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Human papillomavirus (HPV)‐associated cancer continues to evade the immune system by promoting a suppressive tumor microenvironment. Therefore, immunotherapy appears to be a promising approach for targeting HPV‐associated tumors. We hypothesized that valproic acid (VA) as an epigenetic agent combined with avelumab may enhance the antitumor immunity in HPV‐associated solid tumors. We performed bulk RNA‐sequencing (RNA‐Seq) on total peripheral blood mononuclear cells (PBMCs) of seven nonresponders (NRs) and four responders (Rs). A total of 39 samples (e.g., pretreatment, post‐VA, postavelumab, and endpoint) were analyzed. Also, we quantified plasma analytes and performed flow cytometry. We observed a differential pattern in immune response following treatment with VA and/or avelumab in NRs vs. Rs. A significant upregulation of transcripts associated with NETosis [the formation of neutrophil extracellular traps (NETs)] and neutrophil degranulation pathways was linked to the presence of a myeloid‐derived suppressor cell signature in NRs. We noted the elevation of IL‐8/IL‐18 cytokines and a distinct transcriptome signature at the baseline and endpoint in NRs. By using the receiver operator characteristics, we identified a cutoff value for the plasma IL‐8/IL‐18 to discriminate NRs from Rs. We found differential therapeutic effects for VA and avelumab in NRs vs. Rs. Thus, our results imply that measuring the plasma IL‐8/IL‐18 and bulk RNA‐Seq of PBMCs may serve as valuable biomarkers to predict immunotherapy outcomes. [ABSTRACT FROM AUTHOR]

Plant‐parasitic cyst nematodes use a stylet to deliver effector proteins produced in oesophageal gland cells into root cells to cause disease in plants. These effectors are deployed to modulate plant defence responses and developmental programmes for the formation of a specialized feeding site called a syncytium. The Hg2D01 effector gene, coding for a novel 185‐amino‐acid secreted protein, was previously shown to be up‐regulated in the dorsal gland of parasitic juveniles of the soybean cyst nematode Heterodera glycines, but its function has remained unknown. Genome analyses revealed that Hg2D01 belongs to a highly diversified effector gene family in the genomes of H. glycines and the sugar beet cyst nematode Heterodera schachtii. For functional studies using the model Arabidopsis thaliana–H. schachtii pathosystem, we cloned the orthologous Hs2D01 sequence from H. schachtii. We demonstrate that Hs2D01 is a cytoplasmic effector that interacts with the intracellular kinase domain of HAESA (HAE), a cell surface‐associated leucine‐rich repeat (LRR) receptor‐like kinase (RLK) involved in signalling the activation of cell wall‐remodelling enzymes important for cell separation during abscission and lateral root emergence. Furthermore, we show that AtHAE is expressed in the syncytium and, therefore, could serve as a viable host target for Hs2D01. Infective juveniles effectively penetrated the roots of HAE and HAESA‐LIKE2 (HSL2) double mutant plants; however, fewer nematodes developed on the roots, consistent with a role for this receptor family in nematode infection. Taken together, our results suggest that the Hs2D01–AtHAE interaction may play an important role in sugar beet cyst nematode parasitism. [ABSTRACT FROM AUTHOR]

Different functions are used to account for turbulence strength in the atmospheric boundary layer for different stability regimes. These functions are one of the sources for differences among different atmospheric models' predictions and associated biases. Also, turbulence strength is underrepresented in some of the resistance formulations. To address these issues with dry deposition, firstly we take advantage of three‐dimensional (3‐D) turbulence information in estimating resistances by proposing and validating a 3‐D turbulence velocity scale that is relevant for different stability regimes of boundary layer. Secondly, we hypothesize and validate that friction velocity measured by 3‐D sonic anemometer can be effectively replaced by the new turbulence velocity scale multiplied by the von Karman constant. Finally, we (a) present a set of resistance formulations for ozone (O3) based on the 3‐D turbulence velocity scale; (b) intercompare estimations of such resistances with those obtained using existing formulations; and, (c) evaluate simulated O3 fluxes using a single‐point dry deposition model against long‐term observations of O3 fluxes at the Harvard Forest (MA) site. Results indicate that the new resistance formulations work very well in simulating surface latent heat and O3 fluxes when compared to respective existing formulations and measurements at a decadal time scale. Findings from this research may help to improve the capability of dry deposition schemes for better estimation of dry deposition fluxes and create opportunities for the development of a community dry deposition model for use in regional/global air quality models. Plain Language Summary: Chaotic air motions control the amount of pollutant transfer to the surface during dry conditions, which can impact ecosystems, and is a helpful process that can reduce human exposure to air pollutants. Existing pollutant transfer equations use adjustment methods to account for chaotic air motions for different dry conditions. These methods can be sources of errors in estimating pollutant transfer. To avoid using such methods, we propose and evaluate a new velocity parameter derived from using chaotic air energy, which is estimated using other air parameters. Then, we validate the new velocity parameter using sophisticated instrument measurements for chaotic motions. Further, we assume and prove that a constant fraction of that new velocity parameter can be used to avoid adjustment methods and accurately represent strength of chaotic air motions. Finally, we use that new velocity parameter in developing new equations that estimate ozone transfer via various routes to the surface. We used a computer based tool to validate new equations using decadal measurements of ozone fluidities at the Harvard Forest site. Results indicate that our new equations work very well in estimating pollutant transfer. This research has the potential to help manifest a community science package for use in mathematical models. Key Points: Turbulence velocity scale is introduced to represent 3‐D turbulence strength in the estimation of dry depositionProven measured friction velocity can be replaced by von Karman constant and turbulence velocity scale product to avoid stability functionsNew formulations based on turbulence velocity scale simulated realistic surface latent heat and ozone deposition fluxes at decadal time scales [ABSTRACT FROM AUTHOR]

