Common Features of Environmental Mycobacterium chelonae from Colorado Using Partial and Whole Genomic Sequence Analyses.

Nontuberculous mycobacteria (NTM) are environmentally acquired opportunistic pathogens that cause chronic lung disease in susceptible individuals. While presumed to be ubiquitous in built and natural environments, NTM environmental studies are limited. While environmental sampling campaigns have been performed in geographic areas of high NTM disease burden, NTM species diversity is less defined among areas of lower disease burden like Colorado. In Colorado, metals such as molybdenum have been correlated with increased risk for NTM infection, yet environmental NTM species diversity has not yet been widely studied. Based on prior regression modeling, three areas of predicted high, moderate, and low NTM risk were identified for environmental sampling in Colorado. Ice, plumbing biofilms, and sink tap water samples were collected from publicly accessible freshwater sources. All samples were microbiologically cultured and NTM were identified using partial rpoB gene sequencing. From these samples, areas of moderate risk were more likely to be NTM positive. NTM recovery from ice was more common than recovery from plumbing biofilms or tap water. Overall, nine different NTM species were identified, including clinically important Mycobacterium chelonae. MinION technology was used to whole genome sequence and compare mutational differences between six M. chelonae genomes, representing three environmental isolates from this study and three other M. chelonae isolates from other sources. Drug resistance genes and prophages were common findings among environmentally derived M. chelonae, promoting the need for expanded environmental sampling campaigns to improve our current understanding of NTM species abundance while opening new avenues for improved targeted drug therapies.

Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance.

Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai'i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai'i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).

Complete genome assembly of Hawai'i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria.

Nontuberculous mycobacteria (NTM) are ubiquitous environmental opportunistic pathogens that can cause chronic lung disease. Within the United States, Hawai'i has the highest incidence of NTM lung disease, though the precise reasons are yet to be fully elucidated. One possibility is the high prevalence of NTM in the Hawai'i environment acting as a potential reservoir for opportunistic NTM infections. Through our previous initiatives to collect and characterize NTM in Hawai'i, community scientists of Hawai'i have collected thousands of environmental samples for sequencing. Here, these community scientists were invited for the first time into a high school lab in O'ahu for a genomic sequencing workshop, where participants sequenced four of the collected isolate genomic samples using the Oxford Nanopore Technologies MinION sequencer. Participants generated high quality long read data that when combined with short read Illumina data yielded complete bacterial genomic assemblies suitable for in-depth analysis. The gene annotation analysis identified a suite of genes that might help NTM thrive in the Hawai'i environment. Further, we found evidence of co-occurring methylobacteria, revealed from the sequencing data, suggesting that in some cases methylobacteria and NTM may coexist in the same niche, challenging previously accepted paradigms. The sequencing efforts presented here generated novel insights regarding the potential survival strategies and microbial interactions of NTM in the geographic hot spot of Hawai'i. We highlight the contributions of community scientists and present an activity that can be reimplemented as a workshop or classroom activity by other research groups to engage their local communities.

High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors.

Single-cell nanopore sequencing of full-length mRNAs transforms single-cell multi-omics studies. However, challenges include high sequencing errors and dependence on short-reads and/or barcode whitelists. To address these, we develop scNanoGPS to calculate same-cell genotypes (mutations) and phenotypes (gene/isoform expressions) without short-read nor whitelist guidance. We apply scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell-lines. Standalone, scNanoGPS deconvolutes error-prone long-reads into single-cells and single-molecules, and simultaneously accesses both phenotypes and genotypes of individual cells. Our analyses reveal that tumor and stroma/immune cells express distinct combination of isoforms (DCIs). In a kidney tumor, we identify 924 DCI genes involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Transcriptome-wide mutation analyses identify many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting the critical roles of different mutant populations in tumors. Together, scNanoGPS facilitates applications of single-cell long-read sequencing technologies.

Delineating genotypes and phenotypes of individual cells from long-read single cell transcriptomes.

Single-cell nanopore sequencing of full-length mRNAs (scNanoRNAseq) is transforming singlecell multi-omics studies. However, challenges include computational complexity and dependence on short-read curation. To address this, we developed a comprehensive toolkit, scNanoGPS to calculate same-cell genotypes-phenotypes without short-read guidance. We applied scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell lines. Standalone, scNanoGPS accurately deconvoluted error-prone long-reads into single-cells and single-molecules. Further, scNanoGPS simultaneously accessed both phenotypes (expressions/isoforms) and genotypes (mutations) of individual cells. Our analyses revealed that tumor and stroma/immune cells often expressed significantly distinct combinations of isoforms (DCIs). In a kidney tumor, we identified 924 genes with DCIs involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Moreover, transcriptome-wide mutation analyses identified many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting critical roles of different populations in tumors. Together, scNanoGPS facilitates applications of single-cell long-read sequencing.

