Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal

A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.

Cell Sorter Cleaning Practices and Their Impact on Instrument Sterility

Cells isolated using electrostatic cell sorters are subsequently evaluated in a variety of in vitro and in vivo applications. Thus, manipulations to the cells during the pre- and post-sort processing as well as when the cells are being analyzed by and passing through the sorter fluidics has the potential to affect the experimental results. There are many variables to consider when seeking to preserve cellular integrity and function during the cell-sorting process. A previous study by the Association of Biomolecular Resource Facilities Flow Cytometry Research Group (FCRG) investigated downstream effects on different cell types as a function of sorting variables such as pressure, nozzle size, and temperature. This multisite study revealed site-to-site variability based on differential gene expression when the same cell type and sort conditions were used. These results indicated the possibility that environmental factors such as the presence of contaminants in the sorter fluidics could exhibit effects on downstream molecular assays (ie, endotoxins or RNases). In the study described here, the FCRG sought to better understand how sorters are maintained and evaluated for contaminants such as bacteria, endotoxin, and RNases. In addition, the efficacy of an endotoxin decontamination method was evaluated. The results demonstrated that the majority of sorters in shared resource laboratories are free of RNase activity and bacteria; however, many are contaminated with endotoxin. The efficacy of a hydrogen peroxide cleaning procedure was tested and found to exhibit only a short-term effectiveness in eliminating endotoxin contamination.

Tumor-initiating stem cell shapes its microenvironment into an immunosuppressive barrier and pro-tumorigenic niche

Tumor-initiating stem cells (TSCs) are critical for drug resistance and immune escape. However, the mutual regulations between TSC and tumor microenvironment (TME) remain unclear. Using DNA-label retaining, single-cell RNA sequencing (scRNA-seq), and other approaches, we investigated intestinal adenoma in response to chemoradiotherapy (CRT), thus identifying therapy-resistant TSCs (TrTSCs). We find bidirectional crosstalk between TSCs and TME using CellPhoneDB analysis. An intriguing finding is that TSCs shape TME into a landscape that favors TSCs for immunosuppression and propagation. Using adenoma-organoid co-cultures, niche-cell depletion, and lineaging tracing, we characterize a functional role of cyclooxygenase-2 (Cox-2)-dependent signaling, predominantly occurring between tumor-associated monocytes and macrophages (TAMMs) and TrTSCs. We show that TAMMs promote TrTSC proliferation through prostaglandin E2 (PGE2)-PTGER4(EP4) signaling, which enhances β-catenin activity via AKT phosphorylation. Thus, our study shows that the bidirectional crosstalk between TrTSC and TME results in a pro-tumorigenic and immunosuppressive contexture.

Evaluating the Effects of Cell Sorting on Gene Expression

Cell sorting is a commonly used technology to isolate highly purified cell populations for downstream applications. Because the sorted cells are destined for further analysis, i.e., gene expression assays or functional assays, ensuring that the sorting process itself has little effect on the cells is of utmost importance. Previous studies examining the effects of sorting on cellular function have primarily focused on a specific cell type or condition. One of the goals of the Flow Cytometry Research Group of the Association of Biomolecular Resource Facilities is to establish best practice guidelines for cell sorting conditions that minimize cell stress, perturbation, or injury to the sorted cell population. In this study, the effects of nozzle size, sample pressure, UV exposure, and instrument type were evaluated for their effects on gene expression and cell cycle using both established cell lines and primary cells across several flow cytometry shared facilities. Results indicate that nozzle size and pressure, as well as UV exposure and instrument type, have only minor effects on gene expression, which were diminished by subsequent culturing of the sorted cells. In this assessment, these data demonstrate that cell sorting itself, regardless of instrumentation used, has minimal effects on downstream cellular applications.

