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DNA methylation is implicated in a surprising diversity of regulatory, evolutionary processes and diseases in eukaryotes. The introduction of whole-genome bisulfite sequencing has enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness of methylome data in understanding a variety of genomic phenomena. As the number of publicly available whole-genome bisulfite sequencing studies reaches into the hundreds, reliable and convenient tools for comparing and analyzing methylomes become increasingly important. We present MethPipe, a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.

The representation and integration of internal and external cues is crucial for any organism to execute appropriate behaviors. In insects, a highly conserved region of the brain, the central complex (CX), functions in the representation of spatial information and behavioral states, as well as the transformation of this information into desired navigational commands. How does this relatively invariant structure enable the incorporation of information from the diversity of anatomical, behavioral, and ecological niches occupied by insects? Here, we examine the input channels to the CX in the context of their development and evolution. Insect brains develop from ~ 100 neuroblasts per hemisphere that divide systematically to form “lineages” of sister neurons, that project to their target neuropils along anatomically characteristic tracts. Overlaying this developmental tract information onto the recently generated Drosophila “hemibrain” connectome and integrating this information with the anatomical and physiological recording of neurons in other species, we observe neuropil and lineage-specific innervation, connectivity, and activity profiles in CX input channels. We posit that the proliferative potential of neuroblasts and the lineage-based architecture of information channels enable the modification of neural networks across existing, novel, and deprecated modalities in a species-specific manner, thus forming the substrate for the evolution and diversification of insect navigational circuits.

In insects and mammals, olfactory experience in early life alters olfactory behavior and function in later life. In the vinegar fly Drosophila , flies chronically exposed to a high concentration of a monomolecular odor exhibit reduced behavioral aversion to the familiar odor when it is reencountered. This change in olfactory behavior has been attributed to selective decreases in the sensitivity of second-order olfactory projection neurons (PNs) in the antennal lobe that respond to the overrepresented odor. However, since odorant compounds do not occur at similarly high concentrations in natural sources, the role of odor experience-dependent plasticity in natural environments is unclear. Here, we investigated olfactory plasticity in the antennal lobe of flies chronically exposed to odors at concentrations that are typically encountered in natural odor sources. These stimuli were chosen to each strongly and selectively excite a single class of primary olfactory receptor neuron (ORN), thus facilitating a rigorous assessment of the selectivity of olfactory plasticity for PNs directly excited by overrepresented stimuli. Unexpectedly, we found that chronic exposure to three such odors did not result in decreased PN sensitivity but rather mildly increased responses to weak stimuli in most PN types. Odor-evoked PN activity in response to stronger stimuli was mostly unaffected by odor experience. When present, plasticity was observed broadly in multiple PN types and thus was not selective for PNs receiving direct input from the chronically active ORNs. We further investigated the DL5 olfactory coding channel and found that chronic odor-mediated excitation of its input ORNs did not affect PN intrinsic properties, local inhibitory innervation, ORN responses or ORN-PN synaptic strength; however, broad-acting lateral excitation evoked by some odors was increased. These results show that PN odor coding is only mildly affected by strong persistent activation of a single olfactory input, highlighting the stability of early stages of insect olfactory processing to significant perturbations in the sensory environment.

Sensory stimuli fluctuate on many timescales but short-term plasticity causes synapses to act as temporal filters, limiting the range of frequencies they can transmit. Here, the authors show how the interaction of multiple synaptic and circuit mechanisms can reduce synaptic depression to promote faithful coding of both fast and slow stimuli. Sensory stimuli fluctuate on many timescales. However, short-term plasticity causes synapses to act as temporal filters, limiting the range of frequencies that they can transmit. How synapses in vivo might transmit a range of frequencies in spite of short-term plasticity is poorly understood. The first synapse in the Drosophila olfactory system exhibits short-term depression, but can transmit broadband signals. Here we describe two mechanisms that broaden the frequency characteristics of this synapse. First, two distinct excitatory postsynaptic currents transmit signals on different timescales. Second, presynaptic inhibition dynamically updates synaptic properties to promote accurate transmission of signals across a wide range of frequencies. Inhibition is transient, but grows slowly, and simulations reveal that these two features of inhibition promote broadband synaptic transmission. Dynamic inhibition is often thought to restrict the temporal patterns that a neuron responds to, but our results illustrate a different idea: inhibition can expand the bandwidth of neural coding.