Background: Heavy alcohol use, including binge drinking, is associated with high morbidity and mortality among men who have sex with men (MSM). Self‐reported alcohol measures may lead to inaccurate estimates due to recall and social desirability biases. Objective alcohol biomarkers like phosphatidylethanol (PEth) can be used to corroborate self‐report and could help to inform treatment approaches and research strategies for alcohol using MSM. Methods: From 2015 to 2020, alcohol using MSM ≥18 years were enrolled in a randomized controlled trial evaluating the efficacy of naltrexone in reducing binge drinking. Using this trial's baseline data, we applied multivariable logistic regression to identify the correlates of high PEth levels (i.e., ≥87 ng/ml) and concordance between PEth levels and self‐reported heavy drinking. Results: Of 118 MSM, 64% had PEth levels ≥87 ng/ml and 72% had PEth levels that were concordant with self‐reported heavy alcohol use. Factors significantly associated in separate models with elevated PEth levels were income ≥$60,000 (adjusted odds ratio [aOR] = 4.09; 95% CI = 1.13 to 14.82), being employed (aOR = 4.04; 95% CI = 1.45 to 11.32), episodic cannabis use (aOR = 4.63; 95% CI = 1.27 to 16.92), and any alcohol/substance use prior to or during anal intercourse (aOR = 2.52; 95% CI = 1.08 to 5.90). Living with HIV was associated with significantly lower odds of elevated PEth levels (aOR = 0.23; 95% CI = 0.09 to 0.61). Factors associated with significantly higher concordance between PEth levels and self‐reported heavy alcohol use included at least weekly use of poppers (aOR = 6.41; 95% CI = 1.27 to 32.28) and polysubstance use (aOR = 2.53; 95% CI = 1.02 to 6.27). Living with HIV was associated with lower odds of concordance (aOR = 0.36; 95% CI = 0.14 to 0.97). Conclusions: PEth may enhance the detection of heavy drinking among MSM, including the identification of subpopulations that may benefit from targeted alcohol reduction interventions. However, PEth values for MSM living with HIV showed modest concordance with self‐reported alcohol use and may need to be supplemented with additional biomarkers or evaluated against a different cutoff. [ABSTRACT FROM AUTHOR]

Woody plant encroachment – the conversion of open grasslands and savannas to woodlands – represents one of the gravest threats to grassland biomes worldwide. This is especially true for the Great Plains of the US. We contend that the widespread adoption of pyric herbivory (the synergistic application of fire and grazing) and mixed‐species grazing (cattle [Bos taurus] and goats [Capra spp]) would not only make grasslands and savannas more resilient to woody plant encroachment but would also enhance the profitability and resiliency of livestock production systems. These management strategies control woody plants, increase biodiversity, improve grassland ecosystem function, and favor livestock production. Although this management paradigm holds tremendous potential by mimicking original grassland disturbance regimes, it has not been widely adopted because of cultural constraints. Saving the remaining natural grasslands in the Great Plains and elsewhere will require a widespread shift in cultural norms – facilitated by targeted government incentives and a coordinated program of regional research, extension, and education that involves farmers and ranchers as key stakeholders. [ABSTRACT FROM AUTHOR]

In the skin‐healing field, porcine models are regarded as a useful analogue for human skin due to their numerous anatomical and physiological similarities. Despite the widespread use of porcine models in skin healing studies, the initial origin, recruitment and transition of fibroblasts to matrix‐secreting contractile myofibroblasts are not well defined for this model. In this review, we discuss the merit of the pig as an animal for studying myofibroblast origin, as well as the challenges associated with assessing their contributions to skin healing. Although a variety of wound types (incisional, partial thickness, full thickness, burns) have been investigated in pigs in attempts to mimic diverse injuries in humans, direct comparison of human healing profiles with regards to myofibroblasts shows evident differences. Following injury in porcine models, which often employ juvenile animals, myofibroblasts are described in the developing granulation tissue at 4 days, peaking at Days 7–14, and persisting at 60 days post‐wounding, although variations are evident depending on the specific pig breed. In human wounds, the presence of myofibroblasts is variable and does not correlate with the age of the wound or clinical contraction. Our comparison of porcine myofibroblast‐mediated healing processes with those in humans suggests that further validation of the pig model is essential. Moreover, we identify several limitations evident in experimental design that need to be better controlled, and standardisation of methodologies would be beneficial for the comparison and interpretation of results. In particular, we discuss anatomical location of the wounds, their size and depth, as well as the healing microenvironment (wet vs. moist vs. dry) in pigs and how this could influence myofibroblast recruitment. In summary, although a widespread model used in the skin healing field, further research is required to validate pigs as a useful analogue for human healing with regards to myofibroblasts. [ABSTRACT FROM AUTHOR]

Rock moisture in the vadose zone, while recognized as important, is rarely monitored—in part because adequate instrumentation and installation techniques are lacking. The objectives of this work were (a) to test the applicability of a commercially available capacitance soil moisture sensor (EC‐5, METER Group) for continuously monitoring the water content of weathered limestone; and (b) to contrast the water dynamics of rock matrix with that of rock fractures. At a site in the Edwards Plateau, Texas, we developed a protocol for installing sensors in limestone pits and tested its effectiveness in reducing erroneous readings caused by installation‐induced preferential flow along pit walls. Our results show that rock moisture can be accurately measured with EC‐5 sensors, provided some steps are taken to ensure the quality of the installation. These include protecting the sensors by installing them in horizontal shafts rather than on the exposed pit wall, and use of a sealant. Data gathered over 7 mo after installation showed that rock moisture increased significantly only after a 95‐mm rainfall event. Because of preferential flow, fractures reached peak water content within 2–3 h after peak rainfall—a response that was one to two orders of magnitude faster than in rock matrix. Limestone stored 40–70% of the water after the 95‐mm event, and its water content decreased significantly during summer months. Overall, our results attest to the importance of continuously measuring rock moisture in regions with shallow soils, where it serves as a critical reservoir for vegetation. Core Ideas: EC‐5 sensors proved to be successful for monitoring the water content of weathered limestone. Installation‐induced errors can be avoided by following strict installation protocols. The amount of water infiltrating the weathered rock after large storms can be substantial. Rock moisture increases rapidly after storms as a result of preferential flow through fractures. Rock moisture was more depleted during the summer than during the fall dry season. [ABSTRACT FROM AUTHOR]

