Genome-wide promoter assembly in E. coli measured at single-base resolution

When detected at single-base-pair resolution, the genome-wide location, occupancy level, and structural organization of DNA-binding proteins provide mechanistic insights into genome regulation. Here we use ChIP-exo to provide a near-base-pair resolution view of the epigenomic organization of the Escherichia coli transcription machinery and nucleoid structural proteins at the time when cells are growing exponentially and upon rapid reprogramming (acute heat shock). We examined the site specificity of three sigma factors (RpoD/σ⁷⁰, RpoH/σ³², and RpoN/σ⁵⁴), RNA polymerase (RNAP or RpoA, -B, -C), and two nucleoid proteins (Fis and IHF). We suggest that DNA shape at the flanks of cognate motifs helps drive site specificity. We find that although RNAP and sigma factors occupy active cognate promoters, RpoH and RpoN can occupy quiescent promoters without the presence of RNAP. Thus, promoter-bound sigma factors can be triggered to recruit RNAP by a mechanism that is distinct from an obligatory cycle of free sigma binding RNAP followed by promoter binding. These findings add new dimensions to how sigma factors achieve promoter specificity through DNA sequence and shape, and further define mechanistic steps in regulated genome-wide assembly of RNAP at promoters in E. coli.

RAD52: Paradigm of Synthetic Lethality and New Developments

DNA double-strand breaks and inter-strand cross-links are the most harmful types of DNA damage that cause genomic instability that lead to cancer development. The highest fidelity pathway for repairing damaged double-stranded DNA is termed Homologous recombination (HR). Rad52 is one of the key HR proteins in eukaryotes. Although it is critical for most DNA repair and recombination events in yeast, knockouts of mammalian RAD52 lack any discernable phenotypes. As a consequence, mammalian RAD52 has been long overlooked. That is changing now, as recent work has shown RAD52 to be critical for backup DNA repair pathways in HR-deficient cancer cells. Novel findings have shed light on RAD52's biochemical activities. RAD52 promotes DNA pairing (D-loop formation), single-strand DNA and DNA:RNA annealing, and inverse strand exchange. These activities contribute to its multiple roles in DNA damage repair including HR, single-strand annealing, break-induced replication, and RNA-mediated repair of DNA. The contributions of RAD52 that are essential to the viability of HR-deficient cancer cells are currently under investigation. These new findings make RAD52 an attractive target for the development of anti-cancer therapies against BRCA-deficient cancers.

Transcarotid Arterial Revascularization Adoption Should not Be Hindered by a Concern for a Long Learning Curve

BACKGROUND

Transcarotid arterial revascularization (TCAR) offers a novel technique for carotid artery stenting (CAS) that provides flow reversal in the carotid artery and avoids aortic arch manipulation, thus, potentially lowering ipsilateral and contralateral periprocedural stroke rates. As a new technology, adoption may be limited by concern for learning a new technique. This study seeks to examine the number of cases needed for a surgeon to reach technical proficiency.

METHODS

Retrospective analysis was performed using a prospectively collected database of all TCAR procedures performed in a tertiary health care system between 2016 and 2020. Patient demographics and anatomic characteristics were collected. Intraoperative variables and perioperative outcomes were examined. These variables were collated into groups for the first 4 procedures, procedures 5-8, and after 8. Independent Samples t test, 1-way ANOVA, and logarithmic regression were used to statistically analyze the data.

RESULTS

One-hundred and eighty-seven TCARs were performed by 14 surgeons. One hundred and twenty-two (65%) were male, 59 (32%) were older than 75 years, and 83 (44%) were symptomatic. The most common indications were high-lesions in 87 patients (47%) and recurrent stenosis after CEA in 37 patients (20%). Significant differences were found between the first and second groups of 4 cases when comparing mean operative time (71 vs. 58 min; P = 0.001) and flow reversal time (10.8 vs. 7.9 min; P= 0.004). similar significant differences were found between the first and third groups of 4 cases but not between the second and third groups. There was a reduction in contrast usage and fluoroscopy time after the first 4 cases, however, this did not reach statistical significance. There was no ipsilateral perioperative strokes. One patient had a contralateral stroke on postoperative day 2 due to intracranial atherosclerosis, and there was one perioperative mortality that occurred on postoperative day 3 after discharge.

CONCLUSIONS

Procedural and flow reversal times significantly shorten after 4 TCAR procedures are performed. Other metrics, such as fluoroscopy time and contrast usage, are also decreased. Complications, in general, are minimal. Proficiency in TCAR, as measured by these metrics, is met after performing only 4 procedures.

A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells

Antibodies offer a powerful means to interrogate specific proteins in a complex milieu. However, antibody availability and reliability can be problematic, whereas epitope tagging can be impractical in many cases. To address these limitations, the Protein Capture Reagents Program (PCRP) generated over a thousand renewable monoclonal antibodies (mAbs) against human presumptive chromatin proteins. However, these reagents have not been widely field-tested. We therefore performed a screen to test their ability to enrich genomic regions via chromatin immunoprecipitation (ChIP) and a variety of orthogonal assays. Eight hundred eighty-seven unique antibodies against 681 unique human transcription factors (TFs) were assayed by ultra-high-resolution ChIP-exo/seq, generating approximately 1200 ChIP-exo data sets, primarily in a single pass in one cell type (K562). Subsets of PCRP mAbs were further tested in ChIP-seq, CUT&RUN, STORM super-resolution microscopy, immunoblots, and protein binding microarray (PBM) experiments. About 5% of the tested antibodies displayed high-confidence target (i.e., cognate antigen) enrichment across at least one assay and are strong candidates for additional validation. An additional 34% produced ChIP-exo data that were distinct from background and thus warrant further testing. The remaining 61% were not substantially different from background, and likely require consideration of a much broader survey of cell types and/or assay optimizations. We show and discuss the metrics and challenges to antibody validation in chromatin-based assays.

A high-resolution protein architecture of the budding yeast genome

The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is not well defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP-exo/seq)1,2 to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons and transcription by RNA polymerase (Pol) I, II and III. Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. We find that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex. Positioned insulators protect core promoters from upstream events. A small fraction of promoters evolved an architecture for inducibility, whereby sequence-specific transcription factors (ssTFs) create a nucleosome-depleted region (NDR) that is distinct from an NFR. We describe structural interactions among ssTFs, their cognate cofactors and the genome. These interactions include the nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator and SWI-SNF. Surprisingly, we do not detect interactions between ssTFs and TFIID, suggesting that such interactions do not stably occur. Our model for gene induction involves ssTFs, cofactors and general factors such as TBP and TFIIB, but not TFIID. By contrast, constitutive transcription involves TFIID but not ssTFs engaged with their cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.

Systematic review and meta-analysis of endovascular interventions for Stanford type A aortic dissection

OBJECTIVE

The standard surgical approach to Stanford type A aortic dissection is open repair. However, up to one in four patients will be declined surgery because of prohibitive risk. Patients who are treated nonoperatively have an unacceptably high mortality. Endovascular repair of the ascending aorta is emerging as an alternative treatment for a select group of patients. The reported rates of technical success, mortality, stroke, and reintervention have varied. The objective of the study was to systematically report outcomes for acute type A dissections repaired using an endovascular approach.

METHODS

The systematic review and meta-analysis was conducted in accordance with the PRISMA (preferred reporting items for systematic reviews and meta-analyses) guidelines. We performed online literature database searches through April 2020. The demographic and procedural characteristics of the individual studies were tabulated. Data on technical success, short-term mortality, stroke, and reintervention were extracted and underwent meta-analysis using a random effects model.

RESULTS

Fourteen studies with 80 cases of aortic dissection (55 acute and 25 subacute) were included in the final analysis. A wide variation was found in technique and device design across the studies. The outcomes rates were estimated at 17% (95% confidence interval [CI], 10%-26%) for mortality, 15% (95% CI, 8%-23%) for technical failure, 11% (95% CI, 6%-19%) for stroke and 18% (95% CI, 9%-31%) for reintervention. The mean Downs and Black quality assessment score was 13.9 ± 3.2.

