bluuebunny/crossref_metadata_2025 huggingface dataset:
AnRNAinterference knock‐down of nitrate reductase enhances lipid biosynthesis in the diatomPhaeodactylum tricornutum
Authors: Levitan Orly , Dinamarca Jorge , Zelzion Ehud , Gorbunov Maxim Y. , Falkowski Paul G.
Published: October 2015

When diatoms are stressed for inorganic nitrogen they remodel their intermediate metabolism and redirect carbon towards lipid biosynthesis. However, this response comes at a significant cost reflected in decreased photosynthetic energy conversion efficiency and growth. Here we explore a molecular genetics approach to restrict the assimilation of inorganic nitrogen by knocking down nitrate reductase (NR). The transformant strain,NR21, exhibited about 50% lower expression and activity of the enzyme but simultaneously accumulated over 40% more fatty acids. However, in contrast to nitrogen‐stressed wild‐type (WT) cells, which grow at about 20% of the rate of nitrogen‐replete cells, growth ofNR21 was only reduced by about 30%. Biophysical analyses revealed that the photosynthetic energy conversion efficiency of photosystemIIwas unaffected inNR21; nevertheless, the plastoquinone pool was reduced by 50% at the optimal growth irradiance while in theWTit was over 90% oxidized. Further analyses reveal a 12‐fold increase in the glutamate/glutamine ratio and an increaseNADPHand malonyl‐CoA pool size. Transcriptomic analyses indicate that the knock down resulted in changes in the expression of genes for lipid biosynthesis, as well as the expression of specific transcription factors. Based on these observations, we hypothesize that the allocation of carbon and reductants in diatoms is controlled by a feedback mechanism between intermediate metabolites, the redox state of the plastid and the expression and binding of transcription factors related to stress responses.
Genome‐wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes
Authors: Blaby Ian K. , Blaby‐Haas Crysten E. , Pérez‐Pérez María Esther , Schmollinger Stefan , Fitz‐Gibbon Sorel , Lemaire Stéphane D. , Merchant Sabeeha S.
Published: October 2015

Reactive oxygen species (ROS) are produced by and have the potential to be damaging to all aerobic organisms. In photosynthetic organisms, they are an unavoidable byproduct of electron transfer in both the chloroplast and mitochondrion. Here, we employ the reference unicellular green alga Chlamydomonas reinhardtii to identify the effect of H2O2 on gene expression by monitoring the changes in the transcriptome in a time‐course experiment. Comparison of transcriptomes from cells sampled immediately prior to the addition of H2O2 and 0.5 and 1 h subsequently revealed 1278 differentially abundant transcripts. Of those transcripts that increase in abundance, many encode proteins involved in ROS detoxification, protein degradation and stress responses, whereas among those that decrease are transcripts encoding proteins involved in photosynthesis and central carbon metabolism. In addition to these transcriptomic adjustments, we observe that addition of H2O2 is followed by an accumulation and oxidation of the total intracellular glutathione pool, and a decrease in photosynthetic O2 output. Additionally, we analyze our transcriptomes in the context of changes in transcript abundance in response to singlet O2 (), and relate our H2O2‐induced transcripts to a diurnal transcriptome, where we demonstrate enrichments of H2O2‐induced transcripts early in the light phase, late in the light phase and 2 h prior to light. On this basis several genes that are highlighted in this work may be involved in previously undiscovered stress remediation pathways or acclimation responses.
Thermosolutal Mixed Convection in an Air Filled Ventilated Enclosure With Slot Wise Embedded Heat and Contaminant Sources
Authors: Venkateshwarlu K. , Nayak A. K. , Singh Bhupinder , Katiyar V. K. , Gupta N.
Published: October 2015

Airflow, heat, and contaminant transfer in a mechanically ventilated two-dimensional rectangular enclosure by discrete heat and contaminant sources as well as external forced convection at various inlet and outlet locations is numerically simulated. Two different enclosure configurations are considered. In configuration A, the cold air is injected at the top of the left vertical wall and exited at the bottom of the right vertical wall. In configuration B, the cold air is injected at the lower edge of the left vertical wall and exited at the top of the right vertical wall. The objective of the study is to find the relative locations of inlet and outlet in order to obtain more effective cooling in the core of the enclosure by maximizing the heat and contaminant removal rate and reducing the overall temperature. The developed mathematical model is governed by the two-dimensional continuity, momentum, energy, and concentration equations. The governing equations in Cartesian co-ordinates are solved by finite volume based semi-implicit method for pressure linked-equations (SIMPLE) algorithm based on a staggered grid system. Results are presented for different values of the Reynolds number, Grashof number, Sherwood number, and Buoyancy ratio in the laminar regime. A convective transport visualization technique is used to study the behavior of physical phenomena due to stream function, thermal, and solutal functions. The results indicate that cooling inside the core of the enclosure is most effective when the inlet is kept at the bottom of the left vertical wall.
Real-Time Acoustic and Pressure Characterization of Two-Phase Flow for Quality Control of Expanded Polystyrene Injection Molding Processes
Authors: Magarian James N. , White Robert D. , Matson Douglas M.
Published: October 2015

