bluuebunny/crossref_metadata_2025 huggingface dataset:
Depleted aldehyde dehydrogenase 1A1 (ALDH1A1) reverses cisplatin resistance of human lung adenocarcinoma cell A549/DDP
Authors: Wei Yunyan , Wu Shuangshuang , Xu Wei , Liang Yan , Li Yue , Zhao Weihong , Wu Jianqing
Published: November 2016

Background

Cisplatin is the standard first‐line chemotherapeutic agent for the treatment of non‐small cell lung cancer (NSCLC). However, resistance to chemotherapy has been a major obstacle in the management of NSCLC. Aldehyde dehydrogenase 1A1 (ALDH1A1) overexpression has been observed in a variety of cancers, including lung cancer. The purpose of this study was to investigate the effect of ALDH1A1 expression on cisplatin resistance and explore the mechanism responsible.

Methods

Reverse transcriptase‐PCR was applied to measure the messenger RNA expression of ALDH1A1, while Western blot assay was employed to evaluate the protein expression of ALDH1A1, B‐cell lymphoma 2, Bcl‐2‐like protein 4, phospho‐protein kinase B (p‐AKT) and AKT. A short hairpin RNA was used to knockdown ALDH1A1 expression. A 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide assay was used to determine the effect of ALDH1A1 decrease on cell viability. The cell apoptotic rate was tested using flow cytometry assay.

Results

ALDH1A1 is overexpressed in cisplatin resistant cell line A549/DDP, compared with A549. ALDH1A1 depletion significantly decreased A549/DDP proliferation, increased apoptosis, and reduced cisplatin resistance. In addition, the phosphoinositide 3‐kinase (PI3K)
/
AKT pathway is activated in A549/DDP, and ALDH1A1 knockdown reduced the phosphorylation level of AKT. Moreover, the combination of ALDH1A1‐short hairpin RNA and PI3K/AKT pathway inhibitor LY294002 markedly inhibited cell viability, enhanced apoptotic cell death, and increased cisplatin sensitivity.

Conclusion

These results suggest that ALDH1A1 depletion could reverse cisplatin resistance in human lung cancer cell line A549/DDP, and may act as a potential target for the treatment of lung cancers resistant to cisplatin.
Physiological changes associated with routine nursing procedures in critically ill are common: an observational pilot study
Authors: Engström J. , Bruno E. , Reinius H. , Fröjd C. , Jonsson H. , Sannervik J. , Larsson A.
Published: November 2016

Background

Nursing procedures that are routinely performed in the intensive care unit (ICU) are assumed to have minimal side effects. However, these procedures may sometimes cause physiological changes that negatively affect the patient. We hypothesized that physiological changes associated with routine nursing procedures in the ICU are common.

Methods

A clinical observational study of 16 critically ill patients in a nine‐bed mixed university hospital ICU. All nursing procedures were observed, and physiological data were collected and subsequently analyzed. Minor physiological changes were defined as minimal changes in respiratory or circulatory variables, and major physiological changes were marked as hyper/hypotension, bradycardia/tachycardia, bradypnea/tachypnea, ventilatory distress, and peripheral blood oxygen desaturation.

Results

In the 16 patients, 668 procedures generated 158 major and 692 minor physiological changes during 187 observational hours. The most common procedure was patient position change, which also generated the majority of the physiological changes. The most common major physiological changes were blood oxygen desaturation, ventilatory distress, and hypotension, and the most common minor changes were arterial pressure alteration, coughing, and increase in respiratory rate.

Conclusion

In this pilot study, we examined physiological changes in connection with all regular routine nursing procedures in the ICU. We found that physiological changes were common and sometimes severe.
Progression from unipolar depression to schizophrenia
Authors: Musliner Katherine L. , Munk‐Olsen Trine , Mors Ole , Østergaard Søren D.
Published: November 2016

Objective

To examine progression from unipolar depression (UD) to schizophrenia and to identify groups of UD patients at elevated risk for progression.

Method

Historical prospective cohort study using data from Danish national registers. The sample included 71 932 individuals who received a diagnosis of UD in Denmark between January 1, 1995, and May 31, 2013. Analyses were conducted using Kaplan–Meier estimates and Cox regressions.

Results

The 18.5‐year cumulative incidence of schizophrenia was 5.5% in women and 8.4% in men. The strongest predictors of progression included younger age (adjusted hazard ratio (AHR) for individuals 18–24 vs. 40+ = 7.42, 95% confidence interval = [6.29, 8.74]), psychotic symptoms at index UD diagnosis (AHR = 3.70 [3.18, 4.31]), previous disorder with psychotic features (AHR = 3.71 [3.31, 4.16]), and previous illicit substance use disorder (AHR = 1.66 [1.40, 1.97]). Groups of UD patients with different combinations of risk factors had elevated risk for progression, with 10‐year cumulative incidences ranging from 9% to 62%.

