U7 snRNAs： A Computational Survey

U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for func- tional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase Ⅱ. Based on the results of this search, we discuss the high variability of U7 snRNAs in both se- quence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short se- quence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.     

Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention

Broadly neutralizing antibodies (bNAbs) are promising agents to prevent HIV infection and achieve HIV remission without antiretroviral therapy (ART). As with ART, bNAb combinations are likely needed to cover HIV’s extensive diversity. Not all bNAbs are identical in terms of their breadth, potency, and in vivo longevity (half-life). Given these differences, it is important to optimally select the composition, or dose ratio, of combination bNAb therapies for future clinical studies. We developed a model that synthesizes 1) pharmacokinetics, 2) potency against a wide HIV diversity, 3) interaction models for how drugs work together, and 4) correlates that translate in vitro potency to clinical protection. We found optimization requires drug-specific balances between potency, longevity, and interaction type. As an example, tradeoffs between longevity and potency are shown by comparing a combination therapy to a bi-specific antibody (a single protein merging both bNAbs) that takes the better potency but the worse longevity of the two components. Then, we illustrate a realistic dose ratio optimization of a triple combination of VRC07, 3BNC117, and 10–1074 bNAbs. We apply protection estimates derived from both a non-human primate (NHP) challenge study meta-analysis and the human antibody mediated prevention (AMP) trials. In both cases, we find a 2:1:1 dose emphasizing VRC07 is nearly optimal. Our approach can be immediately applied to optimize the next generation of combination antibody prevention and cure studies.     

Molecular basis for substrate recognition and septum cleavage by AtlA,the major N-acetylglucosaminidase of Enterococcus faecalis

The cleavage of septal peptidoglycan at the end of cell division facilitates the separation of the two daughter cells. The hydrolases involved in this process (called autolysins) are potentially lethal enzymes that can cause cell death; their activity, therefore, must be tightly controlled during cell growth. In Enterococcus faecalis, the N-acetylglucosaminidase AtlA plays a predominant role in cell separation. atlA mutants form long cell chains and are significantly less virulent in the zebrafish model of infection. The attenuated virulence of atlA mutants is underpinned by a limited dissemination of bacterial chains in the host organism and a more efficient uptake by phagocytes that clear the infection. AtlA has structural homologs in other important pathogens, such as Listeria monocytogenes and Salmonella typhimurium, and therefore represents an attractive model to design new inhibitors of bacterial pathogenesis. Here, we provide a 1.45 Å crystal structure of the E. faecalis AtlA catalytic domain that reveals a closed conformation of a conserved β-hairpin and a complex network of hydrogen bonds that bring two catalytic residues to the ideal distance for an inverting mechanism. Based on the model of the AtlA–substrate complex, we identify key residues critical for substrate recognition and septum cleavage during bacterial growth. We propose that this work will provide useful information for the rational design of specific inhibitors targeting this enterococcal virulence factor and its orthologs in other pathogens.     

Elaborate petals and staminodes in eudicots: Diversity, function, and evolution

Petals, a characteristic feature of eudicots, have evolved elaborations in various ways and across diverse clades. In this survey of petal and staminode elaborations throughout the eudicots, based on both new studies and a review of the literature, the diversity of such structures and their functions is discussed. Petal elaborations are primarily present as marginal lobes and ventral lobes of various shapes. Lobation patterns can be loosely classified as pinnate, binate, or ternate. One of these patterns may be dominant within a family (e.g. pinnate in Anisophylleaceae, binate in Caryophyllaceae, ternate in Elaeocarpaceae); transitional forms also occur (e.g. between binate and ternate in Onagraceae). Coronas between the corolla and androecium are found in several groups, for example in several families of Malpighiales or in Apocynaceae. In some clades, petal elaborations are especially prominent and can be used as approximate systematic markers (Anisophylleaceae, Elaeocarpaceae, Rhizophoraceae). Petal elaborations are especially diverse in rosids. In asterids, which are characterized by sympetaly, elaborations are more conspicuous at the level of the architecture of the entire corolla, rather than at the level of individual petals. Evolutionary trends in petal elaboration in certain larger clades are shown and their involvement in floral biological functions is discussed.     

The phenology of sexual reproduction inGinkgo biloba: Ecological and evolutionary implications

This study examines how the latitude of cultivation ofGinkgo biloba affects the timing of all phases of its sexual reproductive cycle, from pollination through germination. Seeds produced by trees growing in warm-temperate climates germinate earlier in the year than seeds produced in cold-temperate climates, and they have a longer period of time available for seedling establishment. The embryos ofG. biloba seeds possess a temperature-dependent developmental-delay mechanism that allows seeds to survive winter by preventing premature germination in the fall. This and other cold-climate adaptations appear to have evolved within the genusGinkgo during the early Cretaceous, when the Northern Hemisphere was undergoing dramatic cooling after a long period of stable, warm conditions.Ginkgo biloba seeds possess an odoriferous sarcotesta that attracts mammalian scavengers in Asia-most notably members of the Carnivora—presumably by mimicking the smell of carrion. Seeds cleaned of their sarcotesta germinated faster and at higher percentages than those with their sarcotesta intact, suggesting that animal dispersal plays an important role in promoting seedling establishment. During the Cretaceous, potential dispersal agents included mammals, birds, and carnivorous dinosaurs.     

Lectinomics I. Relevance of exogenous plant lectins in biomedical diagnostics

This review focuses on utilization of plant lectins as medical diagnostic reagents and tools. The lectin-related diagnostic is aimed at detection of several diseases connected to alteration of the glycosylation profiles of cells and at identification of microbial and viral agents in clinical microbiology. Certain lectins, proposed for or used as diagnostic tools could even recognize those cellular determinants, which are not detected by available antibodies. Broad information is presented on the lectinomics field, illustrating that lectin diagnostics might become practical alternative to antibody-based diagnostic products. In addition, the rising trend of lectin utilization in biomedical diagnostics might initiate a development of innovative methods based on better analytical technologies. Lectin microarray, a rapid and simple methodology, can be viewed as an example for such initiative. This technology could provide simple and efficient screening tools for analysis of glycosylation patterns in biological samples (cellular extracts, tissues and the whole cells), allowing thus personalized detection of changes associated with carbohydrate-related diseases.