Randomized phase III KEYNOTE-045 trial of pembrolizumab versus paclitaxel, docetaxel, or vinflunine in recurrent advanced urothelial cancer: results of >2 years of follow-up

Background

Novel second-line treatments are needed for patients with advanced urothelial cancer (UC). Interim analysis of the phase III KEYNOTE-045 study showed a superior overall survival (OS) benefit of pembrolizumab, a programmed death 1 inhibitor, versus chemotherapy in patients with advanced UC that progressed on platinum-based chemotherapy. Here we report the long-term safety and efficacy outcomes of KEYNOTE-045.

Patients and methods

Adult patients with histologically/cytologically confirmed UC whose disease progressed after first-line, platinum-containing chemotherapy were enrolled. Patients were randomly assigned 1 : 1 to receive pembrolizumab [200 mg every 3 weeks (Q3W)] or investigator’s choice of paclitaxel (175 mg/m² Q3W), docetaxel (75 mg/m² Q3W), or vinflunine (320 mg/m² Q3W). Primary end points were OS and progression-free survival (PFS) per Response Evaluation Criteria in Solid Tumors, version 1.1 (RECIST v1.1) by blinded independent central radiology review (BICR). A key secondary end point was objective response rate per RECIST v1.1 by BICR.

Results

A total of 542 patients were enrolled (pembrolizumab, n = 270; chemotherapy, n = 272). Median follow-up as of 26 October 2017 was 27.7 months. Median 1- and 2-year OS rates were higher with pembrolizumab (44.2% and 26.9%, respectively) than chemotherapy (29.8% and 14.3%, respectively). PFS rates did not differ between treatment arms; however, 1- and 2-year PFS rates were higher with pembrolizumab. The objective response rate was also higher with pembrolizumab (21.1% versus 11.0%). Median duration of response to pembrolizumab was not reached (range 1.6+ to 30.0+ months) versus chemotherapy (4.4 months; range 1.4+ to 29.9+ months). Pembrolizumab had lower rates of any grade (62.0% versus 90.6%) and grade ≥3 (16.5% versus 50.2%) treatment-related adverse events than chemotherapy.

Conclusions

Long-term results (>2 years’ follow-up) were consistent with those of previously reported analyses, demonstrating continued clinical benefit of pembrolizumab over chemotherapy for efficacy and safety for treatment of locally advanced/metastatic, platinum-refractory UC.

Trial registration

ClinicalTrials.gov: NCT02256436.

Enhanced degradation of polycyclic aromatic hydrocarbons by biodegradation combined with a modified Fenton reaction

A study has been conducted to enhance degradation of a mixture of polycyclic aromatic hydrocarbons (PAHs) by combining biodegradation with hydrogen peroxide oxidation in a former manufactured gas plant (MGP) soil. An active bacterial consortium enriched from the MGP surface soil (0-2 m) biodegraded more than 90% of PAHs including 2-, 3-, and 4-ring hydrocarbons in a model soil. The consortium was also able to transform about 50% of 4- and 5-ring hydrocarbons in the MGP soil. As a chemical oxidant, Fenton's reagent (H2O2 + Fe2+) was very efficient in the destruction of a mixture of PAHs (i.e., naphthalene (NAP), fluorene (FLU), phenanthrene (PHE), anthracene (ANT), pyrene (PYR), chrysene (CHR), and benzo(a)pyrene (BaP)) in the model soil; noticeably, 84.5% and 96.7% of initial PYR and BaP were degraded, respectively. In the MGP soil, the same treatment destroyed more than 80% of 2- and 3-ring hydrocarbons and 20-40% of 4- and 5-ring compounds. However, the low pH requirement (pH 2-3) for optimum Fenton reaction made the process incompatible with biological treatment and posed potential hazards to the soil ecosystem where the reagent was used. In order to overcome such limitation, a modified Fenton-type reaction was performed at near neutral pH by using ferric ions and chelating agents such as catechol and gallic acid. By the combined treatment of the modified Fenton reaction and biodegradation, more than 98% of 2- or 3-ring hydrocarbons and between 70% and 85% of 4- or 5-ring compounds were degraded in the MGP soil, while maintaining its pH about 6-6.5.