Cancer is a disease of somatic mutations. These cellular mutations compete to dominate their microenvironment and dictate the disease outcome. While a therapeutic approach to target‐specific oncogenic driver mutations helps to manage the disease, subsequent molecular evolution of tumor cells threatens to overtake therapeutic progress. There is a need for rapid, high‐throughput, unbiased in vitro discovery screening platforms that capture the native complexities of the tumor and rapidly identify mutations that confer chemotherapeutic drug resistance. Taking the example of the CDK4/6 inhibitor (CDK4/6i) class of drugs, we show that the pooled in vitro CRISPR screening platform enables rapid discovery of drug resistance mutations in a three‐dimensional (3D) setting. Gene‐edited cancer cell clones assembled into an organotypic multicellular tumor spheroid (MCTS), exposed to CDK4/6i caused selection and enrichment of the most drug‐resistant phenotypes, detectable by next‐gen sequencing after a span of 28 days. The platform was sufficiently sensitive to enrich for even a single drug‐resistant cell within a large, drug‐responsive complex 3D tumor spheroid. The genome‐wide 3D CRISPR‐mediated knockout screen (>18,000 genes) identified several genes whose disruptions conferred resistance to CDK4/6i. Furthermore, multiple novel candidate genes were identified as top hits only in the microphysiological 3D enrichment assay platform and not the conventional 2D assays. Taken together, these findings suggest that including phenotypic 3D resistance profiling in decision trees could improve discovery and reconfirmation of drug resistance mechanisms and afford a platform for exploring noncell autonomous interactions, selection pressures, and clonal competition. [ABSTRACT FROM AUTHOR]

Recent studies have highlighted the functional diversity of dermal fibroblast populations in health and disease, with part of this diversity linked to fibroblast lineage and embryonic origin. Fibroblasts derived from foxd1‐expressing progenitors contribute to the myofibroblast populations present in lung and kidney fibrosis in mice but have not been investigated in the context of dermal wound repair. Using a Cre/Lox system to genetically track populations derived from foxd1‐expressing progenitors, lineage‐positive fibroblasts were identified as a subset of the dermal fibroblast population. During development, lineage‐positive cells were most abundant within the dorsal embryonic tissues, contributing to the developing dermal fibroblast population, and remaining in this niche into adulthood. In adult mice, assessment of fibrosis‐related gene expression in lineage‐positive and lineage‐negative populations isolated from wounded and unwounded dorsal skin was performed, identifying an enrichment of transcripts associated with matrix synthesis and remodeling in the lineage‐positive populations. Using a novel excisional wound model, ventral skin healed with a greatly reduced frequency of foxd1 lineage‐positive cells. This work supports that the embryonic origin of fibroblasts is an important predictor of fibroblast function, but also highlights that within disparate regions, fibroblasts of different lineages likely undergo convergent differentiation contributing to phenotypic similarities. [ABSTRACT FROM AUTHOR]

Malignant melanoma (MM) causes tremendous morbidity and mortality in the solid organ transplant population and may arise in three different clinical scenarios: (1) pretransplant melanoma; (2) de novo melanoma post transplantation and (3) donor‐derived melanoma. This manuscript primarily addresses the first two scenarios with respect to the evaluation and management of pretransplant MM, consideration of transplant candidacy and the occurrence and management of de novo MM post transplantation. The authors outline current evidence describing risks associated with pre‐transplant melanoma to support recently established expert opinion for transplant candidacy. [ABSTRACT FROM AUTHOR]

Background: Body composition is minimally investigated in an immunotherapy era. Specific body composition signals such as myosteatosis may reflect aspects of patients' immunology and thereby their ability to respond to immunotherapies. Ipilimumab is a key checkpoint inhibitor in metastatic melanoma. As an antibody, it may also be more accurately dosed using body composition parameters rather than weight alone. This retrospective study aimed to investigate body composition‐based dosing and outcomes. Methods: Pretreatment computed tomography images from metastatic melanoma, ipilimumab‐treated patients from 2009 to 2014 were used to measure myosteatosis [skeletal muscle radiographic density or SMD, in Hounsfield units (HU)] and surface area (cm2) as previously described. Cut point analysis determined whether a level of ipilimumab dose and myosteatosis demonstrated differences in progression‐free (PFS) and overall survival (OS). Secondary endpoints included objective response rates and toxicities. Results: Of 121 identified, 97 patients were evaluable. Baseline demographics included 56 years median age, 60% male participants, and 23.7% with BRAF mutations. SMD analysis identified cut‐offs of SMD < 42 in those with BMI < 25 kg/m2 and <20 HU in those with BMI ≥ 25 kg/m2, respectively. Low SMD patients had poorer median PFS [2.4 vs. 2.7 months, hazard ratio (HR) 1.76, P = 0.008] and OS (5.4 vs. 17.5 months, HR 2.47, P = 0.001), which remained significant in multivariate modelling. High SMD patients had more immune‐related adverse events, better objective response rates (17.9 vs. 3.3%, P = 0.051), and lower baseline neutrophil‐to‐lymphocyte ratio (21 vs. 39%, P = 0.049). Separately, patients receiving <2.03 mg/cm2 had improved median PFS (3.0 vs. 2.6 months, HR 1.88, P = 0.02) and OS (14.9 vs. 5.7 months, HR 1.98, P = 0.01). Conclusions: Low SMD and receiving >2.03 mg/cm2 are prognostic of poorer melanoma outcomes post ipilimumab. SMD may identify patients with flawed immunology and predict who may better respond to such therapy. Ipilimumab dosing by skeletal muscle index stands in contrast to weight‐based dosing and may demonstrate a more accurate method of antibody dosing. [ABSTRACT FROM AUTHOR]