How Accurate Are the Consistency Labels Used in Hong Kong? An Objective Study of the Consistency of Thickened Liquids Using International Dysphagia Diet Standardisation Initiative and Consistometric Measurements.

OBJECTIVES: The present study objectively examined the consistency (thickness) of labels that are used in Hong Kong for the population with dysphagia using an International Dysphagia Diet Standardisation Initiative (IDDSI) flow test and Bostwick consistometric measurements. METHODS: Liquids were prepared by thickening water to achieve 4 consistency labels (slightly thick, mildly thick, medium thick, and extra thick) according to manufacturer's instructions, employing 2 types of thickening products that are used in Hong Kong, i.e., starch based and gum based. For each consistency label prepared using each thickening product, the IDDSI flow test and consistometric measurements were obtained and compared. RESULTS: The results showed that the actual thickness of liquids was highly dependent on the type of thickener (starch based vs. gum based) used. Thickened liquids prepared using the starch-based thickener were generally thinner than the actual value at a lower concentration. CONCLUSION: Though prepared strictly following the manufacturer's instructions, the thickened liquids fail to faithfully correlate with the standardized norms established according to the IDDSI framework and the objective consistometric measurement using a Bostwick consistometer. Therefore, caution must be exercised when administering a thickened diet following the manufacturer's instructions for patients with dysphagia.

Positional cloning and characterization of the papaya diminutive mutant reveal a truncating mutation in the CpMMS19 gene.

The papaya diminutive mutant exhibits miniature stature, retarded growth and reduced fertility. This undesirable mutation appeared in the variety 'Sunset', the progenitor of the transgenic line 'SunUp', and was accidentally carried forward into breeding populations. The diminutive mutation was mapped to chromosome 2 and fine mapped to scaffold 25. Sequencing of a bacterial artificial chromosome in the fine mapped region led to the identification of the target gene responsible for the diminutive mutant, a gene orthologous to MMS19 with a 36.8 kb deletion co-segregating with the diminutive mutant. The genomic sequence of CpMMS19 is 62 kb, consisting of 20 exons and 19 introns. It encodes a protein of 1143 amino acids while the diminutive allele encodes a truncated protein of 287 amino acids. Expression of the full-length CpMMS19 was able to complement the thermosensitive growth of the yeast mms19 deletion mutant while expression of the diminutive allele resulted in increased thermosensitivity. Over-expression of the diminutive allele in Arabidopsis met18 mutant results in a high frequency of seed abortion. The papaya diminutive phenotype is caused by an alteration in gene function rather than a loss-of-function mutation. SCAR (sequence characterized amplified region) markers were developed for rapid detection of the diminutive allele in breeding populations.

Three-Dimensional Printing for Procedure Rehearsal/Simulation/Planning in Interventional Radiology.

With the advances in affordable three-dimensional (3D) printing technology, 3D reconstruction and patient-specific 3D printed models are establishing a crucial role in the field of medicine for both educational purposes and procedural planning. 3D printed models provide physicians with increased 3D perception and tactile feedback, and enable a team-based approach to operational planning. However, performing an effective 3D reconstruction requires an in-depth understanding of the software features to accurately segment and reconstruct the human anatomy of interest from preacquired image data from multiple modalities such as computer tomography, 3D angiography and magnetic resonance imaging, and the different 3D printers/materials available in the market today. Increased understanding of this technology may benefit radiologists by developing techniques and tricks specific to interventional radiology and establishing a criterion to determine when to use these. Thus, the purpose of this manuscript is to provide physicians with an update on currently available 3D reconstruction software as well as printers and materials. Our initial experience using this technology is introduced based on a specific case of developing a 3D printed aorta for a patient with severe stenosis of the abdominal aorta.

Articulatory Contact Pressure during Bilabial Plosive Production in Esophageal and Tracheoesophageal Speech.

OBJECTIVES: The present study investigated the articulatory contact pressure during the production of bilabial plosives by esophageal (ES), tracheoesophageal (TE), and laryngeal speakers. METHODS: The peak contact pressure (PCP) during bilabial plosive production of /CVCVCVCVCV/ syllable strings of /p/ and /ph/ was obtained from 10 ES, 10 TE, and 10 laryngeal speakers of Cantonese. PCP values were obtained by using a pressure transduction system (Iowa Oral Performance Instrument) during speech production. RESULTS: The results showed that ES speakers exhibited a significantly greater PCP value than TE and laryngeal speakers, as revealed by cheek muscle compression force. In addition, the unaspirated bilabial plosive /p/ was associated with a greater PCP than its aspirated counterpart /ph/. CONCLUSION: The current findings might support the hypothesis of over-exaggerated speech for better intelligibility among alaryngeal speakers. In addition, the increased oral muscular effort could be associated with a compensatory strategy for maintaining a high intraoral pressure or the unique air intake by ES speakers.