A method is proposed for real-time process monitoring for expanded polystyrene (EPS) injection molding systems. The method employs measurement of two variables: vacuum pressure in the EPS supply hose and phase difference between two points along an acoustic standing wave generated within the EPS flow path. High-speed videography is utilized as a secondary means of monitoring the injection molding process. Video data are correlated with pressure and acoustic data to substantiate those variables’ validity as indicators of intended molding system performance. Data show recorded parameter curve shapes to be indicative of key injection molding milestone events, such as valve timing and changes in flow regime.
High school physics and socioeconomics
Authors: White Susan C.
Published: October 2015

In our September column, we noted that Hispanic and African-American seniors were less likely to have taken a high school physics course than their peers, and we suggested that socioeconomic status (SES) played a role in the lower participation. In the figure, we display the proportion of seniors, of physics teachers, and of physics enrollments at schools by SES. While the number of seniors is roughly one-third in each group, physics enrollments differ dramatically by SES. Furthermore, the disparity in enrollments is greater than the disparity in physics teachers; this means that the teachers teaching physics at “better off” schools teach more physics than the physics teachers at “worse off” schools. Thus, a physics teacher at a “better off” school is more likely to teach a majority of their classes in physics.
Thin Film Interference: An Experiment with Microwaves and Paraffin Oil
Authors: D'Anna Michele , Corridoni Tommaso
Published: October 2015

Thin film interference manifests itself in a wide range of visually pleasing situations in everyday life (in the colored effects caused by a drop of oil on water, in soap bubbles, etc.) and is also involved in important technical applications (semi-reflecting mirrors, anti-reflection lenses, etc.). Yet, despite its familiarity, high school students are rarely asked to consider this common phenomenon, in particular from an experimental point of view.
Using Nonprinciple Rays to Form Images in Geometrical Optics
Authors: Marx Jeff , Mian Shabbir
Published: October 2015

Constructing ray diagrams to locate the image of an object formed by thin lenses and mirrors is a staple of many introductory physics courses at the high school and college levels, and has been the subject of some pedagogy-related articles. Our review of textbooks distributed in the United States suggests that the singular approach involves drawing principle rays to locate an object's image. We were pleasantly surprised to read an article in this journal by Suppapittayaporn et al. in which they use an alternative method to construct rays for thin lenses based on a “tilted principle axis” (TPA). In particular, we were struck by the generality of the approach (a single rule for tracing rays as compared to the typical two or three rules), and how it could help students more easily tackle challenging situations, such as multi-lens systems and occluded lenses, where image construction using principle rays may be impractical. In this paper, we provide simple “proofs” for this alternative approach for the case of thin lenses and single refracting surfaces.
Teaching astronomy with case studies
Authors: Slater Timothy F.
Published: October 2015

Breaking the students into small, collaborative learning groups to solve a meaningful task together is one of the most successful and fully evaluated teaching techniques implemented over the last century. Although there are many ways to accomplish small group learning, a long-standing and consistently successful collaborative class activity is to use the case study teaching strategy. The use of case studies is common in medical schools and law schools, but not so common in the teaching of astronomy. Case studies create meaningful conversations among students and with the professor by focusing on life-like dilemmas to be solved. Case study tasks ask audience members to synthesize several ideas or evaluate scenarios that have not been explicitly presented to them in the lecture or in available readings.
Genes, circuits, and precision therapies for autism and related neurodevelopmental disorders
Authors: Sahin Mustafa , Sur Mriganka
Published: October 2015

Help for neurodevelopmental disorders

When the brain does not develop normally, the disabilities that ensue can affect a person for life. Sahin and Sur review how emerging knowledge of the molecular biology behind a suite of neurodevelopmental disorders is shedding light on the group as a whole. The new knowledge offers tantalizing leads toward more effective therapies.

Science
, this issue p.
10.1126/science.aab3897
Gene essentiality and synthetic lethality in haploid human cells
Authors: Blomen Vincent A. , Májek Peter , Jae Lucas T. , Bigenzahn Johannes W. , Nieuwenhuis Joppe , Staring Jacqueline , Sacco Roberto , van Diemen Ferdy R. , Olk Nadine , Stukalov Alexey , Marceau Caleb , Janssen Hans , Carette Jan E. , Bennett Keiryn L. , Colinge Jacques , Superti-Furga Giulio , Brummelkamp Thijn R.
Published: October 2015

Zeroing in on essential human genes

More powerful genetic techniques are helping to define the list of genes required for the life of a human cell. Two papers used the CRISPR genome editing system and a gene trap method in haploid human cells to screen for essential genes (see the Perspective by Boone and Andrews). Wang
et al.
's analysis of multiple cell lines indicates that it may be possible to find tumor-specific dependencies on particular genes. Blomen
et al.
investigate the phenomenon in which nonessential genes are required for fitness in the absence of another gene. Hence, complexity rather than robustness is the human strategy.