Introduction: We report the outcomes of using a combination of cetuximab with radiation therapy (Cetux-RT) to treat a selected group of patients with locally advanced (unresectable) cutaneous squamous cell carcinoma (LA-cSCC). This study presents two-year efficacy and safety data for 8 patients with LA-cSCC treated within a single institution.Methods: Between 2014 and 2017 a total of eight patients (seven males, one female) with LA-cSCC received curative intent treatment with Cetux-RT. All patients received an initial loading dose of cetuximab at 400 mg/m2 seven days prior to radiotherapy, followed by weekly treatment with 250 mg/m2 , continuing through the end of radiotherapy. Radiation doses were 6600 cGy/30 fr (n = 2), 6300 cGy/30fr (n = 2) and 5500 cGy/22 fr (n = 4).Results: The median age was 81 years (range, 55-87). The ECOG performance status of all patients was between 0 and 2. With a median duration of follow-up of 25 months (range 10-48 months), five patients remain in a complete response. After a partial response, another patient has relapsed and is receiving palliative chemotherapy, while two patients have died during the period of follow up (one of whom died following progression of disease, the other of an unrelated cause). Treatment in this group of patients was well tolerated, with most toxicities ≤ grade 2, and no toxicities of grade 4/5 reported.Conclusions: Cetux-RT was well tolerated and provided durable disease control within this patient sample. Our data support the use of the Cetux-RT regimen for selected patients with inoperable LA-cSCC and adequate performance status. [ABSTRACT FROM AUTHOR]

Hydrolysis of ATP by the mitochondrial F‐ATPase is inhibited by a protein called IF1. In the parasitic flagellate, Trypanosoma brucei, this protein, known as TbIF1, is expressed exclusively in the procyclic stage, where the F‐ATPase is synthesizing ATP. In the bloodstream stage, where TbIF1 is absent, the F‐ATPase hydrolyzes ATP made by glycolysis and compensates for the absence of a proton pumping respiratory chain by translocating protons into the intermembrane space, thereby maintaining the essential mitochondrial membrane potential. We have defined regions and amino acid residues of TbIF1 that are required for its inhibitory activity by analyzing the binding of several modified recombinant inhibitors to F1‐ATPase isolated from the procyclic stage of T. brucei. Kinetic measurements revealed that the C‐terminal portion of TbIF1 facilitates homodimerization, but it is not required for the inhibitory activity, similar to the bovine and yeast orthologs. However, in contrast to bovine IF1, the inhibitory capacity of the C‐terminally truncated TbIF1 diminishes with decreasing pH, similar to full length TbIF1. This effect does not involve the dimerization of active dimers to form inactive tetramers. Over a wide pH range, the full length and C‐terminally truncated TbIF1 form dimers and monomers, respectively. TbIF1 has no effect on bovine F1‐ATPase, and this difference in the mechanism of regulation of the F‐ATPase between the host and the parasite could be exploited in the design of drugs to combat human and animal African trypanosomiases. The essential ATPase activity of mitochondrial ATP synthase in the pathogenic stage of Trypanosoma brucei is inhibited by a protein inhibitor TbIF1. TbIF1 forms dimers, acts in a pH‐dependent manner, and does not inhibit a mammalian F1‐ATPase. The inhibition of F1‐ATPase by TbIF1 exhibits several parasite‐specific features. Differences between the parasite and host F1‐ATPase inhibition can be exploited in drug design. [ABSTRACT FROM AUTHOR]

On page three of I Life in Oil: Cofán Survival in the Petroleum Fields of Amazonia i , I was stopped by a photograph of Lucia, Alejandro, and Roberto, three Cofán people whose faces are strikingly rendered in an excellent black and white photograph by Bear Guerra. The two versions of these three persons pulled me into the book, the photography setting a high expectation for what the text might tell me about Cofán life. I suspect that the Cofán, and Cepek's account, have an important part to play in debates of the next few decades, within communities like Dureno, but also around the world. [Extracted from the article]

Objective: We estimated the incidence and prevalence of depression, anxiety disorder, bipolar disorder, and schizophrenia in a population-based cohort with rheumatoid arthritis (RA) as compared to an age-, sex-, and geographically matched cohort without RA.Methods: Using population-based administrative health data from Manitoba, Canada, we identified persons with incident RA between 1989 and 2012, and a cohort from the general population matched 5:1 on year of birth, sex, and region of residence. We applied validated algorithms for depression, anxiety disorder, bipolar disorder, and schizophrenia to determine the annual incidence of these conditions after the diagnosis of RA, and their lifetime and annual period prevalence. We compared findings between cohorts using negative binomial regression models.Results: We identified 10,206 incident cases of RA and 50,960 matched individuals. After adjustment for age, sex, socioeconomic status, region of residence, number of physician visits, and year, the incidence of depression was higher in the RA cohort over the study period (incidence rate ratio [IRR] 1.46 [95% confidence interval (95% CI) 1.35-1.58]), as was the incidence of anxiety disorder (IRR 1.24 [95% CI 1.15-1.34]) and bipolar disorder (IRR 1.21 [95% CI 1.00-1.47]). The incidence of schizophrenia did not differ between groups (IRR 0.96 [95% CI 0.61-1.50]). Incidence rates of psychiatric disorders declined minimally over time. The lifetime and annual period prevalence of depression and anxiety disorder were also higher in the RA than in the matched cohort over the study period.Conclusion: The incidence and prevalence of depression, anxiety disorder, and bipolar disorder are elevated in the RA population as compared to a matched population. [ABSTRACT FROM AUTHOR]