S gene expression and the timing of lysis by bacteriophage lambda

The S gene of bacteriophage lambda encodes the holin required for release of the R endolysin at the onset of phage-induced host lysis. S is the promoter-proximal gene on the single lambda late transcript and spans 107 codons. S has a novel translational initiation region with dual start codons, resulting in the production of two protein products, S105 and S107. Although differing only by the Met-1-Lys-2... N-terminal extension present on S107, the two proteins are thought to have opposing functions, with the shorter polypeptide acting as the lysis effector and the longer one acting as an inhibitor. The expression of wild-type and mutant alleles of the holin gene has been assessed quantitatively with respect to the scheduling of lysis. S mRNA accumulates during the late gene expression period to a final level of about 170 molecules per cell and is maintained at that level for at least the last 15 min before lysis. Total S protein synthesis, partitioned at about 2:1 in favor of the S105 protein compared with the other product, S107, accumulates to a final level of approximately 4,600 molecules per cell. The kinetics of accumulation of S is consistent with a constant translational rate of less than one S protein per mRNA per minute. Mutant alleles with alterations in the translational initiation region were studied to determine how the translational initiation region of S achieves the proper partition of initiation events at the two S start codons and how the synthesis of S105 and S107 relates to lysis timing. The results are discussed in terms of a model for the pathway by which the 30S ribosome-fMet-tRNA complex binds to the translational initiation region of S. In addition, analysis of the relationship between lysis timing and the levels of the two S gene products suggests that S107 inhibits S105, the lethal lysis effector, by a stoichiometric titration.

Biodegradability and biodegradation rate of poly(caprolactone)-starch blend and poly(butylene succinate) biodegradable polymer under aerobic and anaerobic environment

The biodegradability and the biodegradation rate of two kinds biodegradable polymers; poly(caprolactone) (PCL)-starch blend and poly(butylene succinate) (PBS), were investigated under both aerobic and anaerobic conditions. PCL-starch blend was easily degraded, with 88% biodegradability in 44 days under aerobic conditions, and showed a biodegradation rate of 0.07 day(-1), whereas the biodegradability of PBS was only 31% in 80 days under the same conditions, with a biodegradation rate of 0.01 day(-1). Anaerobic bacteria degraded well PCL-starch blend (i.e., 83% biodegradability for 139 days); however, its biodegradation rate was relatively slow (6.1 mL CH(4)/g-VS day) compared to that of cellulose (13.5 mL CH(4)/g-VS day), which was used as a reference material. The PBS was barely degraded under anaerobic conditions, with only 2% biodegradability in 100 days. These results were consistent with the visual changes and FE-SEM images of the two biodegradable polymers after the landfill burial test, showing that only PCL-starch blend had various sized pinholes on the surface due to attack by microorganisms. This result may be use in deciding suitable final disposal approaches of different types of biodegradable polymers in the future.

Dual translational initiation sites control function of the lambda S gene

Lysis gene S of phage lambda has a 107 codon reading frame beginning with the codons Met1-Lys2-Met3. Genetic data have suggested that translational initiation occurs at both Met1 and Met3, generating two polypeptides, S107 and S105 respectively. We have proposed a model in which the proper scheduling of lysis depends on the partition of translational initiations between the two start codons. Here, using in vitro methods, we show that two stem-loop structures, one immediately upstream of the reading frame and a second approximately 10 codons within the gene, control the partitioning event. Utilizing primer-extension inhibition or 'toeprinting', we show that the two S start codons are served by two adjacent Shine-Dalgarno sequences. Moreover, the timing of lysis supported by the wild-type and a number of mutant alleles in vivo can be correlated with the ratio of ternary complex formation over Met1 and Met3 in vitro. Thus the regulation of the S gene is unique in that the products of two adjacent in-frame initiation events have opposing function.

Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation

The cDNAs and genes encoding the intron lariat-debranching enzyme were isolated from the nematode Caenorhabditis elegans and the fission yeast Schizosaccharomyces pombe based on their homology with the Saccharomyces cerevisiae gene. The cDNAs were shown to be functional in an interspecific complementation experiment; they can complement an S. cerevisiae dbr1 null mutant. About 2.5% of budding yeast S. cerevisiae genes have introns, and the accumulation of excised introns in a dbr1 null mutant has little effect on cell growth. In contrast, many S. pombe genes contain introns, and often multiple introns per gene, so that S. pombe is estimated to contain approximately 40 times as many introns as S. cerevisiae. The S. pombe dbr1 gene was disrupted and shown to be nonessential. Like the S. cerevisiae mutant, the S. pombe null mutant accumulated introns to high levels, indicating that intron lariat debranching represents a rate-limiting step in intron degradation in both species. Unlike the S. cerevisiae mutant, the S. pombe dbr1::leu1+ mutant had a severe growth defect and exhibited an aberrant elongated cell shape in addition to an intron accumulation phenotype. The growth defect of the S. pombe dbr1::leu1+ strain suggests that debranching activity is critical for efficient intron RNA degradation and that blocking this pathway interferes with cell growth.

