Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance

Introduction

The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of California established the California SARS-CoV-2 Whole Genome Sequencing (WGS) Initiative, or "California COVIDNet". This initiative constituted an unprecedented multi-sector collaborative effort to achieve large-scale genomic surveillance of SARS-CoV-2 across California to monitor the spread of variants within the state, to detect new and emerging variants, and to characterize outbreaks in congregate, workplace, and other settings.

Methods

California COVIDNet consists of 50 laboratory partners that include public health laboratories, private clinical diagnostic laboratories, and academic sequencing facilities as well as expert advisors, scientists, consultants, and contractors. Data management, sample sourcing and processing, and computational infrastructure were major challenges that had to be resolved in the midst of the pandemic chaos in order to conduct SARS-CoV-2 genomic surveillance. Data management, storage, and analytics needs were addressed with both conventional database applications and newer cloud-based data solutions, which also fulfilled computational requirements.

Results

Representative and randomly selected samples were sourced from state-sponsored community testing sites. Since March of 2021, California COVIDNet partners have contributed more than 450,000 SARS-CoV-2 genomes sequenced from remnant samples from both molecular and antigen tests. Combined with genomes from CDC-contracted WGS labs, there are currently nearly 800,000 genomes from all 61 local health jurisdictions (LHJs) in California in the COVIDNet sequence database. More than 5% of all reported positive tests in the state have been sequenced, with similar rates of sequencing across 5 major geographic regions in the state.

Discussion

Implementation of California COVIDNet revealed challenges and limitations in the public health system. These were overcome by engaging in novel partnerships that established a successful genomic surveillance program which provided valuable data to inform the COVID-19 public health response in California. Significantly, California COVIDNet has provided a foundational data framework and computational infrastructure needed to respond to future public health crises.

Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62

Autophagy is a housekeeping mechanism tasked with eliminating misfolded proteins and damaged organelles to maintain cellular homeostasis. Autophagy deficiency results in increased oxidative stress, DNA damage and chronic cellular injury. Among the core genes in the autophagy machinery, ATG7 is required for autophagy initiation and autophagosome formation. Based on the analysis of an extended pedigree of familial cholangiocarcinoma, we determined that all affected family members had a novel germline mutation (c.2000C>T p.Arg659* (p.R659*)) in ATG7. Somatic deletions of ATG7 were identified in the tumors of affected individuals. We applied linked-read sequencing to one tumor sample and demonstrated that the ATG7 somatic deletion and germline mutation were located on distinct alleles, resulting in two hits to ATG7. From a parallel population genetic study, we identified a germline polymorphism of ATG7 (c.1591C>G p.Asp522Glu (p.D522E)) associated with increased risk of cholangiocarcinoma. To characterize the impact of these germline ATG7 variants on autophagy activity, we developed an ATG7-null cell line derived from the human bile duct. The mutant p.R659* ATG7 protein lacked the ability to lipidate its LC3 substrate, leading to complete loss of autophagy and increased p62 levels. Our findings indicate that germline ATG7 variants have the potential to impact autophagy function with implications for cholangiocarcinoma development.

Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations

Cancer genome sequencing has led to important discoveries such as the identification of cancer genes. However, challenges remain in the analysis of cancer genome sequencing. One significant issue is that mutations identified by multiple variant callers are frequently discordant even when using the same genome sequencing data. For insertion and deletion mutations, oftentimes there is no agreement among different callers. Identifying somatic mutations involves read mapping and variant calling, a complicated process that uses many parameters and model tuning. To validate the identification of true mutations, we developed a method using k-mer sequences. First, we characterized the landscape of unique versus non-unique k-mers in the human genome. Second, we developed a software package, KmerVC, to validate the given somatic mutations from sequencing data. Our program validates the occurrence of a mutation based on statistically significant difference in frequency of k-mers with and without a mutation from matched normal and tumor sequences. Third, we tested our method on both simulated and cancer genome sequencing data. Counting k-mer involving mutations effectively validated true positive mutations including insertions and deletions across different individual samples in a reproducible manner. Thus, we demonstrated a straightforward approach for rapidly validating mutations from cancer genome sequencing data.

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

HepG2 is one of the most widely used human cancer cell lines in biomedical research and one of the main cell lines of ENCODE. Although the functional genomic and epigenomic characteristics of HepG2 are extensively studied, its genome sequence has never been comprehensively analyzed and higher order genomic structural features are largely unknown. The high degree of aneuploidy in HepG2 renders traditional genome variant analysis methods challenging and partially ineffective. Correct and complete interpretation of the extensive functional genomics data from HepG2 requires an understanding of the cell line’s genome sequence and genome structure. Using a variety of sequencing and analysis methods, we identified a wide spectrum of genome characteristics in HepG2: copy numbers of chromosomal segments at high resolution, SNVs and Indels (corrected for aneuploidy), regions with loss of heterozygosity, phased haplotypes extending to entire chromosome arms, retrotransposon insertions and structural variants (SVs) including complex and somatic genomic rearrangements. A large number of SVs were phased, sequence assembled and experimentally validated. We re-analyzed published HepG2 datasets for allele-specific expression and DNA methylation and assembled an allele-specific CRISPR/Cas9 targeting map. We demonstrate how deeper insights into genomic regulatory complexity are gained by adopting a genome-integrated framework.

Identification of large rearrangements in cancer genomes with barcode linked reads

Large genomic rearrangements involve inversions, deletions and other structural changes that span Megabase segments of the human genome. This category of genetic aberration is the cause of many hereditary genetic disorders and contributes to pathogenesis of diseases like cancer. We developed a new algorithm called ZoomX for analysing barcode-linked sequence reads—these sequences can be traced to individual high molecular weight DNA molecules (>50 kb). To generate barcode linked sequence reads, we employ a library preparation technology (10X Genomics) that uses droplets to partition and barcode DNA molecules. Using linked read data from whole genome sequencing, we identify large genomic rearrangements, typically greater than 200kb, even when they are only present in low allelic fractions. Our algorithm uses a Poisson scan statistic to identify genomic rearrangement junctions, determine counts of junction-spanning molecules and calculate a Fisher's exact test for determining statistical significance for somatic aberrations. Utilizing a well-characterized human genome, we benchmarked this approach to accurately identify large rearrangement. Subsequently, we demonstrated that our algorithm identifies somatic rearrangements when present in lower allelic fractions as occurs in tumors. We characterized a set of complex cancer rearrangements with multiple classes of structural aberrations and with possible roles in oncogenesis.

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

K562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional genomic and epigenomic characteristics have been extensively studied, its genome sequence and genomic structural features have never been comprehensively analyzed. Such information is essential for the correct interpretation and understanding of the vast troves of existing functional genomics and epigenomics data for K562. We performed and integrated deep-coverage whole-genome (short-insert), mate-pair, and linked-read sequencing as well as karyotyping and array CGH analysis to identify a wide spectrum of genome characteristics in K562: copy numbers (CN) of aneuploid chromosome segments at high-resolution, SNVs and indels (both corrected for CN in aneuploid regions), loss of heterozygosity, megabase-scale phased haplotypes often spanning entire chromosome arms, structural variants (SVs), including small and large-scale complex SVs and nonreference retrotransposon insertions. Many SVs were phased, assembled, and experimentally validated. We identified multiple allele-specific deletions and duplications within the tumor suppressor gene FHIT. Taking aneuploidy into account, we reanalyzed K562 RNA-seq and whole-genome bisulfite sequencing data for allele-specific expression and allele-specific DNA methylation. We also show examples of how deeper insights into regulatory complexity are gained by integrating genomic variant information and structural context with functional genomics and epigenomics data. Furthermore, using K562 haplotype information, we produced an allele-specific CRISPR targeting map. This comprehensive whole-genome analysis serves as a resource for future studies that utilize K562 as well as a framework for the analysis of other cancer genomes.