CONCLUSION

The technique for endovascular repair of type A aortic dissection is feasible and reproducible. The results of our meta-analysis demonstrate an acceptable safety profile for inoperable patients who otherwise would have an extremely poor prognosis. Data from clinical trials are required before the technique can be introduced into routine clinical practice.

Acute stress drives global repression through two independent RNA polymerase II stalling events in Saccharomyces

In multicellular eukaryotes, RNA polymerase (Pol) II pauses transcription ~30-50 bp after initiation. While the budding yeast Saccharomyces has its transcription mechanisms mostly conserved with other eukaryotes, it appears to lack this fundamental promoter-proximal pausing. However, we now report that nearly all yeast genes, including constitutive and inducible genes, manifest two distinct transcriptional stall sites that are brought on by acute environmental signaling (e.g., peroxide stress). Pol II first stalls at the pre-initiation stage before promoter clearance, but after DNA melting and factor acquisition, and may involve inhibited dephosphorylation. The second stall occurs at the +2 nucleosome. It acquires most, but not all, elongation factor interactions. Its regulation may include Bur1/Spt4/5. Our results suggest that a double Pol II stall is a mechanism to downregulate essentially all genes in concert.

Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes

The ChIP-exo assay precisely delineates protein-DNA crosslinking patterns by combining chromatin immunoprecipitation with 5' to 3' exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects crosslinking efficiencies. Therefore, the spatial organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between its subunits. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of coordinately bound regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. By producing consistent measurements of protein-DNA crosslinking strengths across multiple proteins, our approach enables characterization of relative spatial organization within a regulatory complex. Applying our approach to collections of ChIP-exo data, we demonstrate that it can recover aspects of regulatory complex spatial organization at yeast ribosomal protein genes and yeast tRNA genes. We also demonstrate the ability to quantify changes in protein-DNA complex organization across conditions by applying our approach to analyze Drosophila Pol II transcriptional components. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of spatial organization within protein-DNA complexes.

Vegetation and terrain drivers of infiltration depth along a semiarid hillslope

An improved understanding of the drivers controlling infiltration patterns in semiarid regions is of key importance, as they have important implications for ecosystem productivity, retention of resources and the restoration of degraded areas. The infiltration depth variability (ΔInf) in vegetation patches at the hillslope scale can be driven by different factors along the hillslope. Here we investigate the effects of vegetation and terrain attributes under hypothesis that these attributes exert a major control in ΔInf within the patches. We characterise the ΔInf within vegetation patches at a semiarid hillslope located at the Jornada Experimental Range at dry antecedent conditions preceding two winter frontal rainfall events. We measured these events that are typical during winter conditions, and are characterised by low intensity (0.67 and 4.48 mm h^-1) and a total rainfall of 10.4 and 4.6 mm. High precision geo-referenced wetting front depth measurements were taken at various locations within the vegetation patches using differential GPS. Vegetation and terrain attributes were analysed to explain the ΔInf among the vegetation patches. The infiltration depths in the periphery of the patches were in general considerably deeper than those in the centre. The observations suggest that the upslope margin of the patches received additional water in the form of runon from upslope adjacent bare soil. Patch orientation with regard to the slope dictated the effect of the rest of the patch attributes and the distance to the hillslope crest on ΔInf. We found that primarily patch orientation, followed by shape and size modulate lateral surface water transport through their effects on overland flow paths and water retention; something that would be obscured under more simplistic characterisations based on bare versus uniform vegetated soil discrimination.

Genome-wide determinants of sequence-specific DNA binding of general regulatory factors

General regulatory factors (GRFs), such as Reb1, Abf1, Rap1, Mcm1, and Cbf1, positionally organize yeast chromatin through interactions with a core consensus DNA sequence. It is assumed that sequence recognition via direct base readout suffices for specificity and that spurious nonfunctional sites are rendered inaccessible by chromatin. We tested these assumptions through genome-wide mapping of GRFs in vivo and in purified biochemical systems at near–base pair (bp) resolution using several ChIP-exo–based assays. We find that computationally predicted DNA shape features (e.g., minor groove width, helix twist, base roll, and propeller twist) that are not defined by a unique consensus sequence are embedded in the nonunique portions of GRF motifs and contribute critically to sequence-specific binding. This dual source specificity occurs at GRF sites in promoter regions where chromatin organization starts. Outside of promoter regions, strong consensus sites lack the shape component and consequently lack an intrinsic ability to bind cognate GRFs, without regard to influences from chromatin. However, sites having a weak consensus and low intrinsic affinity do exist in these regions but are rendered inaccessible in a chromatin environment. Thus, GRF site-specificity is achieved through integration of favorable DNA sequence and shape readouts in promoter regions and by chromatin-based exclusion from fortuitous weak sites within gene bodies. This study further revealed a severe G/C nucleotide cross-linking selectivity inherent in all formaldehyde-based ChIP assays, which includes ChIP-seq. However, for most tested proteins, G/C selectivity did not appreciably affect binding site detection, although it does place limits on the quantitativeness of occupancy levels.

Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock

Gene expression is controlled by a variety of proteins that interact with the genome. Their precise organization and mechanism of action at every promoter remains to be worked out. To better understand the physical interplay among genome-interacting proteins, we examined the temporal binding of a functionally diverse subset of these proteins: nucleosomes (H3), H2AZ (Htz1), SWR (Swr1), RSC (Rsc1, Rsc3, Rsc58, Rsc6, Rsc9, Sth1), SAGA (Spt3, Spt7, Ubp8, Sgf11), Hsf1, TFIID (Spt15/TBP and Taf1), TFIIB (Sua7), TFIIH (Ssl2), FACT (Spt16), Pol II (Rpb3), and Pol II carboxyl-terminal domain (CTD) phosphorylation at serines 2, 5, and 7. They were examined under normal and acute heat shock conditions, using the ultrahigh resolution genome-wide ChIP-exo assay in Saccharomyces cerevisiae Our findings reveal a precise positional organization of proteins bound at most genes, some of which rapidly reorganize within minutes of heat shock. This includes more precise positional transitions of Pol II CTD phosphorylation along the 5' ends of genes than previously seen. Reorganization upon heat shock includes colocalization of SAGA with promoter-bound Hsf1, a change in RSC subunit enrichment from gene bodies to promoters, and Pol II accumulation within promoter/+1 nucleosome regions. Most of these events are widespread and not necessarily coupled to changes in gene expression. Together, these findings reveal protein-genome interactions that are robustly reprogrammed in precise and uniform ways far beyond what is elicited by changes in gene expression.

The expression of an exogenous ACC deaminase by the endophyte Serratia grimesii BXF1 promotes the early nodulation and growth of common bean

Ethylene acts as an inhibitor of the nodulation process of leguminous plants. However, some bacteria can decrease deleterious ethylene levels by the action of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase which degrades ACC, the ethylene precursor in all higher plants. Co-inoculation of rhizobia with endophytes enhances the rhizobial symbiotic efficiency with legumes, improving both nodulation and nitrogen fixation. However, not much is understood about the mechanisms employed by these endophytic bacteria. In this regard, the role of ACC deaminase from endophytic strains in assisting rhizobia in this process has yet to be confirmed. In this study, the role of ACC deaminase in an endophyte's ability to increase Rhizobium tropici nodulation of common bean was evaluated. To assess the effect of ACC deaminase in an endophyte's ability to promote rhizobial nodulation, the endophyte Serratia grimesii BXF1, which does not encode ACC deaminase, was transformed with an exogenous acdS gene. The results obtained indicate that the ACC deaminase-overexpressing transformant strain increased common bean growth, and enhanced the nodulation abilities of R. tropici CIAT899, in both cases compared to the wild-type non-transformed strain. Furthermore, plant inoculation with the ACC deaminase-overproducing strain led to an increased level of plant protection against a seed-borne pathogen.

