Revealing the Nature of Chronic Obstructive Pulmonary Disease Using Self-tracking and Analysis of Contact Patterns: Longitudinal Study.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death and is characterized by a progressive loss of pulmonary function over time with intermittent episodes of exacerbations. Rapid and proactive interventions may reduce the burden of the condition for the patients. Telehealth solutions involving self-tracking of vital parameters such as pulmonary function, oxygen saturation, heart rate, and temperature with synchronous communication of health data may become a powerful solution as they enable health care professionals to react with a proactive and adequate response. We have taken this idea to the next level in the Epital Care Model and organized a person-centered technology-assisted ecosystem to provide health services to COPD patients. OBJECTIVE: The objective is to reveal the nature of COPD by combining technology with a person-centered design aimed to benefit from interactions based on patient-reported outcome data and to assess the needed kind of contacts to best treat exacerbations. We wanted to know the following: (1) What are the incidences of mild, moderate, and severe exacerbations in a mixed population of COPD patients? (2) What are the courses of mild, moderate, and severe exacerbations? And (3) How is the activity and pattern of contacts with health professionals related to the participant conditions? METHODS: Participants were recruited by convenience sampling from November 2013 to December 2015. The participants' sex, age, forced expiratory volume during the first second, pulse rate, and oxygen saturation were registered at entry. During the study, we registered number of days, number of exacerbations, and number of contact notes coded into care and treatment notes. Each participant was classified according to GOLD I-IV and risk factor group A-D. Participants reported their clinical status using a tablet by answering 4 questions and sending 3 semiautomated measurements. RESULTS: Of the 87 participants, 11 were in risk factor group A, 24 in B, 13 in C, and 39 in D. The number of observed days was 31,801 days with 12,470 measurements, 1397 care notes, and 1704 treatment notes. A total of 254 exacerbations were treated and only 18 caused hospitalization. Those in risk factor group D had the highest number of hospitalizations (16), exacerbations (151), and contacts (1910). The initial contacts during the first month declined within 3 months to one-third for care contacts and one-half for treatment contacts and reached a plateau after 4 months. CONCLUSIONS: The majority of COPD patients in risk factor group D can be managed virtually, and only 13% of those with severe exacerbations required hospitalization. Contact to the health care professionals decreases markedly within the first months after enrollment. These results provide a new and detailed insight into the course of COPD. We propose a resilience index for virtual clinical management making it easier to compare results across settings.

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages.

BACKGROUND: It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches (16S rRNA gene transcript amplicon coupled to shotgun mRNA sequencing) to study the legacy effects of a century-long soil copper (Cu) pollution on microbial activity and composition, as well as its effect on the capacity of the microbial community to react to temporal fluctuations. RESULTS: Despite evidence of microbial adaptation (e.g., iron homeostasis and avoidance/resistance strategies), increased heterogeneity and richness loss in transcribed gene pools were observed with increasing soil Cu, together with an unexpected predominance of phage mRNA signatures. Apparently, phage activation was either triggered directly by Cu, or indirectly via enhanced expression of DNA repair/SOS response systems in Cu-exposed bacteria. Even though total soil carbon and nitrogen had accumulated with increasing Cu, a reduction in temporally induced mRNA functions was observed. Microbial temporal response groups (TRGs, groups of microbes with a specific temporal response) were heavily affected by Cu, both in abundance and phylogenetic composition. CONCLUSION: Altogether, results point toward a Cu-mediated "decoupling" between environmental fluctuations and microbial activity, where Cu-exposed microbes stopped fulfilling their expected contributions to soil functioning relative to the control. Nevertheless, some functions remained active in February despite Cu, concomitant with an increase in phage mRNA signatures, highlighting that somehow, microbial activity is still happening under these adverse conditions.

Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium.

Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium.

Mercuric reductase genes (merA) and mercury resistance plasmids in High Arctic snow, freshwater and sea-ice brine.