Strategy for Sustaining Cancer Education Services for Underserved Communities.

Innovative strategies are needed to generate resources to replicate and sustain proven, community-based health promotion programs. Authors describe how civic-minded university students can conduct such programs while simultaneously gaining skills that make them competitive graduate school applicants.

Activation of Receptor Activator of Nuclear Factor-κB Ligand and Matrix Metalloproteinase Production in Periodontal Fibroblasts by Endothelin Signaling.

BACKGROUND: Periodontitis is a group of inflammatory diseases affecting the tissues supporting the teeth that will progressively cause the loss of alveolar bone and periodontal ligaments and eventually the dentition. Activation of osteoclast activity by receptor activator of nuclear factor-κB ligand (RANKL) and released enzymes such as matrix metalloproteinases (MMPs) are among the factors involved in the breakdown of the periodontium. However, the mechanisms regulating their production in periodontitis are poorly understood. Endothelin signaling via the activation of the endothelin-A receptor (EDNRA) by endothelin-1 may play a role in the disease because the expression of the receptor and ligand is elevated in the periodontal tissues of patients with periodontitis. METHODS: Cultured primary human periodontal fibroblasts were treated with 20 and 100 nM endothelin-1 for 6 and 24 hours and then collected to assess MMP and RANKL production by immunoblotting. Inhibitors were used to identify the molecular pathways activated by EDNRA in these cells. RESULTS: Endothelin-1 stimulated the production of MMP1, MMP8, and RANKL in a dose- and time-dependent manner; blocking EDNRA function with the antagonist TBC3214 inhibited the response, although EDNRA activation had no effects on osteoprotegerin production. These mechanistic studies indicate that EDNRA activates phospholipase C, which then 1) increases the MMP1 protein levels through activation of the extracellular signal-regulated kinase mitogen-activated protein kinase-dependent pathway and 2) upregulates RANKL by a different pathway. CONCLUSION: These results suggest that EDNRA may function in the breakdown of the periodontal tissues associated with periodontitis by promoting the protein expression of MMPs and RANKL via the phospholipase C pathway.

Disseminating tobacco control information to Asians and Pacific Islanders.

The Asian Grocery Store-Based Cancer Education Program (the Program) is a proven strategy for promoting early breast cancer detection among Asian American women. The authors sought to test whether the same public health model can become an effective strategy for increasing the Asian community's awareness of the California Smokers' Helpline (the Helpline) and thereby, potentially decreasing this community's use of tobacco products. The new module, mainly staffed by four well-trained, volunteer undergraduates, explained the risks of first- and second-hand tobacco exposure and how to access the Helpline's services. A brochure, provided in English, Chinese, Korean, and Vietnamese (the Helpline's available Asian languages), was used to guide the bicultural, bilingual students' tobacco-related discussions with shoppers. The students' repeated presence at the nine partnering Asian grocery stores served as reminders of the Helpline's availability. In its first year of operation, the student trainers reached 1,052 men and 1,419 women with tobacco cessation messages. Equally important, the participating grocery stores' managers did not object to students telling their customers to quit using the tobacco products sold in their stores. The results suggest that the Program's tobacco cessation module is a viable, community-specific, public health strategy. It is also a strategy with the potential for applications to reduce other health threats.

The projected timing of climate departure from recent variability.

Ecological and societal disruptions by modern climate change are critically determined by the time frame over which climates shift beyond historical analogues. Here we present a new index of the year when the projected mean climate of a given location moves to a state continuously outside the bounds of historical variability under alternative greenhouse gas emissions scenarios. Using 1860 to 2005 as the historical period, this index has a global mean of 2069 (±18 years s.d.) for near-surface air temperature under an emissions stabilization scenario and 2047 (±14 years s.d.) under a 'business-as-usual' scenario. Unprecedented climates will occur earliest in the tropics and among low-income countries, highlighting the vulnerability of global biodiversity and the limited governmental capacity to respond to the impacts of climate change. Our findings shed light on the urgency of mitigating greenhouse gas emissions if climates potentially harmful to biodiversity and society are to be prevented.

Rapid divergence and expansion of the X chromosome in papaya.