Use of autotrophic sulfur-oxidizers to remove nitrate from bank filtrate in a permeable reactive barrier system

This study was conducted to evaluate the potential applicability of an in situ biological reactive barrier system to treat nitrate-contaminated bank filtrate. The reactive barrier consisted of sulfur granules as an electron donor and autotrophic sulfur-oxidizing bacteria as a biological component. Limestone was also used to provide alkalinity. The results showed that the autotrophic sulfur oxidizers were successfully colonized on the surfaces of the sulfur particles and removed nitrate from synthetic bank filtrate. The sulfur-oxidizing activity continuously increased with time and then was maintained or slightly decreased after five days of column operation. Maximum nitrate removal efficiency and sulfur oxidation rate were observed at near neutral pH. Over 90% of the initial nitrate dissolved in synthetic bank filtrate was removed in all columns tested with some nitrite accumulation. However, nitrite accumulation was observed mainly during the initial operation period, and the concentration markedly diminished with time. The nitrite concentration in effluent was less than 2 mg-N/l after 12 days of column operation. When influent nitrate concentrations were 30, 40, and 60 mg-N/l and sulfur content in column was 75%, half-order autotrophic denitrification reaction rate constants were 31.73 x 10(-3), 33.3 x 10(-3), and 36.4 x 10(-3) mg(1/2)/l(1/2)min, respectively. Our data on the nitrate distribution profile along the column suggest that an appropriate wall thickness of a reactive barrier for autotrophic denitrification may be 30 cm when influent nitrate concentration is less than 60 mg-N/l.

Combined ozonation and biodegradation for remediation of mixtures of polycyclic aromatic hydrocarbons in soil

A study was conducted to investigate the feasibility of a combined treatment (i.e., ozonation and biodegradation) to overcome the inherent bacterial bioavailability limitation, and hence bioremediation limitation, of polycyclic aromatic hydrocarbons in soil. Ozonation was very efficient in the removal of naphthalene, fluorene, phenanthrene, and anthracene, but not for pyrene, chrysene, and benzo(a)pyrene from soil freshly spiked with the hydrocarbons. A similar result was obtained from coal tar-contaminated soil. Elimination of polycyclic aromatic hydrocarbons increased appreciably in sand containing 0.03% organic carbon, indicating the adverse effect of organic carbon on the efficiency of ozone treatment. In spiked and coal tar-contaminated soils, ozonation followed by biodegradation significantly increased the degradation of various polycyclic aromatic hydrocarbons including chrysene and benzo(a)pyrene which were not degraded by the test bacterial consortium alone. In particular, the effect of the combined treatment was more pronounced in coal tar-contaminated soil than in sterile soil spiked with hydrocarbons, probably due to the augmented biological activity of the introduced consortium. The results suggest that a combined treatment including ozonation and biodegradation may be a promising bioremediation technology in soil contaminated with mixtures of polycyclic aromatic hydrocarbons such as former manufactured gas plant sites.

Observation of tt[over ¯]H Production

The observation of Higgs boson production in association with a top quark-antiquark pair is reported, based on a combined analysis of proton-proton collision data at center-of-mass energies of sqrt[s]=7, 8, and 13 TeV, corresponding to integrated luminosities of up to 5.1, 19.7, and 35.9  fb^{-1}, respectively. The data were collected with the CMS detector at the CERN LHC. The results of statistically independent searches for Higgs bosons produced in conjunction with a top quark-antiquark pair and decaying to pairs of W bosons, Z bosons, photons, τ leptons, or bottom quark jets are combined to maximize sensitivity. An excess of events is observed, with a significance of 5.2 standard deviations, over the expectation from the background-only hypothesis. The corresponding expected significance from the standard model for a Higgs boson mass of 125.09 GeV is 4.2 standard deviations. The combined best fit signal strength normalized to the standard model prediction is 1.26_{-0.26}^{+0.31}.