Naphthalimide end-capped diphenylacetylene: a versatile organic semiconductor for blue light emitting diodes and a donor or an acceptor for solar cells

A novel compound NAI-PVP-NAI was utilized as a blue emissive layer for organic light emitting diodes and as an acceptor and a donor for organic solar cells.

Tuning the Amount of Oxygen Vacancies in Sputter-Deposited SnOx films for Enhancing the Performance of Perovskite Solar Cells

This work demonstrates the effect of oxygen vacancies in SnO_x thin films on the performance of perovskite solar cells. Various SnO_x films with different amounts of oxygen vacancies were deposited by sputtering at different substrate temperatures (25-300 °C). The transmittance of the films decreased from 82 to 66 % with increasing deposition temperature from 25 to 300 °C. Both X-ray photoelectron spectroscopy and electron-spin resonance spectroscopy confirmed that a higher density of oxygen vacancies was created within the SnO_x film at a high substrate temperature, which caused narrowing of the SnO_x bandgap from 4.1 (25 °C) to 3.74 eV (250 °C). Combined ultraviolet photoelectron spectroscopy and UV/Vis spectroscopy showed an excellent conduction band position alignment between the methylammonium lead iodide perovskite layer (3.90 eV) and the SnO_x electron transport layer deposited at 250 °C (3.92 eV). As a result, a significant enhancement of the open-circuit voltage from 0.82 to 1.0 V was achieved, resulting in an increase of the power conversion efficiency of the perovskite solar cells from 11 to 14 %. This research demonstrated a facile approach for controlling the amount of oxygen vacancies in SnO_x thin films to achieve a desirable energy alignment with the perovskite absorber layer for enhanced device performance.

Abstract 4334: Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer

Little is known about the genomic features of brain metastases from colorectal cancer (CRC) and the contributing genetic factors. We conducted an analysis of large-scale structural aberrations, including chromosome aneuploidies, with a method called linked-read whole genome sequencing and a new somatic rearrangement detection software tool (ZoomX) to better understand the genomic architecture of brain metastases from CRC. We resolved on average 145 distal inter- and intra-chromosomal somatic junctions per sample with their exact haplotype information and basepair level breakpoints. In addition, we used a new haplotyping method based on these imbalances to generate cancer chromosome haplotypes of up to 146 Mbp long. We identified extensive chromosomal-level instability (CIN) in these cancer genomes, with an average of 90 large-scale copy number aberrations per sample in sizes ranging from hundreds of Kbp to hundreds of Mbp. A substantial fraction of CIN is likely attributable to earlier chromothripsis events. For example, we identified multiple chromothripsis events disrupting the loci of known cancer genes such as TP53, an essential colon cancer driver. We identified novel rearrangements including an oncogenic gene fusion; e.g. SET/DPP10 among these metastatic samples. A majority of chromosome arms demonstrated an allelic imbalance across all of the samples. In summary, the analysis revealed pervasive chromosome-level genome instability as a potential contributor to devastating brain invasion by CRC. It also demonstrated the advantages of linked-read whole genome sequencing. This approach is cost-effective and represents a high-resolution tool to assess genome-wide rearrangements and to generate megabase-scale haplotypes.

Citation Format: Li C. Xia, John M. Bell, Christina Wood-Bouwens, Daniel A. King, GiWon Shin, Stephanie Greer, Ian D. Connolly, Melanie H. Gephart, Hanlee P. Ji. Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4334.

Vinylene and benzo[c][1,2,5]thiadiazole: effect of the π-spacer unit on the properties of bis(2-oxoindolin-3-ylidene)-benzodifuran-dione containing polymers for n-channel organic field-effect transistors

Two polymers based on (3E,7E)-3,7-bis(2-oxoindolin-3-ylidene)benzo[1,2-b:4,5-b′]difuran-2,6(3H,7H)-dione (BIBDF) coupled with (E)-2-(2-(thiophen-2-yl)vinyl)thiophene (TVT) or dithienylbenzothiadiazole (TBT), namely PBIBDF-TVT and PBIBDF-TBT were synthesized via the Stille coupling reaction. The effect of benzothiadiazole or vinylene-π spacer of the copolymers on optical properties, energy levels, electronic device performance and microstructure were studied. It was found that PBIBDF-TBT based OFET devices, annealed at 180 °C, showed better performance with the highest electron mobility of 2.9 × 10⁻² cm² V s⁻¹ whereas PBIBDF-TVT polymer exhibited 5.0 × 10⁻⁴ cm² V s⁻¹. The two orders of magnitude higher electron mobility of PBIBDF-TBT over PBIBDT-TVT is a clear indicator of the better charge transport ability of this polymer semiconductor arising from its higher crystallinity and better donor–acceptor interaction.

Bottom-gate-top-contact OFET device structure using PBIBDF-TVT and PBIBDF-TBT based polymer semiconductors.

Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy

Genomic instability is a frequently occurring feature of cancer that involves large-scale structural alterations. These somatic changes in chromosome structure include duplication of entire chromosome arms and aneuploidy where chromosomes are duplicated beyond normal diploid content. However, the accurate determination of aneuploidy events in cancer genomes is a challenge. Recent advances in sequencing technology allow the characterization of haplotypes that extend megabases along the human genome using high molecular weight (HMW) DNA. For this study, we employed a library preparation method in which sequence reads have barcodes linked to single HMW DNA molecules. Barcode-linked reads are used to generate extended haplotypes on the order of megabases. We developed a method that leverages haplotypes to identify chromosomal segmental alterations in cancer and uses this information to join haplotypes together, thus extending the range of phased variants. With this approach, we identified mega-haplotypes that encompass entire chromosome arms. We characterized the chromosomal arm changes and aneuploidy events in a manner that offers similar information as a traditional karyotype but with the benefit of DNA sequence resolution. We applied this approach to characterize aneuploidy and chromosomal alterations from a series of primary colorectal cancers.

Abstract 1436: Identification of novel tumor suppressor candidates in familial cholangiocarcinoma using sequencing-based Megabase-scale haplotypes from germline and cancer genomes

Cholangiocarcinoma (bile duct cancer) is a rare epithelial malignancy with an extremely poor prognosis characterized by a 5-year survival of less than 10%. While this tumor type can be amenable to specific combination chemotherapy regimens, it is typically diagnosed at an advanced stage and inevitably progresses towards distant metastasis. We identified a family with a predisposition to cholangiocarcinoma, having multiple affected family members, and sought to identify the underlying germline mutation(s).

We employed linked-read sequencing, a microfluidic technology where high-molecular weight DNA molecules (>20 kb) are partitioned into droplets and labeled with unique barcodes, enabling computational reconstruction of the original large molecules following traditional short-read sequencing, to identify entire megabase-scale regions of the genome that segregate with the disease. We applied this technology to an entire generation of a family predisposed to cholangiocarcinoma, including a mix of 8 affected and unaffected siblings. We additionally utilized each affected individual’s cancer genome to search for a common second hit that would serve as further confirmation. Our analysis yielded a small set of four candidate pathogenic variants. Functional validation of the candidate genes in a zebrafish model, using morpholino-based gene silencing, identified one candidate whose silencing led to a reproducible phenotype consistent with known aspects of the candidate gene’s function. The candidate variant occurs in a TGF family-interacting domain, and has not been extensively characterized in other cancers. Cross-validation with TCGA datasets showed the gene was altered in 5% of cholangiocarcinomas, all of which displayed homozygous deletions. This identification of a germline allele associated with familial cholangiocarcinoma represents a unique discovery with clinical implications for the described family and warrants further investigation in other patients who display features of an inherited cholagniocarcinoma. This finding also raises the possibility of TGF pathway targeting as a therapeutic strategy in select cholangiocarcinomas, and highlights the power of whole-genome phasing to discover novel inherited tumor suppressor variants.