When an odour activates a fly′s antennae asymmetrically, more neurotransmitter is released from olfactory receptor neuron axon branches ipsilateral to the antenna than from contralateral branches. This causes ipsilateral central olfactory neurons to begin spiking earlier and at a higher rate than contralateral neurons, thereby enabling a walking fly to turn towards the odour. Fruitflies’ sense of direction A fruitfly knows right from left when confronted with an asymmetric odour plume. This study demonstrates a neuronal basis for that ability. Rachel Wilson and colleagues show that Drosophila are able to discriminate between odours presented to the right antenna versus the left antenna because each spike arising from the right antenna releases only about two-thirds as much neurotransmitter in the left brain, as compared to the right brain. As a result, central neurons on the right spike a few milliseconds before neurons on the left, and neurons on the right also spike at a slightly higher rate. The brain of a walking fly can detect this subtle asymmetry and initiate a turn to the right before the fly even completes one stride. In Drosophila , most individual olfactory receptor neurons (ORNs) project bilaterally to both sides of the brain 1 , 2 . Having bilateral rather than unilateral projections may represent a useful redundancy. However, bilateral ORN projections to the brain should also compromise the ability to lateralize odours. Nevertheless, walking or flying Drosophila reportedly turn towards the antenna that is more strongly stimulated by odour 3 , 4 , 5 . Here we show that each ORN spike releases approximately 40% more neurotransmitter from the axon branch ipsilateral to the soma than from the contralateral branch. As a result, when an odour activates the antennae asymmetrically, ipsilateral central neurons begin to spike a few milliseconds before contralateral neurons, and at a 30 to 50% higher rate than contralateral neurons. We show that a walking fly can detect a 5% asymmetry in total ORN input to its left and right antennal lobes, and can turn towards the odour in less time than it requires the fly to complete a stride. These results demonstrate that neurotransmitter release properties can be tuned independently at output synapses formed by a single axon onto two target cells with identical functions and morphologies. Our data also show that small differences in spike timing and spike rate can produce reliable differences in olfactory behaviour.

Single-cell mouse embryos were infected in vitro with recombinant lentiviral vectors to generate transgenic mice carrying the green fluorescent protein (GFP) gene driven by a ubiquitously expressing promoter. Eighty percent of founder mice carried at least one copy of the transgene, and 90% of these expressed GFP at high levels. Progeny inherited the transgene(s) and displayed green fluorescence. Mice generated using lentiviral vectors with muscle-specific and T lymphocyte-specific promoters expressed high levels of GFP only in the appropriate cell types. We have also generated transgenic rats that express GFP at high levels, suggesting that this technique can be used to produce other transgenic animal species.

Understanding the computations that take place in brain circuits requires identifying how neurons in those circuits are connected to one another. We describe a technique called TRACT (TRAnsneuronal Control of Transcription) based on ligand-induced intramembrane proteolysis to reveal monosynaptic connections arising from genetically labeled neurons of interest. In this strategy, neurons expressing an artificial ligand (‘donor’ neurons) bind to and activate a genetically-engineered artificial receptor on their synaptic partners (‘receiver’ neurons). Upon ligand-receptor binding at synapses the receptor is cleaved in its transmembrane domain and releases a protein fragment that activates transcription in the synaptic partners. Using TRACT in Drosophila we have confirmed the connectivity between olfactory receptor neurons and their postsynaptic targets, and have discovered potential new connections between neurons in the circadian circuit. Our results demonstrate that the TRACT method can be used to investigate the connectivity of neuronal circuits in the brain. One of the main obstacles to understanding how the brain works is that we know relatively little about how its nerve cells or neurons are connected to one another. These connections make up the brain’s wiring diagram. Current methods for revealing this wiring all have limitations. The most popular method – serial electron microscopy – can reveal the connections in a small region of the brain in great detail, but it cannot show connections between neurons that are far apart. Huang et al. have now created a genetic system for visualizing these connections. For neurons to communicate, one neuron must produce a signal called a ligand. This ligand can then bind to and activate its partner neuron. Huang et al. modified the DNA of neurons so that every time those cells produced a specific ligand, they also produced a red fluorescent protein. Similar modifications ensured that every time the ligand activated a partner neuron, the activated neuron produced a green fluorescent protein. Viewing the red and green neurons under a microscope enabled Huang et al. to see which cells were communicating with which others. While these experiments took place in fruit flies, the same approach should also work in other laboratory animals, including fish, mice and rats. Once we know the wiring diagram of the brain, the next step is to investigate the role of the various connections. To understand how a computer works, for example, we might change the connections between its circuit components and look at how this affects the computer’s output. With this new method, we can change how neurons communicate with one another in the brain, and then look at the effects on behavior. This should provide insights into the workings of the human brain, and clues to what goes wrong in disorders like schizophrenia and autism.