SIGNIFICANCE AND IMPACT OF THE STUDY

In this work, we studied the effect of ACC deaminase production by the bacterial endophyte Serratia grimesi BXF1, and its impact on the nodulation process of common bean. The results obtained indicate that ACC deaminase is an asset to the synergetic interaction between rhizobia and the endophyte, positively contributing to the overall legume-rhizobia symbiosis by regulating inhibitory ethylene levels that might otherwise inhibit nodulation and overall plant growth. The use of rhizobia together with an ACC deaminase-producing endophyte is, therefore, an important strategy for the development of new bacterial inoculants with increased performance.

RAD54 N-terminal domain is a DNA sensor that couples ATP hydrolysis with branch migration of Holliday junctions

In eukaryotes, RAD54 catalyzes branch migration (BM) of Holliday junctions, a basic process during DNA repair, replication, and recombination. RAD54 also stimulates RAD51 recombinase and has other activities. Here, we investigate the structural determinants for different RAD54 activities. We find that the RAD54 N-terminal domain (NTD) is responsible for initiation of BM through two coupled, but distinct steps; specific binding to Holliday junctions and RAD54 oligomerization. Furthermore, we find that the RAD54 oligomeric state can be controlled by NTD phosphorylation at S49, a CDK2 consensus site, which inhibits RAD54 oligomerization and, consequently, BM. Importantly, the effect of phosphorylation on RAD54 oligomerization is specific for BM, as it does not affect stimulation of RAD51 recombinase by RAD54. Thus, the transition of the oligomeric states provides an important control of the biological functions of RAD54 and, likely, other multifunctional proteins.

Chemical characterization of diesel and hydrotreated vegetable oil (HVO) soot after reactive gas probing using diffuse reflectance FTIR spectroscopy (DRIFTS)

A chemical characterization of diesel and hydrotreated vegetable oil (HVO) soot has been developed using diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) before and after the reaction with different probe gases. Samples were generated under combustion conditions corresponding to an urban operation mode of a diesel engine and were reacted with probe gas-phase molecules in a Knudsen flow reactor. Specifically, NH₂OH, O₃ and NO₂ were used as reactants (probes) and selected according to their reactivities towards specific functional groups on the sample surface. Samples of previously ground soot were diluted with KBr and were introduced in a DRIFTS accessory. A comparison between unreacted and reacted soot samples was made in order to establish chemical changes on the soot surface upon reaction. It was concluded that the interface of diesel and HVO soot before reaction mainly consists polycyclic aromatic hydrocarbons, nitro and carbonyl compounds, as well as ether functionalities. The main difference between both soot samples was observed in the band of the C=O groups that in diesel soot was observed at 1719 cm^-1 but not in HVO soot. After reaction with probe gases, it was found that nitro compounds remain on the soot surface, that the degree of unsaturation decreases for reacted samples, and that new spectral bands such as hydroxyl groups are observed.

Molecular Characterization of the Gas-Particle Interface of Soot Sampled from a Diesel Engine Using a Titration Method

Surface functional groups of two different types of combustion aerosols, a conventional diesel (EN 590) and a hydrotreated vegetable oil (HVO) soot, have been investigated using heterogeneous chemistry (i.e., gas-particle surface reactions). A commercial sample of amorphous carbon (Printex XE2-B) was analyzed as a reference substrate. A Knudsen flow reactor was used to carry out the experiments under molecular flow conditions. The selected gases for the titration experiments were: N(CH3)3 for the identification of acidic sites, NH2OH for the presence of carbonyl groups, CF3COOH and HCl for basic sites of different strength, and O3 and NO2 for reducing groups. Reactivity with N(CH3)3 indicates a lower density of acidic functionalities for Printex XE2-B in relation to diesel and HVO soot. Results for NH2OH experiments indicates that commercial amorphous carbon exhibits a lower abundance of available carbonyl groups at the interface compared to the results from diesel and HVO soot, the latter being the one with the largest abundance of carbonyl functions. Reactions with acids indicate the presence of weak basic oxides on the particle surface that preferentially interact with the strong acid CF3COOH. Finally, reactions with O3 and NO2 reveal that diesel and especially HVO have a significantly higher reactivity with both oxidizers compared to that of Printex XE2-B because they have more reducing sites by roughly a factor of 10 and 30, respectively. The kinetics of titration reactions have also been investigated.

The use of heterogeneous chemistry for the characterization of functional groups at the gas/particle interface of soot from a diesel engine at a particular running condition

Two gases, O3 and NO2, were selected to probe the surface of a diesel fuel combustion aerosol sample, diesel soot, and amorphous carbon nanoparticles (PRINTEX XE2-B) using heterogeneous (i.e., gas-surface reactions). The gas uptake to saturation of the probes was measured under molecular flow conditions using a Knudsen flow reactor in order to quantify and characterize surface functional groups. Specifically, O3 and NO2 are used for the titration of oxidizable groups. Diesel soot samples interacted with the probe gases to various extents which points to the coexistence of different functional groups on the same aerosol surface such as reduced groups. The carbonaceous particles displayed significant differences: PRINTEX XE2-B amorphous carbon had a significantly lower surface functional group density of both total and strongly reducing groups despite its significantly larger internal surface area, compared to diesel soot. The uptake kinetics of the gas-phase probe molecules (uptake probabilities) were also measured in order to obtain further information on the reactivity of emitted soot aerosols in order to enable the potential prediction of health effects.

Effusive molecular beam-sampled Knudsen flow reactor coupled to vacuum ultraviolet single photon ionization mass spectrometry using an external free radical source

A new apparatus using vacuum ultraviolet single photon ionization mass spectrometry (VUV SPIMS) of an effusive molecular beam emanating from a Knudsen flow reactor is described. It was designed to study free radical-molecule kinetics over a significant temperature range (300-630 K). Its salient features are: (1) external free radical source, (2) counterpropagating molecular beam and diffuse VUV photon beam meeting in a crossed-beam ion source of a quadrupole mass spectrometer with perpendicular ion extraction, (3) analog detection of the photocurrent of the free radical molecular cation, and (4) possibility of detecting both free radicals and closed shell species in the same apparatus and under identical reaction conditions owing to the presence of photoelectrons generated by the photoelectric effect of the used VUV-photons. The measured thermal molecular beam-to-background ratio was 6.35 ± 0.39 for Ar and 10.86 ± 1.59 for i-C4H10 at 300 K, a factor of 2.52 and 1.50 smaller, respectively, than predicted from basic gas-dynamic considerations. Operating parameters as well as the performance of key elements of the instrument are presented and discussed. Coupled to an external free radical source a steady-state specific exit flow of 1.6 × 10(11) and 5.0 × 10(11) molecule s(-1) cm(-3) of C2H5(●) (ethyl) and t-C4H9(●) (t-butyl) free radicals have been detected using VUV SPIMS at their molecular ion m/z 29 and 57, respectively, at 300 K.

Distinct long-term neurocognitive outcomes after equipotent sevoflurane or isoflurane anaesthesia in immature rats

BACKGROUND

Many anaesthetics when given to young animals cause cell death and learning deficits that persist until much later in life. Recent attempts to compare the relative safety or toxicity between different agents have not adequately controlled for the relative dose of anaesthetic given, thereby making direct comparisons difficult.

METHODS

Isoflurane or sevoflurane were given at 1 minimum alveolar concentration (MAC) for 4 h to postnatal day 7 (P7) rat pups. Beginning at P75 these animals underwent fear conditioning and at P83 Morris water maze testing to assess working memory, short-term memory and early long-term memory using delays of 1 min, 1 h, and 4 h.

RESULTS

No difference between groups was seen in fear conditioning experiments. Morris water maze learning was equivalent between groups, and no difference was seen in working memory. Sevoflurane-treated animals had a deficit in early long-term memory, and isoflurane-treated animals had a deficit in both short-term and early long-term memory.

CONCLUSIONS

Both isoflurane and sevoflurane delivered at 1 MAC for 4 h to immature rats caused a deficit in long-term memory. Isoflurane also caused a deficit in short-term memory. Isoflurane might be more detrimental than sevoflurane in very young animals.