Bacterial reduction in Hg(2+) to Hg(0) , mediated by the mercuric reductase (MerA), is important in the biogeochemical cycling of Hg in temperate environments. Little is known about the occurrence and diversity of merA in the Arctic. Seven merA determinants were identified among bacterial isolates from High Arctic snow, freshwater and sea-ice brine. Three determinants in Bacteriodetes, Firmicutes and Actinobacteria showed < 92% (amino acid) sequence similarity to known merA, while one merA homologue in Alphaproteobacteria and 3 homologues from Betaproteobacteria and Gammaproteobacteria were > 99% similar to known merA's. Phylogenetic analysis showed the Bacteroidetes merA to be part of an early lineage in the mer phylogeny, whereas the Betaproteobacteria and Gammaproteobacteria merA appeared to have evolved recently. Several isolates, in which merA was not detected, were able to reduce Hg(2+) , suggesting presence of unidentified merA genes. About 25% of the isolates contained plasmids, two of which encoded mer operons. One plasmid was a broad host-range IncP-α plasmid. No known incompatibility group could be assigned to the others. The presence of conjugative plasmids, and an incongruent distribution of merA within the taxonomic groups, suggests horizontal transfer of merA as a likely mechanism for High Arctic microbial communities to adapt to changing mercury concentration.

Current strategies for mobilome research.

Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery.

Draft genome sequence of the soil bacterium Burkholderia terrae strain BS001, which interacts with fungal surface structures.

Burkholderia terrae BS001 is a soil bacterium which was originally isolated from the mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a range of fungus-interacting traits which reveal its propensity to actively interact at fungal interfaces. Here, we present the approximately 11.5-Mb (G+C content, 61.52%) draft genome sequence of B. terrae BS001 with the aim of providing insight into the genomic basis of its ecological success in fungus-affected soil settings.

Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data.

BACKGROUND: The increasing interest in small non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs) and recent advances in sequencing technology have yielded large numbers of short (18-32 nt) RNA sequences from different organisms, some of which are derived from small nucleolar RNAs (snoRNAs) and transfer RNAs (tRNAs). We observed that these short ncRNAs frequently cover the entire length of annotated snoRNAs or tRNAs, which suggests that other loci specifying similar ncRNAs can be identified by clusters of short RNA sequences. RESULTS: We combined publicly available datasets of tens of millions of short RNA sequence tags from Drosophila melanogaster, and mapped them to the Drosophila genome. Approximately 6 million perfectly mapping sequence tags were then assembled into 521,302 tag-contigs (TCs) based on tag overlap. Most transposon-derived sequences, exons and annotated miRNAs, tRNAs and snoRNAs are detected by TCs, which show distinct patterns of length and tag-depth for different categories. The typical length and tag-depth of snoRNA-derived TCs was used to predict 7 previously unrecognized box H/ACA and 26 box C/D snoRNA candidates. We also identified one snRNA candidate and 86 loci with a high number of tags that are yet to be annotated, 7 of which have a particular 18mer motif and are located in introns of genes involved in development. A subset of new snoRNA candidates and putative ncRNA candidates was verified by Northern blot. CONCLUSIONS: In this study, we have introduced a new approach to identify new members of known classes of ncRNAs based on the features of TCs corresponding to known ncRNAs. A large number of the identified TCs are yet to be examined experimentally suggesting that many more novel ncRNAs remain to be discovered.

A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family.

Many testis-specific genes from the sex chromosomes are subject to rapid evolution, which can make it difficult to identify murine genes in the human genome. The murine CYPT gene family includes 15 members, but orthologs were undetectable in the human genome. However, using refined homology search, sequences corresponding to the shared promoter region of the CYPT family were identified at 39 loci. Most loci were located immediately upstream of genes belonging to the VCX/Y, SPANX, or CSAG gene families. Sequence comparison of the loci revealed a conserved CYPT promoter-like (CPL) element featuring TATA and CCAAT boxes. The expression of members of the three families harboring the CPL resembled the murine expression of the CYPT family, with weak expression in late pachytene spermatocytes and predominant expression in spermatids, but some genes were also weakly expressed in somatic cells and in other germ cell types. The genomic regions harboring the gene families were rich in direct and inverted segmental duplications (SD), which may facilitate gene conversion and rapid evolution. The conserved CPL and the common expression profiles suggest that the human VCX/Y, SPANX, and CSAG2 gene families together with the murine SPANX gene and the CYPT family may share a common ancestor. Finally, we present evidence that VCX/Y and SPANX may be paralogs with a similar protein structure consisting of C terminal acidic repeats of variable lengths.