Citation Format: Stephanie Greer, Lincoln Nadauld, Billy Lau, Laura Miotke, Erik Hopmans, Christina M. Wood, John M. Bell, David A. Jones, Hanlee P. Ji. Identification of novel tumor suppressor candidates in familial cholangiocarcinoma using sequencing-based Megabase-scale haplotypes from germline and cancer genomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1436. doi:10.1158/1538-7445.AM2017-1436

Molecular Engineering Strategy for High Efficiency Fullerene-Free Organic Solar Cells Using Conjugated 1,8-Naphthalimide and Fluorenone Building Blocks

We designed, synthesized, and characterized a series of novel electron deficient small molecule nonfullerene acceptors based on 1,8-naphthalimide (NAI) and 9-fluorenone (FN) with different branched alkyl chains using various techniques. These molecules are based on an acceptor-donor-acceptor-donor-acceptor (A1-D-A2-D-A1) molecular design configuration with NAI as the end-capping acceptor (A1), FN as electron-withdrawing central (A2) group, and thiophene ring as a donor (D) unit. These materials are named as NAI-FN-NAI (BO) and NAI-FN-NAI (HD) where BO and HD represent butyloctyl and hexyldecyl alkyl groups, respectively. To further modify energy levels of these materials, we converted the weak electron withdrawing ketonic group (C═O) attached to the FN moiety of NAI-FN-NAI (BO) to a stronger electron withdrawing cyano group (C≡N) to obtain the compound NAI-FCN-NAI (BO) by keeping the same alkyl chain. The optical, electrochemical, and thermal properties of the new acceptors were studied. The materials exhibited higher to medium band gaps, low lowest unoccupied molecular orbital (LUMO) energy levels, and highly thermally stable properties. Organic solar cell devices employing conventional poly(3-hexylthiophene) (P3HT) a donor polymer and the newly designed small molecules as the acceptor were investigated. Among all new materials, organic solar cell devices based on NAI-FN-NAI (BO) as an acceptor exhibit the highest performance with an open circuit voltage (V_OC) of 0.88 V, a short-circuit current density (J_SC) of 9.1 mAcm^-2, a fill factor (FF) of 45%, and an overall power conversion efficiency (PCE) of 3.6%. This is the first report of 9-fluorenone based nonfullerene acceptor with P3HT donor in organic solar cell devices with such a promising performance.

Abstract 3602: Linked-Reads enable detailed, phased resolution of structural variation in the cancer genome

Studies have shown that somatic structural variation (SV) plays a key role in the oncogenic process. Traditionally SVs in the cancer genome have been detected using low resolution cytogenetic approaches, such as FISH, or microarray-based techniques. More recently, next-generation sequencing (NGS)-based technologies have been employed to detect SVs, including indels and translocations. However, both short- and long-read NGS-based approaches are limited in their ability to accurately identify SV events and delineate their breakpoints due to the limitations inherent in assembly of billions of short-read sequences across a heterogeneous cancer sample, as well as the costly and burdensome laboratory infrastructure associated with long-read sequencers. We utilized a novel technology that combines microfluidics and molecular barcoding to generate libraries that are sequenced with an Illumina system. Open-source bioinformatics software produces linked-reads that maintain long-range information and single molecule sensitivity.

Cell lines and cancer samples were obtained from commercial sources, and genomic DNA was extracted. DNA sample indexing and partitioning was performed using the 10X Genomicx GemCode instrument. One ng of sample DNA was used as input for each reaction, and DNA molecules were partitioned into droplets to fragment the DNA and introduce molecular barcodes. Following barcoding, droplets were fractured, and library DNA was purified and sequenced on Illumina sequencers. The GemCode Long Ranger software suite was used to map sequencing reads back to original long molecules of DNA, generating reads linked to partition barcodes. Thus we can generate phased sequences covering many 10's to 100's of kilobases.

We first benchmarked the ability to call multiple SV types using a well-characterized germline HapMap sample (NA12878) as well as two recently characterized haploid hydatidiform moles (CHM1 and CHM13) that have been studied with multiple orthogonal technologies. Regions with evidence for structural variation were reassembled into distinct haplotypes. The barcode information allowed us to both phase the structural variants we detected and disambiguate calls within highly repetitive regions, such as segmental duplications. We demonstrated high concordance with alternative approaches across all major classes of SVs, including long insertions and deletions as well as copy-neutral events. In cancer cell lines, we detected well-annotated gene fusions, such as the EML4/ALK and ALK/PTPN3 fusions in the lung cancer cell line NCI-H2228, and the SLC26A/PRKAR2A fusion in the triple negative breast cancer cell line HCC38.

Citation Format: Sofia Kyriazopoulou-Panagiotopoulou, Patrick Marks, Haynes Heaton, Heather Ordonez, Kristina Giorda, Cassandra Jabara, Billy Lau, John M. Bell, Michael Schnall-Levin, Hanlee P. Ji. Linked-Reads enable detailed, phased resolution of structural variation in the cancer genome. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3602.

A genome-wide approach for detecting novel insertion-deletion variants of mid-range size

We present SWAN, a statistical framework for robust detection of genomic structural variants in next-generation sequencing data and an analysis of mid-range size insertion and deletions (<10 Kb) for whole genome analysis and DNA mixtures. To identify these mid-range size events, SWAN collectively uses information from read-pair, read-depth and one end mapped reads through statistical likelihoods based on Poisson field models. SWAN also uses soft-clip/split read remapping to supplement the likelihood analysis and determine variant boundaries. The accuracy of SWAN is demonstrated by in silico spike-ins and by identification of known variants in the NA12878 genome. We used SWAN to identify a series of novel set of mid-range insertion/deletion detection that were confirmed by targeted deep re-sequencing. An R package implementation of SWAN is open source and freely available.

From brittle to ductile: a structure dependent ductility of diamond nanothread

As a potential building block for the next generation of devices/multifunctional materials that are spreading in almost every technology sector, one-dimensional (1D) carbon nanomaterial has received intensive research interests. Recently, a new ultra-thin diamond nanothread (DNT) has joined this palette, which is a 1D structure with poly-benzene sections connected by Stone-Wales (SW) transformation defects. Using large-scale molecular dynamics simulations, we found that this sp(3) bonded DNT can transition from brittle to ductile behaviour by varying the length of the poly-benzene sections, suggesting that DNT possesses entirely different mechanical responses than other 1D carbon allotropes. Analogously, the SW defects behave like a grain boundary that interrupts the consistency of the poly-benzene sections. For a DNT with a fixed length, the yield strength fluctuates in the vicinity of a certain value and is independent of the "grain size". On the other hand, both yield strength and yield strain show a clear dependence on the total length of DNT, which is due to the fact that the failure of the DNT is dominated by the SW defects. Its highly tunable ductility together with its ultra-light density and high Young's modulus makes diamond nanothread ideal for the creation of extremely strong three-dimensional nano-architectures.

