clock caused seriously biased time estimates when the clock is violated, but 2 different rate-drift models produced similar estimates. The prior on times, which incorporates fossil-calibration information, had the greatest impact on posterior time estimation. In particular, the strategies used by the 2 programs to incorporate minimum- and maximum-age bounds led to very different time priors and were responsible for large differences in posterior time estimates in a previous study. The results highlight the critical importance of fossil calibrations to molecular dating and the need for probabilistic modeling of fossil depositions, preservations, and sampling to provide statistical summaries of information in the fossil record concerning species divergence times.

A phylogenetic study of Dipsacaceae, a Mediterranean-centered clade in the Dipsacales, was conducted using nuclear ITS and three chloroplast markers (atpB-rbcL, trnL-trnF, trnS UGA- trnG GCC ). This is the first molecular study to assess Dipsacaceae phylogeny in detail, and includes representatives from all major subclades. Maximum parsimony, maximum likelihood, and Bayesian analyses were carried out on the ITS and plastid datasets separately and in combination. For the most part, the ITS and plastid datasets resulted in similar topologies, and the combined data yielded a well-resolved estimate of Dipsacaceae phylogeny. A small Asian clade composed of Bassecoia and Pterocephalodes hookeri is resolved as sister to the rest of Dipsacaceae. Scabioseae s.str. (Scabiosa, Sixalix, Pterocephalus s.str., Lomelosia, Pycnocomon) and a "Dipknautid" clade (Dipsacus, Cephalaria, Knautia, Pterocephalidum, Succisa, Succisella, Pseudoscabiosa) form the two major lineages within Dipsacaceae. Most of the previously recognized genera are recovered as monophyletic, with the exception of Pycnocomon, which is nested within Lomelosia. We discuss the taxonomic implications of these results and their significance for understanding character evolution, particularly of the epicalyx in relation to seed dispersal.

Aim The clade Campanulaceae in the Cretan area is rich in endemics, with c. 50% of its species having restricted distributions. These species are analysed in the context of a larger phylogeny of the Campanulaceae. Divergence times are calculated and hypotheses of vicariance and dispersal are tested with the aim of understanding whether Cretan lineages represent remnants of an older continental flora. Location The Cretan area: Crete and the Karpathos Islands (Greece). Methods We obtained chloroplast DNA sequence data from rbcL, atpB and matK genes for 102 ingroup taxa, of which 18 are from the Cretan area, 11 are endemics, and two have disjunct, bi-regional distributions. We analysed the data using BEAST, a Bayesian approach that simultaneously infers the phylogeny and divergence times. We calibrated the tree by placing a seed fossil in the phylogeny, and used published age estimates as a prior for the root. Results The phylogenetic reconstruction shows that all Campanula species fall within a well-supported campanuloid clade; however, Campanula is highly polyphyletic. The Cretan endemics do not form a monophyletic group, and species are scattered throughout the campanuloid clade. Therefore, the Cretan taxa did not evolve following a single vicariance or dispersal event. Most Cretan lineages represent remnants of an older continental flora, with the exception of one clade that radiated in situ after island isolation, and one lineage that appears to have arrived by dispersal. Main conclusions Most Cretan species were present in the islands at the time of their isolation, and very little long-distance dispersal to Crete and diversification within Crete has occurred since then. Endemism is probably driven by loss of species on the mainland after island isolation. Species on the islands may have been more widespread in the past, but they are now restricted to often inaccessible areas, probably as a result of human pressure.

The evolutionary origin of vertebrates has been debated ad nauseam by anatomists, paleontologists, embryologists, and physiologists, but it is only now that molecular phylogenetics is providing a more rigorous framework for the placement of vertebrates among their invertebrate relatives that we can begin to arrive at concrete conclusions concerning the nature of ancient ancestors and the sequence in which characteristic anatomical features were acquired. Vertebrates tunicates and cephalochordates together comprise the chordate phylum, which along with echinoderms and hemichordates constitute the deuterostomes. The origin of vertebrates and of jawed vertebrates is characterized by a doubling of the vertebrate genome, leading to hypotheses that this genomic event drove organismal macroevolution. However, this perspective of evolutionary history, based on living organisms alone, is an artifact. Phylogenetic trees that integrate fossil vertebrates among their living relatives demonstrate the gradual and piecemeal assembly of the gnathostome body plan. Unfortunately, it has not been possible to demonstrate gradual assembly of the vertebrate body plan. This is not because vertebrates are irreducibly complex but because many of the characters that distinguish vertebrates from invertebrates are embryological and cellular and, therefore, inherently unfossilizable.

Botella, H., Donoghue, P.C.J and Martinez-Perez, C. 2009. The enameloid microstructure of the oldest known chondrichthyan teeth. — Acta Zoologica (Stockholm) 90 (Suppl. 1): 103‐108 Previous studies on tooth enameloid microstructure in several chondrichthyan taxa spanning the phylogeny of the group provided support for the homology of chondrichthyan tooth enameloid. This hypothesis requires that a single crystallite enameloid (SCE) monolayer must be present in the teeth of the most primitive chondrichthyan. However, the dental microstructure of the earliest sharks has yet to be investigated. We have studied the tooth enameloid microstructure of the two oldest tooth-bearing shark species currently known, Leonodus carlsi Mader (1986) and Celtiberina maderi Wang (1993), from the lowermost Lochkovian (Lower Devonian) of Spain. Our study demonstrates the presence of a SCE monolayer in the teeth of both species. These results show that a superficial cap of SCE is present in the oldest shark teeth known, which suggest its presence in the most basal chondrichthyans.