Declining trends in conception rates in recent birth cohorts of native Danish women: a possible role of deteriorating male reproductive health.

Recent findings of poor semen quality among at least 20% of normal young men in Denmark prompted us to use unique Danish registers on births and induced abortions to evaluate a possible effect of the poor male fecundity on pregnancy rates among their presumed partners--the younger cohorts of women. We have analysed data from the Danish birth and abortion registries as well as the Danish registry for assisted reproduction (ART) and defined a total natural conception rate (TNCR), which is equal to fertility rate plus induced abortion rate minus ART conception rate. A unique personal identification number allowed the linkage of these databases. Our database included 706,270 native Danish women born between 1960 and 1980. We used projections to estimate the fertility of the later cohorts of women who had not yet finished their reproduction. We found that younger cohorts had progressively lower TNCR and that in terms of their total fertility rate, the declining TNCR is compensated by an increasing use of ART. Our hypothesis of an ongoing birth cohort-related decline in fecundity was also supported by our finding of increasing and substantial use of ART in the management of infertility of relatively young couples in the later cohorts. Furthermore, the lower rates of induced abortion among the younger birth cohorts, often viewed as a success of health education programs, may not be fully explained by improved use of contraception. It seems more likely that decreased fecundity because of widespread poor semen quality among younger cohorts of otherwise normal men may explain some of the observed decline in conception rates. This may imply increasing reproductive health problems and lower fertility in the future, which is difficult to reverse in the short term. The current and projected widespread use of ART in Denmark may be a sign of such an emerging public health problem.

Identification and expression profiling of 10 novel spermatid expressed CYPT genes.

To identify candidate genes for poor sperm morphology, we have screened for genes expressed during spermiogenesis. We identified 10 new members of the cysteine-rich perinuclear theca (CYPT) family showing that this family contains at least 15 members, which also includes the casein kinase II target genes. Based on similarity the CYPT sequences could be divided into two groups, Cypt1-10 and the novel members Cypt12-15. The 5'-end of the CYPT family is highly similar to exon1A and part of the first intron of Zfy2. Seven CYPT genes mapped to the X chromosome; six contained an intron and one was intron-less. One CYPT gene mapped to chromosome 3 and one mapped to chromosome 9 which were both intron-less. The upstream region of the CYPT family and Zfy2 genes is conserved. For some the conservation extended over a large region, however, only about 150 nucleotides is conserved among all CYPT members and Zfy2. Nevertheless, the short conserved promoter leads to essentially identical expression profiles for the CYPT family members and Zfy2, which was clearly different from the profile of Zfy1. Expression of the CYPT family and Zfy2 preceded the expression of other spermatid-specific genes such as the transition proteins and the protamines. In situ hybridization revealed a low expression in pachytene spermatocytes from stages IX-X followed by a strong upregulation in spermatids from stage VI with maximum expression in spermatids in stages VII-VIII. The CYPT family may function in the remodeling of the spermatid nucleus before condensation of the DNA.

Analysis of cell-type-specific gene expression during mouse spermatogenesis.

In rodents, changes in gene expression during spermatogenesis can be monitored by sampling testis from each day during postnatal development. However, changes in gene expression at the tissue level can reflect changes in the concentration of an mRNA in a specific cell type, changes in volume of specific cells, or changes in the cell-type composition. This reflects the cellularity of the tissue. Here we have combined techniques that assess the expression profiles of genes at the whole-tissue level, differential display and DNA array, and, at the level of cellularity, in situ hybridization. Combining results from these techniques allows determination of the cell-type-specific gene-expression patterns of many genes during spermatogenesis. Differential display was used to determine expression profiles with high sensitivity and independent of prior knowledge of the sequence, whereas DNA arrays quickly assess the expression profiles of all the genes. This identified three groups of gene-expression profiles. The major group corresponds to genes that are upregulated in spermatocytes during either the mid- or late- pachytene phase of spermatogenesis (stages VII-XI). This pachytene cluster was gradually extinguished in the later spermatid stages but was followed by another cluster of genes expressed in spermatids. Finally, a group of genes was downregulated during spermatogenesis and probably expressed in nongerm cells. We believe that expression of most genes can be described by a combination of these cell-type-specific expression patterns.