Hypersaline water from desalinization plants causes oxidative damage in Posidonia oceanica meadows

Posidonia oceanica is an endemic marine phanerogam of the Mediterranean Sea for that is very sensitive to the environmental changes, especially those related to human activities. The aim of this study was to evaluate the oxidative stress status of P. oceanica meadows exposed to spillage of hypersaline water from a desalination station by using biomarkers. Leaf samples of P. oceanica were obtained from 4 different points exposed to different levels of salinity water. Samples from the area with the highest salinity conditions were 75% shorter than the samples from the control area. Exposure to high salinity induced an increase in the levels of oxidative stress markers (malondialdehyde (MDA) and protein carbonyls). Interestingly, in the area with the highest salinity the activities of glutathione peroxidase, glutathione reductase and glutathione-s-transferase were significantly induced respect to the other studies areas, while catalase (CAT) and superoxide dismutase (SOD) activities were lower. In addition, salinity induced a progressive increase in non-enzymatic antioxidants (polyphenols and glutathione) and in total antioxidant capacity reaching the highest concentrations in samples directly affected by the saline discharge. In conclusion chronic exposure to high salinity induced an increase in total antioxidant capacity in P. oceanica. However, this increase was not enough to protect the plant against oxidative stress as it is evidenced by the raise in oxidative stress markers. The obtained data suggest that high salinity conditions deactivated CAT and SOD antioxidant enzymes and caused an increase in non-enzymatic antioxidants (polyphenols and glutathione) and in glutathione-related enzymes.

Evaluating the Effects of Cell Sorting on Gene Expression

Cell sorting is a commonly used technology to isolate highly purified cell populations for downstream applications. Because the sorted cells are destined for further analysis, i.e., gene expression assays or functional assays, ensuring that the sorting process itself has little effect on the cells is of utmost importance. Previous studies examining the effects of sorting on cellular function have primarily focused on a specific cell type or condition. One of the goals of the Flow Cytometry Research Group of the Association of Biomolecular Resource Facilities is to establish best practice guidelines for cell sorting conditions that minimize cell stress, perturbation, or injury to the sorted cell population. In this study, the effects of nozzle size, sample pressure, UV exposure, and instrument type were evaluated for their effects on gene expression and cell cycle using both established cell lines and primary cells across several flow cytometry shared facilities. Results indicate that nozzle size and pressure, as well as UV exposure and instrument type, have only minor effects on gene expression, which were diminished by subsequent culturing of the sorted cells. In this assessment, these data demonstrate that cell sorting itself, regardless of instrumentation used, has minimal effects on downstream cellular applications.

Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis

Hox genes modulate the properties of hematopoietic stem cells (HSCs) and reacquired Hox expression in progenitors contributes to leukemogenesis. Here, our transcriptome and DNA methylome analyses revealed that Hoxb cluster and retinoid signaling genes are predominantly enriched in LT-HSCs, and this coordinate regulation of Hoxb expression is mediated by a retinoid-dependent cis-regulatory element, distal element RARE (DERARE). Deletion of the DERARE reduced Hoxb expression, resulting in changes to many downstream signaling pathways (e.g., non-canonical Wnt signaling) and loss of HSC self-renewal and reconstitution capacity. DNA methyltransferases mediate DNA methylation on the DERARE, leading to reduced Hoxb cluster expression. Acute myeloid leukemia patients with DNMT3A mutations exhibit DERARE hypomethylation, elevated HOXB expression, and adverse outcomes. CRISPR-Cas9-mediated specific DNA methylation at DERARE attenuated HOXB expression and alleviated leukemogenesis. Collectively, these findings demonstrate pivotal roles for retinoid signaling and the DERARE in maintaining HSCs and preventing leukemogenesis by coordinate regulation of Hoxb genes.

Detecting and Characterizing Protein Self-Assembly In Vivo by Flow Cytometry

Protein self-assembly governs protein function and compartmentalizes cellular processes in space and time. Current methods to study it suffer from low-sensitivity, indirect read-outs, limited throughput, and/or population-level rather than single-cell resolution. We designed a flow cytometry-based single methodology that addresses all of these limitations: Distributed Amphifluoric FRET or DAmFRET. DAmFRET detects and quantifies protein self-assemblies by sensitized emission FRET in vivo, enables deployment across model systems-from yeast to human cells-and achieves sensitive, single-cell, high-throughput read-outs irrespective of protein localization or solubility.