MAVEN observations of the response of Mars to an interplanetary coronal mass ejection

Coupling between the lower and upper atmosphere, combined with loss of gas from the upper atmosphere to space, likely contributed to the thin, cold, dry atmosphere of modern Mars. To help understand ongoing ion loss to space, the Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft made comprehensive measurements of the Mars upper atmosphere, ionosphere, and interactions with the Sun and solar wind during an interplanetary coronal mass ejection impact in March 2015. Responses include changes in the bow shock and magnetosheath, formation of widespread diffuse aurora, and enhancement of pick-up ions. Observations and models both show an enhancement in escape rate of ions to space during the event. Ion loss during solar events early in Mars history may have been a major contributor to the long-term evolution of the Mars atmosphere.

Early MAVEN Deep Dip campaign reveals thermosphere and ionosphere variability

The Mars Atmosphere and Volatile Evolution (MAVEN) mission, during the second of its Deep Dip campaigns, made comprehensive measurements of martian thermosphere and ionosphere composition, structure, and variability at altitudes down to ~130 kilometers in the subsolar region. This altitude range contains the diffusively separated upper atmosphere just above the well-mixed atmosphere, the layer of peak extreme ultraviolet heating and primary reservoir for atmospheric escape. In situ measurements of the upper atmosphere reveal previously unmeasured populations of neutral and charged particles, the homopause altitude at approximately 130 kilometers, and an unexpected level of variability both on an orbit-to-orbit basis and within individual orbits. These observations help constrain volatile escape processes controlled by thermosphere and ionosphere structure and variability.

Investigation on Temperature-Dependent Electrical Conductivity of Carbon Nanotube/Epoxy Composites for Sustainable Energy Applications

Composites with carbon nanotubes are becoming increasingly used in energy storage and electronic devices, due to incorporated excellent properties from carbon nanotubes and polymers. Although their properties make them more attractive than conventional smart materials, their electrical properties have been found to be temperature-dependent which is important to consider for the design of devices. To study the effects of temperature in electrically conductive multi-wall carbon nanotube/epoxy composites, thin films were prepared and the effect of temperature on the resistivity, thermal properties and Raman spectral characteristics of the composite films was evaluated. Resistivity-temperature profiles showed three distinct regions in as-cured samples and only two regions in samples whose thermal histories had been erased. In the vicinity of the glass transition temperature, the as-cured composites exhibited pronounced resistivity and enthalpic relaxation peaks, which both disappeared after erasing the composites' thermal histories by temperature cycling. Combined DSC, Raman spectroscopy, and resistivity-temperature analyses indicated that this phenomenon can be attributed to the physical aging of the epoxy matrix and that, in the region of the observed thermal history-dependent resistivity peaks, structural rearrangement of the conductive carbon nanotube network occurs through a volume expansion/relaxation process. These results have led to an overall greater understanding of the temperature-dependent behaviour of conductive carbon nanotube/epoxy composites, including the positive temperature coefficient effect.

Tuning the resonance properties of 2D carbon nanotube networks towards a mechanical resonator

The capabilities of the mechanical resonator-based nanosensors in detecting ultra-small mass or force shifts have driven a continuing exploration of the palette of nanomaterials for such application purposes. Based on large-scale molecular dynamics simulations, we have assessed the applicability of a new class of carbon nanomaterials for nanoresonator usage, i.e. the single-wall carbon nanotube (SWNT) network. It is found that SWNT networks inherit excellent mechanical properties from the constituent SWNTs, possessing a high natural frequency. However, although a high quality factor is suggested from the simulation results, it is hard to obtain an unambiguous Q-factor due to the existence of vibration modes in addition to the dominant mode. The nonlinearities resulting from these extra vibration modes are found to exist uniformly under various testing conditions including different initial actuations and temperatures. Further testing shows that these modes can be effectively suppressed through the introduction of axial strain, leading to an extremely high quality factor in the order of 10(9) estimated from the SWNT network with 2% tensile strain. Additional studies indicate that the carbon rings connecting the SWNTs can also be used to alter the vibrational properties of the resulting network. This study suggests that the SWNT network can be a good candidate for applications as nanoresonators.

Abstract 4882: Megabase-scale phased haplotypes of genetic aberrations from whole cancer genome sequencing of primary colorectal tumors

Cancer genomes contain multiple types of genetic aberrations that include mutations, deletions, copy number variants and chromosomal rearrangements. Despite advances in next generation sequencing, it remains a major challenge to delineate many of these somatic genomic alterations because of intrinsic complexity of cancer genomes. Haplotyping involves the assignment of genetic variants such as mutations and structural variants to specific segment of homologous chromosomes. Experimentally determined phasing of cancer genomes offers an opportunity to resolve complex genomic structures such as somatic rearrangements, aneuploidy composition and ongoing evolutionary changes. However, contiguous phasing of cancer genomes on a megabase (Mb) scale remains difficult to achieve with sequencing-based approaches.

In this proof-of-concept study, we experimentally determined Mb-scale haplotypes of primary tumor samples via whole genome sequencing. To generate haplotypes, we employed an automated instrument that partitions long DNA fragments into hundreds of thousands of reactions, each of which incorporates a unique, nonrandom barcode into indexed sequencing libraries. Given need to amplify from sparse numbers of molecules and the high efficiency of the automated sequencing library construction process, the DNA requirements for each sample are less than 5 ng.

We sequenced the genomes of primary colorectal cancer samples and their matched normal diploid DNA with an Illumina sequencer. We used the single nucleotide variants to generate Mb-scale haplotype blocks (N50 of 1.2 Mb) with phased haplotype block size of up to 11.3 Mb. We were able to delineate cancer genome haplotypes that cover allelic imbalances, copy number variations such as deletions and other genomic instability events. Structural variants were identified in the context of their position in specific chromosome homologues. Thus, we improved the characterization of somatic genetic aberrations using contiguity mapping and cancer genome haplotypes in the context of whole cancer genome sequencing. Overall, we demonstrated the feasibility and potential utility of conducting contiguous phased haplotypes in whole cancer genome sequencing from primary tumor samples.

Citation Format: Billy Lau, John M. Bell, Michael Schnall-Levin, Mirna Jarosz, Erik Hopmans, Christina M. Wood, Grace X. Zheng, Kristina Giorda, Hanlee P. Ji. Megabase-scale phased haplotypes of genetic aberrations from whole cancer genome sequencing of primary colorectal tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4882. doi:10.1158/1538-7445.AM2015-4882

Abstract 3901: Identification of novel tumor suppressor candidates and characterizing their potential driver role in familial cholangiocarcinoma

Cholangiocarcinoma (bile duct cancer) is an epithelial malignancy originating from the bile duct that connects the liver to the small intestine. This carcinoma, while rare, has an extremely poor prognosis with a 5-year survival of less than 10%. Initial clinical presentation and diagnosis is frequently at an advanced stage and while amenable to specific combination chemotherapy regimens, inevitably progresses towards distal metastasis. Only recently has the molecular genetic underpinnings of this cancer been explored with a number of genome sequencing studies of a limited number of primary tumors.

For this study, we used a multi-faceted approach that integrates the genetic analysis of an extended familial cholangiocarcinoma pedigree with identification of somatic genetic aberrations discovered via primary tumor sequencing of affected family members. Our goal was to identify potential novel tumor suppressor(s) that have not yet been described and are associated with an increased familial risk of cholangiocarcinoma. The extended pedigree was characterized by multiple members with relatively young onset of cholangiocarcinoma and displayed a segregation pattern consistent with an autosomal dominant inheritance pattern. Several members of the family had undergone biopsy or resection and as a result, had primary tumor tissue available for analysis.