Science
, this issue p.
1096
and p.
1092
; see also p.
1028
Draft Genome Sequence of “
Candidatus
Phytoplasma pruni” Strain CX, a Plant-Pathogenic Bacterium
Authors: Lee I.-M. , Shao J. , Bottner-Parker K. D. , Gundersen-Rindal D. E. , Zhao Y. , Davis R. E.
Published: October 2015

“
Candidatus
Phytoplasma pruni” strain CX, belonging to subgroup 16SrIII-A, is a plant-pathogenic bacterium causing economically important diseases in many fruit crops. Here, we report the draft genome sequence, which consists of 598,508 bases, with a G+C content of 27.21 mol%.
Draft Genome Sequence of Burkholderia pseudomallei Strain 350105, Isolated in Hainan, China, in 1976
Authors: Song Lihua , Yu Yonghui , Feng Le , He Jun , Wang Tao , Zhu Hong , Duan Qing
Published: October 2015

Burkholderia pseudomallei
is the etiological agent of the potentially fatal disease melioidosis. Here, we report the draft genome sequence of a virulent water isolate obtained from the Hainan Province of China in 1976,
B. pseudomallei
strain 350105.
Complete Genome Sequence of Bacillus cereus Group Phage TsarBomba
Authors: Erill Ivan , Caruso Steven M.
Published: October 2015

The
Bacillus cereus
group bacteriophage TsarBomba, a double-stranded DNA
Myoviridae
, was isolated from soil collected in Saratov, Russia. TsarBomba was found to be similar to
Bacillus
phages BCP78 and BCU4, and to have a wide host range among
Bacillus cereus
group species.
Draft Genome Sequence of Brazilian Leptospira noguchii Serogroup Panama Strain U73, Isolated from Cattle
Authors: Moreno Luisa Z. , Loureiro Ana P. , Miraglia Fabiana , Matajira Carlos E. C. , Kremer Frederico S. , Eslabao Marcos R. , Dellagostin Odir A. , Lilenbaum Walter , Moreno Andrea M.
Published: October 2015

Leptospira noguchii
is a current zoonotic pathogen in Brazil. Here, we report the draft genome sequence of the Brazilian
L. noguchii
serogroup Panama strain U73, isolated from asymptomatic cattle urine.
Comparison of Whole-Genome Sequences from Two Colony Morphovars of Burkholderia pseudomallei
Authors: Hsueh Pei-Tan , Chen Yao-Shen , Lin Hsi-Hsu , Liu Pei-Ju , Ni Wen-Fan , Liu Mei-Chun , Chen Ya-Lei
Published: October 2015

The entire genomes of two isogenic morphovars (vgh16W and vgh16R) of
Burkholderia pseudomallei
were sequenced. A comparison of the sequences from both strains indicates that they show 99.99% identity, are composed of 22 tandem repeated sequences with <100 bp of indels, and have 199 single-base variants.
Draft Genome Sequence of
Acinetobacter
sp. Strain VT-511 Isolated from the Stomach of a Patient with Gastric Cancer
Authors: Tetz George , Tetz Victor
Published: October 2015

We report the draft genome sequence of
Acinetobacter
sp. strain VT-511, which was obtained from the stomach of a patient with gastric cancer. The genome of
Acinetobacter
sp. VT-511 is composed of approximately 3,416,321 bp and includes 3,214 predicted protein-coding genes.
Child health in Iceland before and after the economic collapse in 2008
Authors: Gunnlaugsson Geir
Published: October 2015

After rapid economic growth, more than 90% of the Icelandic banking system collapsed within 2 weeks in October 2008. A severe economic crisis of historic proportion ensued from which Iceland is still recovering. To protect those most vulnerable, governmental response included policy measures aimed to address the needs of children, families, the elderly, those on social benefits and the unemployed. By the maintenance of free universal healthcare for pregnant women and children, child health has been preserved. Six years later, there is little notable impact of the crisis on key child health indicators. Yet, the proportion of children born small-for-gestational age increased from 2.0% to 3.4%. One important pillar for the outcome is the good coverage and easy access to universal healthcare, educational and social services with highly qualified professionals. Iceland has shown that, by protecting the most vulnerable and maintaining universal access to healthcare, children's health and well-being can be maintained during an economic crisis.
Pseudoangiomatous stromal hyperplasia causing massive breast enlargement
Authors: Bourke Anita Geraldine , Tiang Stephen , Harvey Nathan , McClure Robert
Published: October 2015

Pseudoangiomatous stromal hyperplasia (PASH) of the breast is a benign mesenchymal proliferative process, initially described by Vuitchet al. We report an unusual case of a 46-year-old woman who presented with a 6-week history of bilateral massive, asymmetrical, painful enlargement of her breasts, without a history of trauma. On clinical examination, both breasts were markedly enlarged and oedematous, but there were no discrete palpable masses. Preoperative image-guided core biopsies and surgery showed PASH. PASH is increasingly recognised as an incidental finding on image-guided core biopsy performed for screen detected lesions. There are a few reported cases of PASH presenting as rapid breast enlargement. In our case, the patient presented with painful, asymmetrical, massive breast enlargement. Awareness needs to be raised of this entity as a differential diagnosis in massive, painful breast enlargement.
A well known and important adverse effect of phenytoin in a neurosurgical patient
Authors: Tomar Gaurav Singh , Saxena Anudeep , Kumar Niraj , Goyal Keshav
Published: October 2015