Quantifying Nucleation In Vivo Reveals the Physical Basis of Prion-like Phase Behavior

Protein self-assemblies modulate protein activities over biological timescales that can exceed the lifetimes of the proteins or even the cells that harbor them. We hypothesized that these timescales relate to kinetic barriers inherent to the nucleation of ordered phases. To investigate nucleation barriers in living cells, we developed distributed amphifluoric FRET (DAmFRET). DAmFRET exploits a photoconvertible fluorophore, heterogeneous expression, and large cell numbers to quantify via flow cytometry the extent of a protein's self-assembly as a function of cellular concentration. We show that kinetic barriers limit the nucleation of ordered self-assemblies and that the persistence of the barriers with respect to concentration relates to structure. Supersaturation resulting from sequence-encoded nucleation barriers gave rise to prion behavior and enabled a prion-forming protein, Sup35 PrD, to partition into dynamic intracellular condensates or to form toxic aggregates. Our results suggest that nucleation barriers govern cytoplasmic inheritance, subcellular organization, and proteotoxicity.

A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period

In the developing brain, heightened plasticity during the critical period enables the proper formation of neural circuits. Here, we identify the "navigator" neurons, a group of perinatally born olfactory sensory neurons, as playing an essential role in establishing the olfactory map during the critical period. The navigator axons project circuitously in the olfactory bulb and traverse multiple glomeruli before terminating in perspective glomeruli. These neurons undergo a phase of exuberant axon growth and exhibit a shortened lifespan. Single-cell transcriptome analyses reveal distinct molecular signatures for the navigators. Extending their lifespan prolongs the period of exuberant growth and perturbs axon convergence. Conversely, a genetic ablation experiment indicates that, despite postnatal neurogenesis, only the navigators are endowed with the ability to establish a convergent map. The presence and the proper removal of the navigator neurons are both required to establish tight axon convergence into the glomeruli.

Isolation and characterization of intestinal stem cells based on surface marker combinations and colony-formation assay

BACKGROUND & AIMS

Identification of intestinal stem cells (ISCs) has relied heavily on the use of transgenic reporters in mice, but this approach is limited by mosaic expression patterns and difficult to directly apply to human tissues. We sought to identify reliable surface markers of ISCs and establish a robust functional assay to characterize ISCs from mouse and human tissues.

METHODS

We used immunohistochemistry, real-time reverse-transcription polymerase chain reaction, and fluorescence-activated cell sorting (FACS) to analyze intestinal epithelial cells isolated from mouse and human intestinal tissues. We compared different combinations of surface markers among ISCs isolated based on expression of Lgr5-green fluorescent protein. We developed a culture protocol to facilitate the identification of functional ISCs from mice and then tested the assay with human intestinal crypts and putative ISCs.

RESULTS

CD44(+)CD24(lo)CD166(+) cells, isolated by FACS from mouse small intestine and colon, expressed high levels of stem cell-associated genes. Transit-amplifying cells and progenitor cells were then excluded based on expression of GRP78 or c-Kit. CD44(+)CD24(lo)CD166(+) GRP78(lo/-) putative stem cells from mouse small intestine included Lgr5-GFP(hi) and Lgr5-GFP(med/lo) cells. Incubation of these cells with the GSK inhibitor CHIR99021 and the E-cadherin stabilizer Thiazovivin resulted in colony formation by 25% to 30% of single-sorted ISCs.

CONCLUSIONS

We developed a culture protocol to identify putative ISCs from mouse and human tissues based on cell surface markers. CD44(+)CD24(lo)CD166(+), GRP78(lo/-), and c-Kit(-) facilitated identification of putative stem cells from the mouse small intestine and colon, respectively. CD44(+)CD24(-/lo)CD166(+) also identified putative human ISCs. These findings will facilitate functional studies of mouse and human ISCs.