Relying on a combination of whole genome sequencing, experimentally-derived haplotype phasing, exome sequencing and tumor subclonal identification, we performed a combined germline and somatic analysis on this pedigree. Our analysis included family members both affected and unaffected by biliary cancers. Somatic variant analysis of the tumor samples was used to identify driver mutations that may work in concert with candidate germline mutation to initiate and maintain tumorigenesis. Remarkably, the cancer genome sequencing analysis identified a number of common somatic features among primary tumors found in different family members. Analysis of tumor clonality was derived from copy number and mutation data and further informed our analysis of possible contributing drivers. To further inform the analysis of suspected candidate germline loci, we conducted experimentally-based haplotype phasing covering Megabase segments to better delineate blocks that segregated with affected members. We identified several novel candidate genes with germline mutations with a predicted deleterious effect that segregated to affected individuals and had not been previously noted as polymorphisms or rare variants. Thus, we identified several candidate genes that may be novel tumor suppressor candidates for cholangiocarcinoma and increase the susceptibility to this lethal tumor. Overall, our study has significant implications by shedding light on the genetic basis of cholangiocarcinoma.

Citation Format: Stephanie Greer, Lincoln D. Nadauld, Billy Lau, Laura Miotke, Erik Hopmans, Christina M. Wood, John M. Bell, Hanlee P. Ji. Identification of novel tumor suppressor candidates and characterizing their potential driver role in familial cholangiocarcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3901. doi:10.1158/1538-7445.AM2015-3901

Carbon nanotube-based super nanotubes: tunable thermal conductivity in three dimensions

A numerical study of the tuning of the thermal conductivity of three-dimensional CNT-based nanotubes.

Allele-specific copy number profiling by next-generation DNA sequencing

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. A modified Bayesian information criterion is used to guide model selection for determining the number of copy number events. Falcon is evaluated on in silico spike-in data and applied to the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allows us to draw detailed conclusions regarding the clonal history of the individual's colon cancer.

Abstract 3584: Analysis of colorectal intratumoral genetic heterogeneity by high efficiency and rapid deep targeted sequencing

Metastasis is the most frequent cause of morbidity and mortality in cancer. Metastatic disease lethality is often the result of cancer progression despite treatment. Therapeutic resistance is seen nearly in all cases of metastatic cancer. Genetic studies relying on deep sequencing have shown that many cancers are genetically heterogeneous as a result of diverse clonal populations with delineating and unique set of mutations. Several studies suggest that resistance mutations are present in tumors before the start of treatment and via evolution, clonal populations expand under therapeutic selection. However, these minor allelic mutations that define clonal populations are not typically detectable with typical sequencing coverage (20-50X) employed in whole genome approaches.

Relying on an innovative programmable targeting method that enables us to rapidly configure nearly any region of the human genome and efficiently sequence cancer genomes, we are determining the extent of intratumoral genetic heterogeneity and clonal diversity in colorectal cancer. Our study involves over 120 patients with available clinical data and a subset of matched tumors indicative of tumor progression (e.g. tumor-normal, premalignant-malignant, malignant-metastasis). Via an integrative analysis of TCGA, COSMIC and other genomic data sets of colorectal cancer, we identified the top ranking 53 cancer genes prone to mutation and associated with advanced colorectal cancer by. These top genes are found in known cancer pathways such as the WNT and RAS/RAF pathway and we are analyzing the exons of these genes for mutations, insertions and deletions with a sequencing depth of at least 1000x. Preliminary results have shown that we can readily reach sequencing depths of 7000x with our automated targeting approach and that a minimal sequencing depth of 1000x will enable detection of aberrations present in the sample below 1%. Samples are being analyzed for the overall level of heterogeneity and correlation of clonal mutations to clinical outcome.

For optimal personalized treatment of cancer patients, the analysis of intratumoral genetic heterogeneity may be useful in predicting treatment response and metastatic potential of any given primary colorectal cancer.

Citation Format: Erik S. Hopmans, Hojoon Lee, Laura Miotke, Rowza Tur Rumma, Sue Grimes, John M. Bell, Hanlee P. Ji. Analysis of colorectal intratumoral genetic heterogeneity by high efficiency and rapid deep targeted sequencing. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3584. doi:10.1158/1538-7445.AM2014-3584

Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer

Background

Gastric cancer is the second-leading cause of global cancer deaths, with metastatic disease representing the primary cause of mortality. To identify candidate drivers involved in oncogenesis and tumor evolution, we conduct an extensive genome sequencing analysis of metastatic progression in a diffuse gastric cancer. This involves a comparison between a primary tumor from a hereditary diffuse gastric cancer syndrome proband and its recurrence as an ovarian metastasis.

Results

Both the primary tumor and ovarian metastasis have common biallelic loss-of-function of both the CDH1 and TP53 tumor suppressors, indicating a common genetic origin. While the primary tumor exhibits amplification of the Fibroblast growth factor receptor 2 (FGFR2) gene, the metastasis notably lacks FGFR2 amplification but rather possesses unique biallelic alterations of Transforming growth factor-beta receptor 2 (TGFBR2), indicating the divergent in vivo evolution of a TGFBR2-mutant metastatic clonal population in this patient. As TGFBR2 mutations have not previously been functionally validated in gastric cancer, we modeled the metastatic potential of TGFBR2 loss in a murine three-dimensional primary gastric organoid culture. The Tgfbr2 shRNA knockdown within Cdh1^-/-; Tp53^-/- organoids generates invasion in vitro and robust metastatic tumorigenicity in vivo, confirming Tgfbr2 metastasis suppressor activity.

Conclusions

We document the metastatic differentiation and genetic heterogeneity of diffuse gastric cancer and reveal the potential metastatic role of TGFBR2 loss-of-function. In support of this study, we apply a murine primary organoid culture method capable of recapitulating in vivo metastatic gastric cancer. Overall, we describe an integrated approach to identify and functionally validate putative cancer drivers involved in metastasis.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0428-9) contains supplementary material, which is available to authorized users.

A programmable method for massively parallel targeted sequencing

We have developed a targeted resequencing approach referred to as Oligonucleotide-Selective Sequencing. In this study, we report a series of significant improvements and novel applications of this method whereby the surface of a sequencing flow cell is modified in situ to capture specific genomic regions of interest from a sample and then sequenced. These improvements include a fully automated targeted sequencing platform through the use of a standard Illumina cBot fluidics station. Targeting optimization increased the yield of total on-target sequencing data 2-fold compared to the previous iteration, while simultaneously increasing the percentage of reads that could be mapped to the human genome. The described assays cover up to 1421 genes with a total coverage of 5.5 Megabases (Mb). We demonstrate a 10-fold abundance uniformity of greater than 90% in 1 log distance from the median and a targeting rate of up to 95%. We also sequenced continuous genomic loci up to 1.5 Mb while simultaneously genotyping SNPs and genes. Variants with low minor allele fraction were sensitively detected at levels of 5%. Finally, we determined the exact breakpoint sequence of cancer rearrangements. Overall, this approach has high performance for selective sequencing of genome targets, configuration flexibility and variant calling accuracy.

RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing

Background

Rare single nucleotide variants play an important role in genetic diversity and heterogeneity of specific human disease. For example, an individual clinical sample can harbor rare mutations at minor frequencies. Genetic diversity within an individual clinical sample is oftentimes reflected in rare mutations. Therefore, detecting rare variants prior to treatment may prove to be a useful predictor for therapeutic response. Current rare variant detection algorithms using next generation DNA sequencing are limited by inherent sequencing error rate and platform availability.

Findings

Here we describe an optimized implementation of a rare variant detection algorithm called RVD for use in targeted gene resequencing. RVD is available both as a command-line program and for use in MATLAB and estimates context-specific error using a beta-binomial model to call variants with minor allele frequency (MAF) as low as 0.1%. We show that RVD accepts standard BAM formatted sequence files. We tested RVD analysis on multiple Illumina sequencing platforms, among the most widely used DNA sequencing platforms.