Relationship between early postoperative C-reactive protein elevation and long-term postoperative major adverse cardiovascular and cerebral events in patients undergoing off-pump coronary artery bypass graft surgery: a retrospective study

BACKGROUND

Inflammation plays a key role in the pathogenesis of vascular occlusive diseases, such as myocardial infarction and stroke. Additionally, these conditions are predicted by C-reactive protein (CRP), a general inflammation marker. We hypothesized that the inflammation induced by surgery itself augments vascular occlusive disease. We retrospectively evaluated the relationship between postoperative CRP elevation and postoperative major adverse cardiovascular and cerebral events (MACCE) in patients undergoing off-pump coronary artery bypass surgery (OPCAB).

METHODS

The electronic medical records of 1046 patients who underwent OPCAB were reviewed retrospectively. The relationship between postoperative serum CRP and long-term postoperative MACCE (median follow-up 28 months) was investigated.

RESULTS

Patients were divided into quartiles according to maximum postoperative CRP levels (<18, 18-22, 22-27, ≥27 mg dl(-1)). The adjusted hazard ratios (HRs) were 2.15, 2.45, and 2.81, respectively (P=0.004), compared with the lowest quartile (<18 mg dl(-1)). In the multivariate analysis, the postoperative CRP quartile (HR 2.81; P=0.004), postoperative non-use of statins (HR 1.86; P=0.003), and postoperative maximum troponin I (HR 1.02; P<0.001) independently predicted postoperative MACCE, while preoperative CRP did not (P=0.203). Several parameters were correlated with postoperative maximum CRP level: body temperature (P=0.001) and heart rate (P<0.001) at the end of surgery; intraoperative last lactate (P<0.001) and base excess (P<0.001); and red blood cell transfusion (P=0.019).

CONCLUSIONS

Postoperative CRP elevation was associated with long-term postoperative MACCE in OPCAB patients. This was mitigated by postoperative statin medication. Furthermore, postoperative CRP elevation was associated with intraoperative parameters reflecting hypoperfusion and inflammation.

Human RNA lariat debranching enzyme cDNA complements the phenotypes of Saccharomyces cerevisiae dbr1 and Schizosaccharomyces pombe dbr1 mutants

The cDNA encoding the human RNA lariat debranching enzyme (hDBR1) was identified and cloned by searching the Expressed Sequence Tag (EST) database and screening a HeLa cDNA library, based on predicted amino acid sequence homologies with the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Caenorhabditis elegans debranching enzymes. The hDBR1 cDNA expressed in Escherichia coli showed debranching activity in vitro and was also shown to be functional in an interspecies specific complementation experiment. hDBR1 cDNA in a S. cerevisiae expression vector complemented the intron accumulation phenotype of a S. cerevisiae dbr1 null mutant. Integration of the cDNA for hDBR1 into the ura4 locus of S. pombe also complemented both the intron accumulation and slow growth phenotypes of a S. pombe dbr1 null mutant strain. Comparison of the amino acid sequence of hDBR1 with the other DBR protein sequences showed several conserved regions, with 40, 44 and 43% identity to the S. cerevisiae, S. pombe and C. elegans debranching enzymes, respectively.

L1 Peptide-Conjugated Fibrin Hydrogels Promote Salivary Gland Regeneration

Hyposalivation contributes to dental caries, periodontitis, and microbial infections. Additionally, it impairs activities of daily living (e.g., speaking, chewing, and swallowing). Treatments for hyposalivation are currently limited to medications (e.g., the muscarinic receptor agonists pilocarpine and cevimeline) that induce saliva secretion from residual acinar cells and the use of saliva substitutes. However, given that these therapies provide only temporary relief, the development of alternative treatments to restore gland function is essential. Previous studies demonstrated that laminin 1 (L1) is critical for intact salivary cell cluster formation and organization. However, the full L1 sequence is not suitable for clinical applications, as each protein domain may contribute to unwanted effects, such as degradation, tumorigenesis, and immune responses that, when compounded, outweigh the potential benefits provided by their sum. Although the L1 peptides YIGSR and A99 linked to fibrin hydrogels (FHs) promote intact salivary epithelial formation in vitro, little is known about their role during salivary gland regeneration in vivo. Therefore, the goal of this study was to demonstrate whether L1 peptides conjugated to FHs promote tissue regeneration in a wound-healing model of mouse submandibular glands (mSMGs). Our results suggest that YIGSR-A99 peptides, chemically conjugated to FHs and applied to wounded mSMGs in vivo, formed new organized salivary tissue. In contrast, wounded mSMGs treated with FHs alone or in the absence of a scaffold showed disorganized collagen formation and poor tissue healing. Together these studies indicate that damaged salivary gland tissue can grow and differentiate when treated with FHs containing L1 peptides.