Gum hypertrophy is a well-known and important adverse effect of phenytoin therapy in a neurosurgical patient. We present an interesting case of a 21-year-old man who, following head injury after a road traffic accident, developed status epilepticus diagnosed with gum hypertrophy in the jaws, with ongoing antiepileptics. He was managed conservatively as per hospital protocol.
"Speeding up the road to recovery": The Complex Recovery Assessment and Consultation (CRAC) service
Authors: Davis Le Brun Stephanie
Published: October 2015

The number of bed closures in mental health is on the rise, creating additional pressure on services, including acute mental health services. An efficient way of working is required in order to streamline the acute care pathway and decrease unnecessary delays to length of stay, ensuring all individuals can be offered an inpatient bed when in crisis. The Complex Recovery Assessment and Consultation (CRAC) service was created in order to support acute mental health inpatient clinicians in streamlining hospital stays for service users who present with complex presentations that require lengthier admissions (over 40 days) by offering assessment, advice, and intervention from a rehabilitation perspective. The team was also created to understand why individuals may require a lengthy hospital stay.

Preliminary data showed that requiring a placement on discharge proved to be the most significant factor in increased length of stay and so the team took on a new role of discharge coordinator after around a year of operating. This involved assisting in decreasing any delays out of hospital through improved communication and dedicated time to complete tasks, such as completing paperwork for placement referrals and funding panels. Since taking on this role it was found that the time taken for individuals to be discharged to a rehabilitation or specialist placement decreased; a rehabilitation placement by 13.12 days and a specialist placement by 9.22 days. Discharge to a family address also decreased by 2.9 days and a home address by 2.47 days. Those patients with complex presentations benefit from having one dedicated team to coordinate the discharge process. Their lengthier acute inpatient stay is improved through streamlining care pathways, ultimately decreasing delays in discharge.
The biophysics of bird flight: functional relationships integrate aerodynamics, morphology, kinematics, muscles, and sensors
Authors: Altshuler Douglas L. , Bahlman Joseph W. , Dakin Roslyn , Gaede Andrea H. , Goller Benjamin , Lentink David , Segre Paolo S. , Skandalis Dimitri A.
Published: October 2015

Bird flight is a remarkable adaptation that has allowed the approximately 10 000 extant species to colonize all terrestrial habitats on earth including high elevations, polar regions, distant islands, arid deserts, and many others. Birds exhibit numerous physiological and biomechanical adaptations for flight. Although bird flight is often studied at the level of aerodynamics, morphology, wingbeat kinematics, muscle activity, or sensory guidance independently, in reality these systems are naturally integrated. There has been an abundance of new studies in these mechanistic aspects of avian biology but comparatively less recent work on the physiological ecology of avian flight. Here we review research at the interface of the systems used in flight control and discuss several common themes. Modulation of aerodynamic forces to respond to different challenges is driven by three primary mechanisms: wing velocity about the shoulder, shape within the wing, and angle of attack. For birds that flap, the distinction between velocity and shape modulation synthesizes diverse studies in morphology, wing motion, and motor control. Recently developed tools for studying bird flight are influencing multiple areas of investigation, and in particular the role of sensory systems in flight control. How sensory information is transformed into motor commands in the avian brain remains, however, a largely unexplored frontier.
EXPERIMENTAL INVESTIGATIONS ON INTESTINAL ANASTOMOSIS — A COMPARISON BETWEEN AUTOMATIC AND HAND SUTURING TECHNIQUES
Authors: KHOORJESTAN SANAZ MOSAFER , ROUHI GHOLAMREZA , TOOLABI KARAMOLLAH
Published: October 2015

In this research, intestinal anastomosis was compared in hand and automatic suturing. This work is based on two different experiments: The first one is the tensile test with the aim of finding the maximum breaking strength with the elongation rate of 5[Formula: see text]mm/min; and the second one is the fatigue test with a frequency of 0.2[Formula: see text]Hz and the amplitude of 16, 24 and 32[Formula: see text]mm of stretch in each phase to discover the total number of cycles to failure. For this purpose, 42 fresh bovine intestines were used; 21 specimens for the tensile and 21 for the fatigue test. These two tests were compared by two hand sewing techniques: simple continuous and ford interlocking stitches, and one automatic technique, i.e., the lock stitches. Seven samples were examined for each particular technique. The results of the tensile test indicated that the breaking strength of automatic sutured specimens is significantly greater than those of hand sutured specimens ([Formula: see text]). That might be due to the regularity, as the suturing lines by machines are more regular than suturing by hand. In addition, results showed that automatic sutured specimens failed in greater number of cycles than hand sutured specimens in the fatigue test ([Formula: see text]).
Ecological and Evolutionary Drivers of Geographic Variation in Species Diversity
Authors: Fine Paul V.A.
Published: October 2015