Conclusions

RVD meets a growing need for highly sensitive and specific tools for variant detection. To demonstrate the usefulness of RVD, we carried out a thorough analysis of the software’s performance on synthetic and clinical virus samples sequenced on both an Illumina GAIIx and a MiSeq. We expect RVD can improve understanding the genetics and treatment of common viral diseases including influenza. RVD is available at the following URL:http://dna-discovery.stanford.edu/software/rvd/.

Targeted sequencing library preparation by genomic DNA circularization

BACKGROUND

For next generation DNA sequencing, we have developed a rapid and simple approach for preparing DNA libraries of targeted DNA content. Current protocols for preparing DNA for next-generation targeted sequencing are labor-intensive, require large amounts of starting material, and are prone to artifacts that result from necessary PCR amplification of sequencing libraries. Typically, sample preparation for targeted NGS is a two-step process where (1) the desired regions are selectively captured and (2) the ends of the DNA molecules are modified to render them compatible with any given NGS sequencing platform.

RESULTS

In this proof-of-concept study, we present an integrated approach that combines these two separate steps into one. Our method involves circularization of a specific genomic DNA molecule that directly incorporates the necessary components for conducting sequencing in a single assay and requires only one PCR amplification step. We also show that specific regions of the genome can be targeted and sequenced without any PCR amplification.

CONCLUSION

We anticipate that these rapid targeted libraries will be useful for validation of variants and may have diagnostic application.

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome

Recent exponential growth in the throughput of next-generation DNA sequencing platforms has dramatically spurred the use of accessible and scalable targeted resequencing approaches. This includes candidate region diagnostic resequencing and novel variant validation from whole genome or exome sequencing analysis. We have previously demonstrated that selective genomic circularization is a robust in-solution approach for capturing and resequencing thousands of target human genome loci such as exons and regulatory sequences. To facilitate the design and production of customized capture assays for any given region in the human genome, we developed the Human OligoGenome Resource (http://oligogenome.stanford.edu/). This online database contains over 21 million capture oligonucleotide sequences. It enables one to create customized and highly multiplexed resequencing assays of target regions across the human genome and is not restricted to coding regions. In total, this resource provides 92.1% in silico coverage of the human genome. The online server allows researchers to download a complete repository of oligonucleotide probes and design customized capture assays to target multiple regions throughout the human genome. The website has query tools for selecting and evaluating capture oligonucleotides from specified genomic regions.

Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing

We describe an approach for targeted genome resequencing, called oligonucleotide-selective sequencing (OS-Seq), in which we modify the immobilized lawn of oligonucleotide primers of a next-generation DNA sequencer to function as both a capture and sequencing substrate. We apply OS-Seq to resequence the exons of either 10 or 344 cancer genes from human DNA samples. In our assessment of capture performance, >87% of the captured sequence originated from the intended target region with sequencing coverage falling within a tenfold range for a majority of all targets. Single nucleotide variants (SNVs) called from OS-Seq data agreed with >95% of variants obtained from whole-genome sequencing of the same individual. We also demonstrate mutation discovery from a colorectal cancer tumor sample matched with normal tissue. Overall, we show the robust performance and utility of OS-Seq for the resequencing analysis of human germline and cancer genomes.

A flexible approach for highly multiplexed candidate gene targeted resequencing

We have developed an integrated strategy for targeted resequencing and analysis of gene subsets from the human exome for variants. Our capture technology is geared towards resequencing gene subsets substantially larger than can be done efficiently with simplex or multiplex PCR but smaller in scale than exome sequencing. We describe all the steps from the initial capture assay to single nucleotide variant (SNV) discovery. The capture methodology uses in-solution 80-mer oligonucleotides. To provide optimal flexibility in choosing human gene targets, we designed an in silico set of oligonucleotides, the Human OligoExome, that covers the gene exons annotated by the Consensus Coding Sequencing Project (CCDS). This resource is openly available as an Internet accessible database where one can download capture oligonucleotides sequences for any CCDS gene and design custom capture assays. Using this resource, we demonstrated the flexibility of this assay by custom designing capture assays ranging from 10 to over 100 gene targets with total capture sizes from over 100 Kilobases to nearly one Megabase. We established a method to reduce capture variability and incorporated indexing schemes to increase sample throughput. Our approach has multiple applications that include but are not limited to population targeted resequencing studies of specific gene subsets, validation of variants discovered in whole genome sequencing surveys and possible diagnostic analysis of disease gene subsets. We also present a cost analysis demonstrating its cost-effectiveness for large population studies.

Dissemination and genetic context analysis of bla(VIM-6) among Pseudomonas aeruginosa isolates in Asian-Pacific Nations

VIM-6, previously reported in two strains from Singapore recovered in 2000, was detected in 16 isolates collected in 2006 in India (12 isolates), Indonesia (two), Korea and the Philippines (one each). High genetic variability was observed among VIM-6-producing isolates (12 ribotypes and 11 pulsed-field gel electrophoresis types), but clones were observed in India and Indonesia; bla(VIM-6)-carrying integrons of 3.9 kb and 5 kb were detected, and two of five Indian hospitals yielded isolates with both integrons. These two integrons, bla(VIM-6) was located in the first position, followed by bla(OXA-10) and aacA4. The 5-kb integrons also harboured aadA1 and a 331-bp open reading frame encoding a putative efflux pump.

Outbreak of invasive methicillin-resistant Staphylococcus aureus infection associated with acupuncture and joint injection

OBJECTIVE

To describe an outbreak of invasive methicillin-resistant Staphylococcus aureus (MRSA) infection after percutaneous needle procedures (acupuncture and joint injection) performed by a single medical practitioner.

SETTING

A medical practitioner's office and 4 hospitals in Perth, Western Australia.

PATIENTS

Eight individuals who developed invasive MRSA infection after acupuncture or joint injection performed by the medical practitioner.

METHODS

We performed a prospective and retrospective outbreak investigation, including MRSA colonization surveillance, environmental sampling for MRSA, and detailed molecular typing of MRSA isolates. We performed an infection control audit of the medical practitioner's premises and practices and administered MRSA decolonization therapy to the medical practitioner.

RESULTS

Eight cases of invasive MRSA infection were identified. Seven cases occurred as a cluster in May 2004; another case (identified retrospectively) occurred approximately 15 months earlier in February 2003. The primary sites of infection were the neck, shoulder, lower back, and hip: 5 patients had septic arthritis and bursitis, and 3 had pyomyositis; 3 patients had bacteremia, including 1 patient with possible endocarditis. The medical practitioner was found to be colonized with the same MRSA clone [ST22-MRSA-IV (EMRSA-15)] at 2 time points: shortly after the first case of infection in March 2003 and again in May 2004. After the medical practitioner's premises and practices were audited and he himself received MRSA decolonization therapy, no further cases were identified.

CONCLUSIONS

This outbreak most likely resulted from a breakdown in sterile technique during percutaneous needle procedures, resulting in the transmission of MRSA from the medical practitioner to the patients. This report demonstrates the importance of surveillance and molecular typing in the identification and control of outbreaks of MRSA infection.