Characterization and cytotoxic activity of sulfated derivatives of polysaccharides from Agaricus brasiliensis

Agaricus brasiliensis cell-wall polysaccharides isolated from fruiting body (FR) and mycelium (MI) and their respective sulfated derivatives (FR-S and MI-S) were chemically characterized using elemental analysis, TLC, FT-IR, NMR, HPLC, and thermal analysis. Cytotoxic activity was evaluated against A549 tumor cells by MTT and sulforhodamine assays. The average molecular weight (Mw) of FR and MI was estimated to be 609 and 310 kDa, respectively. FR-S (127 kDa) and MI-S (86 kDa) had lower Mw, probably due to hydrolysis occurring during the sulfation reaction. FR-S and MI-S presented ~14% sulfur content in elemental analysis. Sulfation of samples was characterized by the appearance of two new absorption bands at 1253 and 810 cm(-1) in the infrared spectra, related to S=O and C-S-O sulfate groups, respectively. Through (1)H and (13)C NMR analysis FR-S was characterized as a (1→6)-(1→3)-β-D-glucan fully sulfated at C-4 and C-6 terminal and partially sulfated at C-6 of (1→3)-β-D-glucan moiety. MI-S was shown to be a (1→3)-β-D-gluco-(1→2)-β-D-mannan, partially sulfated at C-2, C-3, C-4, and C-6, and fully sulfated at C-6 of the terminal residues. The combination of high degree of sulfation and low molecular weight was correlated with the increased cytotoxic activity (48 h of treatment) of both FR-S (EC₅₀=605.6 μg/mL) and MI-S (EC₅₀=342.1 μg/mL) compared to the non-sulfated polysaccharides FR and MI (EC₅₀>1500 μg/mL).

Polarity and bypass of DNA heterology during branch migration of Holliday junctions by human RAD54, BLM, and RECQ1 proteins

Several proteins have been shown to catalyze branch migration (BM) of the Holliday junction, a key intermediate in DNA repair and recombination. Here, using joint molecules made by human RAD51 or Escherichia coli RecA, we find that the polarity of the displaced ssDNA strand of the joint molecules defines the polarity of BM of RAD54, BLM, RECQ1, and RuvAB. Our results demonstrate that RAD54, BLM, and RECQ1 promote BM preferentially in the 3'→5' direction, whereas RuvAB drives it in the 5'→3' direction relative to the displaced ssDNA strand. Our data indicate that the helicase activity of BM proteins does not play a role in the heterology bypass. Thus, RAD54 that lacks helicase activity is more efficient in DNA heterology bypass than BLM or REQ1 helicases. Furthermore, we demonstrate that the BLM helicase and BM activities require different protein stoichiometries, indicating that different complexes, monomers and multimers, respectively, are responsible for these two activities. These results define BM as a mechanistically distinct activity of DNA translocating proteins, which may serve an important function in DNA repair and recombination.

Cooperation of RAD51 and RAD54 in regression of a model replication fork

DNA lesions cause stalling of DNA replication forks, which can be lethal for the cell. Homologous recombination (HR) plays an important role in DNA lesion bypass. It is thought that Rad51, a key protein of HR, contributes to the DNA lesion bypass through its DNA strand invasion activity. Here, using model stalled replication forks we found that RAD51 and RAD54 by acting together can promote DNA lesion bypass in vitro through the ‘template-strand switch’ mechanism. This mechanism involves replication fork regression into a Holliday junction (‘chicken foot structure’), DNA synthesis using the nascent lagging DNA strand as a template and fork restoration. Our results demonstrate that RAD54 can catalyze both regression and restoration of model replication forks through its branch migration activity, but shows strong bias toward fork restoration. We find that RAD51 modulates this reaction; by inhibiting fork restoration and stimulating fork regression it promotes accumulation of the chicken foot structure, which we show is essential for DNA lesion bypass by DNA polymerase in vitro. These results indicate that RAD51 in cooperation with RAD54 may have a new role in DNA lesion bypass that is distinct from DNA strand invasion.

Rad54, the motor of homologous recombination

Homologous recombination (HR) performs crucial functions including DNA repair, segregation of homologous chromosomes, propagation of genetic diversity, and maintenance of telomeres. HR is responsible for the repair of DNA double-strand breaks and DNA interstrand cross-links. The process of HR is initiated at the site of DNA breaks and gaps and involves a search for homologous sequences promoted by Rad51 and auxiliary proteins followed by the subsequent invasion of broken DNA ends into the homologous duplex DNA that then serves as a template for repair. The invasion produces a cross-stranded structure, known as the Holliday junction. Here, we describe the properties of Rad54, an important and versatile HR protein that is evolutionarily conserved in eukaryotes. Rad54 is a motor protein that translocates along dsDNA and performs several important functions in HR. The current review focuses on the recently identified Rad54 activities which contribute to the late phase of HR, especially the branch migration of Holliday junctions.

Analyzing the branch migration activities of eukaryotic proteins

The Holliday junction is a key intermediate of DNA repair, recombination, and replication. Branch migration of Holliday junctions is a process in which one DNA strand is progressively exchanged for another. Branch migration of Holliday junctions may serve several important functions such as affecting the length of genetic information transferred between homologous chromosomes during meiosis, restarting stalled replication forks, and ensuring the faithful repair of double strand DNA breaks by homologous recombination. Several proteins that promote branch migration of Holliday junctions have been recently identified. These proteins, which function during DNA replication and repair, possess the ability to bind Holliday junctions and other branched DNA structures and drive their branch migration by translocating along DNA in an ATPase-dependent manner. Here, we describe methods employing a wide range of DNA substrates for studying proteins that catalyze branch migration of Holliday junctions.

A unitary anesthetic binding site at high resolution

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA(A) receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA(A) receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show that apoferritin also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA(A) receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.

The use of heterogeneous chemistry for the characterization of functional groups at the gas/particle interface of soot and TiO2 nanoparticles

Six gases [N(CH(3))(3), NH(2)OH, CF(3)COOH, HCl, NO(2) and O(3)] were selected to probe the surface of seven different types of combustion aerosol samples (amorphous carbon, flame soot) and three types of TiO(2) nanoparticles using heterogeneous, i.e. gas-surface reactions. The gas uptake to saturation of the probes was measured under molecular flow conditions in a Knudsen flow reactor and expressed as a density of surface functional groups on a particular aerosol, namely acidic (carboxylic) and basic (conjugated oxides such as pyrone, N-heterocycle and amine) sites, carbonyl (R(1)-C(O)-R(2)) and oxidizable (olefinic, -OH) groups. The limit of detection was generally well below 1% of a formal monolayer of adsorbed probe gas. With few exceptions most investigated aerosol samples interacted with all probe gases to various extents which points to the coexistence of different functional groups on the same aerosol surface such as acidic and basic groups. Generally, the carbonaceous particles displayed significant differences in surface group density: Printex 60 amorphous carbon had the lowest density of surface functional groups throughout, whereas Diesel soot recovered from a Diesel particulate filter had the largest. The presence of basic oxides on carbonaceous aerosol particles was inferred from the ratio of uptakes of CF(3)COOH and HCl owing to the larger stability of the acetate compared to the chloride counterion in the resulting pyrylium salt. Both soots generated from a rich and a lean hexane diffusion flame had a large density of oxidizable groups similar to amorphous carbon FS 101. TiO(2) 15 had the lowest density of functional groups studied for all probe gases among the three TiO(2) nanoparticles despite the smallest size of its primary particles. The technique used enabled the measurement of the uptake probability of the probe gases on the various supported aerosol samples. The initial uptake probability, gamma(0), of the probe gas onto the supported nanoparticles differed significantly among the various investigated aerosol samples but was roughly correlated with the density of surface groups, as expected.