Noncanonical Wnt signaling maintains hematopoietic stem cells in the niche

Wnt signaling is involved in self-renewal and maintenance of hematopoietic stem cells (HSCs); however, the particular role of noncanonical Wnt signaling in regulating HSCs in vivo is largely unknown. Here, we show Flamingo (Fmi) and Frizzled (Fz) 8, members of noncanonical Wnt signaling, both express in and functionally maintain quiescent long-term HSCs. Fmi regulates Fz8 distribution at the interface between HSCs and N-cadherin(+) osteoblasts (N-cad(+)OBs that enrich osteoprogenitors) in the niche. We further found that N-cad(+)OBs predominantly express noncanonical Wnt ligands and inhibitors of canonical Wnt signaling under homeostasis. Under stress, noncanonical Wnt signaling is attenuated and canonical Wnt signaling is enhanced in activation of HSCs. Mechanistically, noncanonical Wnt signaling mediated by Fz8 suppresses the Ca(2+)-NFAT- IFNγ pathway, directly or indirectly through the CDC42-CK1α complex and also antagonizes canonical Wnt signaling in HSCs. Taken together, our findings demonstrate that noncanonical Wnt signaling maintains quiescent long-term HSCs through Fmi and Fz8 interaction in the niche.

Cohesin proteins promote ribosomal RNA production and protein translation in yeast and human cells

Cohesin is a protein complex known for its essential role in chromosome segregation. However, cohesin and associated factors have additional functions in transcription, DNA damage repair, and chromosome condensation. The human cohesinopathy diseases are thought to stem not from defects in chromosome segregation but from gene expression. The role of cohesin in gene expression is not well understood. We used budding yeast strains bearing mutations analogous to the human cohesinopathy disease alleles under control of their native promoter to study gene expression. These mutations do not significantly affect chromosome segregation. Transcriptional profiling reveals that many targets of the transcriptional activator Gcn4 are induced in the eco1-W216G mutant background. The upregulation of Gcn4 was observed in many cohesin mutants, and this observation suggested protein translation was reduced. We demonstrate that the cohesinopathy mutations eco1-W216G and smc1-Q843Δ are associated with defects in ribosome biogenesis and a reduction in the actively translating fraction of ribosomes, eiF2α-phosphorylation, and (35)S-methionine incorporation, all of which indicate a deficit in protein translation. Metabolic labeling shows that the eco1-W216G and smc1-Q843Δ mutants produce less ribosomal RNA, which is expected to constrain ribosome biogenesis. Further analysis shows that the production of rRNA from an individual repeat is reduced while copy number remains unchanged. Similar defects in rRNA production and protein translation are observed in a human Roberts syndrome cell line. In addition, cohesion is defective specifically at the rDNA locus in the eco1-W216G mutant, as has been previously reported for Roberts syndrome. Collectively, our data suggest that cohesin proteins normally facilitate production of ribosomal RNA and protein translation, and this is one way they can influence gene expression. Reduced translational capacity could contribute to the human cohesinopathies.

Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation

The Spt-Ada-Gcn5-acetyltransferase (SAGA) complex was discovered from Saccharomyces cerevisiae and has been well characterized as an important transcriptional coactivator that interacts both with sequence-specific transcription factors and the TATA-binding protein TBP. SAGA contains a histone acetyltransferase and a ubiquitin protease. In metazoans, SAGA is essential for development, yet little is known about the function of SAGA in differentiating tissue. We analyzed the composition, interacting proteins, and genomic distribution of SAGA in muscle and neuronal tissue of late stage Drosophila melanogaster embryos. The subunit composition of SAGA was the same in each tissue; however, SAGA was associated with considerably more transcription factors in muscle compared with neurons. Consistent with this finding, SAGA was found to occupy more genes specifically in muscle than in neurons. Strikingly, SAGA occupancy was not limited to enhancers and promoters but primarily colocalized with RNA polymerase II within transcribed sequences. SAGA binding peaks at the site of RNA polymerase pausing at the 5' end of transcribed sequences. In addition, many tissue-specific SAGA-bound genes required its ubiquitin protease activity for full expression. These data indicate that in metazoans SAGA plays a prominent post-transcription initiation role in tissue-specific gene expression.