To conclude, at the time of UD diagnosis, the strongest risk factors for progression to schizophrenia include male sex, younger age, past/current psychotic symptoms, and illicit substance use disorders. These clinical predictors may aid in targeting monitoring for schizophrenia among patients with UD.
Towards a New Paradigm in Nano‐Genotoxicology: Facing Complexity of Nanomaterials’ Cellular Interactions and Effects
Authors: Gonzalez Laetitia , Cundari Enrico , Leyns Luc , Kirsch‐Volders Micheline
Published: November 2016

Changes in paradigm contribute to advances in research. The current paradigms for the evaluation of toxicity of chemicals refer to linear or curvilinear dose–response curves with or without threshold and to surface‐dependent induction of oxidative damage for particles. The unique physicochemical properties and biological/genotoxic activity of engineered nanomaterials (NMs) require the development of a new paradigm. Because of their unusual dosimetry and their multiple interactions at NM level (agglomeration/aggregation) and at different cellular and extracellular levels, NMs are likely to have complex modes of action (multiple hits at multiple targets) leading to complex thresholded–non‐thresholded dose–response curves. Understanding their cellular targets and their modes of action will contribute to the production of safe‐by‐design NMs. An integrative, cell‐by‐cell approach for genotoxic effects should be applied to tackle this emerging paradigm in nano‐genotoxicology.
From boundary waters to watersheds: Legal change and the geography of the Great Lakes‐St. Lawrence system
Authors: Benidickson Jamie
Published: November 2016

Key Messages

The legal framework applicable to the geography of the Great Lakes‐St. Lawrence has evolved.

At the time of theBoundary Waters Treatya linear, boundary‐oriented perspective prevailed.

Following theGreat Lakes Water Quality Agreementof 1972, the introduction of basin‐ and ecosystem‐oriented approaches altered the legal framework for the Great Lakes‐St. Lawrence system.
Genetics and genomics of ovarian sex cord‐stromal tumors
Authors: Fuller P.J. , Leung D. , Chu S.
Published: November 2016

Ovarian sex cord‐stromal tumors (SCST) represent approximately 8% of malignant ovarian tumors. The most common are granulosa cell tumors (GCT) which account for approximately 90% of malignant SCST. Recent studies have unraveled the key genomic and genetic events contributing to their pathogenesis. SCST are found in the hereditary syndromes: Peutz‐Jeghers syndrome, Ollier disease and Maffucci syndrome, and DICER1 syndrome. Genomic studies have largely been limited to GCT where a number of recurring chromosomal abnormalities (monsomy and trisomy) have been identified although their contribution to pathogenesis remains unclear. In addition to the recurrent DICER1 mutations reported in non‐hereditary cases of Sertoli cell and Sertoli–Leydig cell tumors, recurrent somatic mutations in both the juvenile (j) and adult (a) forms of GCT have been reported. Approximately 30% of jGCT contain a somatic mutation, the gsp oncogene, while a further 60% have an activating mutation in the AKT gene. In the case of aGCT, a well characterized mutation in the FOXL2 transcription factor (FOXL2 C134W) is found in almost all cases, which arguably defines the disease, although the molecular events that determine the stage, behavior and prognosis of aGCT remain to be determined.
MEG Evidence for Incremental Sentence Composition in the Anterior Temporal Lobe
Authors: Brennan Jonathan R. , Pylkkänen Liina
Published: November 2016

Research investigating the brain basis of language comprehension has associated the left anterior temporal lobe (ATL) with sentence‐level combinatorics. Using magnetoencephalography (MEG), we test the parsing strategy implemented in this brain region. The number of incremental parse steps from a predictive left‐corner parsing strategy that is supported by psycholinguistic research is compared with those from a less‐predictive strategy. We test for a correlation between parse steps and source‐localized MEG activity recorded while participants read a story. Left‐corner parse steps correlated with activity in the left ATL around 350–500 ms after word onset. No other correlations specific to sentence comprehension were observed. These data indicate that the left ATL engages in combinatoric processing that is well characterized by a predictive left‐corner parsing strategy.
Alcohol use disorders in Australia
Authors: Freyer C. H. , Morley K. C. , Haber P. S.
Published: November 2016

Alcohol use disorders are common in Australia and are often unrecognised. Alcohol places a significant burden on our healthcare system by increasing the risk of injuries as well as many chronic medical conditions. Diagnosis requires a high index of suspicion and can be aided by the use of specific questionnaires, such as the Alcohol Use Disorder Identification Test‐C. The current available laboratory tests are of limited sensitivity and specificity, but can nevertheless aid in the diagnosis in some circumstances. Newer tests, such as ethyl‐glucuronide and phosphatidylethanol, are more sensitive and specific but are costly and not widely available. The effective management of alcohol use disorder entails psychosocial or pharmacological treatments or a combination of both. In those who cannot reduce alcohol consumption, harm reduction strategies can be applied to reduce the burden of harm to the drinkers as well as the community at large.
Rates of neutropenia in adults with influenza A or B: a retrospective analysis of hospitalised patients in South East Queensland during 2015
Authors: Higgins P. , Runnegar N. , Bird R. J. , Markey K. A.
Published: November 2016

Neutropenia in adult patients is often attributed to intercurrent viral infections; however, there are limited data describing the frequency or natural history of this phenomenon. We examined all patients presenting to three large hospitals in the Metro South region of South East Queensland with laboratory‐confirmed influenza A or B throughout the 2015 influenza season (January–October). Four hundred and thirty‐six patients were studied and 15.3% of this cohort were neutropenic (absolute neutrophil count <2.0 × 109/L) with no identifiable cause other than the influenza. Importantly, the majority of cases were mild, with absolute neutrophil count remaining >1.0 × 109/L. The incidence of neutropenia was significantly higher in association with influenza B than influenza A (18.3% vs 10.3%). We conclude that mild, transient neutropenia is common among patients with influenza infection and advise that it should not cause alarm or invite specific investigation unless severe or prolonged.
A New “Mormon Moment”? The Book of Mormon in Literary Studies
Authors: Scales Laura Thiemann
Published: November 2016