Rad51 protein stimulates the branch migration activity of Rad54 protein

The Rad51 and Rad54 proteins play important roles during homologous recombination in eukaryotes. Rad51 forms a nucleoprotein filament on single-stranded DNA and performs the initial steps of double strand break repair. Rad54 belongs to the Swi2/Snf2 family of ATP-dependent DNA translocases. We previously showed that Rad54 promotes branch migration of Holliday junctions. Here we find that human Rad51 (hRad51) significantly stimulates the branch migration activity of hRad54. The stimulation appears to be evolutionarily conserved, as yeast Rad51 also stimulates the branch migration activity of yeast Rad54. We further investigated the mechanism of this stimulation. Our results demonstrate that the stimulation of hRad54-promoted branch migration by hRad51 is driven by specific protein-protein interactions, and the active form of the hRad51 filament is more stimulatory than the inactive one. The current results support the hypothesis that the hRad51 conformation state has a strong effect on interaction with hRad54 and ultimately on the function of hRad54 in homologous recombination.

Interactions of human rad54 protein with branched DNA molecules

The Rad54 protein plays an important role during homologous recombination in eukaryotes. The protein belongs to the Swi2/Snf2 family of ATP-dependent DNA translocases. We previously showed that yeast and human Rad54 (hRad54) specifically bind to Holliday junctions and promote branch migration. Here we examined the minimal DNA structural requirements for optimal hRad54 ATPase and branch migration activity. Although a 12-bp double-stranded DNA region of branched DNA is sufficient to induce ATPase activity, the minimal substrate that gave rise to optimal stimulation of the ATP hydrolysis rate consisted of two short double-stranded DNA arms, 15 bp each, combined with a 45-nucleotide single-stranded DNA branch. We showed that hRad54 binds preferentially to the open and not to the stacked conformation of branched DNA. Stoichiometric titration of hRad54 revealed formation of two types of hRad54 complexes with branched DNA substrates. The first of them, a dimer, is responsible for the ATPase activity of the protein. However, branch migration activity requires a significantly higher stoichiometry of hRad54, approximately 10 +/- 2 protein monomers/DNA molecule. This pleomorphism of hRad54 in formation of oligomeric complexes with DNA may correspond to multiple functions of the protein in homologous recombination.

Photoactive analogues of the haloether anesthetics provide high-resolution features from low-affinity interactions

The difficulty in obtaining binding target and site information for low-affinity drugs, like the inhaled anesthetics, has limited identification of their molecular effectors. Because such information can be provided by photoactive analogues, we designed, synthesized, and characterized a novel diazirnyl haloether that closely mimics isoflurane, the most widely used clinical general anesthetic. This compound, H-diaziflurane, is a nontoxic, potent anesthetic that potentiates GABA-gated ion channels in primary cultures of hippocampal neurons. Calorimetric and structural characterizations show that H-diaziflurane binds a model anesthetic host protein with similar energetics as isoflurane and forms photoadducts with residues lining the isoflurane binding site. H-diaziflurane will be immediately useful for identifying targets and sites important for the molecular pharmacology of the inhaled haloether anesthetics.

Uptake of CO2, SO2, HNO3 and HCl on Calcite (CaCO3) at 300 K: Mechanism and the Role of Adsorbed Water

All experimental observations of the uptake of the four title compounds on calcite are consistent with the presence of a reactive bifunctional surface intermediate Ca(OH)(HCO3) that has been proposed in the literature. The uptake of CO2 and SO2 occurs on specific adsorption sites of crystalline CaCO3(s) rather than by dissolution in adsorbed water, H2O(ads). SO2 primarily interacts with the bicarbonate moiety whereas CO2, HNO3 and HCl all react first with the hydroxyl group of the surface intermediate. Subsequently, the latter two react with the bicarbonate group to presumably form Ca(NO3)2 and CaCl2.2H2O. The effective equilibrium constant of the interaction of CO2 with calcite in the presence of H2O(ads) is kappa = deltaCO2/(H2O(ads)[CO2]) = 1.62 x 10(3) bar(-1), where CO2 is the quantity of CO2 adsorbed on CaCO3. The reaction mechanism involves a weakly bound precursor species that is reversibly adsorbed and undergoes rate-controlling concurrent reactions with both functionalities of the surface intermediate. The initial uptake coefficients gamma0 on calcite powder depend on the abundance of H2O(ads) under the present experimental conditions and are on the order of 10(-4) for CO2 and 0.1 for SO2, HNO3 and HCl, with gamma(ss) being significantly smaller than gamma0 for HNO3 and HCl, thus indicating partial saturation of the uptake. At 33% relative humidity and 300 K there are 3.5 layers of H2O adsorbed on calcite that reduce to a fraction of a monolayer of weakly and strongly bound water upon pumping and/or heating.

The heterogeneous interaction of HOCl with solid KBr substrates: The catalytic role of adsorbed halogens

The heterogeneous reactivity of HOCl on solid KBr at ambient temperature has been studied using a Knudsen flow reactor. On solid KBr steady-state uptake experiments reveal the formation of Br- and Cl-containing reaction products formed in secondary reactions such as Br(2), BrCl, HOBr, BrOCl, Cl(2) and Cl(2)O with the latter two predominating in the late stages of the reaction. The uptake coefficient gamma spanning a range between 0.15 and 1 x 10(-3) and product yields of HOCl strongly depend on the nature of the solid sample, whether grain, ground grain or thin sprayed film, as well as on sample processing such as pumping and/or heating. Furthermore, the presence of adsorbed halogen species such as Br(2)(a) are crucial for the kinetics of the reaction of HOCl with solid KBr substrates. The presence of surface-adsorbed water (SAW) leads to deactivation of KBr whereas mechanical stress such as grinding leads to the formation of surface defects that become reaction centers. Desorption of SAW at T > 620 K induces high reactivity of the KBr sample at ambient temperature. A reaction mechanism encompassing all significant observations including unusual autocatalytic activity is given as there is no direct reaction of HOCl with solid KBr. It stresses the importance of adsorbed Br-containing species such as Br(2)(a) and HBr(a) that initiate the heterogeneous chemistry of HOCl on solid KBr in the presence of SAW. The role of surface acidity and SAW for the extent of reaction is emphasized.

Inoculum production of the ectomycorrhizal fungus Pisolithus microcarpus in an airlift bioreactor

Many important tree species in reforestation programs are dependent on ectomycorrhizal symbiosis in order to survive and grow, mainly in poor soils. The exploitation of this symbiosis to increase plant productivity demands the establishment of inoculum production methods. This study aims to propose an inoculum production method of the ectomycorrhizal fungus Pisolithus microcarpus (isolate UFSC-Pt116) using liquid fermentation in an airlift bioreactor with external circulation. The fungus grew as dark dense pellets during a batch fermentation at 25.5 degrees C and air inlet of 0.26-0.43 vvm. The maximum biomass (dry weight) achieved in the airlift bioreactor was approximately 5 g.l(-1) after 10-11 days. The specific growth rate (micro(x)) in the exponential phase was 0.576 day(-1), the yield factor (Y(X/S)) 0.418, and the productivity (P(X)) 0.480 g.l(-1).day(-1). This specific growth rate was higher than that observed by other authors during fermentation processes with other Pisolithus isolates. The method seems to be very suitable for biomass production of this fungus. However, new studies on the fungus growth morphology in this system, as well as on the efficiency of the process for the cultivation of other ectomycorrhizal fungi, are necessary. It is also necessary to test the infectivity and efficiency of the inoculum towards the hosts.

[The "Participatory" Movement]

This study reports the trajectory of the Participatory Movement (MP), which was created in opposition to the policies carried out by the Brazilian Association of Nursing (ABEn). This article, written by the first president elected of the "participatory" movement, presents the principles of the movement, its organization, the struggle for leadership, and the work developed in the first administration.