Observation of Higgs Boson Decay to Bottom Quarks

The observation of the standard model (SM) Higgs boson decay to a pair of bottom quarks is presented. The main contribution to this result is from processes in which Higgs bosons are produced in association with a W or Z boson (VH), and are searched for in final states including 0, 1, or 2 charged leptons and two identified bottom quark jets. The results from the measurement of these processes in a data sample recorded by the CMS experiment in 2017, comprising 41.3  fb^{-1} of proton-proton collisions at sqrt[s]=13  TeV, are described. When combined with previous VH measurements using data collected at sqrt[s]=7, 8, and 13 TeV, an excess of events is observed at m_{H}=125  GeV with a significance of 4.8 standard deviations, where the expectation for the SM Higgs boson is 4.9. The corresponding measured signal strength is 1.01±0.22. The combination of this result with searches by the CMS experiment for H→bb[over ¯] in other production processes yields an observed (expected) significance of 5.6 (5.5) standard deviations and a signal strength of 1.04±0.20.

Peripheral blood extrathymic CD4(+)CD8(+) T cells with high cytotoxic activity are from the same lineage as CD4(+)CD8(-) T cells in cynomolgus monkeys

We have previously reported that CD4/CD8 double-positive (DP) T cells with the resting memory phenotype are present in the periphery of healthy cynomolgus monkeys. In the present study, we performed functional studies on the T cells. The expression of CD4 and CD8 on DP, CD4 single-positive (SP) or CD8 SP T cells was stable in cultures with either mitogen or anti-CD3 antibody stimulation. In spite of lacking CD28 expression, DP T cells showed similar proliferative ability and apoptosis sensitivity to CD4 SP and CD8 SP T cells. DP T cells showed both helper and cytotoxic activities. Although the helper activity of DP T cells was lower than that of CD4 SP T cells, cytotoxic activity was comparable to that of CD8 SP T cells. Fresh DP T cells killed target cells mainly by the perforin-granzyme pathway. In addition, fresh DP T cells expressed a high level of mRNA for IFN-gamma and produced a high level of IFN-gamma when they were activated by anti-CD3 antibody ligation. On the other hand, several expanded DP T cell clones shared TCR V(beta) with expanded CD4 SP T cell clones, strongly suggesting that those two corresponding clones with DP and CD4 SP phenotypes might be derived from the same ancestor T cell. These results showed that the DP T cells are a novel T cell subset with functions overlapping with those of CD4 SP and CD8 SP T cells, and that they might play protective and regulatory roles in secondary immune response in cynomolgus monkeys.

Plus-strand strong-stop DNA synthesis in retrotransposon Ty1

Reverse transcription in the yeast retrotransposon Ty1 follows the general "rules" of retroviral replication overall. However, some details of the retroviral and Ty1 reverse transcription processes are different. We have identified and determined the structure of plus-strand strong-stop DNA and examined the effect of polypurine tract deletion mutations on its synthesis. Furthermore, we have defined the stop signal for plus-strand strong-stop DNA synthesis as an unusual 2'-O-ribosylated nucleotide in the primer tRNA. Full-length plus-strand strong-stop DNA, following strand transfer, would have a terminal 2-base mismatch with minus-strand DNA. These findings indicate that the mechanism of plus-strand strong-stop DNA transfer in Ty1 differs from that of the retroviral transfer and suggest that full-length plus-strand strong-stop DNA is not a direct intermediate in Ty1 retrotransposition.