Despite deep popular interest in Mormon culture, scholars have not given significant attention to the religion's central scripture. The Book of Mormon is relevant to literary studies at a moment when the turn to religion and debates over the secularization thesis have captured scholarly attention. Until recently, scholarship on The Book of Mormon was largely polemical and divided between apologists and skeptics. The rise of the new Mormon history beginning in the 1960s helped bring studies of Mormonism tentatively into the mainstream academy. Historians and scholars of religious studies have examined the reception of The Book of Mormon, the rise of the religion in early American culture, and the story of its founder, Joseph Smith. By studying the long‐neglected internal workings of the text, literary critics have the opportunity to bring new scholarly techniques to bear on this highly influential American scripture.
Parenting without Protection: How Legal Status Ambiguity Affects Lesbian and Gay Parenthood
Authors: Gash Alison , Raiskin Judith
Published: November 2016

Through the lens of lesbian and gay parenthood we ask how individuals who experience “legal status ambiguity”—that which emerges when legal fluctuations combine with divided attitudes, ignorance of the law, and autonomous institutional gatekeepers—exercise their legal rights and responsibilities. The results from thirty-one interviews with lesbian and gay parents in Oregon and their six adult children suggest that the state's fluctuating legal and social climates for lesbian and gay parenting between 1985 and 2013 presented significant challenges for two generations of same-sex parents. Although both cohorts created and utilized a range of legal and social mechanisms to assert their legal rights, they found these rights to be controlled as much by gatekeeper perspectives as by legal force. After the 2015Obergefellruling on marriage equality, lesbian and gay parenting status remains a site of ongoing legal and social contestation, providing insight into the risks and challenges of legal status ambiguity.
Convergent evolution of social hybridogenesis in Messor harvester ants
Authors: Romiguier Jonathan , Fournier Axel , Yek Sze Huei , Keller Laurent
Published: November 2016

Sexual reproduction generally requires no more than two partners. Here, we show convergent evolution of social hybridogenesis, a reproductive system requiring three reproductive partners in harvester ants. In this unorthodox reproductive system, two distinct genetic lineages live in sympatry and queens have to mate with males of their own lineage to produce queens along with males of the alternative lineage to produce workers. Using a large transcriptomic data set of nine species, we show that social hybridogenesis evolved at least three times independently in the genus Messor. Moreover, a study of 13 populations of Messor barbarus revealed that this mode of reproduction is fixed in the whole range of this ecologically dominant species. Finally, we show that workers can produce males carrying genes of the two genetic lineages, raising the possibility of rare gene flow between lineages contributing to the long‐term maintenance of pairs of interdependent lineages. These results emphasize the evolutionary importance of social hybridogenesis, a major transition possibly linked to the peculiar ecology of harvester ants.
Factors associated with bone marrow stem cell yield for pediatric allogeneic stem cell transplantation: The impact of donor characteristics
Authors: Fettah Ali , Özbek Namık , Özgüner Meltem , Azık Fatih , Işık Pamir , Avcı Zekai , Yaralı Neşe , Uçkan Duygu , Tunç Bahattin
Published: November 2016

The aim of this study was to investigate the effects of donor characteristics onCD34+cell yield in BM harvest. Between April 2010 and November 2013, consecutive donors who underwent BM harvesting in our BM transplantation unit were retrospectively investigated. Donors were classified into two groups: those who donated BM without mobilization (steady‐state BM donors) and those who received G‐CSFfor stem cell mobilization (G‐CSF‐primed BM donors). Donor characteristics (age, gender, race, body weight, BMI, and laboratory factors including donor's leukocyte, platelet, and monocyte) and their relationship with total nuclear cell andCD34+cell numbers has been evaluated. A total of 64 healthy related donors (29 males/35 females, median age 11.2 years; 49 [76.6%] younger than 18 and 36 [56.3%] younger than 12 years) were included in the study. The medianCD34+cell yield in the harvest was 0.12×106/L (0.02‐0.21) inSS‐BMdonors and 0.18×106/L (0.09‐0.67) inGP‐BMdonors (P=.03). Median ofCD34+cell count given to recipients was 2.6×106/recipient body weight (1.3‐19.3) inSS‐BMyields and 3.8×106/recipient body weight (1.1‐10.2) inGP‐BMyields, respectively. Multiple regression analysis showed that donor height and pre‐G‐CSFplatelet were the most important parameters to obtain a sufficient BM harvest. Our data suggest that the shorter donors and the donors with higher thrombocyte counts may offer more hematopoietic stem cell. The height and thrombocyte count of the donors should be taken into consideration before planning the targetedCD34+cell count especially for pediatric donors.
Cellular and viral peptides bind multiple sites on the N‐terminal domain of clathrin
Authors: Muenzner Julia , Traub Linton M. , Kelly Bernard T. , Graham Stephen C.
Published: November 2016