Recent studies have generated an explosion of phylogenetic and biogeographic data and have provided new tools to investigate the processes driving large-scale gradients in species diversity. Fossils and phylogenetic studies of plants and animals demonstrate that tropical regions are the source for almost all groups of organisms, and these groups are composed of a mixture of ancient and recently derived lineages. These findings are consistent with the hypothesis that the large extent of tropical environments during the past 10–50 million years, together with greater climatic stability, has promoted speciation and reduced extinction rates. Energy availability appears to only indirectly contribute to global patterns of species diversity, especially considering how some marine diversity gradients can be completely decoupled from temperature and productivity gradients. Instead, climate stability and time–integrated area together determine the baselines of both terrestrial and marine global diversity patterns. Biotic interactions likely augment diversification and coexistence in the tropics.
Modeling Species and Community Responses to Past, Present, and Future Episodes of Climatic and Ecological Change
Authors: Maguire Kaitlin C. , Nieto-Lugilde Diego , Fitzpatrick Matthew C. , Williams John W. , Blois Jessica L.
Published: October 2015

There is an urgent need to understand species and community responses to climatic and ecological changes to predict biodiversity patterns given anticipated global change. The current distribution of species and the environment provide a limited perspective to study and predict ecological responses; therefore, biodiversity responses to past environmental changes must be examined. The rapid development of ecological niche models (ENMs) and their use in reconstructing past species distributions has facilitated inclusion of past observations into predictive models. Paleodata offer an opportunity to test the predictive ability of ENMs and their underlying assumptions. However, paleodata remain underutilized despite the rapidly growing field of paleoinformatics. New modeling methods that incorporate species associations, coupled with paleodata, provide more robust approaches to studying species and community responses, especially given the predicted emergence of no-analog climates and communities in the future.
Integrative and Conjugative Elements (ICEs): What They Do and How They Work
Authors: Johnson Christopher M. , Grossman Alan D.
Published: October 2015

Horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. Integrative and conjugative elements (ICEs, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. Induction of ICE gene expression leads to excision, production of the conserved conjugation machinery (a type IV secretion system), and the potential to transfer DNA to appropriate recipients. ICEs typically contain cargo genes that are not usually related to the ICE life cycle and that confer phenotypes to host cells. We summarize the life cycle and discovery of ICEs, some of the regulatory mechanisms, and how the types of cargo have influenced our view of ICEs. We discuss how ICEs can acquire new cargo genes and describe challenges to the field and various perspectives on ICE biology.
The PI3K/AKT Pathway as a Target for Cancer Treatment
Authors: Mayer Ingrid A. , Arteaga Carlos L.
Published: October 2015

Anticancer targeted therapies are designed to exploit a particular vulnerability in the tumor, which in most cases results from its dependence on an oncogene and/or loss of a tumor suppressor. Genes in the phosphoinositide 3-kinase (PI3K)/AKT pathway are the most frequently altered in human cancers. Aberrant activation of this pathway, as a result of these somatic alterations, is associated with cellular transformation, tumorigenesis, cancer progression, and drug resistance. Several drugs targeting PI3K/ATK are currently in clinical trials, alone or in combination, in both solid tumors and hematologic malignancies. These drugs are the focus of this review.
Adaptive Optics Ophthalmoscopy
Authors: Roorda Austin , Duncan Jacque L.
Published: October 2015

This review starts with a brief history and description of adaptive optics (AO) technology, followed by a showcase of the latest capabilities of AO systems for imaging the human retina and by an extensive review of the literature on clinical uses of AO. It then concludes with a discussion on future directions and guidance on usage and interpretation of images from AO systems for the eye.
Zebrafish Models of Retinal Disease
Authors: Link Brian A. , Collery Ross F.
Published: October 2015

Visual defects affect a large proportion of humanity, have a significant negative impact on quality of life, and cause significant economic burden. The wide variety of visual disorders and the large number of gene mutations responsible require a flexible animal model system to carry out research for possible causes and cures for the blinding conditions. With eyes similar to humans in structure and function, zebrafish are an important vertebrate model organism that is being used to study genetic and environmental eye diseases, including myopia, glaucoma, retinitis pigmentosa, ciliopathies, albinism, and diabetes. This review details the use of zebrafish in modeling human ocular diseases.
Impact of mechanical ventilation on the pathophysiology of progressive acute lung injury
Authors: Nieman Gary F. , Gatto Louis A. , Habashi Nader M.
Published: October 2015