Abstract: To quantify differences between dry deposition algorithms commonly used in North America, five models were selected to calculate dry deposition velocity (Vd) for O3 and SO2 over a temperate mixed forest in southern Ontario, Canada, where a 5‐year flux database had previously been developed. The models performed better in summer than in winter with correlation coefficients for hourly Vd between models and measurements being approximately 0.6 and 0.3, respectively. Differences in mean Vd values between models were on the order of a factor of 2 in both summer and winter. All models produced lower Vd values than the measurements of O3 in summer and SO2 in summer and winter, although the measured Vd may be biased. There was not a consistent tendency in the models to overpredict or underpredict for O3 in winter. Several models produced magnitudes of the diel variation of Vd (O3) comparable to the measurements, while all models produced slightly smaller diel variations than the measurements of Vd (SO2) in summer. A few models produced larger diel variations than the measurements of Vd for O3 and SO2 in winter. Model differences were mainly due to different surface resistance parameterizations for stomatal and nonstomatal uptake pathways, while differences in aerodynamic and quasi‐laminar resistances played only a minor role. It is recommended to use ensemble modeling results for ecosystem impact assessment studies, which provides mean values of all the used models and thus can avoid too much overestimations or underestimations. [ABSTRACT FROM AUTHOR]

The F‐ATPases (also called the F1Fo‐ATPases or ATP synthases) are multi‐subunit membrane‐bound molecular machines that produce ATP in bacteria and in eukaryotic mitochondria and chloroplasts. The structures and enzymic mechanisms of their F1‐catalytic domains are highly conserved in all species investigated hitherto. However, there is evidence that the F‐ATPases from the group of protozoa known as Euglenozoa have novel features. Therefore, we have isolated pure and active F1‐ATPase from the euglenozoan parasite, Trypanosoma brucei, and characterized it. All of the usual eukaryotic subunits (α, β, γ, δ, and ε) were present in the enzyme, and, in addition, two unique features were detected. First, each of the three α‐subunits in the F1‐domain has been cleaved by proteolysis in vivo at two sites eight residues apart, producing two assembled fragments. Second, the T. brucei F1‐ATPase has an additional subunit, called p18, present in three copies per complex. Suppression of expression of p18 affected in vitro growth of both the insect and infectious mammalian forms of T. brucei. It also reduced the levels of monomeric and multimeric F‐ATPase complexes and diminished the in vivo hydrolytic activity of the enzyme significantly. These observations imply that p18 plays a role in the assembly of the F1 domain. These unique features of the F1‐ATPase extend the list of special characteristics of the F‐ATPase from T. brucei, and also, demonstrate that the architecture of the F1‐ATPase complex is not strictly conserved in eukaryotes. [ABSTRACT FROM AUTHOR]

Lichens are actually made up of several organisms living in a community, and have their own spectacular varieties and color combinations, which are a source of tourism inspiration, through naturalism with a hand lens. The book is very well-structured to accommodate readers as they wander through the subject matter, guided and sometimes brought up short by images, maps, photographs, and drawings. Thinking about this elegant book brings to mind an intricate list, something that might appear in a novel by Umberto Eco or Salman Rushdie. [Extracted from the article]

The extracellular adherence protein (Eap) plays a crucial role in pathogenesis and survival of Staphylococcus aureus by inhibiting the classical and lectin pathways of complement. We have previously shown that Eap binds with nanomolar affinity to complement C4b and disrupts the initial interaction between C4b and C2, thereby inhibiting formation of the classical and lectin pathway C3 pro-convertase. Although an underlying mechanism has been identified, the structural basis for Eap binding to C4b is poorly understood. Here, we show that Eap domains 3 and 4 each contain a low-affinity, but saturable binding site for C4b. Taking advantage of the high lysine content of Eap, we used a zero-length crosslinking approach to map the Eap binding site to both the α′- and γ-chains of C4b. We also probed the C4b/Eap interface through a chemical footprinting approach involving lysine modification, proteolytic digestion, and mass spectrometry. This identified seven lysines in Eap that undergo changes in solvent exposure upon C4b binding. We found that simultaneous mutation of these lysines to either alanine or glutamate diminished C4b binding and complement inhibition by Eap. Together, our results provide insight into Eap recognition of C4b, and suggest that the repeating domains that comprise Eap are capable of multiple ligand-binding modes. [ABSTRACT FROM AUTHOR]

The protein methylome in mammalian mitochondria has been little studied until recently. Here, we describe that lysine-368 of human citrate synthase is methylated and that the modifying enzyme, localized in the mitochondrial matrix, is methyltransferase-like protein 12 (METTL12), a member of the family of 7β-strand methyltransferases. Lysine-368 is near the active site of citrate synthase, but removal of methylation has no effect on its activity. In mitochondria, it is possible that some or all of the enzymes of the citric acid cycle, including citrate synthase, are organized in metabolons to facilitate the channelling of substrates between participating enzymes. Thus, possible roles for the methylation of Lys-368 are in controlling substrate channelling itself, or in influencing protein-protein interactions in the metabolon. [ABSTRACT FROM AUTHOR]

The p300/CBP-associated factor (PCAF) and related GCN5 bromodomain-containing lysine acetyl transferases are members of subfamily I of the bromodomain phylogenetic tree. Iterative cycles of rational inhibitor design and biophysical characterization led to the discovery of the triazolopthalazine-based L-45 (dubbed L-Moses) as the first potent, selective, and cell-active PCAF bromodomain (Brd) inhibitor. Synthesis from readily available (1R,2S)-(−)-norephedrine furnished L-45 in enantiopure form. L-45 was shown to disrupt PCAF-Brd histone H3.3 interaction in cells using a nanoBRET assay, and a co-crystal structure of L-45 with the homologous Brd PfGCN5 from Plasmodium falciparum rationalizes the high selectivity for PCAF and GCN5 bromodomains. Compound L-45 shows no observable cytotoxicity in peripheral blood mononuclear cells (PBMC), good cell-permeability, and metabolic stability in human and mouse liver microsomes, supporting its potential for in vivo use. [ABSTRACT FROM AUTHOR]