Differences in delta13C and delta15N stable isotopes in the pearly razorfish Xyrichtys novacula related to the sex, location and spawning period

In the present study, Xyrichtys novacula (Labridae) were sampled at five locations around the islands of Ibiza and Formentera (western Mediterranean Sea). Isotopic signatures of delta13C, delta15N and the C:N ratio were analysed in relation to locality, sex and size differences. delta13C and delta15N partitioning was also studied in the reproductive spawning period. There were significant differences in the delta13C signature between localities for both sexes, but not for delta15N. Sex differences were also found with a mean +/-s.e. value of -17.38 +/- 0.06 per thousand delta13C and 8.36 +/- 0.05 per thousand delta(15)N for females and -17.17 +/- 0.07 per thousand delta13C and 8.80 +/- 0.06 per thousand delta15N for males. Increasing total length in both sexes was positively correlated with delta15N enrichment and a significant positive linear regression was established for both variables. During the reproductive spawning period, there were changes in delta13C fractioning with enrichment in postspawning females and males (with respect to prespawning and spawning periods) and delta(15)N impoverishment in postspawning females (with respect to prespawning and spawning periods). Xyrichtys novacula uses local food sources, as confirmed by delta(13)C and delta(15)N, and females and males use different food sources, thus avoiding intraspecific competition. This was confirmed by delta15N enrichment as size increased. Spawning leads to special requirements for gonad maturation, which is reflected in the isotopic signatures for both sexes.

Muscle and scale isotopic offset of three fish species in the Mediterranean Sea: Dentex dentex, Argyrosomus regius and Xyrichtys novacula

Diet information of organisms was traditionally acquired by the use of lethal techniques (gut content or muscle delta(13)C and delta(15)N isotopic ratios). An increase in the number of isotopic ratio studies and the vulnerability of some species have led to increased use of non-lethal methodologies for conservation purposes. In the present work we have compared the delta(13)C and delta(15)N isotopic signals of muscle and scales of three different fish species in order to test fish-scale sampling as a non-lethal technique in fish trophodynamics. A positive correlation was found between muscle and scales in Argyrosomus regius and Xyrichtys novacula, while Dentex dentex showed no correlation due to the small length range of this species. The isotopic offset (Delta(13)C and Delta(15)N) between muscle and scales was significantly different among species (analysis of variance (ANOVA), p < 0.001) with Tukey's post-hoc HSD indicating a tissue offset difference (p < 0.001) for both stable isotopes in all species, except for Delta(13)C between A. regius and X. novacula and for Delta(15)N between D. dentex and X. novacula (p > 0.05). Mean delta(13)C and delta(15)N values between species showed significant differences (paired t-test, p < 0.01) between muscle and scale with an enrichment for delta(13)C and a depletion for delta(15)N. Spatial differences were found in the Delta(13)C of X. novacula between the studied locations, while no differences were found for Delta(15)N, indicating that non-geographical differences should be considered in the application of scales instead of muscle for (15)N, while for (13)C differences in the geographical isotopic offset should be considered.

Stable isotopes and metal contamination in caged marine mussel Mytilus galloprovincialis

Metal concentrations and isotopic composition were measured in different tissues of the mussel Mytilus galloprovincialis in waters of the Balearic Islands (Western Mediterranean) in order to assess pollution levels. The isotopic composition was correlated with lead, cadmium, selenium and nickel obtained from the digestive gland and foot of the mussels. Significant negative correlations were found between cadmium, selenium and zinc and the mussel foot, mainly for (13)C. Significant correlations were also found between lead and cadmium and the digestive gland. Pearson correlations indicated that the (13)C isotopic signal in foot is a good proxy for the concentration of metals such as lead, cadmium, selenium and zinc. Similarly, (15)N isotopic signatures in the digestive gland reflected the lead and cadmium concentration.