Salmonella Enteritidis is a major foodborne pathogen for which chickens serve as reservoir hosts. Reducing Salmonella Enteritidis carriage in chickens would reduce contamination of poultry meat and eggs with this pathogen. We investigated the prophylactic efficacy of feed supplemented with caprylic acid (CA), a natural, generally recognized as safe eight-carbon fatty acid, for reducing Salmonella Enteritidis colonization in chicks. One hundred commercial day-old chicks were randomly divided into five groups of 20 birds each: CA control (no Salmonella Enteritidis, CA), positive control (Salmonella Enteritidis, no CA), negative control (no Salmonella Enteritidis, no CA), and 0.7 or 1% CA. Water and feed were provided ad libitum. On day 8, birds were inoculated with 5.0 log CFU of Salmonella Enteritidis by crop gavage. Six birds from each group were euthanized on days 1, 7, and 10 after challenge, and Salmonella Enteritidis populations in the cecum, small intestine, cloaca, crop, liver, and spleen were enumerated. The study was replicated three times. CA supplementation at 0.7 and 1% consistently decreased Salmonella Enteritidis populations recovered from the treated birds. Salmonella Enteritidis counts in the tissue samples of CA-treated chicks were significantly lower (P < 0.05) than those of control birds on days 7 and 10 after challenge. Feed intake and body weight did not differ between the groups. Histological examination revealed no pathological changes in the cecum and liver of CA-supplemented birds. The results suggest that prophylactic CA supplementation through feed can reduce Salmonella Enteritidis colonization in day-old chicks and may be a useful treatment for reducing Salmonella Enteritidis carriage in chickens.

Evolutionary biologists often wish to explore the impact of a particular historical event (e.g., the origin of a novel morphological trait, an episode of biogeographic dispersal, or the onset of an ecological association) on rates of diversification (speciation minus extinction). We describe a Bayesian approach for evaluating the correlation between such events and differential rates of diversification that relies on cross-validation predictive densities. This approach exploits estimates of the marginal posterior probability for the rate of diversification (in the unaffected part of the tree) and the marginal probability for the timing of the event to generate a predictive distribution of species diversity that would be expected had the event not occurred. The realized species diversity can then be compared to this predictive diversity distribution to assess whether rates of diversification associated with the event are significantly higher or lower than expected. Although simple, this Bayesian approach provides a robust inference framework that accommodates various sources of uncertainty, including error associated with estimates of divergence times, diversification-rate parameters, and event history. Furthermore, the proposed approach is relatively flexible, allowing exploration of various types of events (including changes in discrete morphological traits, episodes of biogeographic movement, etc.) under both hypothesis-testing and data-exploration inference scenarios. Importantly, the cross-validation predictive densities approach facilitates evaluation of both replicated and unique historical events. We demonstrate this approach with empirical examples concerning the impact of morphological and biogeographic events on rates of diversification in Adoxaceae and Lupinus , respectively.

The genetics underlying flower symmetry shifts between radial and bilateral symmetry has been intensively studied in the model Antirrhinum majus. Understanding the conservation or diversification of this genetic pathway in other plants is of special interest in understanding angiosperm evolution and ecology. Evidence from Antirrhinum indicates that TCP and MYB transcription factors, especially CYCLOIDEA (CYC), DICHOTOMA (DICH), DIVARICATA (DIV), and RADIALIS (RAD) play a role in specifying dorsal identity (CYC, DICH, and RAD) and ventral identity (DIV) in the corolla and androecium of monosymmetric (bilateral) flowers. Previous data indicate that the ECE clade of TCP genes (including CYC and DICH) underwent two duplication events around the diversification of the core eudicots. In this study, we examined the duplication events within Dipsacales, which contains both radially and bilaterally symmetrical flowered species. Additionally, we report here the phylogenetic relationships of the DIV-like genes across core eudicots. Like TCP genes, we found three core eudicot clades of DIV-like genes, with duplications occurring around the diversification of the core eudicots, which we name DIV1, DIV2, and DIV3. The Antirrhinum genes, DIVARICATA and its sister DVL1, fall into the DIV1 clade. We also found additional duplications within these clades in Dipsacales. Specifically, the Caprifoliaceae (bilaterally symmetrical clade) duplicated independently in each of the three core eudicot DIV clades. Using reverse transcription polymerase chain reaction (rtPCR), we showed that most of these copies are expressed across floral tissues in the Dipsacales species Heptacodium miconioides. One copy, DipsDIV1A (orthologous to DIV and DVL1), was expressed in a dorsal-ventral pattern. DipsDIV1A was expressed only in petal tissue, in both dorsal and ventral regions but was lacking from lateral petals. We argue that this suggests that DipsDIV1A may be expressed in a similar pattern to DIV in Antirrhinum, suggesting a broad conservation of this pathway. Finally, DIV contains a large intron near the beginning of the second MYB domain, which shows promise as a highly variable molecular marker for phylogenetic studies.

Microscopy and Microanalysis, 15 (2), ISSN:1431-9276, ISSN:1435-8115

We integrate climatic niche models and dated phylogenies to characterize the evolution of climatic niches in Oenothera sections Anogra and Kleinia (Onagraceae), and from that we make inferences on diversification in relation to climate. The evolution of climatic tolerances in Anogra + Kleinia has been heterogeneous, across phylogenetic groups and across different dimensions of climate. All the extant taxa occur in semiarid to arid conditions (annual precipitation of 10.1-49.1 cm and high temperatures in the warmest month of 28.5 degrees-40.1 degrees C), but there is striking variation among taxa in their climatic tolerances, especially temperature (minimum temperatures in the coldest month of -14.0 degrees to 5.3 degrees C) and summer versus winter precipitation (precipitation in the warmest quarter of 0.6-19.4 cm). Climatic disparity is especially pronounced in two subclades (californica, deltoides) that radiated in the southwestern United States and California, apparently including both divergent and convergent evolution of climatic tolerances. This niche evolution is remarkable, given the probable timescale of the radiation (approximately 1 million years). We suggest that the spatiotemporal climatic heterogeneity of western North America has served as a driver of diversification. Our data are also consistent with Axelrod's hypothesis that the spread of arid conditions in western North America stimulated diversification of arid-adapted lineages.