Grillparzer's Der arme Spielmann exemplifies the truth that the nineteenth-century German novella, although informed by the philosophical and cultural legacy of German idealist aesthetics, also embodies a narrative critique of it. The poetic realist novella in German should therefore be read in the context of German idealist aesthetics but never reduced to the terms which that aesthetics defines. This essay challenges, through a detailed analysis of Grillparzer's text, the view that German poetic realism expresses an idea of art which is supposed to be transcendent of the world of economic necessity and social facts. On the contrary, Grillparzer's novella is shown to highlight the contradiction between that world and the way its central character experiences 'art'. Unlike the major modes of idealist aesthetics, and despite its concern with the 'formless art' of music, this text does not endorse an idea of artistic creation derived from the non-verbal arts, in which art more embodies than represents the real. Grillparzer's text does not hide but rather foregrounds the process of literary creation. It emphasises the distance between any supposedly disengaged realism and the actuality of experience. The essay both argues this thesis in detail in relation to Grillparzer's Der arme Spielmann and shows its relevance to the reassessment of German poetic realism in German as a whole. [ABSTRACT FROM AUTHOR]

The structures of F-ATPases have predominantly been determined from mitochondrial enzymes, and those of the enzymes in eubacteria have been less studied. Paracoccus denitrificans is a member of the α-proteobacteria and is related to the extinct protomitochondrion that became engulfed by the ancestor of eukaryotic cells. The P. denitrificans F-ATPase is an example of a eubacterial F-ATPase that can carry out ATP synthesis only, whereas many others can catalyse both the synthesis and the hydrolysis of ATP. Inhibition of the ATP hydrolytic activity of the P. denitrificans F-ATPase involves the ζ inhibitor protein, an α-helical protein that binds to the catalytic F1 domain of the enzyme. This domain is a complex of three α-subunits and three β-subunits, and one copy of each of the γ-, δ- and ɛ-subunits. Attempts to crystallize the F1-ζ inhibitor complex yielded crystals of a subcomplex of the catalytic domain containing the α- and β-subunits only. Its structure was determined to 2.3 Å resolution and consists of a heterodimer of one α-subunit and one β-subunit. It has no bound nucleotides, and it corresponds to the `open' or `empty' catalytic interface found in other F-ATPases. The main significance of this structure is that it aids in the determination of the structure of the intact membrane-bound F-ATPase, which has been crystallized. [ABSTRACT FROM AUTHOR]

Books reviewed in this section are: Andrew Darley Visual Digital Culture: Surface Play and Spectacle in New Media Genres Guy Peploe S. J. Peploe 1871–1935 Edward Lucie-Smith Lives of the Great Twentieth-Century Artists Petrine Archer-Straw Negrophilia: Avant-Garde Paris and Black Culture in the 1920s Pierre Cailler Maurice Denis: Catalogue Raisonné de l'oeuvre grave et lithographie Jill-Elyse Grossvogel Clause-Emile Schuffenecker: Catalogue Raisonné I Ed by Salim Kemal and Ivan Gaskell Politics and Aesthetics in the Arts Terry Matz The Daybook of Saints. A Celebration of Saints Throughout the Year [ABSTRACT FROM AUTHOR]

Background: The zebrafish genetic mutant iguana ( igu) has defects in the ciliary basal body protein Dzip1, causing improper cilia formation. Dzip1 also interacts with the downstream transcriptional activators of Hedgehog (Hh), the Gli proteins, and Hh signaling is disrupted in igu mutants. Hh governs a wide range of developmental processes, including stabilizing developing blood vessels to prevent hemorrhage. Using igu mutant embryos and embryos treated with the Hh pathway antagonist cyclopamine, we conducted a microarray to determine genes involved in Hh signaling mediating vascular stability. Results: We identified 40 genes with significantly altered expression in both igu mutants and cyclopamine-treated embryos. For a subset of these, we used in situ hybridization to determine localization during embryonic development and confirm the expression changes seen on the array. Conclusions: Through comparing gene expression changes in a genetic model of vascular instability with a chemical inhibition of Hh signaling, we identified a set of 40 differentially expressed genes with potential roles in vascular stabilization. Developmental Dynamics 244:211-223, 2015. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Rifampicin resistance, a defining attribute of multidrug-resistant tuberculosis, is conferred by mutations in the β subunit of RNA polymerase. Sequencing of rifampicin-resistant ( RIF- R) clinical isolates of M ycobacterium tuberculosis revealed, in addition to RIF- R mutations, enrichment of potential compensatory mutations around the double-psi β-barrel domain of the β′ subunit comprising the catalytic site and the exit tunnel for newly synthesized RNA. Sequential introduction of the resistance allele followed by the compensatory allele in isogenic M ycobacterium smegmatis showed that these mutations respectively caused and compensated a starvation enhanced growth defect by altering RNA polymerase activity. While specific combinations of resistance and compensatory alleles converged in divergent lineages, other combinations recurred among related isolates suggesting transmission of compensated RIF- R strains. These findings suggest nutrient poor growth conditions impose larger selective pressure on RIF- R organisms that results in the selection of compensatory mutations in a domain involved in catalysis and starvation control of RNA polymerase transcription. [ABSTRACT FROM AUTHOR]