The earliest description of what is now known as the acute respiratory distress syndrome (ARDS) was a highly lethal double pneumonia. Ashbaugh and colleagues (Ashbaugh DG, Bigelow DB, Petty TL, Levine BE Lancet 2: 319-323, 1967) correctly identified the disease as ARDS in 1967. Their initial study showing the positive effect of mechanical ventilation with positive end-expiratory pressure (PEEP) on ARDS mortality was dampened when it was discovered that improperly used mechanical ventilation can cause a secondary ventilator-induced lung injury (VILI), thereby greatly exacerbating ARDS mortality. This Synthesis Report will review the pathophysiology of ARDS and VILI from a mechanical stress-strain perspective. Although inflammation is also an important component of VILI pathology, it is secondary to the mechanical damage caused by excessive strain. The mechanical breath will be deconstructed to show that multiple parameters that comprise the breath—airway pressure, flows, volumes, and the duration during which they are applied to each breath—are critical to lung injury and protection. Specifically, the mechanisms by which a properly set mechanical breath can reduce the development of excessive fluid flux and pulmonary edema, which are a hallmark of ARDS pathology, are reviewed. Using our knowledge of how multiple parameters in the mechanical breath affect lung physiology, the optimal combination of pressures, volumes, flows, and durations that should offer maximum lung protection are postulated.
WDR5 Supports an N-Myc Transcriptional Complex That Drives a Protumorigenic Gene Expression Signature in Neuroblastoma
Authors: Sun Yuting , Bell Jessica L. , Carter Daniel , Gherardi Samuele , Poulos Rebecca C. , Milazzo Giorgio , Wong Jason W.H. , Al-Awar Rima , Tee Andrew E. , Liu Pei Y. , Liu Bing , Atmadibrata Bernard , Wong Matthew , Trahair Toby , Zhao Quan , Shohet Jason M. , Haupt Ygal , Schulte Johannes H. , Brown Peter J. , Arrowsmith Cheryl H. , Vedadi Masoud , MacKenzie Karen L. , Hüttelmaier Stefan , Perini Giovanni , Marshall Glenn M. , Braithwaite Antony , Liu Tao
Published: October 2015

MYCN gene amplification in neuroblastoma drives a gene expression program that correlates strongly with aggressive disease. Mechanistically, trimethylation of histone H3 lysine 4 (H3K4) at target gene promoters is a strict prerequisite for this transcriptional program to be enacted. WDR5 is a histone H3K4 presenter that has been found to have an essential role in H3K4 trimethylation. For this reason, in this study, we investigated the relationship between WDR5-mediated H3K4 trimethylation and N-Myc transcriptional programs in neuroblastoma cells. N-Myc upregulated WDR5 expression in neuroblastoma cells. Gene expression analysis revealed that WDR5 target genes included those with MYC-binding elements at promoters such as MDM2. We showed that WDR5 could form a protein complex at the MDM2 promoter with N-Myc, but not p53, leading to histone H3K4 trimethylation and activation of MDM2 transcription. RNAi-mediated attenuation of WDR5 upregulated expression of wild-type but not mutant p53, an effect associated with growth inhibition and apoptosis. Similarly, a small-molecule antagonist of WDR5 reduced N-Myc/WDR5 complex formation, N-Myc target gene expression, and cell growth in neuroblastoma cells. In MYCN-transgenic mice, WDR5 was overexpressed in precancerous ganglion and neuroblastoma cells compared with normal ganglion cells. Clinically, elevated levels of WDR5 in neuroblastoma specimens were an independent predictor of poor overall survival. Overall, our results identify WDR5 as a key cofactor for N-Myc–regulated transcriptional activation and tumorigenesis and as a novel therapeutic target for MYCN-amplified neuroblastomas. Cancer Res; 75(23); 5143–54. ©2015 AACR.
Abstract A07: Combining CTLA4 and PD-L1 blockade leads to complete eradication of metastatic osteosarcoma
Authors: Lussier Danielle M. , Johnson John L. , Hingorani Pooja , Blattman Joseph N.
Published: October 2015

Osteosarcoma remains one of the most common bone cancers in children and adolescents. While conventional therapy can be effective at reducing or stabilizing primary osteosarcoma tumors, metastatic disease is typically refractory to treatment. Previously, we have investigated the role of PD-1 in limiting the efficacy of CTL to mediate metastatic osteosarcoma immune control. Blockade of PD-1/PD-L1 interactions in metastatic osteosarcoma dramatically improves survival outcomes by enhancing the function of osteosarcoma-specific CTL. However, PD-1/PD-L1 blockade treated mice still succumb to disease due to the development of PD-L1 antibody resistance. Combinational CTLA-4 and PD-L1 blockade treated mice were able to completely eradicate metastatic osteosarcoma, and generate immunity to disease. These results suggest that blockade of PD-1/PD-L1 interactions in patients with metastatic osteosarcoma may lead to tumor resistance, requiring combinational immunotherapies to combat disease.

Citation Format: Danielle M. Lussier, John L. Johnson, Pooja Hingorani, Joseph N. Blattman. Combining CTLA4 and PD-L1 blockade leads to complete eradication of metastatic osteosarcoma. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A07.
Abstract A17: The role of radiation-induced TGF-β in the generation of MDSCs
Authors: Gonzalez-Junca Alba , Pelicciotta Ilenia , Discroll Kyla Elizabeth , Barcellos-Hoff Mary Helen
Published: October 2015

Myeloid derived suppressor cells (MDSCs) are a subset of myeloid precursors that are only present in pathological situations such as pathogen infection and cancer. Very little is known about the regulation of this cells as well as the regulation of its immunosuppressive function. We are interested in whether MDSC abundance is regulated by tumor cells secreted factors as a means to evade anti-tumor immune responses and how this might be affected by radiation therapy. Our hypothesis is that radiation therapy activation of TGFβ, which has a prominent role in the induction and maintenance of MDSC, promotes MDSC in the tumor microenvironment, thereby limiting tumor control. To test this we first established co-cultures of tumor cell lines and freshly isolated PBMCs from normal donors. MDSC are rarely in healthy donor mono-cultures (less than 1%). However, co-culture with either MDA-MB231 breast cancer cell line or with U118-MG glioma cancer cells resulted in a significant enrichment in the population of MDSCs (up to 12%). We then isolated cells based on CD33 expression for functional characterization. Compared to CD33- cells, the CD33+ population expresses significantly higher levels of ARG1, PDL1, IL10 and TGFB1, which are markers of active MDSC. This model will be modified by co-culture with irradiated tumor cell lines in conjunction with TGFβ inhibitors in ongoing studies. We can postulate that the combination of radiotherapy and TGFβ inhibitors, which are nowadays in clinical trials for different cancer types, could have important therapeutic benefits.