Short peptide motifs in unstructured regions of clathrin‐adaptor proteins recruit clathrin to membranes to facilitate post‐Golgi membrane transport. Three consensus clathrin‐binding peptide sequences have been identified and structural studies show that each binds distinct sites on the clathrin heavy chain N‐terminal domain (NTD). A fourth binding site for adaptors on NTD has been functionally identified but not structurally characterised. We have solved high resolution structures of NTD bound to peptide motifs from the cellular clathrin adaptors β2 adaptin and amphiphysin plus a putative viral clathrin adaptor, hepatitis D virus large antigen (HDAg‐L). Surprisingly, with each peptide we observe simultaneous peptide binding at multiple sites on NTD and viral peptides binding to the same sites as cellular peptides. Peptides containing clathrin‐box motifs (CBMs) with the consensus sequence LΦxΦ[DE] bind at the ‘arrestin box’ on NTD, between β‐propeller blades 4 and 5, which had previously been thought to bind a distinct consensus sequence. Further, we structurally define the fourth peptide binding site on NTD, which we term the Royle box. In vitro binding assays show that clathrin is more readily captured by cellular CBMs than by HDAg‐L, and site‐directed mutagenesis confirms that multiple binding sites on NTD contribute to efficient capture by CBM peptides.
Navigating veterinary borderlands: ‘heiferlumps’, epidemiological boundaries and the control of animal disease in New Zealand
Authors: Enticott Gareth
Published: November 2016

This paper analyses the importance of boundaries in the control of animal disease. On the one hand, establishing geographical and disciplinary boundaries is seen to be vital to the control of disease. In practice, however, boundaries are unstable, disrupted and frequently transgressed. Disease and its diagnosis vary in space, while disciplinary boundaries between epidemiology, laboratory and clinical practices can collapse from the non‐coherence of disease. Drawing on the concepts of ‘disciplinary borderlands’ and fluid space, the paper analyses how uncertainty over disease diagnosis establishes a veterinary borderland in which disciplines are merged and combined and difficult to tell apart. From archival research and interviews of key informants, the paper describes the history of the control of bovine tuberculosis (bTB) in New Zealand. Focusing on disputes around the diagnosis of bTB in the West Coast region, the paper shows how the problem of non‐specificity (locally referred to as ‘heiferlumps’) undermined attempts to impose a universal version of disease and control policy. In this new veterinary borderland, attempts to manage the non‐coherence of disease shifted from denial to viewing disease as a moral problem in which farmers’ own knowledges were central to the definition and management of disease. In doing so, boundaries between traditional disease disciplines were broken down, and new hybrid veterinary practices established to create geographically variable disease control rules and procedures. In conclusion, the paper considers the wider consequences for the management of animal disease arising from greater farmer involvement in animal disease management.
The Mechanics of Single Cell and Collective Migration of Tumor Cells
Authors: Lintz Marianne , Muñoz Adam , Reinhart-King Cynthia A.
Published: November 2016

Metastasis is a dynamic process in which cancer cells navigate the tumor microenvironment, largely guided by external chemical and mechanical cues. Our current understanding of metastatic cell migration has relied primarily on studies of single cell migration, most of which have been performed using two-dimensional (2D) cell culture techniques and, more recently, using three-dimensional (3D) scaffolds. However, the current paradigm focused on single cell movements is shifting toward the idea that collective migration is likely one of the primary modes of migration during metastasis of many solid tumors. Not surprisingly, the mechanics of collective migration differ significantly from single cell movements. As such, techniques must be developed that enable in-depth analysis of collective migration, and those for examining single cell migration should be adopted and modified to study collective migration to allow for accurate comparison of the two. In this review, we will describe engineering approaches for studying metastatic migration, both single cell and collective, and how these approaches have yielded significant insight into the mechanics governing each process.
New Indices for Optimal Design of Redundantly Actuated Parallel Manipulators
Authors: Li Qinchuan , Zhang Ningbin , Wang Feibo
Published: November 2016

Redundantly actuated parallel manipulators (PMs) receive growing interest due to their reduced singularity and enlarged workspace. This paper proposes new indices for optimal design and analysis of redundantly actuated PMs by evaluating their motion/force transmissibility. First, we proposed a method to extract a multi-DOF (degrees-of-freedom) redundantly actuated PM into several subsidiary one-DOF PMs with two or more actuators by locking some actuators in an ergodic manner. Then, a new index of output transmission performance is proposed by investigating the mean value of the instantaneous power produced by the multiple actuation wrenches and one twist of the moving platform of one-DOF PMs. A local transmission index (LTI) is defined as the minimum value of the index of output and input transmission performance. A global transmission index (GTI) is then established based on the LTI. The proposed LTI and GTI are coordinate-free and have clear physical interpretation. Finally, the validity and universality of the new indices are demonstrated by optimization and analysis of redundantly actuated lower-mobility PMs with extra articulated six-DOF or limited-DOF limbs.
A New Methodology of Finding Optimal Toolpath and Tooling Strategies for Robotic-Assisted Arthroplasty
Authors: Kianmajd Babak , Soshi Masakazu
Published: November 2016

Robotic total hip arthroplasty is a procedure in which a milling operation is performed on the femur followed by insertion of a prosthetic implant. Although surgeons operate the robots, they do not control the choice of robotic tools and cutting strategies of the robot. Toolpath parameters, such as feedrate, tool geometry, and spindle speeds, govern the cutting forces of the robot. This research covers a methodological approach for finding optimal parameters such that cutting forces and surgical times are reduced. Many different types of orthopedic surgical burs were retrofitted into an advanced computer numerically controlled (CNC) machine, and the characteristics of each tool were evaluated. A simulation cutting model was then developed to find the parameters that could remove the most material in the fastest amount of time without violating any of the safety constraints of surgery. The new methodology proposed not only finds the theoretical optimal parameters but also expedites the process of finding sufficient parameters for orthopedic surgery.
Sensitivity to Zone Covering of the Map of Passive Turbulence Control to Flow-Induced Motions for a Circular Cylinder at 30,000 ≤ Re ≤ 120,000
Authors: Park Hongrae , Kim Eun Soo , Bernitsas Michael M.
Published: November 2016