Assessment of environmental pollution at Balearic Islands applying oxidative stress biomarkers in the mussel Mytilus galloprovincialis

The antioxidant enzyme response of the mussel Mytilus galloprovincialis to different degree of pollution was investigated. Antioxidant enzyme activities - catalase (CAT), glutathione peroxidase (GSH-PX), glutathione reductase (GR), superoxide dismutase (SOD) - and malondialdehyde (MDA) concentration were measured in gills and digestive glands of mussels. Mussels from the same origin were transplanted along the Balearic coastal waters in eight stations characterized by a different degree of contamination and human impacts. Antioxidant enzyme activities showed an adaptive response to increase the activities in the more polluted areas. CAT, GR and SOD in gills and CAT and GR in digestive gland presented significant differences between polluted and non-polluted stations. No significant differences were observed in MDA concentration indicating that the antioxidant response is capable to avoid the lipid peroxidation. The use of biomarkers such as CAT and GR in gills and digestive glands of the mussel M. galloprovincialis is a good tool to categorize differences between polluted and non-polluted areas.

Organic compounds temporal trends at some invertebrate species from the Balearics, Western Mediterranean

Concentrations of persistent organic pollutants (POPs) such as hexachlorobenzene (HCB), dichlore diphenyl trichloretane (DDT), polychlorinated biphenyls (PCBs), and gamma-hexachlorocyclohexane (gamma-HCH or lindane) were determined in tissue of marine benthic invertebrates such as Mytilus galloprovincialis, Chamelea gallina, Venus verrucosa, Lithophaga lithophaga and Paracentrotus lividus. Species were selected due to their habitat, trophic level, feeding behaviour and their consumption. Invertebrate species were systematically sampled from December 1996 to December 2005 from several sites along the Balearic Islands. The highest concentrations of PCBs (785ng/g lipid) were found in M. galloprovincialis while the lowest concentrations were found in the sea-urchin P. lividus (193ng/g lipid). Among the 7 PCB quantified congeners the higher values are mainly obtained for CB138 and CB153. All bivalves presented higher PCBs contents than the sea-urchin P. lividus are possibly linked with the bioaccumulation process of POPs throughout the food web and to differential detoxifying mechanisms. The concentration of SigmaDDT exceeds that of HCB and gamma-HCH at all species and sampling stations. DDT concentrations ranged from 0.4ng/g ww at the bivalve C. gallina in 2002, to values of 15.8ng/g ww at the bivalve L. lithophaga in 1998. The values obtained for the organic compounds (HCH, HCB, PCBs, DDT) depend upon the place and year of sampling and are compared to values found by other authors for the mussel M. galloprovincialis in other Mediterranean areas. gamma-HCH and HCB were found in lower concentrations than the other POPs.

Psychophysical and electrophysiologic support for a left hemisphere temporal processing advantage

OBJECTIVE

The objective of this study was to investigate cerebral asymmetries for the detection of brief temporal events in a group of 22 dextrals using psychophysical measures.

BACKGROUND

By combining electrophysiologic and psychophysical measures, it should be possible to demonstrate that the right ear advantage reported in previous studies is the result of a left hemisphere temporal processing advantage rather than a rightward attentional bias.

METHOD

Bursts of white noise lasting 300 milliseconds were delivered unilaterally to the participants' ears. Half of the stimuli contained a gap lasting either 4 or 6 milliseconds. Participants indicated whether or not the noise burst contained a gap. Asymmetries in alpha and beta activity at left and right temporal lobe sites were measured during the task.

RESULTS

The psychophysical data confirmed previous reports of faster response times (RTs) and lower levels of error for the right ear (RE). There was no asymmetry in alpha activity between the left and right temporal lobes; however, there was a higher level of beta activity in the left temporal lobe.

CONCLUSIONS

The electrophysiological data suggest that the perceptual asymmetry is not the result of a nonspecific rightward attentional bias but that of a left hemisphere specialization for the detection of brief temporal events. The relation between atypical temporal processing asymmetries and developmental learning disorders is discussed.