Citation Format: Alba Gonzalez-Junca, Ilenia Pelicciotta, Kyla Elizabeth Discroll, Mary Helen Barcellos-Hoff. The role of radiation-induced TGF-β in the generation of MDSCs. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A17.
Abstract A40: Agonistic CD40 antibody combined with chemotherapy drives TLR4/MyD88 independent regression of pancreatic tumors in a T cell dependent manner
Authors: Byrne Katelyn T. , Vonderheide Robert H.
Published: October 2015

This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR07) of the Conference Proceedings.

Citation Format: Katelyn T. Byrne, Robert H. Vonderheide. Agonistic CD40 antibody combined with chemotherapy drives TLR4/MyD88 independent regression of pancreatic tumors in a T cell dependent manner. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A40.
Abstract A44: Checkpoint inhibition of adaptive immunity by IL-9 can be disrupted to achieve rapid T cell sensitization and rejection of progressive tumor challenges
Authors: Hoelzinger Dominique B. , Dominguez Ana Lucia , Cohen Peter A. , Gendler Sandra J.
Published: October 2015

Interleukin 9 (IL-9), the signature Th9 cytokine, is associated with T regulatory cell function, parasite expulsion and allergic airway inflammation. Because IL-9 can promote a tolerogenic/immunosuppressive environment, we used IL-9 knock-out (IL-9ko) mice to estimate the role of endogenous IL-9 in the biology of two aggressive breast cancers, TUBO and 4T1, and CT26 a colon carcinoma. Merely eliminating endogenous IL-9 enabled efficient sensitization of host T cells leading to early rejection of growing tumors. Duplicate tumor challenges simply grew progressively in wildtype mice. Interestingly, tumor rejection occurred without additional vaccines or immunomodulatory therapies. The IL-9ko mice acquired immunologic memory, which actively protected from residual disease and tumor rechallenges. The ability of a normally lethal tumor challenge to stimulate an enduring therapeutic response in IL-9ko mice was linked to the activation of CD8+ T cells, as IL-9ko mice failed to be cured if either CD8+ or CD4+ T cells were depleted. Importantly, T cells from tumor-rejecting IL-9ko mice retained effector competence in wildtype mice, and treatments with neutralizing anti-IL-9 significantly slowed tumor progression in wildtype mice. IL-9 inhibits the immune system's ability to prime effective immunological memory after exposure to growing tumor; it therefore functions as a checkpoint inhibitor of adaptive immunity. Optimization of IL-9 neutralization may play a unique role in immunotherapy.

Citation Format: Dominique B. Hoelzinger, Ana Lucia Dominguez, Peter A. Cohen, Sandra J. Gendler. Checkpoint inhibition of adaptive immunity by IL-9 can be disrupted to achieve rapid T cell sensitization and rejection of progressive tumor challenges. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A44.
Abstract A54: Laser-assisted intradermal delivery of Xcl1-specific fusion vaccines induces potent antitumor response
Authors: Terhorst Dorothea , Terhorst Dorothea , Fossum Even , Bogen Bjarne , Henri Sandrine , Malissen Bernard
Published: October 2015

Dendritic cells (DCs) are highly efficient specialized antigen-presenting cells and have been regarded as promising targets in cancer immunotherapy. Cross-presentation of antigen by a subset of DCs, the CD8α-type DCs to CD8+ T cells is a fundamentally important mechanism in the defense against pathogens and tumors. In human and mice, CD8α-type DCs that are able to cross present uniquely express the chemokine receptor Xcr1 that binds the Xcl1 chemokine. We targeted antigens to cross- presenting CD8α-type DCs using Xcl1 inserted in dimeric vaccine molecules. Bivalent Xcl1 fusion vaccines bind specifically to and chemoattract CD8α-type DCs in a Xcr1 dependent manner.

With its easy accessibility and rich network of DCs, the skin appeals as a promising target site for vaccination. Using the PLEASE® laser microporation system, we specifically applied Xcl1 fusion vaccines into the murine dermis and targeted the cross-presenting CD8α-type dermal DCs. A single application of Xcl1 coupled to the modelantigen Ovalbumin (OVA) on the dermis of the mouse ear skin produced enhanced CD4 and CD8 T-cell responses, even in the absence of adjuvants. The first T-cell response was limited to the ear draining lymph node. This suggests that the application of antigens by laser microporation to the ear leads to a first localized immune response and thus limiting the possible amount of systemic side effects. However, such targeting of Xcl1-OVA also produced a striking enhancement of antibody responses. When the mice were challenged with B16 melanoma expressing OVA, treatment with the Xcl1-OVA could prevent development or mediate eradication of subcutaneous solid B16-OVA melanoma.