Aquatic ecosystems are important components of landscape carbon budgets. In lake-rich landscapes, both lakes and streams may be important sources of carbon gases (CO2 and CH4) to the atmosphere, but the processes that control gas concentrations and emissions in these interconnected landscapes have not been adequately addressed. We use multiple data sets that vary in their spatial and temporal extent during 2001-2012 to investigate the carbon gas source strength of streams in a lake-rich landscape and to determine the contribution of lakes, metabolism, and groundwater to stream CO2 and CH4. We show that streams emit roughly the same mass of CO2 (23.4 Gg C yr−1; 0.49 mol CO2 m−2 d−1) as lakes at a regional scale (27 Gg C yr−1) and that stream CH4 emissions (189 Mg C yr−1; 8.46 mmol CH4 m−2 d−1) are an important component of the regional greenhouse gas balance. Gas transfer velocity variability (range = 0.34 to 13.5 m d−1) contributed to the variability of gas flux in this landscape. Groundwater inputs and in-stream metabolism control stream gas supersaturation at the landscape scale, while carbon cycling in lakes and deep groundwaters does not control downstream gas emissions. Our results indicate the need to consider connectivity of all aquatic ecosystems (lakes, streams, wetlands, and groundwater) in lake-rich landscapes and their connections with the terrestrial environment in order to understand the full nature of the carbon cycle. [ABSTRACT FROM AUTHOR]

Private-sector institutions offering English for speakers of other languages ( ESOL) in postcompulsory contexts are distinctive in terms of their dual nature: As businesses, their principal raison d'etre is to turn a profit for their owners and shareholders, but at the same time they are educational institutions that are expected, at least in regulated environments, to adhere to established professional and ethical standards. ESOL teachers are professional educators trained in a humanistic academic tradition. When employed in private-sector English language centres, how do such professionals come to terms with the challenges of practising in a manifestly commercial environment? This article employs a services perspective to explore tensions between commercial and educational or professional imperatives in ESOL. It considers the challenges facing ESOL teachers in functioning as so-called market-oriented teachers (Fredriksson, ), able both to uphold the tenets of their profession and to support the business strategy and commercial practices of their employer. Although it is unlikely that strains in the ESOL business-education relationship can be entirely dispelled, examples of good practice suggest that a mutually beneficial alliance of the commercial and the educational is possible, resulting in profitable, professional, and ethical private-sector ESOL organisations. [ABSTRACT FROM AUTHOR]

Abscission is the process by which plants discard organs in response to environmental cues/stressors, or as part of their normal development. Abscission has been studied throughout the history of the plant sciences and in numerous species. Although long studied at the anatomical and physiological levels, abscission has only been elucidated at the molecular and genetic levels within the last two decades, primarily with the use of the model plant Arabidopsis thaliana. This has led to the discovery of numerous genes involved at all steps of abscission, including key pathways involving receptor-like protein kinases (RLKs). This review covers the current knowledge of abscission research, highlighting the role of RLKs. [ABSTRACT FROM AUTHOR]

Endothelial cells regulate many aspects of vascular physiology, including vasculogenesis and angiogenesis. The S100 family of calcium-binding proteins regulates many aspects of cell function but their roles in vascular physiology are less well understood. Herein, we investigated the expression and function of S100-related family members in endothelial cells. Analysis of total endothelial m RNAs using a human gene chip array revealed significant gene expression of the S100 calcium-binding protein family members S100A6, S100A10, S100A11 and S100A13. We then examined the expression and functional properties of the major S100 family member, S100A6, in vascular endothelial cells. Comparison of primary and transformed human cells revealed significant differences in S100A6 protein levels in these cells. In primary human endothelial cells, S100A6 was present in both the nucleus and the cytoplasm. To assess the function of endothelial S100A6, we depleted protein levels using RNA interference and this caused increased cell-cycle arrest in the G2/ M phase under different conditions. S100A6 depletion caused a decrease in both cyclin-dependent kinase 1 ( CDK1) and phospho- CDK1 levels, which are essential for eukaryote cell-cycle progression. S100A6 depletion also decreased expression of CDK1, cyclin A1 ( CCNA1) and cyclin B ( CCNB1) genes with effects on cell-cycle progression. Depletion of endothelial S100A6 levels also elevated β-galactosidase expression, which is an important hallmark of cellular senescence and exit from the mammalian cell cycle. We thus propose that S100A6 has an important role in regulating endothelial commitment to, and progression through, the cell cycle. [ABSTRACT FROM AUTHOR]

In the human systemic amyloidoses caused by mutant or wild-type transthyretin (TTR), deposition occurs at a distance from the site of synthesis. The TTR synthesized and secreted by the hepatocyte circulates in plasma, then deposits in target tissues far from the producing cell, a pattern reproduced in mice transgenic for multiple copies of the human wild-type TTR gene. By 2 yr of age, half of the transgenic males show cardiac deposition resembling human senile systemic amyloidosis. However, as early as 3 mo of age, when there are no deposits, cardiac gene transcription differs from that of nontransgenic littermates, primarily in the expression of a large number of genes associated with inflammation and the immune response. At 24 mo, the hearts with histologically proven TTR deposits show expression of stress response genes, exuberant mitochondrial gene transcription, and increased expression of genes associated with apoptosis, relative to the hearts without TTR deposition. These 24-mo-old hearts with TTR deposits also show a decrease in transcription of inflammatory genes relative to that in the younger transgenic mice. After 2 yr of expressing large amounts of human TTR, the livers of the transgenic mice without cardiac deposition display chaperone gene expression and evidence of an activated unfolded protein response, while the livers of animals with cardiac TTR deposition display neither, showing increased transcription of interferon-responsive inflammatory genes and those encoding an antioxidant response. With time, in animals with cardiac deposition, it appears that hepatic proteostatic capacity is diminished, exposing the heart to a greater load of misfolded TTR with subsequent extracellular deposition. Hence systemic (cardiac) TTR deposition may be the direct result of the diminution in the distant chaperoning capacity of the liver related to age or long-standing exposure to misfolded TTR, or both. [ABSTRACT FROM AUTHOR]