Prostaglandin f2alpha treatment in vivo, but not in vitro, stimulates protein kinase C-activated superoxide production by nonsteroidogenic cells of the rat corpus luteum

Luteal regression is associated with the generation of reactive oxygen species (ROS). To determine the nature of the ROS generator, cells isolated from luteinized rat ovaries were examined for ROS production using luminol-amplified chemiluminescence (LCL). Cells cultured for 2-48 h exhibited minimal LCL, but there was a significant (30- to 50-fold), rapid (maximum at 3-5 min), and dose-dependent increase in LCL in response to phorbol ester (phorbol 12-myristate 13-acetate; TPA; ED50 = 0.03 microM) and diacylglycerol (1,2-dioctanoyl-glycerol; ED50 = 30 microM). The TPA-induced response was cell number dependent and was virtually abolished by superoxide dismutase, freezing, or heating (95 degrees C for 5 min). Zymosan, known to induce a phagocytic response in leukocytes, stimulated a superoxide (O2-.) response with a slow onset (maximum at 40 to 60 min) and a maximum about one third of that observed for TPA. The response to TPA and zymosan was inhibited by the NADPH/NADH-oxidase inhibitor, diphenylene iodonium (ID50 = 5 microM for TPA), but not by the mitochondrial inhibitors, potassium cyanide, rotenone, or sodium azide. Fractionation of cells by centrifugal elutriation showed that TPA-stimulated O2-. production coeluted with the nonsteroidogenic cells and that little, if any, O2-. generation coeluted with the steroidogenic cells. Cells isolated 1, 2, and 4 h after in vivo treatment with a luteolytic dose of prostaglandin F2alpha (PGF2alpha) showed a significant increase in TPA-stimulated O2-. production at 2 h, whereas luteal cells or corpora lutea incubated directly with 1 microM PGF2alpha did not show any increase in response. Corpora lutea isolated from naturally regressed ovaries (18 days after ovulation) showed a significantly elevated level of TPA-stimulated O2-. production. In conclusion, there is a superoxide generator in luteinized ovaries that is activated through a protein kinase C pathway, localized in nonsteroidogenic cells, transiently increased during PGF2alpha-induced luteolysis in vivo, and elevated during natural luteal regression.

Cellular distribution of 5-lipoxygenase and leukotriene receptors in postsurgical peritoneal wound repair

Products of the eicosanoid pathways, namely prostaglandins and leukotrienes, are known to play a key role in inflammatory and immune responses, as well as other wound cellular activities of wounded tissue. The objective of this study was to determine whether surgically induced intraperitoneal and incisional wounds in the rat express 5-lipoxygenase and contain binding sites for leukotrienes and whether their levels change during the course of healing. With the use of a specific monoclonal antibody generated against 5-lipoxygenase, the enzyme was immunohistochemically localized in various wound cells during postsurgical days 2 to 35. The inflammatory cells within the wound were the major cell types containing 5-lipoxygenase immunoreactive protein, followed by fibroblasts in the incisional and peritoneal fibrous adhesions, striated muscle, and the vasculature. The greatest level of immunostaining was observed during the first 2 weeks after surgery, which decreased to near unwounded levels by day 35. Light microscope autoradiographic binding studies using (3)H-leukotrienes indicated that the peritoneal/incisional wounds and unwounded tissues contain specific (3)H-leukotriene C(4) and (3)H-leukotriene D(4) but not (3)H-leukotriene B(4) binding sites. Quantitative grain analysis (net grain density/100 microm(2)), representing specific (3)H-leukotriene C(4) and (3)H-leukotriene D(4) binding sites calculated for different cell types in the wound and unwounded regions showed that (3)H-leukotriene C(4) binding was highest over the striated muscle proximal to the injury and incisional and peritoneal granulation tissue fibroblasts. The net grain density over these cells increased by 3-, 2.5-, and 2-fold by day 14, respectively, and declined to the control values by day 21 after injury (p < 0.05). The pattern of (3)H-leukotriene D(4) binding was similar to that observed for (3)H-leukotriene C(4), but with a lower density. The grain density for (3)H-leukotriene C(4) and (3)H-leukotriene D(4) in arteriolar endothelial and smooth muscle cells remained unchanged. These data suggest that the products of the lipoxygenase pathway through the presence of their specific receptors may play an important role in peritoneal wound repair and adhesion formation.

The effect of surgical glove powder on proliferation of human skin fibroblast and monocyte/macrophage

The effect of surgical glove powders (Biosorb, Keoflo, and CaCO3) and Hydrocote (powder-free lubricating agent, Biogel) was examined on human skin fibroblasts and monocyte/macrophage cell lines (U937 and HL-60). Glove powders (0.1-100 micrograms/ml) in the presence of 10% fetal bovine serum (FBS) had no significant effect on the rate of 3H-thymidine uptake and proliferation of these cells after 48 h and 7 days of exposure, respectively. However, they inhibited HL-60 growth after 10 days, and Biosorb and CaCO3 inhibited U937 after 10-21 days of exposure compared with control. In the presence of low serum (0.5%), Biosorb, but not Keoflo, CaCO3, and Hydrocote, inhibited HL-60 cells after the third day of exposure (p < 0.05), whereas they were without any effect on U937 cells. Further incubation resulted in a significant decrease in cell density in all treatments, as well as controls, because of cell death. In the presence of 2% serum, glove powder-treated HL-60 significantly increased in cell numbers during the first 3 days, and the cells became stationary thereafter, whereas Keoflo and CaCO3-stimulated U937 reached a maximal by 9 days of treatment. Coculturing of fibroblasts directly with macrophages (0.4-5 x 10(5) cells per dish) or incubation with macrophage culture-conditioned media (CCM) stimulated quiescent fibroblast growth equal to that induced by 10% and 0.5% serum, respectively (p < 0.05). However, incubation of fibroblasts with glove powder-treated HL-60 CCM (except CaCO3) inhibited (p < 0.05) and CCM from Biosorb-treated U937 stimulated (p < 0.05) fibroblast proliferation. The CCM from glove powder-treated HL-60 and U937 did not have any significant effect on the rate of 3H-thymidine incorporation into fibroblasts compared with controls. The present observations suggest that glove powder action on fibroblast and macrophage growth in vitro depends on both the serum concentration of the culture medium and the length of exposure. The results imply that glove powders may have an adverse effect in vivo by directly influencing the biologic activity of macrophages, as well as other cell types, leading to alterations in the early phases of wound healing.

Expression of transforming growth factor-beta (TGF beta) isoforms and TGF beta type II receptor messenger ribonucleic acid and protein, and the effect of TGF beta s on endometrial stromal cell growth and protein degradation in vitro

Reverse transcription-polymerase chain reaction analysis of total RNA and immunocytochemical observations revealed that human endometrial glandular epithelial and stromal cells in primary culture express messenger RNAs and proteins for transforming growth factor-beta 1 (TGF beta 1), TGF beta 2, and TGF beta 3 as well as TGF beta type II receptor. The epithelial and stromal cells synthesize and secrete into their culture-conditioned medium 2.6 +/- 0.3 and 1.4 +/- 0.2 ng TGF beta 1/10(6) cells, respectively; after transient acidification of the medium, the TGF beta 1 levels were 18.1 +/- 0.4 and 7.8 +/- 0.7 ng/10(6) cells. These cells also contain specific binding sites for [125I]TGF beta 1, indicated by light microscope autoradiography. TGF beta s at 0.01-10 ng/ml neither stimulated or inhibited subconfluent quiescent stromal cells under serum-free condition nor altered the mitogenic action of 10% fetal bovine serum. However, in the presence of 2% fetal bovine serum, which induced half-maximal stimulation of [3H]thymidine incorporation, TGF beta 1 and TGF beta 2 at 0.1-0.5 ng/ml and TGF beta 3 at 0.1-2.5 ng/ml significantly stimulated the rate of [3H]thymidine incorporation into quiescent stromal cells (P < 0.005); they were ineffective at higher concentrations. TGF beta s did not have any effect on cell proliferation, as determined by cell counting; however, at 0.1 ng/ml and higher concentrations, TGF beta s significantly reduced the metabolic activity of stromal cells, as determined by colorimetric 3-(4,5-dimethylthiazol-2-yl)2, 5-diphenyltetrazolium bromide assay (P < 0.05). The stimulatory and inhibitory actions of TGF beta s in both assays were reversible using 5-10 micrograms/ml TGF beta 1- and TGF beta 2- and 3-6 micrograms/ml TGF beta 3-specific neutralizing antibodies. TGF beta 1 at 1 ng/ml had no significant effect on long-lived protein degradation, assayed by incorporation of [14C]valine into newly synthesized protein by stromal cells, and was similar to the effect of epidermal growth factor or platelet-derived growth factor-BB (10 ng/ml). The data suggest that the TGF beta expression by various endometrial cell types in an autocrine/paracrine manner acts as a negative regulator essential for restraining endometrial growth and transition from proliferation to differentiation stages during the secretory phase after mitogenic stimulation during the proliferative phase of the menstrual cycle.