Although the relationship between ontogeny and phylogeny has been of long-standing interest to palaeontolo- gists, the fossil record has provided little insight into the development of long extinct organisms. This has changed with the discovery of numerous assemblages of fossilized invertebrate embryos and larvae, but realising their evolu- tionary significance is hampered by a paucity of data on the relationship between ontogeny and taphonomy. We describe the results of an experimental taphonomy study of the devel- opment of the anostracan brine shrimp Artemia salina, which show that in conditions of aqueous aerobic and anaer- obic autolysis and microbial decay, the developmental stages exhibit differential preservation potential. The most decay resistant developmental stage is the diapause cyst, encapulsat- ing the gastrula, in which the gross morphology of the embryo can be maintained for 18 months or more in simple anaerobic conditions. Otherwise, the embryo shrinks within the cyst and cellular and tissue detail of breaks down as lipid droplets coalesce. Postembryonic excysted larvae decay more rapidly. The rate of decay is similar among all larval stages with the exception of the L4 larva, which resists cuticle fail- ure for longer than later developmental stages. The larvae decay leading to liquefaction of the muscles and viscera, leav- ing an intact but empty and progressively shrunken and dis- torted cuticle that eventually loses structural integrity and collapses. Our experimental results provide an explanatory model for the phenomenal abundance of putative diapause stage embryos, in the absence of postembryonic stages, as seen in the Ediacaran Doushantuo Formation of South China and the incompleteness of fossilized developmental sequences of embryos and larvae more generally. It also cau- tions against the association of developmental stages in fossil deposits without additional evidence. Finally, the pattern of decay seen in larvae provides an explanation for the preser- vation style of Orsten-type Lagerstatten where preservation of cuticular detail can be astonishingly fine, but extends internally to muscles and viscera only rarely.

The intrinsic damage response is activated by DNA damage that arises during the cell division process. The ability of the cell to repair this damage during proliferation is important for normal cell growth and, when disrupted, may lead to increased mutagenesis and tumorigenesis. The atypical CDK activator, Spy1, was previously shown to promote cell survival, prevent apoptosis and inhibit checkpoint activation in response to DNA damage. Prior studies have shown that Spy1 is upregulated in breast carcinomas and accelerates mammary tumorigenesis in vivo. In this report, first, we demonstrate that the ability of Spy1 to inhibit apoptosis and bypass UV-induced checkpoint activation is dependent on the presence of the gene regulatory protein p53 and the CKI p21. Second, we demonstrate that Spy1 expression has the following effects: prevents repair of cyclobutane pyrimidine dimers through bypass of nucleotide excision repair; increases the cellular mutation frequency; and reduces the formation of cyclin E induced gammaH2A.X foci. Lastly, we show that knockdown of endogenous Spy1 leads to gammaH2A.X foci formation, Chk1 phosphorylation and proliferation defects, demonstrating a functional role for Spy1 in the intrinsic DNA damage response. These results also demonstrate that Spy1 fulfills a novel regulatory role in the intrinsic DNA damage response and maintains the balance between checkpoint activation, apoptosis, repair and cell cycle progression in response to exogenous or intrinsic damage. Furthermore, the overexpression of Spy1 as a contributing factor in cancer progression will most likely be confined to p53-positive cells.

The use of benzodiazepine anxiolytics and hypnotics continues to excite controversy. Views differ from expert to expert and from country to country as to the extent of the problem, or even whether long-term benzodiazepine use actually constitutes a problem. The adverse effects of these drugs have been extensively documented and their effectiveness is being increasingly questioned. Discontinuation is usually beneficial as it is followed by improved psychomotor and cognitive functioning, particularly in the elderly. The potential for dependence and addiction have also become more apparent. The licensing of SSRIs for anxiety disorders has widened the prescribers' therapeutic choices (although this group of medications also have their own adverse effects). Melatonin agonists show promise in some forms of insomnia. Accordingly, it is now even more imperative that long-term benzodiazepine users be reviewed with respect to possible discontinuation. Strategies for discontinuation start with primary-care practitioners, who are still the main prescribers.This review sets out the stratagems that have been evaluated, concentrating on those of a pharmacological nature. Simple interventions include basic monitoring of repeat prescriptions and assessment by the doctor. Even a letter from the primary-care practitioner pointing out the continuing usage of benzodiazepines and questioning their need can result in reduction or cessation of use. Pharmacists also have a role to play in monitoring the use of benzodiazepines, although mobilizing their assistance is not yet routine. Such stratagems can avoid the use of specialist back-up services such as psychiatrists, home care, and addiction and alcohol misuse treatment facilities.Pharmacological interventions for benzodiazepine dependence have been reviewed in detail in a recent Cochrane review, but only eight studies proved adequate for analysis. Carbamazepine was the only drug that appeared to have any useful adjunctive properties for assisting in the discontinuation of benzodiazepines but the available data are insufficient for recommendations to be made regarding its use. Antidepressants can help if the patient is depressed before withdrawal or develops a depressive syndrome during withdrawal. The clearest strategy was to taper the medication; abrupt cessation can only be justified if a very serious adverse effect supervenes during treatment. No clear evidence suggests the optimum rate of tapering, and schedules vary from 4 weeks to several years. Our recommendation is to aim for withdrawal in6 months, otherwise the withdrawal process can become the morbid focus of the patient's existence. Substitution of diazepam for another benzodiazepine can be helpful, at least logistically, as diazepam is available in a liquid formulation.Psychological interventions range from simple support through counselling to expert cognitive-behavioural therapy (CBT). Group therapy may be helpful as it at least provides support from other patients. The value of counselling is not established and it can be quite time consuming. CBT needs to be administered by fully trained and experienced personnel but seems effective, particularly in obviating relapse.The outcome of successful withdrawal is gratifying, both in terms of improved functioning and abstinence from the benzodiazepine usage. Economic benefits also ensue.Some of the principles of withdrawing benzodiazepines are listed. Antidepressants may be helpful, as may some symptomatic remedies. Care must be taken not to substitute one drug dependence problem for the original one.

