Using genetic approaches, particle image velocimetry and an inert tracer of cytoplasmic streaming, we have made a mechanistic connection between the motor proteins (myosins XI), cargo transported by these motors (distinct endomembrane compartment defined by membrane-anchored MyoB receptors) and the process of cytoplasmic streaming in plant cells. It is shown...
To characterize the mechanism through which myosin XI-K attaches to its principal endomembrane cargo, a yeast two-hybrid library of Arabidopsis thaliana cDNAs was screened using the myosin cargo binding domain as bait. This screen identified two previously uncharacterized transmembrane proteins (hereinafter myosin binding proteins or MyoB1/2) that share a myosin...
The improvement of the agricultural and wine-making qualities of the grapevine (Vitis vinifera) is hampered by adherence to traditional varieties, the recalcitrance of this plant to genetic modifications, and public resistance to genetically modified organism (GMO) technologies. To address these challenges, we developed an RNA virus-based vector for the introduction...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
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, and Evolution of the Myosin
Gene Family in Plants1[W][OA]
ValeraV. Peremyslov, Todd C. Mockler
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
Papain-like leader proteases are found in diverse families of human, animal, plant, and fungal positive-strand RNA viruses. In addition to autocatalytic processing, these proteases play a variety of roles in the virus life cycle. In particular, the leader protease (L-Pro) of a prototype member of the Closterovirus genus, Beet yellows...
Beet yellows virus (BYV) is a filamentous, positive-strand RNA virus that belongs to the family Closteroviridae. BYV particles encapsidate a 15.5 kb RNA and posses complex polar architecture. A long virion body is formed by the major capsid protein(CP), whereas the minor capsid protein (CPm) assembles a short tail that...
More than half of the recognized genera of positive strand RNA viruses employ polyprotein processing as one of the strategies for their genome expression. Normally, this processing is mediated by virus-encoded proteinases that belong to the trypsin-like or papain-like family. In particular, papain-like, leader proteinases were found in diverse families...
Important progress in understanding replication, interactions with host plants, and evolution of closteroviruses enabled engineering of several vectors for gene expression and virus-induced gene silencing. Due to the broad host range of closteroviruses, these vectors expanded vector applicability to include important woody plants such as citrus and grapevine. Furthermore, large...
Deep sequencing analysis of an asymptomatic grapevine revealed a virome containing five RNA viruses and a viroid. Of these, Grapevine leafroll-associated virus 7 (GLRaV-7), an unassigned closterovirus, was by far the most prominently represented sequence in the analysis. Graft-inoculation of the infection to another grape variety confirmed the lack of...
The advent of improved DNA sequencing technologies has allowed the analysis of various microbial communities. Bloom-forming freshwater cyanobacteria can produce toxins and taste-and-odor compounds that can negatively affect drinking water supplies. Here, I have employed second- and third-generation sequencing technologies to characterize bloom-forming freshwater cyanobacterial genomes and their associated heterotrophic...
Viruses are obligatory parasites that depend on host cellular factors for their replication as well as for their local and systemic
movement to establish infection. Although myosin motors are thought to contribute to plant virus infection, their exact roles
in the specific infection steps have not been addressed. Here we...
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of Tobacco Mosaic Virus
Amari, K., Di Donato, M., Dolja, V. V., Heinlein, M. (2014) Myosins VIII and
Grapevine leafroll disease (GLD) is one of the most important grapevine viral diseases affecting grapevines worldwide. The impact on vine health, crop yield, and quality is difficult to assess due to a high number of variables, but significant economic losses are consistently reported over the lifespan of a vineyard if...
Virus-infected plants accumulate abundant, 21–24 nucleotide viral siRNAs which are generated by the evolutionary
conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids.
Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in...
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,
Kristin Kasschau3, Valerian V. Dolja3, Patricia Otten4, Laurent Farinelli4, Mikhail M. Pooggin1*
1
Background:
The Amazon River runs nearly 6500 km across the South American continent before emptying into the western tropical North Atlantic Ocean. In terms of both volume and watershed area, it is the world’s largest riverine system, affecting elemental cycling on a global scale.
Results:
A quantitative inventory of genes...
Agrobacterium tumefaciens is a plant pathogenic bacteria which incites
crown gall tumors. Although virulence has been associated with a
97-156 Mdalton "tumor-inducing" (Ti) plasmid, few potential plasmid gene
products have been identified. The objective of this study was to
identify plasmid-coded gene products through a comparison of protein
fingerprints of...
Pallidosis is a disease of strawberry identified in 1957 with an unknown etiology. Two previously uncharacterized viruses in strawberry, Strawberry pallidosis associated virus (SPaV) and Beet pseudo-yellows virus (BPYV), have been found associated with disease symptoms. The complete nucleotide sequence of both viruses was determined and molecular detection protocols developed....
Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental...
Protists are microscopic eukaryotic
microbes that are ubiquitous, diverse,
and major participants in oceanic food
webs and in marine biogeochemical
cycles. The study and characterization
of protists has a long and distinguished
tradition. Even with this history, the
extraordinary species diversity and variety
of interactions of protists in the sea...
Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems,
usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided
into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be
specific to deep water. Here we examine the...
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subclade-specific
genomic features have been identified (Grote et al.,
2012). The subclade V representative
Since nucleic acids were first extracted directly from the environment and sequenced, metagenomics has grown to one of the most data-rich and pervasive techniques for understanding the taxonomic and functional diversity of microbial communities. In the last decade, cheaper sequencing has democratized the application of metagenomics and generated billions of...