X chromosomes have long been thought to conserve the structure and gene content of the ancestral autosome from which the sex chromosomes evolved. We compared the recently evolved papaya sex chromosomes with a homologous autosome of a close relative, the monoecious Vasconcellea monoica, to infer changes since recombination stopped between the papaya sex chromosomes. We sequenced 12 V. monoica bacterial artificial chromosomes, 11 corresponding to the papaya X-specific region, and 1 to a papaya autosomal region. The combined V. monoica X-orthologous sequences are much shorter (1.10 Mb) than the corresponding papaya region (2.56 Mb). Given that the V. monoica genome is 41% larger than that of papaya, this finding suggests considerable expansion of the papaya X; expansion is supported by a higher repetitive sequence content of the X compared with the papaya autosomal sequence. The alignable regions include 27 transcript-encoding sequences, only 6 of which are functional X/V. monoica gene pairs. Sequence divergence from the V. monoica orthologs is almost identical for papaya X and Y alleles; the Carica-Vasconcellea split therefore occurred before the papaya sex chromosomes stopped recombining, making V. monoica a suitable outgroup for inferring changes in papaya sex chromosomes. The papaya X and the hermaphrodite-specific region of the Y(h) chromosome and V. monoica have all gained and lost genes, including a surprising amount of changes in the X.

Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution.

Sex determination in papaya is controlled by a recently evolved XY chromosome pair, with two slightly different Y chromosomes controlling the development of males (Y) and hermaphrodites (Y(h)). To study the events of early sex chromosome evolution, we sequenced the hermaphrodite-specific region of the Y(h) chromosome (HSY) and its X counterpart, yielding an 8.1-megabase (Mb) HSY pseudomolecule, and a 3.5-Mb sequence for the corresponding X region. The HSY is larger than the X region, mostly due to retrotransposon insertions. The papaya HSY differs from the X region by two large-scale inversions, the first of which likely caused the recombination suppression between the X and Y(h) chromosomes, followed by numerous additional chromosomal rearrangements. Altogether, including the X and/or HSY regions, 124 transcription units were annotated, including 50 functional pairs present in both the X and HSY. Ten HSY genes had functional homologs elsewhere in the papaya autosomal regions, suggesting movement of genes onto the HSY, whereas the X region had none. Sequence divergence between 70 transcripts shared by the X and HSY revealed two evolutionary strata in the X chromosome, corresponding to the two inversions on the HSY, the older of which evolved about 7.0 million years ago. Gene content differences between the HSY and X are greatest in the older stratum, whereas the gene content and order of the collinear regions are identical. Our findings support theoretical models of early sex chromosome evolution.

A physical map of the papaya genome with integrated genetic map and genome sequence.

BACKGROUND: Papaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced because of its agricultural importance, unique biological features, and successful application of transgenic papaya for resistance to papaya ringspot virus. As a part of the genome sequencing project, we constructed a BAC-based physical map using a high information-content fingerprinting approach to assist whole genome shotgun sequence assembly. RESULTS: The physical map consists of 963 contigs, representing 9.4x genome equivalents, and was integrated with the genetic map and genome sequence using BAC end sequences and a sequence-tagged high-density genetic map. The estimated genome coverage of the physical map is about 95.8%, while 72.4% of the genome was aligned to the genetic map. A total of 1,181 high quality overgo (overlapping oligonucleotide) probes representing conserved sequences in Arabidopsis and genetically mapped loci in Brassica were anchored on the physical map, which provides a foundation for comparative genomics in the Brassicales. The integrated genetic and physical map aligned with the genome sequence revealed recombination hotspots as well as regions suppressed for recombination across the genome, particularly on the recently evolved sex chromosomes. Suppression of recombination spread to the adjacent region of the male specific region of the Y chromosome (MSY), and recombination rates were recovered gradually and then exceeded the genome average. Recombination hotspots were observed at about 10 Mb away on both sides of the MSY, showing 7-fold increase compared with the genome wide average, demonstrating the dynamics of recombination of the sex chromosomes. CONCLUSION: A BAC-based physical map of papaya was constructed and integrated with the genetic map and genome sequence. The integrated map facilitated the draft genome assembly, and is a valuable resource for comparative genomics and map-based cloning of agronomically and economically important genes and for sex chromosome research.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

Dialysis in nursing homes.

The number of geriatric end-stage renal disease (ESRD) patients in the United States is increasing disproportionately to other age groups on dialysis. Thus there will be more dialysis patients that will require the assistance of nursing homes or extended care facilities. Nursing homes may be beneficial for the geriatric patient in terms of social and physical rehabilitation. Many of these facilities, however, may not take care of or may not have the capacity to adequately care for dialysis patients. Such patients have a higher rate of peritonitis when on peritoneal dialysis (PD) and have higher mortality rates on hemodialysis (HD) or PD compared to similar dialysis patients in the community. Cooperation and communication between the dialysis center and the nursing home, given the complex management issues involved in the care of these patients, are essential. One promising approach to the care of elderly dialysis patients is an integration of nursing home and dialysis unit. Although another approach could be to more fully utilize the services of adult day care centers, this has proven logistically difficult and has not been reported to be successful since it was first suggested more than a decade ago.