Recessive dystrophic epidermolysis bullosa (RDEB) is an inherited disorder characterized by skin fragility, blistering, and multiple skin wounds with no currently approved or consistently effective treatment. It is due to mutations in the gene encoding type VII collagen (C7). Using recombinant human C7 (rhC7) purified from human dermal fibroblasts (FB-rhC7), we showed previously that intravenously injected rhC7 distributed to engrafted RDEB skin, incorporated into its dermal–epidermal junction (DEJ), and reversed the RDEB disease phenotype. Human dermal fibroblasts, however, are not used for commercial production of therapeutic proteins. Therefore, we generated rhC7 from Chinese hamster ovary (CHO) cells. The CHO–derived recombinant type VII collagen (CHO-rhC7), similar to FB-rhC7, was secreted as a correctly folded, disulfide-bonded, helical trimer resistant to protease degradation. CHO-rhC7 bound to fibronectin and promoted human keratinocyte migration in vitro. A single dose of CHO-rhC7, administered intravenously into new-born C7-null RDEB mice, incorporated into the DEJ of multiple skin sites, tongue and esophagus, restored anchoring fibrils, improved dermal–epidermal adherence, and increased the animals’ life span. Furthermore, no circulating or tissue-bound anti-C7 antibodies were observed in the mice. These data demonstrate the efficacy of CHO-rhC7 in a preclinical murine model of RDEB.

IL-1β and TNF-α are canonical immune response mediators that play key regulatory roles in a wide range of inflammatory responses to both chronic and acute conditions. Here we employ an automated microscopy platform for the analysis of messenger RNA (mRNA) expression of IL-1β and TNF-α at the single-cell level. The amount of IL-1β and TNF-α mRNA expressed in a human monocytic leukemia cell line (THP-1) is visualized and counted using single-molecule fluorescent in-situ hybridization (smFISH) following exposure of the cells to lipopolysaccharide (LPS), an outer-membrane component of Gram-negative bacteria. We show that the small molecule inhibitors MG132 (a 26S proteasome inhibitor used to block NF-κB signaling) and U0126 (a MAPK Kinase inhibitor used to block CCAAT-enhancer-binding proteins C/EBP) successfully block IL-1β and TNF-α mRNA expression. Based upon this single-cell mRNA expression data, we screened 36 different mathematical models of gene expression, and found two similar models that capture the effects by which the drugs U0126 and MG132 affect the rates at which the genes transition into highly activated states. When their parameters were informed by the action of each drug independently, both models were able to predict the effects of the combined drug treatment. From our data and models, we postulate that IL-1β is activated by both NF-κB and C/EBP, while TNF-α is predominantly activated by NF-κB. Our combined single-cell experimental and modeling efforts show the interconnection between these two genes and demonstrates how the single-cell responses, including the distribution shapes, mean expression, and kinetics of gene expression, change with inhibition.

Human epidermal growth factor receptor 2 ( HER2, ERBB2 ) is an important critical predictive marker in patients with invasive breast cancer. It is thus imperative to ensure accuracy and precision in HER2 and ERBB2 testing. In 2007, the American Society of Clinical Oncology and College of American Pathologists (ASCO/CAP) proposed new guidelines for immunohistochemistry and fluorescence in-situ hybridization scoring in an effort to improve accuracy and utility of these companion diagnostic tests. The goal of the 2007 guidelines was to improve concordance rates between the diagnostic tests and decrease the number of inconclusive cases. This study examines the impact in concordance rates and number of inconclusive cases based on the recent change in guidelines in a large study cohort. HER2 immunohistochemistry and ERBB2 fluorescence in-situ hybridization were performed on all specimens from our facility from years 2003 through 2010 ( n =1437). Cases from 2003–2007 ( n =1016) were scored using Food and Drug Administration guidelines, with immunohistochemical 3+ cases staining >10% of tumor cells and fluorescence in-situ hybridization amplification cutoff value of 2.0. The 2007 guidelines were implemented and scored accordingly for cases from 2008–2010 ( n =421), with immunohistochemical 3+ cases staining >30% of tumor cells and fluorescence in-situ hybridization amplification cutoff value of 2.2. We compared concordance rates before and after 2007 guidelines. For the 2003–2007 study population, the concordance rate between the assays was 97.6% with a corresponding kappa coefficient ( k ) of 0.90. For the 2008–2010 study population, concordance rate was 97.6% with a corresponding k of 0.89. There was no significant difference in number of inconclusive rates before and after 2007 guidelines. In our study, implementation of the new ASCO/CAP 2007 HER2 guidelines did not show a significant difference in concordance rates and did not decrease the number of inconclusive cases.