Microscopic and spectroscopic study of self-ordering in poly(3-hexylthiophene)/carbon nanotubes nanocomposites

Poly(3-hexylthiophene)-single-walled carbon nanotubes (SWNTs) composites were studied using UV-visible absorbance and Raman spectroscopy, scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). Monolayers of regioregular poly(3-hexyl thiophene) (rrP3HT) adsorbed on SWNTs have been imaged using scanning tunneling microscopy (STM) to obtain measurements of the chiral angles at which the thiophene polymer chains wrap around individual carbon nanotubes (41-48 degrees with respect to nanotube axis) and polymer interchain spacings (1.68 angstroms). The rrP3HT interchain distance is greater for rrP3HT monolayers adsorbed onto the curved surfaces of SWNTs than on the flat surfaces of highly ordered pyrolytic graphite samples (1.4 angstroms). UV-vis spectroscopic data provided strong evidence for increased interchain interactions in composites of rrP3HT and SWNTs compared to the pure polymer. The STM local-probe studies of the native polymer and the composites further confirmed that the rrP3HT interacts with carbon nanotubes to produce a highly ordered material at the molecular level.

Multiple pollinator visits to Mimulus ringens (Phrymaceae) flowers increase mate number and seed set within fruits

The timing and effectiveness of pollinator visitation to flowers is an important factor influencing mating patterns and reproductive success. Multiple pollinator probes to a flower may increase both the quantity and genetic diversity of progeny, especially if single probes deposit insufficient pollen for maximal seed set or if the interval between probes is brief. When pollen carryover is limited, sequential pollen loads may also differ markedly in sire representation. We hypothesized that these conditions help explain high levels of multiple paternity in Mimulus ringens fruits. We documented all bee visits to individual flowers, quantified resulting seed set, and determined paternity for 20 seeds per fruit. Most (76%) flowers received multiple probes, and the interval between probes was usually <30 min. Flowers probed multiple times produced 44% more seeds than flowers probed once. All fruits were multiply sired. Flowers receiving a single probe averaged 3.12 outcross sires per fruit, indicating that single probes deposit pollen from several donors. Multiple paternity was even greater after three or more probes (4.92 outcross sires), demonstrating that sequential visits bring pollen from donors not represented in the initial probe.

Two-Dimensional Crystal Growth and Stacking of Bis(phthalocyaninato) Rare Earth Sandwich Complexes at the 1-Phenyloctane/Graphite Interface

Initial stages of two-dimensional crystal growth of the double-decker sandwich complex Lu(Pc*)2 [Pc* = 2,3,9,10,16,17,23,24-octakis(octyloxy)phthalocyaninato] have been studied by scanning tunneling microscopy at the liquid/solid interface between 1-phenyloctane and highly oriented pyrolytic graphite. High-resolution images strongly suggest alignment of the double-decker molecules into monolayers with the phthalocyanine rings parallel to the surface. Domains were observed with either hexagonal or quadrate packing motifs, and the growing interface of the layer was imaged. Molecular resolution was achieved, and the face of the phthalocyanine rings appeared as somewhat diffuse circular features. The alkyl chains are proposed to be interdigitating to maintain planar side-by-side packing.

Patterns of multiple paternity in fruits of Mimulus ringens (Phrymaceae)

Multiply sired fruits provide unambiguous evidence that pollen from two or more donors was deposited on a stigma and successfully fertilized ovules. Such multiple paternity within fruits can have important consequences for both parental and offspring fitness, but little is known about the frequency of multiple paternity or the mechanisms causing it. In this study we quantify the extent of multiple paternity in replicate experimental arrays of Mimulus ringens (square-stem monkeyflower) and use observations of pollinator behavior to infer mechanisms generating multiply sired fruits. In each array, floral displays were trimmed to two, four, eight, or 16 flowers per plant to span the range of display sizes observed in nature. In our sample of 204 fruits, more than 95% had two or more outcross pollen donors. The number of sires per fruit averaged 4.63 ± 0.10 (mean ± 1 SE), including selfs, and did not vary significantly with floral display treatment. Patterns of bumble bee foraging, combined with limited pollen carryover, suggest that observed levels of multiple paternity cannot be fully explained by single probes that deposited mixed pollen loads. Multiple probes to flowers, each delivering pollen from 1-3 different sires, are more likely to have caused the observed patterns. These sequential visits may reduce the potential for pollen competition and female choice based on pollen tube growth rate.

Antimicrobial activities of garenoxacin (BMS 284756) against Asia-Pacific region clinical isolates from the SENTRY program, 1999 to 2001

Between 1999 and 2001, 16,731 isolates from the Asia-Pacific Region were tested in the SENTRY Program for susceptibility to six fluoroquinolones including garenoxacin. Garenoxacin was four- to eightfold less active against Enterobacteriaceae than ciprofloxacin, although both drugs inhibited similar percentages at 1 microg/ml. Garenoxacin was more active against gram-positive species than all other fluoroquinolones except gemifloxacin. For Staphylococcus aureus, oxacillin resistance was high in many participating countries (Japan, 67%; Taiwan, 60%; Hong Kong, 55%; Singapore, 52%), with corresponding high levels of ciprofloxacin resistance (57 to 99%) in oxacillin-resistant S. aureus (ORSA). Of the ciprofloxacin-resistant ORSA isolates, the garenoxacin MIC was >4 microg/ml for only 9% of them. For Streptococcus pneumoniae, penicillin nonsusceptibility and macrolide resistance were high in many countries. No relationship was seen between penicillin and garenoxacin susceptibility, with all isolates being susceptible at <2 microg/ml. There was, however, a partial correlation between ciprofloxacin and garenoxacin MICs. For ciprofloxacin-resistant isolates for which garenoxacin MICs were 0.25 to 1 microg/liter, mutations in both the ParC and GyrA regions of the quinolone resistance-determining region could be demonstrated. No mutations conferring high-level resistance were detected. Garenoxacin shows useful activity against a wide range of organisms from the Asia-Pacific region. In particular, it has good activity against S. aureus and S. pneumoniae, although there is evidence that low-level resistance is present in those organisms with ciprofloxacin resistance.

Prevalence of extended-spectrum beta-lactamase-producing Enterobacter cloacae in the Asia-Pacific region: results from the SENTRY Antimicrobial Surveillance Program, 1998 to 2001

Enterobacter cloacae strains from hospitalized patients with a range of infections were collected by 17 laboratories in the Asia-Pacific region and South Africa. Isolates for which ceftriaxone MICs were above 1 microg/ml and/or ceftazidime MICs were above 2 microg/ml, as well as 46 strains for which ceftriaxone and/or ceftazidime MICs were at or below these values, were screened for levels of extended-spectrum beta-lactamase (ESBL) production through the use of broth microdilution for the detection of clavulanate enhancement of the activity of ceftriaxone, ceftazidime, and cefepime. Of the isolates examined, ceftriaxone and/or ceftazidime had elevated MICs for 44%, of which 36% were ESBL positive. ESBL-positive strains were commonly susceptible to piperacillin-tazobactam and more frequently resistant to several other antimicrobials studied. A cefepime MIC above 0.25 microg/ml had the highest sensitivity (100%) and specificity (74%) for predicting the presence of an ESBL.

The influence of floral display size on selfing rates in Mimulus ringens

Pollinators often visit several flowers in sequence on plants with large floral displays. This foraging pattern is expected to influence the rate of self-fertilization in self-compatible taxa. To quantify the effects of daily floral display on pollinator movements and selfing, we experimentally manipulated flower number in four replicate (cloned) arrays of Mimulus ringens (Scrophulariaceae), each consisting of genets with unique combinations of homozygous marker genotypes. Four display classes (two, four, eight and 16 flowers) were present in each array. Pollinator visitation rate per flower and seed set per fruit were unaffected by display. However, flower number strongly influenced the frequency of within-plant pollinator movements, which increased from 13.8% of probes on two-flower displays to 77.6% of probes on 16-flower displays. The proportion of within-plant movements was significantly correlated with selfing (r = 0.993). The increase from 22.9% selfing on two-flower displays to 37.3% selfing on 16-flower displays reflects changes in the extent of geitonogamous self-pollination. We estimate that approximately half of all selfing on 16-flower displays resulted from geitonogamy. Selfing also varied dramatically among fruits within display classes. Nested ANOVA indicates that differences among flowers on two-flower ramets accounted for 45.4% of the variation in selfing, differences among genets accounted for 16.1% of the variation, and statistical and sampling error accounted for 38.5% of the variation. Differences among flowers within ramets may reflect the order of sequential floral probes on a display.