Fossilized embryos with extraordinary cellular preservation appear in the Late Neoproterozoic and Cambrian, coincident with the appearance of animal body fossils. It has been hypothesized that microbial processes are responsible for preservation and mineralization of organic tissues. However, the actions of microbes in preservation of embryos have not been demonstrated experimentally. Here, we show that bacterial biofilms assemble rapidly in dead marine embryos and form remarkable pseudomorphs in which the bacterial biofilm replaces and exquisitely models details of cellular organization and structure. The experimental model was the decay of cleavage stage embryos similar in size and morphology to fossil embryos. The data show that embryo preservation takes place in 3 distinct steps: ( i ) blockage of autolysis by reducing or anaerobic conditions, ( ii ) rapid formation of microbial biofilms that consume the embryo but form a replica that retains cell organization and morphology, and ( iii ) bacterially catalyzed mineralization. Major bacterial taxa in embryo decay biofilms were identified by using 16S rDNA sequencing. Decay processes were similar in different taphonomic conditions, but the composition of bacterial populations depended on specific conditions. Experimental taphonomy generates preservation states similar to those in fossil embryos. The data show how fossilization of soft tissues in sediments can be mediated by bacterial replacement and mineralization, providing a foundation for experimentally creating biofilms from defined microbial species to model fossilization as a biological process.

Salmonella Enteritidis and Campylobacter jejuni are 2 major foodborne pathogens in the United States, estimated to cause more than 3 million cases of human illness annually. Chickens are the natural hosts of these bacteria, and their drinking water can be a source of S. Enteritidis and C. jejuni, contributing to the colonization of birds. In this study, trans-cinnamaldehyde (TC), a natural, generally recognized as safe ingredient in cinnamon oil was evaluated for its efficacy to inactivate S. Enteritidis and C. jejuni in the drinking water of chickens. Well water containing 0, 0.016, 0.03, and 0.06% TC was inoculated with a 5-strain mixture of S. Enteritidis or C. jejuni (˜6 log10 cells/mL). Water samples containing 1% chicken feces or feed were also included. The samples were incubated at 12.5 or 25°C for 7 d and analyzed for bacterial populations on d 0, 1, 3, 5, and 7. Duplicate samples of treatments and control were included, and the study was replicated 3 times. Trans-cinnamaldehyde at 0.06% inactivated Salmonella completely after 24 h in water with 1% feces at both temperatures. In water containing 1% feed, TC (0.06%) reduced S. Enteritidis to undetectable levels after 3 d at 12.5°C or 7 d at 25°C. Presence of feed or feces in water reduced the antibacterial effect (P 0.001) on the antibacterial property of TC on C. jejuni. Results indicate that TC is effective in killing S. Enteritidis and C. jejuni in chicken drinking water and may decrease the likelihood that water will contribute to colonization of chickens by these pathogens.

Variable rates of molecular evolution have been documented across the tree of life, but the cause of this observed variation within and among clades remains uncertain. In plants, it has been suggested that life history traits are correlated with the rate of molecular evolution, but previous studies have yielded conflicting results. Exceptionally large phylogenies of five major angiosperm clades demonstrate that rates of molecular evolution are consistently low in trees and shrubs, with relatively long generation times, as compared with related herbaceous plants, which generally have shorter generation times. Herbs show much higher rates of molecular change but also much higher variance in rates. Correlates of life history attributes have long been of interest to biologists, and our results demonstrate how changes in the rate of molecular evolution that are linked to life history traits can affect measurements of the tempo of evolution as well as our ability to identify and conserve biodiversity.

Recent phylogenetic analyses of the Dipsacales strongly support a Caprifolieae clade within Caprifoliaceae including Leycesteria, Triosteum, Symphoricarpos, and Lonicera. Relationships within Caprifolieae, however, remain quite uncertain, and the monophyly of Lonicera, the most species-rich of the traditional genera, and its subdivisions, need to be evaluated. In this study we used sequences of the ITS region of nuclear ribosomal DNA and five chloroplast non-coding regions (rpoB–trnC spacer, atpB–rbcL spacer, trnS–trnG spacer, petN–psbM spacer, and psbM–trnD spacer) to address these problems. Our results indicate that Heptacodium is sister to Caprifolieae, Triosteum is sister to the remaining genera within the tribe, and Leycesteria and Symphoricarpos form a clade that is sister to a monophyletic Lonicera. Within Lonicera, the major split is between subgenus Caprifolium and subgenus Lonicera. Within subgenus Lonicera, sections Coeloxylosteum, Isoxylosteum, and Nintooa are nested within the paraph...

