Epidemic management and control through risk-dependent individual contact interventions

Testing, contact tracing, and isolation (TTI) is an epidemic management and control approach that is difficult to implement at scale because it relies on manual tracing of contacts. Exposure notification apps have been developed to digitally scale up TTI by harnessing contact data obtained from mobile devices; however, exposure notification apps provide users only with limited binary information when they have been directly exposed to a known infection source. Here we demonstrate a scalable improvement to TTI and exposure notification apps that uses data assimilation (DA) on a contact network. Network DA exploits diverse sources of health data together with the proximity data from mobile devices that exposure notification apps rely upon. It provides users with continuously assessed individual risks of exposure and infection, which can form the basis for targeting individual contact interventions. Simulations of the early COVID-19 epidemic in New York City are used to establish proof-of-concept. In the simulations, network DA identifies up to a factor 2 more infections than contact tracing when both harness the same contact data and diagnostic test data. This remains true even when only a relatively small fraction of the population uses network DA. When a sufficiently large fraction of the population (≳ 75%) uses network DA and complies with individual contact interventions, targeting contact interventions with network DA reduces deaths by up to a factor 4 relative to TTI. Network DA can be implemented by expanding the computational backend of existing exposure notification apps, thus greatly enhancing their capabilities. Implemented at scale, it has the potential to precisely and effectively control future epidemics while minimizing economic disruption.     

Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer

DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.     

Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide

Six terrestrial ecosystems in the USA were exposed to elevated atmospheric CO(2) in single or multifactorial experiments for more than a decade to assess potential impacts. We retrospectively assessed soil bacterial community responses in all six-field experiments and found ecosystem-specific and common patterns of soil bacterial community response to elevated CO(2) . Soil bacterial composition differed greatly across the six ecosystems. No common effect of elevated atmospheric CO(2) on bacterial biomass, richness and community composition across all of the ecosystems was identified, although significant responses were detected in individual ecosystems. The most striking common trend across the sites was a decrease of up to 3.5-fold in the relative abundance of Acidobacteria Group 1 bacteria in soils exposed to elevated CO(2) or other climate factors. The Acidobacteria Group 1 response observed in exploratory 16S rRNA gene clone library surveys was validated in one ecosystem by 100-fold deeper sequencing and semi-quantitative PCR assays. Collectively, the 16S rRNA gene sequencing approach revealed influences of elevated CO(2) on multiple ecosystems. Although few common trends across the ecosystems were detected in the small surveys, the trends may be harbingers of more substantive changes in less abundant, more sensitive taxa that can only be detected by deeper surveys. Representative bacterial 16S rRNA gene clone sequences were deposited in GenBank with Accession No. JQ366086–JQ387568.     

Group‐Size Effect on Vigilance and Foraging in a Predator‐Free Population of Feral Goats (Capra hircus) on the Isle of Rum,NW Scotland

Many previous studies have found that as group size increases, individual vigilance levels decrease and forage intake increases (group‐size effect), but few such studies have considered the impact of within‐group interactions and other confounding factors on the direction of group‐size effects. A free‐ranging population of feral goats (Capra hircus), with little predation threat, was studied on the Isle of Rum (northwest Scotland), from Jun. to Nov. 2000, to investigate the effects of group size on individual vigilance levels and foraging efficiency after taking into account the effect of confounding factors (e.g. sex, season, time of day, habitat, predation risk) and within‐group interactions (via changes in movement rates while feeding). Our results show that, while group size exerted a negative influence on individual vigilance levels and a positive effect on movement rate, foraging efficiency never increased with group size and even decreased at certain times of day. There was no sex difference in individual vigilance in feral goats, but foraging efficiency was higher in females than in males. Goats were more vigilant in fall than in summer. The results imply that the benefits for foraging obtained from the reduced vigilance level in larger groups may be constrained or offset by increased interaction (or competition) within larger groups even in a population that faces negligible predation risk.     

The conformation of endothelin-1 in aqueous solution: NMR-derived constraints combined with distance geometry and molecular dynamics calculations

The aqueous solution conformation of the bicyclic, 21 amino acid vasoconstrictor peptide, endothelin-1, has been determined using two dimensional NMR and a combination of distance geometry and molecular dynamics. The dominant structural feature is a helical region between Lys9 and Cys15 characterized by strong NHi-NHi+1 NOEs and several long range NOEs spanning 3 to 5 residues. Solvent inaccessibility and possible hydrogen bonding in the Cys3-Cys11 loop is suggested by the temperature independence of the chemical shifts of several amide protons. There is no evidence for association of the C-terminal hexapeptide with the bicyclic region.     

Nerve growth factor biosynthesis: Isolation and characterization of a guinea pig prostate kallikrein

Guinea pig prostate contains one major soluble esteropeptidase activity. The protein has been purified and characterized and found to be a glycoprotein comprised of a single polypeptide chain. The molecular weight of the deglycosylated protein is approximately 26,000. The esteropeptidase has a similar K_m for lysine and arginine synthetic substrates, although the V_max for arginine is much greater than that for lysine. Amino-terminal sequence analysis has also revealed a marked degree of homology to mouse γ-nerve growth factor (NGF) and the kallikrein family of serine proteases. In contrast to γ-NGF, however, the guinea pig enzyme does not appear to form stable complexes with β-NGF.     

Autoradiographic Method for Isolation of Diverse Microbial Species with Unique Catabolic Traits

A novel autoradiographic method for isolation of bacteria with unique catabolic traits was developed to overcome many of the limitations of traditional selective enrichment techniques. The method consists of five steps. (i) An environmental sample is directly plated (without enrichment) on a microporous filter atop a solid medium that allows cultivation of diverse kinds of microorganisms. (ii) Once colonies form, two replicas of the filter are prepared and the colonies are regrown. (iii) The replica filters are starved 24 to 72 h to deplete intracellular carbon reserves and then (iv) placed on Na(inf2)(sup35)SO(inf4)-containing solid media with and without a test compound. (v) Following an incubation period, the replica filters are exposed to film in order to identify colonies that incorporate more (sup35)S into cell biomass in the presence of the test compound than in its absence, providing presumptive evidence for metabolism of the compound. The colonies identified in this manner can be recovered from the master filter. To demonstrate this technique, bacteria capable of degrading benzoate were isolated from a single soil slurry by traditional enrichment as well as by autoradiography. From the enrichment culture, a single isolate able to degrade benzoate was obtained. In contrast, 18 distinct strains were obtained by purifying 19 putative benzoate-degrading colonies identified by autoradiography. Each of the 18 strains was able to completely transform the substrate, as determined by high-performance liquid chromatography analyses. The doubling times of a subset of the isolates grown in benzoate medium ranged from 1.4 to 17.1 h, whereas the doubling time of the isolate obtained by enrichment was 2.0 h. These data demonstrate that the method described here can be used to obtain a collection of diverse organisms able to metabolize a specific compound.