Human Deltex 3-like (DTX3L) is a member of the Deltex family of proteins. Initially identified as a B-lymphoma and BAL-associated protein, DTX3L is an E3 ligase that regulates subcellular localization of its partner protein, BAL, by a dynamic nucleocytoplasmic trafficking mechanism. Unlike other members of the Deltex family of proteins, DTX3L lacks the highly basic N-terminal motif and the central proline-rich motif present in other Deltex proteins, and instead contains other unique N-terminal domains. The C-terminal domains are, however, homologous with other members of the Deltex family of proteins; these include a RING domain and a previously unidentified C-terminal domain. In this study, we report the high-resolution crystal structure of this previously uncharacterized C-terminal domain of human DTX3L, which we term the Deltex C-terminal domain. Proteins 2012. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Summary [ABSTRACT FROM AUTHOR]

The thalassemia syndromes are associated with cardiovascular complications, which differ with the varying phenotypes encountered. The well-recognized paradigm of heart failure induced by myocardial iron overload, in thalassemia major (TM), has now been joined by pulmonary arterial hypertension (mostly seen in thalassemia intermedia) among other more subtle disorders of the cardiovascular system, including endothelial dysfunction. Cardiovascular magnetic resonance (T2*) has allowed cardiac iron load to be quantified noninvasively, and the routine measurement of T2* has been associated with a marked improvement in the outlook for patients with TM, in particular. Echocardiography remains an indispensable tool in the cardiovascular assessment of patients, it provides many insights into cardiovascular function, and its use allows improved management of patients. It is particularly suited to assess diastolic function, diagnose intracardiac masses (usually thrombus), and assess right ventricular function and pulmonary pressure. [ABSTRACT FROM AUTHOR]

The AMP-activated protein kinase (AMPK) is a highly conserved trimeric protein complex that is responsible for energy homeostasis in eukaryotic cells. Here, a 1.9 Å resolution crystal structure of the isolated kinase domain from the α2 subunit of human AMPK, the first from a multicellular organism, is presented. This human form adopts a catalytically inactive state with distorted ATP-binding and substrate-binding sites. The ATP site is affected by changes in the base of the activation loop, which has moved into an inhibited DFG-out conformation. The substrate-binding site is disturbed by changes within the AMPKα2 catalytic loop that further distort the enzyme from a catalytically active form. Similar structural rearrangements have been observed in a yeast AMPK homologue in response to the binding of its auto-inhibitory domain; restructuring of the kinase catalytic loop is therefore a conserved feature of the AMPK protein family and is likely to represent an inhibitory mechanism that is utilized during function. [ABSTRACT FROM AUTHOR]

Vascular endothelial growth factor A (VEGF-A)-induced signaling through VEGF receptor 2 (VEGFR2) regulates both physiological and pathological angiogenesis in mammals. However, the temporal and spatial mechanism underlying VEGFR2-mediated intracellular signaling is not clear. Here, we define a pathway for VEGFR2 trafficking and proteolysis that regulates VEGF-A-stimulated signaling and endothelial cell migration. Ligand-stimulated VEGFR2 activation and ubiquitination preceded proteolysis and cytoplasmic domain removal associated with endosomes. A soluble VEGFR2 cytoplasmic domain fragment displayed tyrosine phosphorylation and activation of downstream intracellular signaling. Perturbation of endocytosis by the depletion of either clathrin heavy chain or an ESCRT-0 subunit caused differential effects on ligand-stimulated VEGFR2 proteolysis and signaling. This novel VEGFR2 proteolysis was blocked by the inhibitors of 26S proteasome activity. Inhibition of proteasome activity prolonged VEGF-A-induced intracellular signaling to c-Akt and endothelial nitric oxide synthase (eNOS). VEGF-A-stimulated endothelial cell migration was dependent on VEGFR2 and VEGFR tyrosine kinase activity. Inhibition of proteasome activity in this assay stimulated VEGF-A-mediated endothelial cell migration. VEGFR2 endocytosis, ubiquitination and proteolysis could also be stimulated by a protein kinase C-dependent pathway. Thus, removal of the VEGFR2 carboxyl terminus linked to phosphorylation, ubiquitination and trafficking is necessary for VEGF-stimulated endothelial signaling and cell migration. [ABSTRACT FROM AUTHOR]

Ephrin receptor tyrosine kinase A3 (EphA3, EC 2.7.10.1) is a member of a unique branch of the kinome in which downstream signaling occurs in both ligand- and receptor-expressing cells. Consequently, the ephrins and ephrin receptor tyrosine kinases often mediate processes involving cell–cell contact, including cellular adhesion or repulsion, developmental remodeling and neuronal mapping. The receptor is also frequently overexpressed in invasive cancers, including breast, small-cell lung and gastrointestinal cancers. However, little is known about direct substrates of EphA3 kinase and no chemical probes are available. Using a library approach, we found a short peptide sequence that is a good substrate for EphA3 and is suitable for co-crystallization studies. Complex structures show multiple contacts between kinase and substrates; in particular, two residues undergo conformational changes and by mutation are found to be important for substrate binding and turnover. In addition, a difference in catalytic efficiency between EPH kinase family members is observed. These results provide insight into the mechanism of substrate binding to these developmentally integral enzymes. [ABSTRACT FROM AUTHOR]

The article discusses the establishment of riparian buffers as an effective method for the reduction of nutrient input into streams, despite the lack of understanding regarding underlying biogeochemical processes. The focus of the article is a 4-year study examining the effects of riparian zone restoration on the biogeochemical cycle of nitrogen (N) in a mountain pasture degraded by cattle. N cycles were compared using three experimental treatments which include restoration with vegetation regrowth, a simulated effects model of continuous grazing, and degraded riparian area with simulated soil compaction and vegetation removal. Soil solution concentrations of nitrate (NO3-), denitrification rates, and changes in nutrient cycling mechanisms are presented.