Activating mutations within fibroblast growth factor receptor 3 (FGFR3), a receptor tyrosine kinase, are responsible for human skeletal dysplasias including achondroplasia and the neonatal lethal syndromes, Thanatophoric Dysplasia (TD) type I and II. Several of these same FGFR3 mutations have also been identified somatically in human cancers, including multiple myeloma, bladder carcinoma, and cervical cancer. Based on reports that strongly activated mutants of FGFR3 such as the TDII (K650E) mutant signal preferentially from within the secretory pathway, the inhibitory properties of nordihydroguaiartic acid (NDGA), which blocks protein transport through the Golgi, were investigated. NDGA was able to inhibit FGFR3 autophosphorylation both in vitro and in vivo. In addition, signaling molecules downstream of FGFR3 activation such as signal transducers and activators of transcription (STAT)1, STAT3, and mitogen-activated protein kinase (MAPK) were inhibited by NDGA treatment. Using HEK293 cells expressing activated FGFR3-TDII, together with several multiple myeloma cell lines expressing activated forms of FGFR3, NDGA generally resulted in a decrease in MAPK activation by 1 hour, and resulted in increased apoptosis over 24 hours. The effects of NDGA on activated FGFR3 derivatives targeted either to the plasma membrane or the cytoplasm were also examined. These results suggest that inhibitory small molecules such as NDGA that target a specific subcellular compartment may be beneficial in the inhibition of activated receptors such as FGFR3 that signal from the same compartment. [Cancer Res 2008;68(18):7362–70]

Ilemoraspis kirkinskayae is a poorly known genus of Osteostraci (stem-gnathostome) yet is one of the most distinct in terms of its anatomy and biogeography. It is paleobiogeographically isolated from all but one other genus of Osteostraci on the Altaid microcontinents and is one of the few genera to survive into the Middle Devonian. Discovery of a new locality in Khakassia, Russia, has yielded a number of exceptionally well-preserved specimens of the genus and subsequently a wealth of new anatomical information. A new reconstruction of Ilemoraspis is provided, including postcranial anatomy and a sensory line extending onto the trunk. The latter is a novel observation for the Osteostraci and allows the proposal of a scenario for the evolution of trunk lateral lines. New anatomical data for I. kirkinskayae allow testing of established hypotheses on its affinity. Our analyses yield two equally parsimonious solutions that appear unlikely on the basis of comparative anatomy or paleobiogeographic grounds, respectively. This situation is likely to be a consequence of the sporadic sampling of osteostracans in central Asia.

Using a low-copy nuclear gene region ( LEAFY second intron) we show multiple instances of allopolyploid speciation in Persicaria (Polygonaceae), which includes many important weeds. Fifteen species seem to be allopolyploids, which is higher than the number found in previous comparisons of chloroplast DNA and nuclear ribosomal internal transcribed spacer (nrITS) phylogenies. This underestimation of the extent of allopolyploidy is due in at least three cases to homogenization of nrITS toward the maternal lineage. One of the diploid species, P. lapathifolia , has been involved in at least six cases of allopolyploid speciation. Of the diploids, this species is the most widespread geographically and ecologically and also bears more numerous and conspicuous flowers, illustrating ecologic factors that may influence hybridization frequency. With a few exceptions, especially the narrowly endemic hexaploid, P. puritanorum , the allopolyploid species also are widespread, plastic, ecological generalists. Hybridization events fostered by human introductions may be fueling the production of new species that have the potential to become aggressive weeds.

Interspecific hybridization followed by polyploidization appears to have played a major role in plant diversification, but quantifying the contribution of this mechanism to diversification within taxonomically complex clades remains difficult. Incongruence among gene trees can provide critical insights, especially when combined with data on chromosome numbers, morphology, and geography. To further test our previous hypothesis on hybrid speciation in Persicaria (Polygonaceae), we performed molecular phylogenetic studies using three cpDNA regions and nuclear ITS sequences, with an emphasis on sampling within section Eupersicaria. Our analyses revealed major conflicts between the combined cpDNA tree and the nrITS tree; a variety of incongruence tests rejected stochastic error as the cause of incongruence in most cases. On the basis of our tree incongruence results and information on chromosome numbers, we hypothesize that the origin of 10 polyploid species involved interspecific hybridization. Our studies also support the recognition of several previously named species that have been treated as belonging within other species. Repeated allotetraploidy (as distinct from radiation at the tetraploid level) now appears to be the key mechanism governing the diversification of this taxonomically challenging group.

Phylogenetic studies are revealing that major ecological niches are more conserved through evolutionary history than expected, implying that adaptations to major climate changes have not readily been accomplished in all lineages. Phylogenetic niche conservatism has important consequences for the assembly of both local communities and the regional species pools from which these are drawn. If corridors for movement are available, newly emerging environments will tend to be filled by species that filter in from areas in which the relevant adaptations have already evolved, as opposed to being filled by in situ evolution of these adaptations. Examples include intercontinental disjunctions of tropical plants, the spread of plant lineages around the Northern Hemisphere after the evolution of cold tolerance, and the radiation of northern alpine plants into the Andes. These observations highlight the role of phylogenetic knowledge and historical biogeography in explanations of global biodiversity patterns. They also have implications for the future of biodiversity.

Intramolecular hydroamination of several aminoalkynes catalyzed by silver-phenanthroline complexes is reported. This catalyst system complements previous protocols by employing air- and moisture-stable complexes without compromising activity or reaction control. Some of the hydroamination products are subject to a useful aerobic oxidation. Silver-phenanthroline complexes have successfully demonstrated efficacy in the desymmetrization of a prochiral diyne.

Hemlock, Tsuga (Pinaceae), has a disjunct distribution in North America and Asia. To examine the biogeographic history of Tsuga, phylogenetic relationships among multiple accessions of all nine species were inferred using chloroplast DNA sequences and multiple cloned sequences of the nuclear ribosomal ITS region. Analysis of chloroplast and ITS sequences resolve a clade that includes the two western North American species, T. heterophylla and T. mertensiana, and a clade of Asian species within which one of the eastern North American species, T. caroliniana, is nested. The other eastern North American species, T. canadensis, is sister to the Asian clade. Tsuga chinensis from Taiwan did not group with T. chinensis from mainland China, and T. sieboldii from Ullung Island did not group with T. sieboldii from Japan suggesting that the taxonomic status of these distinct populations should be reevaluated. The Himalayan species, T. dumosa, was in conflicting positions in the chloroplast and ITS trees, suggesting that it may be of hybrid origin. Likelihood-based biogeographic inference with divergence time estimates infers an Eocene basal crown group diversification and an initial widespread circumpolar distribution with subsequent vicariance and extinction events leading to the current disjunct distribution.