This thesis uses both feminist and new historic theories to argue that the women's romance novels The Last September (1929) by Elizabeth Bowen and The Country Girl's Trilogy (1960, 1962, 1964) by Edna O'Brien are tragic bildungsroman that subvert and challenge the Irish patriarchal marriage expectations of their respective time...
Fungi and Actinobacteria are essential actors in global biogeochemical cycles of carbon and nutrients, and have both been recently appreciated for their roles in marine ecosystems. However, the diversity and distribution of these ubiquitous, but low-abundance microbes in deep-sea habitats remains poorly understood, particularly in chemosynthetic habitats such as methane...
SAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world's oceans, where they play a major role in the ocean carbon cycle. Correlations between the phylogenetic branching order and spatiotemporal patterns in cell distributions from planktonic ocean environments indicate that SAR11 has evolved into...
Metal-organic polyhedra (MOPs) are discrete molecules comprised of a metal and interconnecting ligands. The resulting MOP structures are porous cages, and to date, they have shown great promise toward gas capture. Ammonia is a hazardous gas that is produced in enormous quantities for use in fertilizers. In this talk, I...
Deep learning is becoming the latest trend in sensitive applications, such as healthcare, criminal justice, and finance. As these new applications emerge, adversaries are circumventing them.
Further, there have been concerns about the possibility of bias and discrimination in predictive applications.
In order to address these issues, we propose an...
Threshold-based time of arrival (TOA) estimation is a technique for high-precision indoor localization. Existing threshold selection methods, such as xed thresh- old and normalized threshold methods, do not consider the signal-to-noise radio (SNR) value at the receiver. This is not desired for high-precision positioning. A proper threshold value depends on...
Certain plant-associated prokaryotes such as Corynebacteriurn
fascians and Agrobacterium tumefaciens are known to produce substantial
levels of cytokinins. In view of the fragmentary and
presumptive evidence available on the quantitative and qualitative
levels of cytokinins produced by A. tumefaciens, it was decided to
conduct a study of the cytokinins produced...
Microbial activity within elevated CO2 and oxygen depleted environments changes with
density driven stratification overturn in the seasonally anoxic region of Devil’s Hole,
Bermuda. The temperature gradient developed during the summer months creates a
natural laboratory to study bacterial and virus population density and microbial
community dynamics in the anoxic...
Microbial activity within elevated CO2 and oxygen depleted environments changes with
density driven stratification overturn in the seasonally anoxic region of Devil’s Hole,
Bermuda. The temperature gradient developed during the summer months creates a
natural laboratory to study bacterial and virus population density and microbial
community dynamics in the anoxic...
The lagoons spanning Alaska’s Beaufort Sea coast provide a unique habitat for arctic wildlife. These lagoons and the food webs they support face extreme seasonality with nine months of ice cover followed by a spring thaw that pulses a large amount of freshwater and nutrients into the lagoons. Bacteria link...
One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis....
Background: DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood.
Results: We surveyed DNA methylation from...
Hatcheries are often perceived as a source of pathogen amplification, potentially increasing disease risk to free-ranging populations; at the same time, free-ranging fishes may introduce pathogens into hatcheries through untreated water sources. Many pathogens exist naturally within the environment (with the exception of introduced pathogens) and the presence of a...
Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative
capacity of plant species, and may be especially important for long-lived
organisms with complex life cycles, including forest trees. Diverse environmental
stresses and hybridization/polyploidization events can create reversible heritable
epigenetic marks that can be transmitted to subsequent generations...
Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly...
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Genomics
Workbench (v 4.9) with a minimum length fraction of 80% and a similarity of at least 95%.
Fig 1
Marine sediments are one of the largest habitats for microbial life on earth. These microorganisms play critical roles in biogeochemical cycling both within the subsurface and between the sediment and water columns. However, microbial communities in sediments are highly heterogeneous and the factors defining microbial community structure and metabolic function...
Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of
natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally
much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454
sequencing of...
Pancreatic beta cells produce and release insulin, a vital hormone that regulates blood glucose levels, and their dysfunction contributes to the development of diabetes mellitus. Dietary zinc deficiency and exposure to the toxicant inorganic arsenic have both independently been associated with diabetes, although the effects of their combination on pancreatic...
Large equine facilities are comprised of many different departments (areas) that are necessary for the proper care and maintenance of horses. The placement of departments is often inefficient due to the slow growth of equine facilities. As a result, facility layout becomes a crucial aspect requiring explicit consideration because mandatory...
A critical component in diabetes management is diabetes self-management education (DSME). Additionally, poor self-management behavior and negative health outcomes are associated with participants that do not complete diabetes education (Gurdiacci et al., 2007). Despite the widespread use of DSME, many do not obtain the wide range of benefits these programs...
This thesis argues for the importance of justice of recognition not only for humans, but the entire non-human world in the face of environmental destruction and climate crisis. The common response to the degradation of the world’s ecological sphere is to act with technological, scientific, and material based responses. However,...
A computer program called SAPWOOD which possesses the
capability of performing linear or nonlinear, static or
dynamic response including seismic excitation for wood-framed
buildings with semirigid connection systems is
presented in this study. Program SAPWOOD is a modification
of the program NONSAP by adding new elements such as a
linkage...
Historically, the difficulty of obtaining pure cultures of abundant marine
microbial plankton has an obstacle to reconstructing the underlying
mechanisms of biogeochemistry in the ocean. While a number of dominant
marine species from the ocean surface have been cultured, the dominant
microbial plankton of the dark ocean proved far more...