We conclude that targeting of dimeric fusion vaccine molecules to dermal CD8α-type DCs by use of Xcl1 represents a novel and promising method for inducing cytotoxic T cell reponses. Targeting the right dendritic cell subset in the right cutaneous compartment via PLEASE® laser microporation is a promising approach for immunotherapy also e.g. against allergies and pathogens.

Citation Format: Dorothea Terhorst, Dorothea Terhorst, Even Fossum, Bjarne Bogen, Sandrine Henri, Bernard Malissen. Laser-assisted intradermal delivery of Xcl1-specific fusion vaccines induces potent antitumor response. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A54.
Abstract A57: Determine a transcriptional mechanism novel to tumor infiltrating T cell dysfunction
Authors: Waugh Katherine A. , Leach Sonia , Slansky Jill E.
Published: October 2015

This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR03) of the Conference Proceedings.

Citation Format: Katherine A. Waugh, Sonia Leach, Jill E. Slansky. Determine a transcriptional mechanism novel to tumor infiltrating T cell dysfunction. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A57.
Abstract A58: JAK1 deficiency as a novel mechanism of tumor immune escape in uterine cancer
Authors: Ren Yuan , Zhang Yonghong , Liu Richard Z. , Fenstermacher David A. , Wright Kenneth L. , Teer Jamie K. , Wu Jie
Published: October 2015

Recognition of MHC class I antigens on the surface of tumor cells is an essential process in the effector phase of CD8+ cytotoxic T lymphocyte (CTL)-mediated anti-tumor response. Presentation of MHC class I antigens on tumor cells is regulated by the JAK1/JAK2-mediated interferon-γ signaling pathway. We analyzed the targeted exome sequencing data of 3,274 human tumors from 48 different tissues in the Total Cancer Care (TCC) tumor bank and found JAK1 truncating mutations in 36 of 635 gynecologic tumors. The highest JAK1 truncating mutation rate (9.5%) was found in endometrial cancer. These truncating mutations result in the loss of the JAK1 protein tyrosine kinase (PTK) domain that is located in the C-terminal region. JAK1 truncating mutations in cancer cell lines of the Cancer Cell Line Encyclopedia (CCLE) databank also occur most often in endometrial cancer cells. Analysis of mutation sites identified three mutation hot spots. Re-sequencing of cancer cell lines, primary tumors, and matched normal tissues confirmed JAK1 mutations and revealed that these JAK1 mutations are somatic. Besides JAK1, recurrent JAK2 loss-of-function (LOF) mutations were also found in TCC tumors but at lower rates. Similar to JAK1, the highest rate of LOF JAK2 mutations was found in endometrial/uterine cancer. No JAK1 or JAK2 truncating mutation was identified in 130 samples from hematological malignancies. Functional assays showed that JAK1 deficient cancer cells were defective in interferon-γ-induced expression of tumor antigen processing machinery proteins LMP2 and TAP1 and cell surface expression of HLA molecules. These data identify recurrent JAK1 deficiency in endometrial cancer that impairs tumor antigen presentation by the MHC class I complex to CTLs. While PTKs have been perceived mostly as oncogenes and PTK inhibitors, including JAK inhibitors, have been developed for cancer therapy, our findings suggest that JAK1 is a novel tumor suppressor and that LOF JAK1 mutations allow tumor immune escape. Our findings also raise caution about the use of JAK inhibitors as therapeutic agents in solid tumors.

Citation Format: Yuan Ren, Yonghong Zhang, Richard Z. Liu, David A. Fenstermacher, Kenneth L. Wright, Jamie K. Teer, Jie Wu. JAK1 deficiency as a novel mechanism of tumor immune escape in uterine cancer. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A58.
Abstract A63: The role of DARC in the immunological tumor microenvironment of breast cancer
Authors: Davis Melissa B. , Monteil Michele , Hire Rupali , Howerth Elizabeth W.
Published: October 2015

The Duffy Antigen Receptor for Chemokines (DARC or ACKR1) gene regulates circulating levels of inflammatory chemokines and major alleles of the gene are associated with a myriad of clinical outcomes. There are two unique isoforms of DARC which are expressed from distinct separate promoters, but little is known about the expression or regulation of these isoforms. Using quantitative RT-PCR and Immunohistochemical studies of lymphoblastic cells from relevant ancestry groups, we recently found that a DARC polymorphism, the Duffy Null (Fy-) allele found almost exclusively in African ancestry groups, is associated with altered regulation of these isoforms. Our data indicates that people of African ancestry who carry the Fy- allele will have an altered expression pattern of DARC isoforms. Thusly, we investigated whether the Fy- allele is associated with distinct recruitment of monocytes to breast tumor epithelia, regulated by DARC modulated chemokines. This may translate into a suite of distinct inflammatory responses correlated with specific chemokine action and may explain the disparate clinical outcomes of breast cancer in this population.

Citation Format: Melissa B. Davis, Michele Monteil, Rupali Hire, Elizabeth W. Howerth. The role of DARC in the immunological tumor microenvironment of breast cancer. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A63.