Experimental analyses of decay in a tunicate deuterostome and three lophotrochozoans indicate that the controls on decay and preservation of embryos, identified previously based on echinoids, are more generally applicable. Four stages of decay are identified regardless of the environment of death and decay. Embryos decay rapidly in oxic and anoxic conditions, although the gross morphology of embryos is maintained for longer under anoxic conditions. Under anoxic reducing conditions, the gross morphology of the embryos is maintained for the longest period of time, compatible with the timescale required for bacterially mediated mineralization of soft tissues. All four stages of decay were encountered under all environmental conditions, matching the spectrum of preservational qualities encountered in all fossil embryo assemblages. The preservation potential of embryos of deuterostomes and lophotrochozoans is at odds with the lack of such embryos in the fossil record. Rather, the fossil record of embryos, as sparse as it is, is dominated by forms interpreted as ecdysozoans, cnidarians, and stem-metazoans. The dearth of deuterostome and lophotrochozoan embryos may be explained by the fact that ecdysozoans, at least, tend to deposit their eggs in the sediment rather than through broadcast spawning. However, fossil embryos remain very rare and the main controlling factor on their fossilization may be the unique conspiracy of environmental conditions at a couple of sites. The preponderance of fossilized embryos of direct developers should not be used in evidence against the existence of indirect development at this time in animal evolutionary history.

Relationships within the Polygonaceae have been recently examined using rbcL sequences, with an emphasis on Polygonum and its segregates. Here we test these results with respect to Polygonum (sensu lato) with an expanded dataset, including additional species and gene regions. Specifically, we focus on inferring the relationships of Eupersicaria (Polygonum sect. Persicaria in many prior treatments), using the chloroplast genes rbcL, trnL-F, trnK intron-matK, and psbA-trnH IGS, and nuclear ribosomal ITS sequences. We conclude that Eupersicaria is monophyletic and most closely related to Tovara and Echinocaulon. In turn, this clade is most closely related to Cephalophilon. The sister group of this entire Persicaria clade contains Bistorta and a clade including Aconogonon and Koenigia, which supports the monophyly of the Persicarieae. Within Eupersicaria there appears to be a deep split between P. amphibia and the remaining species, and there is strong conflict regarding the placement of P. punctata. These results set the stage for a more detailed phylogenetic analysis of Eupersicaria.

Phylogenetic analyses of chloroplast DNA sequences, morphology, and combined data have provided consistent support for many of the major branches within the angiosperm clade Dipsacales. Here we use sequences from three mitochondrial loci to test the existing broad scale phylogeny and in an attempt to resolve several relationships that have remained uncertain. Parsimony, maximum likelihood, and Bayesian analyses of a combined mitochondrial data set recover trees broadly consistent with previous studies, although resolution and support are lower than in the largest chloroplast analyses. Combining chloroplast and mitochondrial data results in a generally well-resolved and very strongly supported topology but the previously recognized problem areas remain. To investigate why these relationships have been difficult to resolve we conducted a series of experiments using different data partitions and heterogeneous substitution models. Usually more complex modeling schemes are favored regardless of the partitions recognized but model choice had little effect on topology or support values. In contrast there are consistent but weakly supported differences in the topologies recovered from coding and non-coding matrices. These conflicts directly correspond to relationships that were poorly resolved in analyses of the full combined chloroplast-mitochondrial data set. We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas.

Recent phylogenetic analyses based on molecular markers have resulted in a solid phylogeny of Viburnum with 12 well-defined clades. This has allowed us to focus on character evolution, endocarp and seed characters in particular. Members of Viburnum bear drupes that differ considerably between clades. Characters such as pyrene shape and grooving, number of fibrous layers, seed coat anatomy, and seed rumination are phylogenetically highly valuable. Our results largely agree with the results based on molecular data and provide several additional insights. The position of V. clemensae as sister to the rest of Viburnum is supported by several characters. The early diversification of V. clemensae might explain its highly derived features. Furthermore, our results give an indication of the possible paraphyly of the Megalotinus clade, confirm the paraphyly of Hara's section Solenotinus, and support the split of Hara's section Odontotinus into four well-defined clades. Endocarp and seed characters are mainly useful at the level of individual clades. Several characters, however, are useful at higher taxonomic levels. The presence of small, amorphous crystals in the endosperm, for example, is most likely to be apomorphic for Viburnum within the order Dipsacales. ispartof: International journal of plant sciences vol:169 issue:3 pages:409-431 status: published

The causal basis of vertebrate complexity has been sought in genome duplication events (GDEs) that occurred during the emergence of vertebrates, but evidence beyond coincidence is wanting. MicroRNAs (miRNAs) have recently been identified as a viable causal factor in increasing organismal complexity through the action of these ≈22-nt noncoding RNAs in regulating gene expression. Because miRNAs are continuously being added to animalian genomes, and, once integrated into a gene regulatory network, are strongly conserved in primary sequence and rarely secondarily lost, their evolutionary history can be accurately reconstructed. Here, using a combination of Northern analyses and genomic searches, we show that 41 miRNA families evolved at the base of Vertebrata, as they are found and/or detected in lamprey, but not in either ascidians or amphioxus (or any other nonchordate taxon). When placed into temporal context, the rate of miRNA acquisition and the extent of phenotypic evolution are anomalously high early in vertebrate history, far outstripping any other episode in chordate evolution. The genomic position of miRNA paralogues in humans, together with gene trees incorporating lamprey orthologues, indicates that although GDEs can account for an increase in the diversity of miRNA family members, which occurred before the last common ancestor of all living vertebrates, GDEs cannot account for the origin of these novel families themselves. We hypothesize that lying behind the origin of vertebrate complexity is the dramatic expansion of the noncoding RNA inventory including miRNAs, rather than an increase in the protein-encoding inventory caused by GDEs.