Conservation of a dual-start motif in P22 lysis gene regulation

Gene 13 of bacteriophage P22 is functionally equivalent to lambda lysis gene S. Gene S codes for two products, the polypeptides S105 and S107, produced from translational initiation events at the third and first codon, respectively. We have shown that the two polypeptides have opposing functions in lysis: S105 is the lethal lysis effector, and S107 acts as an inhibitor of lysis (U. Bläsi, K. Nam, D. Hartz, L. Gold, and R. Young, EMBO J. 11:3501-3510, 1989). Gene 13 has a 108-codon reading frame and its product begins with a similar motif: Met-1-Lys-2-Lys-3-Met-4. Here, we present in vivo and in vitro evidence for the expression of a 13(108) and a 13(105) product and show that the lambda lysis control mechanisms is evolutionarily conserved in phage P22. In this case 13(108), like S107 in lambda, functions as the inhibitor of the lysis effector 13(105). Although the DNA sequences upstream of the S and 13 gene starts showed less homology, the same structural characteristics, i.e., stem-loop structures immediately upstream and about 10 codons downstream of the start region, were present in both reading frames. Using in vitro mutagenesis and toeprinting, we show that the upstream stem-loop structures of genes 13 and S, containing the Shine-Dalgarno sequence for initiations at Met-1, are interchangeable. Moreover, our data indicate that the stability of the secondary structures present in the translational initiation regions of genes S and 13 is set to create a particular ratio of initiation events at Met-1 and Met-3 or Met-4. The ratio of effector to inhibitor was much higher in P22 than in lambda. We propose that this reflects less transcriptional readthrough at the late terminator t(R) and suggests that the dual-start motif in genes 13 and S may be important for establishment of maintenance of the lysogenic state.

Role of loosely bound humic substances and humin in the bioavailability of phenanthrene aged in soil

A study was conducted to determine a possible role of loosely bound humic substances (i.e., humic and fulvic acids) in bioavailability of aged phenanthrene with time. In this study, long-term residence of phenanthrene in soil is defined as aging or sequestration, and the effect was determined by the declined bioavailability to bacteria of the polycyclic aromatic hydrocarbon with increased residence time. After 1, 7, and 100 days of aging of phenanthrene in Lima loam, about 90-93% of initial phenanthrene was recovered from the humin-mineral fraction of Lima loam whereas less than 12% was found in humic and fulvic acids of the same soil. Mineralization rates of phenanthrene aged in the humin-mineral fraction significantly decreased with time by the test bacterium P5-2. In terms of extents of mineralization, the difference with time was not appreciable, but still significant at P<0.05. Additional decreases in the rates and extents of mineralization were observed with the whole soil (i.e. Lima loam) to which phenanthrene had been aged. Data suggest that major sequestration sites for phenanthrene may reside in the humin-mineral fraction, and probably humic and fulvic acids may act as a physico-chemical barrier to bacterial degradation so that the compound's bioavailability may be limited.

A novel H1 mutation in the keratin 1 chain in epidermolytic hyperkeratosis

We report a novel mutation in a case of epidermolytic hyperkeratosis that results in a proline for arginine substitution in the penultimate residue position of the H1 subdomain of the keratin 1 chain, which is near the beginning of the rod domain. This causes a severe clinical disease classified as PS-2. Therefore, the H1 subdomain is probably equally important for the maintenance of keratin intermediate filament integrity as the rod domain. Since earlier concepts had implied that mutations in the H1 subdomain produce milder disease, this case suggests that attempts to correlate mutations with disease presentation remain problematic.

An alanine to proline mutation in the 1A rod domain of the keratin 10 chain in epidermolytic hyperkeratosis

We report a mutation in a case of epidermolytic hyperkeratosis that results in a proline for alanine substitution in the residue position 12 of the 1A subdomain of the keratin 10 chain (codon 158). The disease phenotype is consistent with the inappropriate substitution of a proline near the beginning of the rod domain, because it is likely to seriously disrupt the structural organization of coiled-coil molecules within keratin intermediate filaments. Mutations/substitutions in this position have not been reported in any keratin disease. Position 12 is an alanine in all intermediate filament chains, and lies in the outer b heptad position of the coiled-coil. In vitro peptide interference assembly assays revealed that substitutions that alter residue size or charge at this position primarily interfere with keratin filament elongation.

PAH utilization by Pseudomonas rhodesiae KK1 isolated from a former manufactured-gas plant site

Pseudomonas rhodesiae KK1 was isolated from a former manufactured-gas plant site, due to its ability to grow rapidly in a mixture of polycyclic aromatic hydrocarbons (PAHs). Radiorespirometric analysis revealed that strain KK1 was found to be able to mineralize anthracene, naphthalene and phenanthrene. Notably, phenanthrene-grown cells were able to mineralize anthracene much more rapidly than naphthalene-grown cells. Comparative analysis of amino acid sequences from 17 randomly selected dioxygenases capable of hydroxylating unactivated aromatic nuclei indicated that the enzymes for catabolism of PAHs, such as naphthalene and phenanthrene, might exist redundantly in strain KK1. Northern hybridization for cells grown on naphthalene or phenanthrene, using the putative naphthalene or phenanthrene dioxygenase gene fragment as a probe, suggested that the enzyme for naphthalene catabolism might share some homology in deduced amino acid sequences with phenanthrene dioxygenases. Also, it was found that three lipids (17:0 cyclo, 18:1 omega7c, 19:0 cyclo) increased in response to both naphthalene and phenanthrene, while the shift of other lipids varied from substrate to substrate.