Passive turbulence control (PTC) in the form of two straight roughness strips with variable width, and thickness about equal to the boundary layer thickness, is used to modify the flow-induced motions (FIM) of a rigid circular cylinder. The cylinder is supported by two end springs and the flow is in the TrSL3, high-lift, regime. The PTC-to-FIM Map, developed in the previous work, revealed zones of weak suppression (WS), strong suppression (SS), hard galloping (HG), and soft galloping (SG). In this paper, the sensitivity of the PTC-to-FIM map to: (a) the width of PTC covering, (b) PTC covering a single or multiple zones, and (c) PTC being straight or staggered is studied experimentally. Experiments are conducted in the low turbulence free surface water channel of the University of Michigan, Ann Arbor, MI. Fixed parameters are: cylinder diameter D = 8.89 cm, m* = 1.725, spring stiffness K = 763 N/m, aspect ratio l/D = 10.29, and damping ratio ζ = 0.019. Variable parameters are circumferential PTC location αPTC∈ (0–180 deg), Reynolds number Re ∈ (30,000–120,000), flow velocity U∈ (0.36–1.45 m/s). Measured quantities are amplitude ratio A/D, frequency ratio fosc/fn,w, and synchronization range. As long as the roughness distribution is limited to remain within a zone, the width of the strips does not affect the FIM response. When multiple zones are covered, the strong suppression zone dominates the FIM.
Experimental Study on a New Type of Water Shutoff Agent Used in Fractured Low Permeability Reservoir
Authors: Zhang Lei , Pu Chunsheng , Cui Shuxia , Nasir Khan , Liu Yang
Published: November 2016

In order to effectively plug the fracture channeling-path in the high water cut fractured low permeability reservoir, a new type of water shutoff agent is developed by bottle tests and its injectivity and plugging performance in fractures are systematically studied by rheology and fractured core displacement experiment. The gelant consists of modified starch, dimethyl diallyl ammonium chloride, N,N′-methylene diacrylamide, and potassium persulfate, which behaves as a Newtonian with a good flowing capacity that allows its accurate positioning in the fractures. After gelatinization, the gel has high elastic modulus and viscous modulus. During the gelant injection into the fractured core, the filtration from fracture into matrix of the gelant leads to a difference between the injection volume of the gelant and the plugged fracture volume. Thus, a mathematical model for calculating filtration volume is established and applied in plugging experiment very well. After plugging, the two block cores can be tightly cemented together by the starch gel. The experiments show that the water shutoff agent and the mathematical model of filtration can be used to effectively plug the fracture channeling-path in the high water cut fractured low permeability reservoir.
Study of alternate hardmasks for extreme ultraviolet patterning
Authors: De Silva Anuja , Seshadri Indira , Arceo Abraham , Petrillo Karen , Meli Luciana , Mendoza Brock , Yao Yiping , Belyansky Michael , Halle Scott , Felix Nelson M.
Published: November 2016

Traditional patterning stacks for deep ultraviolet patterning have been based on a trilayer scheme with an organic planarizing layer, silicon antireflective coating or organic bottom antireflective coating, and photoresist. At an extreme ultraviolet (EUV) wavelength, there is no longer a need for reflectivity control. This offers an opportunity to look at different types of underlayers for patterning at sub-36 nm pitch length scales. An alternate hardmask can be used to develop a low aspect ratio patterning stack that can enable a larger process window at sub-36 nm pitch resolution. The hardmask layer under the resist has the potential for secondary electron generation at the resist/hardmask interface to improve resist sensitivity. This work explores EUV patterning on deposited hardmasks of various types such as silicon oxides and metal hardmasks. It also details the challenges of patterning directly on an alternate underlayer and approaches for improving patterning performance on such layers.
Atom-by-atom assembly of defect-free one-dimensional cold atom arrays
Authors: Endres Manuel , Bernien Hannes , Keesling Alexander , Levine Harry , Anschuetz Eric R. , Krajenbrink Alexandre , Senko Crystal , Vuletic Vladan , Greiner Markus , Lukin Mikhail D.
Published: November 2016

Making perfect atomic arrays

Arrays of atoms can be a useful resource for quantum information. However, loading atoms into arrays is typically a stochastic process, which leads to imperfections. Two groups have now performed defect-free assembly of atoms into arrays (see the Perspective by Regal). The researchers first loaded the atoms stochastically and imaged the system. They then shuttled the atoms around to form perfect arrays. Barredo
et al.
worked with two-dimensional arrays, creating a variety of spatial configurations. Endres
et al.
manipulated atoms along a line. By further cooling down the atoms and generating interactions among them, the techniques may also find use in quantum simulation.