Synopsis Little attention has been paid to the suprageneric classification for conodonts and existing schemes have been formulated without attention to homology, diagnosis and definition. We propose that cladistics providesan appropriate methodology to test existingschemes of classification and in which to explore the evolutionary relationships of conodonts. The development of a multielement taxonomy and a concept of homology based upon the position, not morphology, of elements within the apparatus provide the ideal foundation for the application of cladistics to conodonts. In an attempt to unravel the evolutionary relationships between ‘complex’ conodonts (prioniodontids and derivative lineages) we have compiled a data matrix based upon 95 characters and 61 representative taxa. The dataset was analysed using parsimony and the resulting hypotheses were assessed using a number of measures of support. These included bootstrap, Bremer Support and double‐decay; we also compared levels of homoplasy to those ex...

Many of the features that distinguish the vertebrates from other chordates are derived from the neural crest, and it has long been argued that the emergence of this multipotent embryonic population was a key innovation underpinning vertebrate evolution. More recently, however, a number of studies have suggested that the evolution of the neural crest was less sudden than previously believed. This has exposed the fact that neural crest, as evidenced by its repertoire of derivative cell types, has evolved through vertebrate evolution. In this light, attempts to derive a typological definition of neural crest, in terms of molecular signatures or networks, are unfounded. We propose a less restrictive, embryological definition of this cell type that facilitates, rather than precludes, investigating the evolution of neural crest. While the evolutionary origin of neural crest has attracted much attention, its subsequent evolution has received almost no attention and yet it is more readily open to experimental investigation and has greater relevance to understanding vertebrate evolution. Finally, we provide a brief outline of how the evolutionary emergence of neural crest potentiality may have proceeded, and how it may be investigated.

The intramolecular hydroamination of carbon-carbon π-bonds is an effective method for the rapid construction of nitrogen heterocycles. The rapid evaluation of suitable ligands using virtual screening will aid in the development of a stereoselective analogue of the reaction by predicting effective substrate/ligand combinations. Electronic structure calculations of the relevant transition structures for different nucleophiles and alkynes at the B3LYP/ LACVP* level of theory are presented. They provide the basis for the development of a transition state force field by the Q2MM method, which is discussed in detail. The parameter development and performance for the transition state force field is presented.

An efficient multiresidue method was successfully applied to the determination of fluoroquinolones (FQs) in chicken serum. In this method, FQs are extracted from matrix with ammoniacal acetonitrile, and the extracts are defatted and then evaporated. After addition of basic phosphate buffer and filtration, the samples are analyzed by liquid chromatography-fluorescence-mass spectrometryn (multiple mass spectrometry; MSn). This approach allows for simultaneous quantitation (fluorescence) and confirmation (MSn) of the FQs. Using this method, 8 FQs were determined in fortified chicken serum at levels of 10, 20, 50, and 100 ng/g. Recoveries ranged from 7199, with excellent relative standard deviations (

Bacteriophages used to treat infections are typically amplified in a pathogenic host. However, this practice introduces the risk of administering any remaining bacteriophage-resistant pathogen during bacteriophage application if separation techniques are less than perfect. In this study, bacteriophage isolates capable of replicating in both Salmonella and Klebsiella oxytoca were identified and applied to poultry carcasses. These Wide-Host-Range bacteriophages (WHR) were amplified using the non-pathogenic bacteria, Klebsiella oxytoca in tryptic soy broth until a titer of approximately 10⁹ PFU/mL was obtained. WHR and Klebsiella oxytoca were not separated prior to treatment of carcasses. Fresh processed chicken carcasses were inoculated with either Salmonella enteritidis (SE) or S. typhimurium (ST), sprayed with 5 mL of WHR and rinsed with sterile water. Samples were enriched, plated on XLD agar and evaluated for Salmonella-typical colonies. In four separate trials, WHR significantly reduced the recovery of SE. No SE was detected in two trials and a greater than 70% reduction was seen in the other two trials. ST was also significantly reduced in the two trials in which it was included (p

This is an abbreviated version of a paper that appears in full in the Electronic supplement to Taxon. Phylogenetic definitions are provided for the names of 20 clades of vascular plants (plus 33 others in the electronic supplement). Emphasis has been placed on well-supported clades that are widely known to non-specialists and/or have a deep origin within Tracheophyta or Angiospermae. These treatments follow the draft PhyloCode and illustrate the application ofphylogenetic nomenclature in a variety of nomenclatural and phylogenetic contexts. Phylogenetic nomenclature promotes precision in distinguishing crown, apomorphy-based, and total clades, thereby improving communication about character evolution and divergence times. To make these distinctions more transparent without increasing the number of entirely different names that must be learned, the following naming conventions (which have been adopted in the most recent draft of the PhyloCode) are employed here: widely known names are applied to crown clades, and the corresponding total clade (i.e., crown plus stem) is named "Pan-X", where "X" is the name of the crown (e.g., Pan-Spermatophyta for the total clade of plants that share more recent ancestry with extant seed plants than with any other crown clade). If a name "X" that is based etymologically on an apomorphy is applied to the crown, the name "Apo-X" is applied to the clade for which this trait is synapomorphic (e.g., Apo-Spermatophyta for the clade originating from the first plant with seeds). Crown clade names can be defined by three kinds of definitions, two of which are used here: standard node-based and branch-modified node-based. The latter is particularly useful when outgroup relationships of a crown clade are better known than basal relationships within the clade. Criteria and approaches used here to choose among competing preexisting names for a clade, to select a definition type, to choose appropriate specifiers, and (in some cases) to restrict the use of a name to certain phylogenetic contexts may be widely applicable when naming other clades. The phylogenetic definitions proposed here should help focus future discussions of the PhyloCode on real definitions rather than simplified hypothetical ones.

