Spinach curly top virus: A Newly Described \u3ci\u3eCurtovirus\u3c/i\u3e Species from Southwest Texas with Incongruent Gene Phylogenies

A curtovirus associated with a disease of spinach was isolated in southwest Texas during 1996. Disease symptoms included severe stunting and chlorosis, with younger leaves curled, distorted, and dwarfed. Viral DNA was purified and an infectious clone obtained. Agroinoculation using a construct bearing full-length tandem repeats of the cloned viral genome resulted in systemic infection of species in six of seven plant families tested, indicating that the virus has a wide host range. Symptoms produced in spinach agroinoculated with cloned viral DNA were similar to those observed in the field. Viral single-stranded and double-stranded DNA forms typical of curtovirus infection were detected in host plants by Southern blot hybridization. The complete sequence of the infectious clone comprised 2,925 nucleotides, with seven open reading frames encoding proteins homologous to those of other curtoviruses. Complete genome comparisons revealed that the spinach curtovirus shared 64.2 to 83.9% nucleotide sequence identity relative to four previously characterized curtovirus species: Beet curly top virus, Beet severe curly top virus, Beet mild curly top virus, and Hor.semdi.sh curly top virus. Phylogenetic analysis of individual open reading frames indicated that the evolutionary history of the three virion-sense genes was different from that of the four complementary-sense genes, suggesting that recombination among curtoviruses may have occurred. Collectively, these results indicate that the spinach curtovirus characterized here represents a newly described species of the genus Curtovirus, for which we propose the name Spinach curly top virus

Neuroendocrine Disruption: More than Hormones are Upset

Only a small proportion of the published research on endocrine-disrupting chemicals (EDC) directly examined effects on neuroendocrine processes. There is an expanding body of evidence that anthropogenic chemicals exert effects on neuroendocrine systems and that these changes might impact peripheral organ systems and physiological processes. Neuroendocrine disruption extends the concept of endocrine disruption to include the full breadth of integrative physiology (i.e., more than hormones are upset). Pollutants may also disrupt numerous other neurochemical pathways to affect an animal's capacity to reproduce, develop and grow, or deal with stress and other challenges. Several examples are presented in this review, from both vertebrates and invertebrates, illustrating that diverse environmental pollutants including pharmaceuticals, organochlorine pesticides, and industrial contaminants have the potential to disrupt neuroendocrine control mechanisms. While most investigations on EDC are carried out with vertebrate models, an attempt is also made to highlight the importance of research on invertebrate neuroendocrine disruption. The neurophysiology of many invertebrates is well described and many of their neurotransmitters are similar or identical to those in vertebrates; therefore, lessons learned from one group of organisms may help us understand potential adverse effects in others. This review argues for the adoption of systems biology and integrative physiology to address the effects of EDC. Effects of pulp and paper mill effluents on fish reproduction are a good example of where relatively narrow hypothesis testing strategies (e.g., whether or not pollutants are sex steroid mimics) have only partially solved a major problem in environmental biology. It is clear that a global, integrative physiological approach, including improved understanding of neuroendocrine control mechanisms, is warranted to fully understand the impacts of pulp and paper mill effluents. Neuroendocrine disruptors are defined as pollutants in the environment that are capable of acting as agonists/antagonists or modulators of the synthesis and/or metabolism of neuropeptides, neurotransmitters, or neurohormones, which subsequently alter diverse physiological, behavioral, or hormonal processes to affect an animal's capacity to reproduce, develop and grow, or deal with stress and other challenges. By adopting a definition of neuroendocrine disruption that encompasses both direct physiological targets and their indirect downstream effects, from the level of the individual to the ecosystem, a more comprehensive picture of the consequences of environmentally relevant EDC exposure may emerge