Science
, this issue p.
972
, p.
1021
; see also p.
1024
Novel Viruses Isolated from Mosquitoes in Pantanal, Brazil
Authors: Pauvolid-Corrêa Alex , Solberg Owen , Couto-Lima Dinair , Nogueira Rita Maria , Langevin Stanley , Komar Nicholas
Published: November 2016

Genomic sequences are described from five novel viruses and divergent strains of Brejeira and Guaico Culex viruses from mosquitoes collected in Pantanal, Brazil, in 2010.
Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151
Authors: Leski Tomasz A. , Taitt Chris R. , Bangura Umaru , Ansumana Rashid , Stenger David A. , Wang Zheng , Vora Gary J.
Published: November 2016

Citrobacter freundiiis a Gram-negative opportunistic pathogen that is increasingly being recognized as a causative agent of hospital-acquired urinary tract infections and an important reservoir of antimicrobial resistance determinants. In this report, we describe the finished genome sequence ofC. freundiistrain SL151, a highly multidrug-resistant human urine isolate.
Biochemical and genetic analysis of hydrogen metabolism in Escherichia coli: the hydB gene
Authors: Sankar P , Shanmugam K T
Published: November 2016

Production of active hydrogenase by Escherichia coli requires several gene products. One of the essential genes, hydB, is encoded by a DNA fragment of approximately 1.0 kilobase. The hydB gene produced a protein with an apparent molecular weight of 32,000. The hydB gene was transcribed only under anaerobic conditions. Oxygen and nitrate repressed transcription of this gene. hydB gene transcription also required sigma 60, the product of the rpoN gene.
Role of the Bradyrhizobium japonicum ntrC gene product in differential regulation of the glutamine synthetase II gene (glnII)
Authors: Martin G B , Chapman K A , Chelm B K
Published: November 2016

We isolated the ntrC gene from Bradyrhizobium japonicum, the endosymbiont of soybean (Glycine max), and examined its role in regulating nitrogen assimilation. Two independent ntrC mutants were constructed by gene replacement techniques. One mutant was unable to produce NtrC protein, while the other constitutively produced a stable, truncated NtrC protein. Both ntrC mutants were unable to utilize potassium nitrate as a sole nitrogen source. In contrast to wild-type B. japonicum, the NtrC null mutant lacked glnII transcripts in aerobic, nitrogen-starved cultures. However, the truncated-NtrC mutant expressed glnII in both nitrogen-starved and nitrogen-excess cultures. Both mutants expressed glnII under oxygen-limited culture conditions and in symbiotic cells. These results suggest that nitrogen assimilation in B. japonicum is regulated in response to both nitrogen limitation and oxygen limitation and that separate regulatory networks exist in free-living and symbiotic cells.
Oxygen-dependent inactivation of ribulose 1,5-bisphosphate carboxylase/oxygenase in crude extracts of Rhodospirillum rubrum and establishment of a model inactivation system with purified enzyme
Authors: Cook L S , Im H , Tabita F R
Published: November 2016

Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBPC/O) was inactivated in crude extracts of Rhodospirillum rubrum under atmospheric levels of oxygen; no inactivation occurred under an atmosphere of argon. RuBP carboxylase activity did not decrease in dialyzed extracts, indicating that a dialyzable factor was required for inactivation. The inactivation was inhibited by catalase. Purified RuBPC/O is relatively oxygen stable, as no loss of activity was observed after 4 h under an oxygen atmosphere. The aerobic inactivation catalyzed by endogenous factors in crude extracts was mimicked by using a model system containing purified enzyme, ascorbate, and FeSO4 or FeCl3. Dithiothreitol was found to substitute for ascorbate in the model system. Preincubation of the purified enzyme with RuBP led to enhanced inactivation, whereas Mg2+ and HCO3- significantly protected against inactivation. Unlike the inactivation catalyzed by endogenous factors from extracts of R. rubrum, inactivation in the model system was not inhibited by catalase. It is proposed that ascorbate and iron, in the presence of oxygen, generate a reactive oxygen species which reacts with a residue at the activation site, rendering the enzyme inactive.
Rhizobium meliloti host range nodH gene determines production of an alfalfa-specific extracellular signal
Authors: Faucher C , Maillet F , Vasse J , Rosenberg C , van Brussel A A , Truchet G , Dénarié J
Published: November 2016

The Rhizobium meliloti nodH gene is involved in determining host range specificity. By comparison with the wild-type strain, NodH mutants exhibit a change in host specificity. That is, although NodH mutants lose the ability to elicit root hair curling (Hac-), infection threads (Inf-), and nodule meristem formation (Nod-) on the homologous host alfalfa, they gain the ability to be Hac+ Inf+ Nod+ on a nonhomologous host such as common vetch. Using root hair deformation (Had) bioassays on alfalfa and vetch, we have demonstrated that sterile supernatant solutions of R. meliloti cultures, in which the nod genes had been induced by the plant flavone luteolin, contained symbiotic extracellular signals. The wild-type strain produced at least one Had signal active on alfalfa (HadA). The NodH- mutants did not produce this signal but produced at least one factor active on vetch (HadV). Mutants altered in the common nodABC genes produced neither of the Had factors. This result suggests that the nodABC operon determines the production of a common symbiotic factor which is modified by the NodH product into an alfalfa-specific signal. An absolute correlation was observed between the specificity of the symbiotic behavior of rhizobial cells and the Had specificity of their sterile filtrates. This indicates that the R. meliloti nodH gene determines host range by helping to mediate the production of a specific extracellular signal.
Characterization of the tetracycline resistance gene of plasmid pT181 of Staphylococcus aureus
Authors: Mojumdar M , Khan S A
Published: November 2016