Geo-referenced archive databases on mountain organisms are very promising tools for achieving a better understanding of mountain biodiversity and predicting its changes. The Global Mountain Biodiversity Assessment (GMBA) of DIVERSITAS, in cooperation with the Global Biodiversity Information Facility, encourages a global effort to mine biodiversity databases on mountain organisms. The wide range of climatic conditions and topographies across the world's mountains offers an unparalleled opportunity for developing and testing biodiversity theory. The power of openly accessible, interconnected electronic databases for scientific biodiversity research, which by far exceeds the original intent of archiving for mainly taxonomic purposes, has been illustrated. There is an urgent need to increase the amount and quality of geo-referenced data on mountain biodiversity provided online, in order to meet the challenges of global change in mountains.

Speedy/RINGO family members bind and activate cyclin dependent kinases (CDKs), although these proteins have no homology to known cyclin proteins. Members of this family are required for and enhance meiotic maturation, in addition to having novel roles in regulating the mitotic mammalian cell cycle and the DNA damage response. Here we discuss how the specialized functions of these proteins differ from classical cyclin-mediated activation of CDKs. Through atypical activation of CDKs, bypass of conventional inhibitory mechanisms, and unique substrate selection, Speedy/RINGO proteins contribute to cell cycle, checkpoint, and apoptotic regulation. Furthermore, we address the recently established correlation between Spy1 and cancer in terms of the specialized functions of the Speedy/RINGO family.

Phylogenetic thinking has infiltrated many areas of biological research, but has had little impact on studies of global ecology or climate change. Here, we illustrate how phylogenetic information can be relevant to understanding vegetation-atmosphere dynamics at ecosystem or global scales by re-analyzing a data set of carbonic anhydrase (CA) activity in leaves that was used to estimate terrestrial gross primary productivity. The original calculations relied on what appeared to be low CA activity exclusively in C4 grasses, but our analyses indicate that such activity might instead characterize the PACCAD grass lineage, which includes many widespread C3 species. We outline how phylogenetics can guide better taxon sampling of key physiological traits, and discuss how the emerging field of phyloinformatics presents a promising new framework for scaling from organism physiology to global processes.

The rhodium-catalyzed hydrogenation reaction of enamides is studied computationally using the B3LYP/LACVP** level of theory for a range of ligands and substrates. Two model bidentate phosphine ligands, 1,2-bis(dimethylphosphino)ethane (DMPE) and (Z)-1,2-bis(dimethylphosphino) ethene (ZDMP), and two chiral bidentate phosphine ligands, (R,R)-MeDuPHOS and (R,R)-tetramethylbisoxaphospinane (TMBOP), are investigated in the hydrogenation of alpha-formamidoacrylonitrile as a model substrate. The ZDMP ligand is then studied for three additional substrates: N-(2-propenyl)formamide, (Z)-3-formamido-2-butenenitrile, and (E)-3-formamido-2-butenenitrile. The potential-energy surfaces calculated for the four ligands and alpha-formamidoacrylonitrile are in general agreement with previous computational studies using QM/MM (ONIOM) methods but show consistently higher relative barriers rather than lower. The calculated potential-energy surfaces of hydrogenations of various substrates with a common ligand indicate a mechanistic change based on substrate. The sequence of hydrogen transfer to the two olefinic carbons is calculated to change based on substrate electronics. This has a significant impact on the origins of enantioselectivity for such varied substrates as the first hydride transfer to the substrate is calculated to be irreversible for all substrates, independent of whether it occurs at the alpha or beta carbon of the olefin.

Clarifying the evolution and mechanisms for photosynthetic productivity is a key to both improving crops and understanding plant evolution and habitat distributions. Current theory recognizes a role for the hydraulics of water transport as a potential determinant of photosynthetic productivity based on comparative data across disparate species. However, there has never been rigorous support for the maintenance of this relationship during an evolutionary radiation. We tested this theory for 30 species of Viburnum, diverse in leaf shape and photosynthetic anatomy, grown in a common garden. We found strong support for a fundamental requirement for leaf hydraulic capacity (Kleaf) in determining photosynthetic capacity (Amax), as these traits diversified across this lineage in tight coordination, with their proportionality modulated by the climate experienced in the species' range. Variation in Kleaf arose from differences in venation architecture that influenced xylem and especially outside-xylem flow pathways. These findings substantiate an evolutionary basis for the coordination of hydraulic and photosynthetic physiology across species, and their co-dependence on climate, establishing a fundamental role for water transport in the evolution of the photosynthetic rate. As photosynthesis requires water, its transport to and within leaves is a potential determinant of photosynthetic productivity. This comparison of 30 species of Viburnum shows how variations in venation architecture constrain photosynthetic rate.

The rhodium catalyzed asymmetric hydrogenation of enamides to generate amino acid products and derivatives is a widely used method to generate unnatural amino acids. The choice of a chiral ligand is of utmost importance in this reaction and is often based on high throughput screening or simply trial and error. A virtual screening method can greatly increase the speed of the ligand screening process by calculating expected enantiomeric excesses from relative energies of diastereomeric transition states. Utilizing the Q2MM method, new molecular mechanics parameters are derived to model the hydride transfer transition state in the reaction. The new parameters were based off of structures calculated at the B3LYP/LACVP** level of theory and added to the MM3* force field. The new parameters were validated against a test set of experimental data utilizing a wide range of bis-phosphine ligands. The computational model agreed with experimental data well overall, with an unsigned mean error of 0.6 kcal/mol against a set of 18 data points from experiment. The major errors in the computational model were due either to large energetic errors at high e.e., still resulting in qualitative agreement, or cases where large steric interactions prevent the reaction from proceeding as expected.