Synaptonemal complex formation: where does it start?

The synaptonemal complex is a prominent, evolutionarily conserved feature of meiotic prophase. The assembly of this structure is closely linked to meiotic recombination. A recent study in budding yeast reveals an unexpected role in centromere pairing for a protein component of the synaptonemal complex, Zip1. These findings have implications for synaptonemal complex formation.     

Free cholesterol in atherosclerotic plaques: where does it come from?

PURPOSE OF REVIEW: Free cholesterol in plaques is an emerging contributing factor to lesion instability and, until recently, apoptosis of lipid-laden macrophages was considered the major source of free cholesterol. The validity of this concept is beginning to be challenged since there is recent evidence of erythrocyte membrane-derived cholesterol in plaques. Therefore, intraplaque hemorrhage may not be a passive event, as once considered as studies continue to support the relationship of intraplaque hemorrhage and necrotic core expansion. RECENT FINDINGS: The association of intraplaque hemorrhage, accumulated free cholesterol, and necrotic core expansion is beginning to unfold and recent MRI studies suggest the value of intraplaque hemorrhage as a predictor of recurrent cerebrovascular events. The amount of erythrocyte membrane-derived cholesterol is also suggested to be a measure of lesion vulnerability in acute coronary syndromes. Recent inhibitors studies of vascular permeability factors further emphasize the importance of intraplaque hemorrhage in plaque progression. Finally, DNA microarray analysis is starting to reveal key molecules involved in the accumulation of free cholesterol that are selectively induced in high-risk plaques. SUMMARY: These recent findings emphasize the importance of intraplaque hemorrhage as a contributor of free cholesterol in plaques and point to its provocative role in lesion destabilization.     

The restoration of biodiversity: where has research been and where does it need to go?

The practice of ecological restoration is a primary option for increasing levels of biodiversity by modifying human-altered ecosystems. The scientific discipline of restoration ecology provides conceptual guidance and tests of restoration strategies, with the ultimate goal of predictive landscape restoration. I construct a conceptual model for restoration of biodiversity, based on site-level (e.g., biotic and abiotic) conditions, landscape (e.g, interpatch connectivity and patch geometry), and historical factors (e.g., species arrival order and land-use legacies). I then ask how well restoration ecology has addressed the various components of this model. During the past decade, restoration research has focused largely on how the restoration of site-level factors promotes species diversity-primarily of plants. Relatively little attention has been paid to how landscape or historical factors interplay with restoration, how restoration influences functional and genetic components of biodiversity, or how a suite of less-studied taxa might be restored. I suggest that the high level of variation seen in restoration outcomes might be explained, at least in part, by the contingencies placed on site-level restoration by landscape and historical factors and then present a number of avenues for future research to address these often ignored linkages in the biodiversity restoration model. Such work will require carefully conducted restoration experiments set across multiple sites and many years. It is my hope that by considering how space and time influence restoration, we might move restoration ecology in a direction of stronger prediction, conducted across landscapes, thus providing feasible restoration strategies that work at scales over which biodiversity conservation occurs.     

Who is where in the Plastisphere,and why does it matter?

To fully understand how plastic is affecting the ocean, we need to understand how marine life interacts directly with it. Besides their ecological relevance, microbes can affect the distribution, degradation and transfer of plastics to the rest of the marine food web. From amplicon sequencing and scanning electron microscopy, we know that a diverse array of microorganisms rapidly associate with plastic marine debris in the form of biofouling and biofilms, also known as the “Plastisphere.” However, observation of multiple microbial interactions in situ, at small spatial scales in the Plastisphere, has been a challenge. In this issue of Molecular Ecology Resources, Schlundt et al. apply the combination labelling and spectral imaging – fluorescence in situ hybridization to study microbial communities on plastic marine debris. The images demonstrate the colocalization of abundant bacterial groups on plastic marine debris at a relatively high taxonomic and spatial resolution while also visualizing biofouling of eukaryotes, such as diatoms and bryozoans. This modern imaging technology provides new possibilities to address questions regarding the ecology of marine microbes on plastic marine debris and describe more specific impacts of plastic pollution in the marine food webs.     

Coexistence of competing parasitoids: which is the fugitive and where does it hide?