Insulin-like growth factor I (IGF-I), IGF-I receptors, and IGF binding proteins 1-4 in human uterine tissue: tissue localization and IGF-I action in endometrial stromal and myometrial smooth muscle cells in vitro

The objective of the present study was to elucidate the presence and cellular distribution of insulin-like growth factor I (IGF-I), IGF-I receptor (IGF-IR), and IGF binding proteins (IGFBPs) in human uterine tissue at various reproductive stages, and to determine the effect of IGF-I and its interaction with epidermal growth factor (EGF) and platelet-derived growth factor (PDGF) in endometrial stromal and myometrial smooth muscle cells in primary culture. Using specific antibodies, immunohistochemical observations indicated that luminal and glandular epithelial cells were the major sites of immunoreactive IGF-I, IGF-IR, and IGFBPs 1-4, followed by myometrial smooth muscle and endometrial stromal cells. The immunostaining intensity of IGF-I, IGF-IR, and IGFBPs in endometrial but not myometrial tissue was cycle-dependent and higher in the late proliferative and early/mid-secretory periods than in the late secretory and postmenopausal periods, with little immunostaining at the early proliferative phase of the menstrual cycle. Stromal and smooth cells in primary cell culture also contained immunoreactive IGF-I, IGF-IR, and IGFBPs. IGF-I at 10-100 ng/ml stimulated 3H-thymidine incorporation in quiescent stromal and smooth muscle cells with maximal effect at 100 ng/ml (p < 0.05). However, in the presence of 2% serum, which induces half-maximal stimulation, IGF-I (100 ng/ml) further increased the rate of 3H-thymidine incorporation in stromal but not smooth muscle cells (p < 0.05). The effect of IGF-I was significantly lower than that induced by EGF (10 ng/ml), PDGF-BB (10 ng/ml) and their combination (p < 0.005), and higher in stromal cells from proliferative, than secretory phase of the cycle in the presence of 2% fetal bovine serum, but not serum-free condition (p < 0.005). The effect of IGF-I on myometrial smooth muscle cells was significantly higher than that induced by EGF, but lower than that induced by PDGF-BB or by EGF+PDGF-BB, without the cycle specificity seen with stromal cells. EGF, PDGF-BB, and their combination with IGF-I, but not IGF-I alone, stimulated stromal and smooth muscle cell growth as determined by a cell proliferation assay. The results indicate that human uterine tissue at various reproductive stages contains immunoreactive IGF-I, IGF-IR, and IGFBPs 1-4. Although IGF-I alone was found to be a weak mitogenic factor for stromal and smooth muscle cells, by interacting with EGF and PDGF-BB in a cycle-dependent manner it may regulate the growth and differentiation of these and other uterine cell types.

Cellular distribution of epidermal growth factor, transforming growth factor-α, and epidermal growth factor receptor in fascia and peritoneum during healing in the rat: an autoradiographic and immunohistochemical study

The presence and cellular distribution of epidermal growth factor (EGF), TGF-alpha, and EGF-R were determined in the rat fascial and peritoneal tissue during healing of an incisional injury by means of immunohistochemistry and autoradiographic techniques. The immunostaining intensity for EGF in the regenerating wound area was substantially higher during the first 14 days, then decreased to near prewound levels during 14 to 35 days after surgery. Within the wound area, the most intense immunostaining occurred with inflammatory cells, followed by fascial striated muscle and arterioles, whereas fibroblasts in the regenerating area contained very low immunostaining intensity. The immunostaining pattern for TGF-alpha with the use of three separate polyclonal antibodies that were directed against the amino and carboxy termini of TGF-alpha precursor and a fragment of the mature 50-amino-acid form of TGF-alpha was similar to that seen with EGF and persisted until 28 days after injury. However, fibroblasts in the regenerating area immunostained intensely for TGF-alpha but not for EGF. Quantitative autoradiography of iodine 125-labeled EGF binding and immunohistochemical studies of the EGF-R with monoclonal antibodies that were directed against the extracellular binding domain of EGF-R demonstrated the presence of specific EGF-R in regenerating fascial and peritoneal tissue. Net grain density (100 microm(2)), representing specific binding of (125)I-EGF, was calculated for different cell types in the wound. The grain density over fascial striated muscle, migratory fibroblasts and peritoneal fibroblasts increased by two and one half, three, and four times, respectively, at 7 days and decreased to the values in adjacent unwounded tissue by 21 days after injury (p < 0.05). Immunostaining for the EGF-R generated similar patterns, which persisted for 14 days after injury. The grain density and immunostaining for EGF-R over the arterioles in the wound did not change during the course of healing and was similar to that of the uninjured regions. In summary, these observations indicate that the local levels of EGF, TGF-alpha, and EGF-R increase during the early phases of healing in fascial and peritoneal injury, which suggests a role for these growth factors in the normal mechanism of fascial/peritoneal wound healing and fibrous adhesion formation.

Five-minute treatments with fluorouracil, floxuridine, and mitomycin have long-term effects on human Tenon's capsule fibroblasts

Proliferating human Tenon's capsule fibroblasts were exposed for 5 minutes to a wide range of concentrations of fluorouracil, floxuridine, and mitomycin. High concentrations of all three agents had prolonged effects on cell proliferation and morphologic characteristics compared with untreated control cells up to 36 days. The highest concentrations of both floxuridine (15,000 micrograms/mL) and mitomycin (1000 micrograms/mL) had an apparent cidal effect, reducing cell numbers below initial cell density. In contrast, although the highest concentration of fluorouracil (25,000 micrograms/mL) inhibited cell proliferation by more than 50% relative to the untreated control cells at 36 days, the cell numbers still increased fourfold compared with the initial cell density. These results demonstrate that 5-minute treatments with high concentrations of these drugs have prolonged effects on the proliferation of human Tenon's capsule fibroblasts in vitro. Single-dose regimens using high concentrations of these drugs at the time of operation may achieve results similar to those of protocols that involve repeated applications.

Platelet-derived growth factor (PDGF), epidermal growth factor (EGF), and EGF and PDGF beta-receptors in human endometrial tissue: localization and in vitro action

Human endometrial tissue and primary stromal cell culture contain immunoreactive epidermal growth factor (EGF), platelet-derived growth factor (PDGF)-AB as well as EGF and PDGF-beta receptors. The immunostaining for EGF, EGF receptor, and PDGF beta-receptor were associated with endometrial luminal and glandular epithelial and stromal cells, whereas only the stromal cells contain immunoreactive PDGF-AB. The immunostaining intensity of EGF, EGF receptor, and PDGF-AB was similar in both phases of the menstrual cycle, whereas, PDGF-beta receptor immunostaining was highest in proliferative phase and considerably reduced, particularly in luminal and glandular epithelial cells in the secretory phase. In addition primary stromal cell cultures express EGF, PDGF-AB, and contain EGF and PDGF-beta receptors, and very low levels of PDGF-alpha receptor. 3H-Thymidine incorporation indicate that after 48 h of incubation in serum-free medium approximately 75-80% of stromal cells are quiescent. Incubation of quiescent stromal cells with 10% fetal bovine serum stimulate 3H-thymidine incorporation in a time-dependent manner reaching maximal after 30-48 h, with a doubling time of 38.2 h. EGF (1.5-15 ng/ml) stimulates 3H-thymidine incorporation by quiescent stromal cells (P less than 0.001). This effect was significantly reduced at concentrations above 15 ng/ml (P less than 0.005). PDGF-AB (3-10 ng/ml) and PDGF-BB (0.5-10 ng/ml) also stimulate 3H-thymidine incorporation in quiescent stromal cells compared to controls (P less than 0.005). The action of EGF (15 ng/ml) and PDGF-AB (10 ng/ml) was time dependent, reaching maximal after 36 and 48 h of incubation (P less than 0.002). Addition of PDGF-AB (10 ng/ml) to EGF (15 ng/ml) significantly enhanced the action of EGF or PDGF-AB used individually (P less than 0.001). 17 beta-estradiol or progesterone at 1 microM did not stimulate 3H-thymidine incorporation, although they were stimulatory in combination (P less than 0.001), they did not alter the action of EGF or PDGF when added in combination. These observations provide further evidence that human endometrial tissue contains specific immunoreactive EGF receptors. It also demonstrates the presence of immunoreactive EGF, PDGF-AB, and PDGF-beta receptors in endometrial tissue as well as stromal cells in primary culture. Both EGF and PDGF are mitogenic for endometrial stromal cells, suggesting an autocrine/paracrine role in modulation of endometrial cell growth and differentiation.