Some genetic and biochemical properties of the tetracycline resistance element of the Staphylococcus aureus plasmid pT181 have been studied. Resequencing of a portion of the tetracycline resistance gene (tet) showed the presence of a single open reading frame of 1,299 nucleotides capable of encoding a polypeptide of 433 amino acids. Analysis of BAL 31 nuclease-generated deletion mutants of the tet gene showed the presence of two complementation groups within this region. Northern blot hybridizations demonstrated that the tet gene encodes a single mRNA, and its initiation site has been mapped by S1 nuclease protection experiments. We also identified an approximately 52,000-dalton tetracycline-inducible polypeptide in Bacillus subtilis minicells carrying pT181. Induction of the tet gene by tetracycline resulted in a 4-fold increase in the levels of TET mRNA and at least a 15-fold increase in the amount of TET protein in B. subtilis minicells.
Molecular cloning, expression, and regulation in Escherichia coli K-12 of a chromosome-mediated aerobactin iron transport system from a human invasive isolate of E. coli K1
Authors: Valvano M A , Crosa J H
Published: November 2016

We have cloned chromosomal genes determining the aerobactin iron transport system from the Escherichia coli K1 strain VW187. Mapping and hybridization experiments showed that the VW187 aerobactin region was identical to that of the plasmid ColV-K30. However, in the E. coli K-12 background, the biosynthesis of both siderophore and ferric aerobactin receptor encoded by the VW187-derived recombinant plasmids was not repressed by iron to the same extent found when a recombinant plasmid derived from pColV-K30 was used. RNA-DNA dot-blot hybridization experiments demonstrated that the aerobactin-specific mRNA synthesized by the VW187-derived clones was not iron regulated in E. coli K-12. In contrast, the synthesis of aerobactin and its receptor in strain VW187 was completely repressed by iron regardless of whether the recombinant plasmids originated from VW187 or pColV-K30. Similar results were obtained with gene fusions in which a promoterless lac operon was placed under the control of aerobactin promoter regions of either chromosome- or plasmid-mediated aerobactin systems. DNA sequencing of the chromosomal aerobactin promoter region showed changes in bases located immediately upstream to the -35 region compared with the corresponding region in pColV-K30, which is known to be part of the binding site for the Fur repressor protein.
Cytochrome components of nitrate- and sulfate-respiring Desulfovibrio desulfuricans ATCC 27774
Authors: Liu M C , Costa C , Coutinho I B , Moura J J , Moura I , Xavier A V , LeGall J
Published: November 2016

Three multiheme c-type cytochromes--the tetraheme cytochrome c3 (molecular weight [MW] 13,500), a dodecaheme cytochrome c (MW 40,800), and a "split-Soret" cytochrome c (MW 51,540), which is a dimer with 2 hemes per subunit (MW 26,300)--were isolated from the soluble fraction of Desulfovibrio desulfuricans (ATCC 27774) grown under nitrate- or sulfate-respiring conditions. Two of them, the dodecaheme and the split-Soret cytochromes, showed no similarities to any of the c-type cytochromes isolated from other sulfate-reducing bacteria, while the tetraheme cytochrome c3 appeared to be analogous to the cytochrome c3 found in other sulfate-reducing bacteria. For all three multiheme c-type cytochromes isolated, the homologous proteins from nitrate- and sulfate-grown cells were indistinguishable in amino acid composition, physical properties, and spectroscopic characteristics. It therefore appears that the same c-type cytochrome components are present when D. desulfuricans ATCC 27774 cells are grown under either condition. This is in contrast to the considerable difference found in Pseudomonas perfectomarina (Liu et al., J. Bacteriol. 154:278-286, 1983), a marine denitrifier, when the cells are grown on nitrate or oxygen as the terminal electron acceptor. In addition, two spectroscopy methods capable of revealing minute structural variations in proteins provided identical information about the tetraheme cytochrome c3 from nitrate-grown and sulfate-grown cells.
Transformation of Schwanniomyces occidentalis with an ADE2 gene cloned from S. occidentalis
Authors: Klein R D , Favreau M A
Published: November 2016

We have developed an efficient transformation system for the industrial yeast Schwanniomyces occidentalis (formerly Schwanniomyces castellii). The transformation system is based on ade2 mutants of S. occidentalis deficient for phosphoribosylaminoimidazole carboxylase that were generated by mutagenesis. As a selectable marker, we isolated and characterized the S. occidentalis ADE2 gene by complementation in an ade2 strain of Saccharomyces cerevisiae. S. occidentalis was transformed with the recombinant plasmid pADE, consisting of a 4.5-kilobase-pair (kbp) DNA fragment from S. occidentalis containing the ADE2 gene inserted into the S. cerevisiae expression vector pYcDE8 by a modification of the spheroplasting procedure of Beggs (J. D. Beggs, Nature [London] 275:104-108, 1978). Intact plasmids were recovered in Escherichia coli from whole-cell lysates of ADE+ transformants, indicating that plasmids were replicating autonomously. High-molecular-mass species of pADE2 were found by Southern hybridization analysis of intact genomic DNA preparations. The shift to higher molecular mass of these plasmids during electrophoresis in the presence ethidium bromide after exposure to shortwave UV suggests that they exist in a supercoiled form in the transformed host. Subclones of the 4.5-kbp insert indicated that ADE2-complementing activity and sequences conferring autonomous replication in S. occidentalis were located within a 2.7-kbp EcoRI-SphI fragment. Plasmids containing this region cloned into the bacterial vector pUC19 complemented ade2 mutants of S. occidentalis with efficiencies identical to those of the original plasmid pADE.
Regulation of the galactose-inducible lac operon and the histidine utilization operons in pts mutants of Klebsiella aerogenes
Authors: Baldauf S L , Cardani M A , Bender R A
Published: November 2016