Most insects harbour a community of parasitoids that coexist in spite of competition for resources. One potential mechanism for coexistence of competitors is a tradeoff between dispersiveness and local competitive ability. Here we present a study of competition between the specialized parasitoids Hyposoter horticola and Cotesia melitaearum sharing the Glanville fritillary butterfly, Melitaea cinxia . Within one host generation, the parasitoid larvae interact inside the host during each of the three C. melitaearum generations. We founds that in the summer when the host is small, the solitary H. horticola is the superior competitor, suppressing the gregarious C. melitaearum as eggs or small larvae. When multiparasitism occurs in the autumn the two parasitoid species engage in physical combat and C. melitaearum is favoured. Finally, a previous study showed that in the third C. melitaearum generation the univoltine H. horticola grows quickly during its final instar, excluding young C. melitaearum simply through limited time and resources. We found that contrary to expectations of the evolution of gregariousness, C. melitaearum , which lives in sibling groups, has biting mandibles in the first instar while the solitary H. horticola has suctorial mouthparts. Previous studies suggest that the two parasitoids co-exist because H. Horticola is dispersive and C. melitaearum is a strong local competitor. However, putting together the results of this experiment and out recent understanding of the adult wasp foraging behaviours and large scale population dynamics, we conclude that H. horticola is both a superior local competitor and more dispersive than C. melitaearum . Cotesia melitaearum has no impact on the population dynamics of H. horticola , persisting as a fugitive using a small fraction the larvae left unparasitized by H. horticola .     

Subfunctionalization: How often does it occur? How long does it take?

The mechanisms responsible for the preservation of duplicate genes have been debated for more than 70 years. Recently, Lynch and Force have proposed a new explanation: subfunctionalization--after duplication the two gene copies specialize to perform complementary functions. We investigate the probability that subfunctionalization occurs, the amount of time after duplication that it takes for the outcome to be resolved, and the relationship of these quantities to the population size and mutation rates.     

Intra‐individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

Next‐generation sequencing allows access to a large quantity of genomic data. In plants, several studies used whole chloroplast genome sequences for inferring phylogeography or phylogeny. Even though the chloroplast is a haploid organelle, NGS plastome data identified a nonnegligible number of intra‐individual polymorphic SNPs. Such observations could have several causes such as sequencing errors, the presence of heteroplasmy or transfer of chloroplast sequences in the nuclear and mitochondrial genomes. The occurrence of allelic diversity has practical important impacts on the identification of diversity, the analysis of the chloroplast data and beyond that, significant evolutionary questions. In this study, we show that the observed intra‐individual polymorphism of chloroplast sequence data is probably the result of plastid DNA transferred into the mitochondrial and/or the nuclear genomes. We further assess nine different bioinformatics pipelines’ error rates for SNP and genotypes calling using SNPs identified in Sanger sequencing. Specific pipelines are adequate to deal with this issue, optimizing both specificity and sensitivity. Our results will allow a proper use of whole chloroplast NGS sequence and will allow a better handling of NGS chloroplast sequence diversity.     

Modulating social behavior with oxytocin: How does it work? What does it mean?

Among its many roles in body and brain, oxytocin influences social behavior. Understanding the precise nature of this influence is crucial, both within the broader theoretical context of neurobiology, social neuroscience and brain evolution, but also within a clinical context of disorders such as anxiety, schizophrenia, and autism. Research exploring oxytocin's role in human social behavior is difficult owing to its release in both body and brain and its interactive effects with other hormones and neuromodulators. Additional difficulties are due to the intricacies of the blood-brain barrier and oxytocin's instability, which creates measurement issues. Questions concerning how to interpret behavioral results of human experiments manipulating oxytocin are thus made all the more pressing. The current paper discusses several such questions. We highlight unresolved fundamental issues about what exactly happens when oxytocin is administered intranasally, whether such oxytocin does in fact reach appropriate receptors in brain, and whether central or peripheral influences account for the observed behavioral effects. We also highlight the deeper conceptual issue of whether the human data should be narrowly interpreted as implicating a specific role for oxytocin in complex social cognition, such a generosity, trust, or mentalizing, or more broadly interpreted as implicating a lower-level general effect on general states and dispositions, such as anxiety and social motivation. Using several influential studies, we show how seemingly specific, higher-level social-cognitive effects can emerge via a process by which oxytocin's broad influence is channeled into a specific social behavior in a context of an appropriate social and research setting. This article is part of a Special Issue entitled Oxytocin, Vasopressin, and Social Behavior.     