The linear framework: using graph theory to reveal the algebra and thermodynamics of biomolecular systems

The linear framework uses finite, directed graphs with labelled edges to model biomolecular systems. Graph vertices represent biochemical species or molecular states, edges represent reactions or transitions and labels represent rates. The graph yields a linear dynamics for molecular concentrations or state probabilities, with the graph Laplacian as the operator, and the labels encode the nonlinear interactions between system and environment. The labels can be specified by vertices of other graphs or by conservation laws or, when the environment consists of thermodynamic reservoirs, they may be constants. In the latter case, the graphs correspond to infinitesimal generators of Markov processes. The key advantage of the framework has been that steady states are determined as rational algebraic functions of the labels by the Matrix-Tree theorems of graph theory. When the system is at thermodynamic equilibrium, this prescription recovers equilibrium statistical mechanics but it continues to hold for non-equilibrium steady states. The framework goes beyond other graph-based approaches in treating the graph as a mathematical object, for which general theorems can be formulated that accommodate biomolecular complexity. It has been particularly effective at analysing enzyme-catalysed modification systems and input-output responses.

A novel glutamic acid to aspartic acid mutation near the end of the 2B rod domain in the keratin 1 chain in epidermolytic hyperkeratosis

We report a mutation in a mild case of epidermolytic hyperkeratosis that results in a glutamic acid to aspartic acid substitution in a novel location, codon 477 or position 106 of the 2B rod domain of the keratin 1 chain. This residue has been conserved in all intermediate filament chains and lies near the beginning of the highly conserved helix termination sequence and just prior to the predicted molecular overlap region. Keratin filaments assembled in vitro from chains bearing this substitution are abnormal, indicating that the glutamic acid residue is critically involved in ionic interactions in intermediate levels of filament structure.

Search for a Narrow Resonance Lighter than 200 GeV Decaying to a Pair of Muons in Proton-Proton Collisions at sqrt[s]=13 TeV

A search is presented for a narrow resonance decaying to a pair of oppositely charged muons using sqrt[s]=13  TeV proton-proton collision data recorded at the LHC. In the 45-75 and 110-200 GeV resonance mass ranges, the search is based on conventional triggering and event reconstruction techniques. In the 11.5-45 GeV mass range, the search uses data collected with dimuon triggers with low transverse momentum thresholds, recorded at high rate by storing a reduced amount of trigger-level information. The data correspond to integrated luminosities of 137 and 96.6  fb^{-1} for conventional and high-rate triggering, respectively. No significant resonant peaks are observed in the probed mass ranges. The search sets the most stringent constraints to date on a dark photon in the ∼30-75 and 110-200 GeV mass ranges.

Measurement of Prompt D^{0} Meson Azimuthal Anisotropy in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The prompt D^{0} meson azimuthal anisotropy coefficients, v_{2} and v_{3}, are measured at midrapidity (|y|<1.0) in Pb-Pb collisions at a center-of-mass energy sqrt[s_{NN}]=5.02  TeV per nucleon pair with data collected by the CMS experiment. The measurement is performed in the transverse momentum (p_{T}) range of 1 to 40  GeV/c, for central and midcentral collisions. The v_{2} coefficient is found to be positive throughout the p_{T} range studied. The first measurement of the prompt D^{0} meson v_{3} coefficient is performed, and values up to 0.07 are observed for p_{T} around 4  GeV/c. Compared to measurements of charged particles, a similar p_{T} dependence, but smaller magnitude for p_{T}<6  GeV/c, is found for prompt D^{0} meson v_{2} and v_{3} coefficients. The results are consistent with the presence of collective motion of charm quarks at low p_{T} and a path length dependence of charm quark energy loss at high p_{T}, thereby providing new constraints on the theoretical description of the interactions between charm quarks and the quark-gluon plasma.