Galactose appears to be the physiological inducer of the chromosomal lac operon in Klebsiella aerogenes. Both lactose and galactose are poor inducers in strains having a functional galactose catabolism (gal) operon, but both are excellent inducers in gal mutants. Thus the slow growth of K. aerogenes on lactose reflects the rapid degradation of the inducer. Several pts mutations were characterized and shown to affect both inducer exclusion and permanent catabolite repression. The beta-galactosidase of pts mutants cannot be induced at all by lactose, and pts mutants appear to have a permanent and constitutive inducer exclusion phenotype. In addition, pts mutants show a reduced rate of glucose metabolism, leading to slower growth on glucose and a reduced degree of glucose-mediated permanent catabolite repression. The crr-type pseudorevertants of pts mutations relieve the constitutive inducer exclusion for lac but do not restore the full level of glucose-mediated permanent catabolite repression and only slightly weaken the glucose-mediated inducer exclusion. Except for weakening the glucose-mediated permanent catabolite repression, pts and crr mutations have no effect on expression of the histidine utilization (hut) operons.
Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis
Authors: MacNeil D J
Published: November 2016

Streptomyces avermitilis contains a unique restriction system that restricts plasmid DNA containing N6-methyladenine or 5-methylcytosine. Shuttle vectors isolated from Escherichia coli RR1 or plasmids isolated from modification-proficient Streptomyces spp. cannot be directly introduced into S. avermitilis. This restriction barrier can be overcome by first transferring plasmids into Streptomyces lividans or a modification-deficient E. coli strain and then into S. avermitilis. The transformation frequency was reduced greater than 1,000-fold when plasmid DNA was modified by dam or TaqI methylases to contain N6-methyladenine or by AluI, HhaI, HphI methylases to contain 5-methylcytosine. Methyl-specific restriction appears to be common in Streptomyces spp., since either N6-methyladenine-specific or 5-methylcytosine-specific restriction was observed in seven of nine strains tested.
Purification, characterization, and primary structure of Escherichia coli protease VII with specificity for paired basic residues: identity of protease VII and OmpT
Authors: Sugimura K , Nishihara T
Published: November 2016

Escherichia coli cells were found to contain a novel outer membrane-associated protease, designated protease VII (K. Sugimura and N. Higashi, J. Bacteriol. 170:3650-3654, 1988). This enzyme was purified to homogeneity and exhibited an apparent molecular weight of 36,000 on sodium dodecyl sulfate gels and 180,000 on a TSK G-3000SW column in the presence of Triton X-100. It was capable of cleaving several peptides at the center of paired basic residues but not at single basic residues, implying that it is distinct from trypsinlike proteases. Protease VII was most active at pH 6.0 and was sensitive to a serine protease inhibitor, diisopropylfluorophosphate, and to the bivalent cations Zn2+, Cu2+, and Fe2+. The nucleotide sequence of a protease VII gene-carrying DNA fragment, which had been cloned by complementation analysis (K. Sugimura, Biochem. Biophys. Res. Commun. 153:753-759, 1988) was determined. It carried two putative promoter regions and a putative Shine-Dalgarno sequence in addition to the complete structural gene, which encoded pre-protease VII of 317 amino acid residues, with the N-terminal 20 residues being a signal peptide. By comparing their amino acid sequences, protease VII and OmpT, which specifically cleaves ferric enterobactin receptor protein, were found to be identical.
Induction of cat-86 by chloramphenicol and amino acid starvation in relaxed mutants of Bacillus subtilis
Authors: Ambulos N P , Rogers E J , Alexieva Z , Lovett P S
Published: November 2016

The chloramphenicol acetyltransferase gene cat-86 is induced through a mechanism that is a variation of classical attenuation. Induction results from the destabilization of an RNA stem-loop that normally sequesters the cat-86 ribosome-binding site. Destabilization of the stem-loop is due to the stalling of a ribosome in the leader region of cat-86 mRNA at a position that places the A site of the stalled ribosome at leader codon 6. Two events can stall ribosomes at the correct location to induce cat-86 translation: addition of chloramphenicol to cells and starvation of cells for the amino acid specified by leader codon 6. Induction by amino acid starvation is an anomaly because translation of the cat-86 coding sequence requires all 20 amino acids. To explain this apparent contradiction we postulated that amino acid starvation triggers intracellular proteolysis, thereby providing levels of the deprived amino acid sufficient for cat-86 translation. Here we show that a mutation in relA, the structural gene for stringent factor, blocks intracellular proteolysis that is normally triggered by amino acid starvation. The relA mutation also blocks induction of cat-86 by amino acid starvation, but the mutation does not interfere with chloramphenicol induction. Induction by amino acid starvation can be demonstrated in relA mutant cells if the depleted amino acid is restored at very low levels (e.g., 2 micrograms/ml). A mutation in relC, which may be the gene for ribosomal protein L11, blocks induction of cat-86 by either chloramphenicol or amino acid starvation. We believe this effect is due to a structural alteration of the ribosome resulting from the relC mutation and not to the relaxed phenotype of the cells.