Antimicrobial resistance trends in community-acquired respiratory tract pathogens in the Western Pacific Region and South Africa: report from the SENTRY antimicrobial surveillance program, (1998-1999) including an in vitro evaluation of BMS284756

From 1998 to 1999, a large number of community-acquired respiratory tract isolates of Streptococcus pneumoniae (n=566), Haemophilus influenzae (n=513) and Moraxella catarrhalis (n=228) were collected from 15 centres in Australia, Hong Kong, Japan, China, the Philippines, Singapore, South Africa and Taiwan through the SENTRY Antimicrobial Surveillance Program. Isolates were tested against 26 antimicrobial agents using the NCCLS-recommended methods. Overall, 40% of S. pneumoniae isolates were resistant to penicillin with 18% of strains having high-level resistance (MIC > or =2 mg/l). Rates of erythromycin and clindamycin resistance were 41 and 23%, respectively. Penicillin-resistant strains showed high rates of resistance to other antimicrobial agents: 96% to trimethoprim-sulphamethoxazole (TMP-SMX), 84% to tetracycline and 81% to erythromycin. A significant proportion of penicillin-susceptible strains was also resistant to erythromycin (21%), tetracycline (29%) and TMP-SMZ (26%). Small numbers of strains were resistant to levofloxacin (0.7%), trovafloxacin (0.4%) and grepafloxacin (1.3%) where as all strains remained uniformly susceptible to quinupristin/dalfopristin and BMS284756 (MIC(90), 0.06 mg/l), a new desfluoroquinolone. beta-lactamases were, produced by 20% H. influenzae isolates and only rare strains showed intrinsic resistance to amoxycillin. Other beta-lactam agents showed good activity with rates of resistance less than 2% and all isolates showed susceptibility to cefixime, ceftibuten, cefepime and cefotaxime. Rates of resistance to tetracycline and chloramphenicol were also relatively low at 3%. The majority (98%) of M. catarrhalis isolates was found to be beta-lactamase-positive and resistant to penicillins, however, resistance to erythromycin and tetracycline was also low at 1.8%. Both H. influenzae and M. catarrhalis isolates were uniformly susceptible to the new desfluoroquinolone and tested fluoroquinolones.

Home testing of fructosamine improves glycemic control in patients with diabetes

OBJECTIVE

To determine whether weekly fructosamine testing at home by patients with type 2 diabetes, combined with therapeutic intervention when necessary on the basis of the results, would lead to improved glycemic control in comparison with usual care during a 3-month period.

METHODS

In a prospective study, 25 patients with glycosylated hemoglobin (HbA1c) values above 8.0% were randomized into 2 groups. Both groups, a glucose-only testing group (14 patients with an initial mean HbA1c of 9.4 +/- 0.9%) and a combined glucose plus fructosamine testing group (11 patients with an initial mean HbA1c of 9.2 +/- 0.7%), received therapeutic intervention at the time of randomization. Both groups were instructed to perform blood glucose testing up to four times per day. The combined glucose plus fructosamine testing group was also instructed to perform weekly fructosamine testing in addition to the glucose testing and to telephone the investigator if their home-testing fructosamine value exceeded 350 mmol/L (approximately equivalent to HbA1c of 7.8%), whereupon the investigator implemented further interventions. Both groups returned in 3 months, at which time HbA1c testing was repeated in order to determine whether glycemic control had changed.

RESULTS

The study results after 3 months showed that the HbA1c values in the combined glucose plus fructosamine testing group decreased from 9.2 +/- 0.7% to 8.0 +/- 0.5% (P<0.0001). In contrast, the HbA1c values in the glucose-only testing group declined from 9.4 +/- 0.9% to 9.1 +/- 1.3%, a difference that was not significant.

CONCLUSION

In the 3 months after a change in therapy for type 2 diabetes, weekly home testing of fructosamine, combined with therapeutic interventions based on the results, led to a more rapid and significant improvement in glycemic control than did the usual regimen of glucose-only testing.

Lack of association of the (AAAT)6 allele of the GXAlu tetranucleotide repeat in intron 27b of the NF1 gene with autism

A novel allele of the GXAlu tetranucleotide repeat in intron 27b of the neurofibromatosis 1 (NF1) gene has recently been reported to be present in 4.7% of autistic patients but not in controls. We have found the novel GXAlu allele absent in 204 patients from the South Carolina Autism Project and 200 controls. The autism population studied includes a significant number of patients with hypotonia, stereotyped behaviors, or postural, gait, and motor abnormalities similar to those seen in the patients previously reported to possess the novel GXAlu allele. This suggests that the novel (AAAT)6 GXAlu allele is not associated with autism.

Chronic valproate treatment decreases the in vivo turnover of arachidonic acid in brain phospholipids: a possible common effect of mood stabilizers

Both (Li(+)) and valproic acid (VPA) are effective in treating bipolar disorder, but the pathway by which either works, and whether it is common to both drugs, is not agreed upon. We recently reported, using an in vivo fatty acid model, that Li(+) reduces the turnover rate of the second messenger arachidonic acid (AA) by 80% in brain phospholipids of the awake rat, without changing turnover rates of docosahexaenoic or palmitic acid. Reduced AA turnover was accompanied by down-regulation of gene expression and protein levels of an AA-specific cytosolic phospholipase A(2) (cPLA(2)). To see if VPA had the same effect on AA turnover, we used our in vivo fatty acid model in rats chronically administered VPA (200 mg/kg, i.p. for 30 days). Like Li(+), VPA treatment significantly decreased AA turnover within brain phospholipids (by 28-33%), although it had no effect on cPLA(2) protein levels. Thus, both mood stabilizers, Li(+) and VPA have a common action in reducing AA turnover in brain phospholipids, albeit by different mechanisms.

Methicillin-resistant Staphylococcal aureus evolution in Australia over 35 years

Australia has a long association methicillin-resistant Staphylococcus aureus (MRSA). Its unique geographic and demographic features have led to the emergence and spread of three types of MRSA over 35 years. Classical multiresistant hospital-acquired MRSA were first noted in Australia in 1965. By the end of the 1970s, strains of this type of MRSA were well established in the complex tertiary care hospitals in the capital cities on the eastern seaboard of mainland Australia. Characterized by resistance to beta-lactams, erythromycin, tetracycline, gentamicin, and trimethoprim-sulfamethoxazole, these strains have persisted and diversified genetically and have acquired a variety of new resistances. They have proven pathogenicity and are a prominent cause of hospital infection in the endemic institutions. More recently they have become endemic in some central state tertiary care hospitals. Community-acquired strains of MRSA first appeared in the north of Western Australia in the mid-1980s. Strains have subsequently appeared in the south of the state and in the two adjacent central states, and are more frequently isolated from Aboriginal patients. Although harboring few or no additional resistances apart from resistance to beta-lactams initially, these strains are also accumulating additional resistances. A different variety of community-acquired MRSA has recently been noted in eastern Australia. It has a similar antibiogram to the western strains, but an entirely different epidemiology, resembling that currently being experienced in parts of New Zealand, and associated with patients of south Pacific island origin.