A new view of electrochemistry at highly oriented pyrolytic graphite

Major new insights on electrochemical processes at graphite electrodes are reported, following extensive investigations of two of the most studied redox couples, Fe(CN)64–/3– and Ru(NH3)63+/2+. Experiments have been carried out on five different grades of highly oriented pyrolytic graphite (HOPG) that vary in step-edge height and surface coverage. Significantly, the same electrochemical characteristic is observed on all surfaces, independent of surface quality: initial cyclic voltammetry (CV) is close to reversible on freshly cleaved surfaces (>400 measurements for Fe(CN)64–/3– and >100 for Ru(NH3)63+/2+), in marked contrast to previous studies that have found very slow electron transfer (ET) kinetics, with an interpretation that ET only occurs at step edges. Significantly, high spatial resolution electrochemical imaging with scanning electrochemical cell microscopy, on the highest quality mechanically cleaved HOPG, demonstrates definitively that the pristine basal surface supports fast ET, and that ET is not confined to step edges. However, the history of the HOPG surface strongly influences the electrochemical behavior. Thus, Fe(CN)64–/3– shows markedly diminished ET kinetics with either extended exposure of the HOPG surface to the ambient environment or repeated CV measurements. In situ atomic force microscopy (AFM) reveals that the deterioration in apparent ET kinetics is coupled with the deposition of material on the HOPG electrode, while conducting-AFM highlights that, after cleaving, the local surface conductivity of HOPG deteriorates significantly with time. These observations and new insights are not only important for graphite, but have significant implications for electrochemistry at related carbon materials such as graphene and carbon nanotubes

A new method for studying activity and reaction kinetics of photocatalytic water oxidation systems using a bubbling reactor

A novel method is proposed for studying kinetics and overall activity of water oxidation (WO) catalysts using a bubbling reactor, where oxygen concentration is measured simultaneously in the liquid and in the gaseous phase. Total oxygen evolution is obtained from direct integration. The actual rate of oxygen formation as a function of time, RO2(t) not accessible to direct measurement with batch reactors, is calculated from raw data through a simple but comprehensive mathematical model, taking into account mass transfer phenomena occurring in the system. Data concerning the activity of a nanostructured Co3O4 catalyst dispersed on a mesoporous silica (MSU-H), in the presence of tris(2,2'-bipyridyl)Ruthenium [Ru(bpy)3]2+ as sensitizer and Na2S2O8 as sacrificial reactant, are used to illustrate data processing. Behaviour of the system is complicated by the occurrence, besides WO reaction, of the degradation of the sensitizer. Increase of sweeping gas flow increases RO2(t), by decreasing diffusional limitations to the reactions in the system: conditions for minimizing those were established. Data reported show that the assumption generally made of equilibrium between gaseous and liquid phase through Henry's law is incorrect, the more so the smaller the apparent mass transfer coefficient, kLa. An additional reason for removing oxygen from the liquid phase through bubbling is the occurrence of a parasitic reaction of molecular oxygen with the sensitizer. The method seems to yield reliable values of both kLa and the set of RO2(t) values: the former scales with the flow of sweeping gas, as expected; RO2(t) curves are in qualitative agreement with accepted reaction mechanisms. Results concerning RO2(t) lend support to our previous kinetic studies (M. Armandi et. al., ACS Catal. 2013, 3, 1272) where the reaction rate was assumed as constant for the first ~ 15 min. Availability of RO2(t) data not too biased by diffusional limitations opens the way to realistic studies of the kinetic features of WO heterogeneous reactions, in the present case as well as in many other

HMMerThread: Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition

Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10), a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in proteins based on weak sequence similarity. Our predictions open up new avenues for biological and medical studies. Genome-wide HMMerThread domains are available at http://vm1-hmmerthread.age.mpg.de

Electrochemical and Photoelectrochemical Investigation of Water Oxidation with Hematite Electrodes

Atomic layer deposition (ALD) was utilized to deposit uniform thin films of hematite (α-Fe2O3) on transparent conductive substrates for photocatalytic water oxidation studies. Comparison of the oxidation of water to the oxidation of a fast redox shuttle allowed for new insight in determining the rate limiting processes of water oxidation at hematite electrodes. It was found that an additional overpotential is needed to initiate water oxidation compared to the fast redox shuttle. A combination of electrochemical impedance spectroscopy, photoelectrochemical and electrochemical measurements were employed to determine the cause of the additional overpotential. It was found that photogenerated holes initially oxidize the electrode surface under water oxidation conditions, which is attributed to the first step in water oxidation. A critical number of these surface intermediates need to be generated in order for the subsequent hole-transfer steps to proceed. At higher applied potentials, the behavior of the electrode is virtually identical while oxidizing either water or the fast redox shuttle; the slight discrepancy is attributed to a shift in potential associated with Fermi level pinning by the surface states in the absence of a redox shuttle. A water oxidation mechanism is proposed to interpret these results