Impact factor in cytopathology journals: what does it reflect and how much does it matter?

B. AbdullGaffar
Impact factor in cytopathology journals: what does it reflect and how much does it matter? Objective: To study the trends of impact factor (IF) in four cytopathology journals. To investigate the factors that might influence IF in cytopathology literature and whether IF has any impact on cytopathology practice. Methods: The IFs of four cytopathology journals were searched from 2005 to 2009. The IFs and their relationships with the types and number of publications, publishers, the official societies, readership, the quality of their contents, the topics covered and the levels of evidence were compared. Results: Cancer Cytopathology (CC) had the highest IF. Acta Cytologica (AC) had the lowest IF, which appeared to be in decline. Cytopathology (C) and Diagnostic Cytopathology (DC) had a slow but steady increase in their IF. Components that might influence these differences could include the category and the society of the journal, targeted readers and certain types of publications. Publishers, the number of publications, the types of topics covered and the levels of evidence probably have no major effect on IF. Conclusions: IF has its own benefits and original applications. IF is a quantitative measure that does not reflect the levels of evidence in cytopathology journals. IF should not be abandoned because it might encourage competition between cytopathology journals, but it should not dictate their contents.     

Symmetry breakage in the vertebrate embryo: When does it happen and how does it work?

Asymmetric development of the vertebrate embryo has fascinated embryologists for over a century. Much has been learned since the asymmetric Nodal signaling cascade in the left lateral plate mesoderm was detected, and began to be unraveled over the past decade or two. When and how symmetry is initially broken, however, has remained a matter of debate. Two essentially mutually exclusive models prevail. Cilia-driven leftward flow of extracellular fluids occurs in mammalian, fish and amphibian embryos. A great deal of experimental evidence indicates that this flow is indeed required for symmetry breaking. An alternative model has argued, however, that flow simply acts as an amplification step for early asymmetric cues generated by ion flux during the first cleavage divisions. In this review we critically evaluate the experimental basis of both models. Although a number of open questions persist, the available evidence is best compatible with flow-based symmetry breakage as the archetypical mode of symmetry breakage.     

Complexin: does it deserve its name?

Knockout and other perturbations of complexins have provided important insights and elicited controversies about their role in neurotransmitter release. New work by Yang et?al. in this issue of Neuron adds important detail and complexity to existing concepts-particularly on the nature of a Ca(2+)-dependent complexin-synaptotagmin switch for the triggering of exocytosis. But it also provokes thoughts about alternative interpretations, which might result in a simpler model of complexin function.     

Single-molecule biology: what is it and how does it work?

Biochemistry and structural biology are undergoing a dramatic revolution. Until now, we have tried to study subtle and complex biological processes by crude in vitro techniques, looking at average behaviors of vast numbers of molecules under conditions usually remote from those existing in the cell. Researchers have realized the limitations of this approach, but none other has been available. Now, we can not only observe the nuances of the behaviors of individual molecules but prod and probe them as well. Perhaps most important is the emerging ability to carry out such observations and manipulations within the living cell. The long-awaited leap to an in vivo biochemistry is at last underway.     

MLL: How complex does it get?

The mixed lineage leukemia (MLL) gene encodes a very large nuclear protein homologous to Drosophila trithorax (trx). MLL is required for the proper maintenance of HOX gene expression during development and hematopoiesis. The exact regulatory mechanism of HOX gene expression by MLL is poorly understood, but it is believed that MLL functions at the level of chromatin organization. MLL was identified as a common target of chromosomal translocations associated with human acute leukemias. About 50 different MLL fusion partners have been isolated to date, and while similarities exist between groups of partners, there exists no unifying property shared by all the partners. MLL gene rearrangements are found in leukemias with both lymphoid and myeloid phenotypes and are often associated with infant and secondary leukemias. The immature phenotype of the leukemic blasts suggests an important role for MLL in the early stages of hematopoietic development. Mll homozygous mutant mice are embryonic lethal and exhibit deficiencies in yolk sac hematopoiesis. Recently, two different MLL-containing protein complexes have been isolated. These and other gain- and loss-of-function experiments have provided insight into normal MLL function and altered functions of MLL fusion proteins. This article reviews the progress made toward understanding the function of the wild-type MLL protein. While many advances in understanding this multifaceted protein have been made since its discovery, many challenging questions remain to be answered.