Presence of epidermal growth factor, platelet-derived growth factor, and their receptors in human myometrial tissue and smooth muscle cells: their action in smooth muscle cells in vitro

Immunohistochemical observations indicate that human myometrial smooth muscle cells express epidermal growth factor (EGF) and platelet-derived growth factor (PDGF)-AB and contain EGF and PDGF-beta receptors with no variation in intensity with phases of the menstrual cycle. Furthermore, immunofluorescent microscopic studies revealed that primary myometrial smooth muscle cell cultures also express EGF, PDGF-AB, and contain EGF and PDGF-beta, but not alpha-receptor. Incubation of subconfluent smooth muscle cells in serum-free medium leads to quiescence within 48 h as demonstrated by 3H-thymidine incorporation and labeling index. Exposure of quiescent cells to 10% fetal bovine serum stimulates resumption of DNA synthesis and proliferation in a time-dependent manner with a doubling time of 41.6 h. EGF (1.5-50 ng/ml) and PDGF-AB (1-10 ng/ml) in a dose- and time-dependent manner significantly stimulated 3H-thymidine incorporation by quiescent myometrial smooth muscle cells (P less than 0.05). Combinations of EGF (15 ng/ml) and PDGF-AB (10 ng/ml) significantly increased 3H-thymidine incorporation induced by either growth factor alone (P less than 0.05). PDGF-BB at 10 ng/ml also stimulated 3H-thymidine incorporation and its effect was similar to that induced by PDGF-AB at the same concentration. 17 beta-Estradiol (E2) at 1 microM inhibited 3H-thymidine incorporation by the smooth muscle cells (P less than 0.05). E2 also reduced the stimulatory effect of EGF (15 ng/ml) and PDGF (3 ng/ml). Progesterone at 1 microM either alone or in combination with E2 did not have any effect on 3H-thymidine incorporation or alter the mitogenic action of EGF and PDGF. The effect of EGF and PDGF on cell growth and 3H-thymidine incorporation by myometrial smooth muscle cells was independent of phases of the menstrual cycle. In summary, the results of present studies indicate that human myometrial tissue and myometrial smooth muscle cells in primary culture locally produce EGF and PDGF-AB and contain EGF and PDGF-beta, but not alpha-receptors. Moreover, the myometrial smooth muscle cells in culture respond to the mitogenic action of EGF and PDGF.

Possible role of prostaglandins in the regulation of mouse myoblasts

A differentiation-defective mouse myoblast subclone (DD-1), cells of which do not fuse into myotubes nor synthesize muscle-specific proteins, was employed to help define the role of eicosanoids in mouse myoblast differentiation. We observed by hplc, tlc, and radioimmunoassay that the DD-1 cells release strikingly higher levels of cyclooxygenase pathway products prostaglandin E2 and F2 alpha into the culture medium than the parental non-differentiation-defective cells (DZ). In contrast, the levels of 15-hydroxyeicosatetraenoic acid (15-HETE), a lipoxygenase product, and a putatively identified second lipoxygenase product (LLP) did not differ greatly in the two cell types. The DD-1 cells also have strikingly higher levels of cyclooxygenase activity than the parental cells as determined by intact and broken cell assays. Additional fusion-defective clones were isolated on the basis of their flattened appearance and ability to grow in "mitogen-poor" medium and these cells also released strikingly higher levels of prostaglandins E2 and F2 alpha into the growth medium. The "turn on" of the cyclooxygenase pathway in the DD-1 cells and other fusion-defective cells is consistent with the hypothesis that the products of this pathway contribute to the inability of myoblasts to fuse with one another. This hypothesis is supported by the observation that there is a dose-dependent decrease in fusion of DZ cells when PGE2 is added to commitment medium.

Antarctic Ozone Depletion Chemistry: Reactions of N2O5 with H2O and HCl on Ice Surfaces

The reactions of dinitrogen pentoxide (N(2)O(5)) with H(2)O and hydrochloric acid (HCl) were studied on ice surfaces in a Knudsen cell flow reactor. The N(2)O(5) reacted on ice at 185 K to form condensed-phase nitric acid (HNO(3)). This reaction may provide a sink for odd nitrogen (NO(x)) during the polar winter, a requirement in nearly all models of Antarctic ozone depletion. A lower limit to the sticking coefficient, gamma, for N(2)O(5) on ice is 1 x 10(-3). Moreover, N(2)O(5) reacted on HCl-ice surfaces at 185 K, with gamma greater than 3 x 10(-3). This reaction, which produced gaseous nitryl chloride (ClNO(2)) and condensed-phase HNO(3), proceeded until all of the HCl within the ice was depleted. The ClNO(2), which did not react or condense on ice at 185 K, can be readily photolyzed in the Antarctic spring to form atomic chlorine for catalytic ozone destruction cycles. The other photolysis product, gaseous nitrogen dioxide (NO(2)), may be important in the partitioning of NO(x) between gaseous and condensed phases in the Antarctic winter.

Reconstruction of the chest wall. Procedures and nursing care

Large defects of the chest wall can be reconstructed with healthy, well-vascularized soft tissue flaps from adjacent areas of the torso. Such treatment extends the capabilities of surgeons and operating room staff and improves the quality of life for many patients with complicated clinical problems. It requires close cooperation among surgeons, operating room staff, and consulting personnel.

Reaction of Chlorine Nitrate with Hydrogen Chloride and Water at Antarctic Stratospheric Temperatures

Laboratory studies of heterogeneous reactions important for ozone depletion over Antarctica are reported. The reaction of chlorine nitrate (ClONO(2)) with H(2)0 and hydrogen chloride (HCl) on surfaces that simulate polar stratospheric clouds [ice and nitric acid (HNO(3))-ice and sulfuric acid] are studied at temperatures relevant to the Antarctic stratosphere. The reaction of ClONO(2) on ice and certain mixtures of HNO(3) and ice proceeded readily. The sticking coefficient of ClONO(2) on ice of 0.009 +/- 0.002 was observed. A reaction produced gas-phase hypochlorous acid (HOCl) and condensed-phase HNO(3); HOC1 underwent a secondary reaction on ice producing dichlorine monoxide (Cl(2)O). In addition to the reaction with H(2)0, ClONO(2) reacted with HCl on ice to form gas-phase chlorine (Cl(2)) and condensed-phase HNO(3.) Essentially all of the HCl in the bulk of the ice can react with ClONO(2) on the ice surface. The gaseous products of the above reactions, HOCl, Cl(2)0, and Cl(2), could readily photolyze in the Antarctic spring to produce active chlorine for ozone depletion. Furthermore, the formation of condensed-phase HNO(3) could serve as a sink for odd nitrogen species that would otherwise scavenge the active chlorine.

Attributional change and the importance of baseline recording a case illustration

This single case study illustrates how attention to baseline measures prevented premature conclusions regarding the impact of a conditioning procedure upon aggressive, acting-out behavior. Five disruptive behaviors were initially delineated so that frequency distributions could be obtained. During the course of this 15-day observational period, a significant reduction in the number of these aggressive responses was noted. The proposed conditioning procedure was therefore never required. Explanations as well as implications regarding the observed alteration in behavior were discussed.