Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection

Host anti-viral factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill in this knowledge gap, we perform a genome-wide CRISPR dropout screen and integrate analyses of the multi-omics data of the CRISPR screen, genome-wide association studies, single-cell RNA-Seq, and host-virus proteins or protein/RNA interactome. This study uncovers many host factors that are currently underappreciated, including the components of V-ATPases, ESCRT, and N-glycosylation pathways that modulate viral entry and/or replication. The cohesin complex is also identified as an anti-viral pathway, suggesting an important role of three-dimensional chromatin organization in mediating host-viral interaction. Furthermore, we discover another anti-viral regulator KLF5, a transcriptional factor involved in sphingolipid metabolism, which is up-regulated, and harbors genetic variations linked to COVID-19 patients with severe symptoms. Anti-viral effects of three identified candidates (DAZAP2/VTA1/KLF5) are confirmed individually. Molecular characterization of DAZAP2/VTA1/KLF5-knockout cells highlights the involvement of genes related to the coagulation system in determining the severity of COVID-19. Together, our results provide further resources for understanding the host anti-viral network during SARS-CoV-2 infection and may help develop new countermeasure strategies.

Evaluating institutional fit for the conservation of threatened species

Recovery and conservation of threatened species require adequate institutional responses. We tested an approach to systematically identify and measure how an institutional framework acknowledges threats and required responses for the recovery of endangered species. We measured institutional functional fit with a drivers-pressure-state-impacts-response (DPSIR) model integrated with a quantitative text mining method and qualitative analysis of statutory instruments to examine regulatory responses that support the recovery of 2 endangered species native to Australia, the bridled nailtail wallaby (Onychogalea fraenata) and the Eastern Bristlebird (Dasyornis brachypterus). The key components of the DPSIR model were present in the institutional framework at statutory and operational levels, but some institutional gaps remained in the protection and recovery of the Eastern Bristlebird, including feral predator control, weed control, and grazing management in some locations. However, regulatory frameworks varied in their geographic scope and the application and implementation of many instruments remained optional. Quantitative text mining can be used to quickly navigate a large volume of regulatory documents, but challenges remain in selection of terms, queries of co-occurrence, and interpretation of word frequency counts. To inform policy, we recommend that quantitative assessments of institutional fit be complemented with qualitative analysis and interpreted in light of the sociopolitical and institutional context.

Review of Philippine Health Laws and its Implication to HTA Institutionalization

Objective

To identify the implications of health legislations on the direction of health technology assessment (HTA) institutionalization in the Philippines.

Methods

We reviewed 15 health laws and extracted information using a preset data extraction tool. The collected data was then subjected to the KJ (Kawakita Jiro) method to group similar provisions, taking into account their respective implications to the HTA direction. Once grouped, a core concept was identified that captured the underlying provisions within the group. After which, the core concepts were tabulated and matched with the core components of HTA institutionalization to identify specific policy implication to HTA.

Results

Three major paradigms emerged that are considered important in the institutionalization of HTA. First, common among the health laws are the need for the provision or expansion of benefit packages through the Philippine Health Insurance Corporation. Aside from the benefit packages, the reviewed laws also require delivery of new health services that entail the use of specific health technologies. Lastly, as a consequence of the need for new health services, equity concerns became evident in relation to the identified health services specifically in terms of socioeconomic divide, geographical location and disease status.

Discussion and Conclusions

The three paradigms identified from the review of health laws indicate synergism and antagonism to the HTA-related policy content of the Philippines' UHC Law. Some identify the need for HTA before being funded by the government while others do not explicitly state this. Despite the health laws requiring expansion or creation of benefit packages and delivery of new health services, there is still a need to undergo HTA in order to ensure efficient use of resources. The presence of these laws should not be tantamount to exception of undergoing HTA process but rather should be taken as a guide for priority-setting of topics for assessment.

Key messages

In the process of institutionalizing HTA, existing legislations on health can help map out areas of priority for assessment. Many health policies preceded the signing of the Universal Health Care Law, thus it is important to review them to determine provisions that are synergistic or antagonistic to the content of UHC Law.

Key considerations and challenges in the application of social-network research for environmental decision making

Attempts to better understand the social context in which conservation and environmental decisions are made has led to increased interest in human social networks. To improve the use of social-network analysis in conservation, we reviewed recent studies in the literature in which such methods were applied. In our review, we looked for problems in research design and analysis that limit the utility of network analysis. Nineteen of 55 articles published from January 2016 to June 2019 exhibited at least 1 of the following problems: application of analytical methods inadequate or sensitive to incomplete network data; application of statistical approaches that ignore dependency in the network; or lack of connection between the theoretical base, research question, and choice of analytical techniques. By drawing attention to these specific areas of concern and highlighting research frontiers and challenges, including causality, network dynamics, and new approaches, we responded to calls for increasing the rigorous application of social science in conservation.

Residual impact of aged nZVI on heavy metal-polluted soils

In the present study, the residual toxicity and impact of aged nZVI after a leaching experiment on heavy metal (Pb, Zn) polluted soils was evaluated. No negative effects on physico-chemical soil properties were observed after aged nZVI exposure. The application of nZVI to soil produced a significant increase in Fe availability. The impact on soil biodiversity was assessed by fluorescence in situ hybridization (FISH). A significant effect of nZVI application on microbial structure has been recorded in the Pb-polluted soil nZVI-treated. Soil bacteria molecular response, evaluated by RT-qPCR using exposure biomarkers (pykA, katB) showed a decrease in the cellular activity (pykA) due to enhanced intracellular oxidative stress (katB). Moreover, ecotoxicological standardised test on Caenorhabditis elegans (C. elegans) showed a decrease in the growth endpoint in the Pb-polluted soil, and particularly in the nZVI-treated. A different pattern has been observed in Zn-polluted soils: no changes in soil biodiversity, an increase in biological activity and a significant decrease of Zn toxicity on C. elegans growth were observed after aged nZVI exposure. The results reported indicated that the pollutant and its nZVI interaction should be considered to design soil nanoremediation strategies to immobilise heavy metals.

[Colonic fermentation in humans: effect of the ingestion of meat associated to milk]

The amount of breath H2 produced for 6 h following the ingestion of 240 ml of milk was used as an index of the rate of colonic fermentation of undigested lactose in 8 lactase non-persistent Guatemalan adults. Treatments in separate days included milk alone, milk with 400 g cooked beef, lactose pre-hydrolyzed milk with the same amount of beef, beef alone and fasting for 6 h. Excess excretion of H2, calculated as the mean area under the curve were 178 +/- 31 ppm h with milk alone, 50 +/- 17 with milk plus beef, -1 +/- 26 with prehydrolyzed milk (p > 0.001). Peak increments of breath H2 followed the same trend: all 8 subjects over 20 ppm with milk alone, 2 with milk plus beef and none with hydrolyzed milk, beef alone or fasting. Thus, cooked beef significantly reduces the rate of appearance of intact lactose in the large bowel of lactase deficient adults.

Test-retest reproducibility of the relative dose response for vitamin A status in Guatemalan adults: issues of diagnostic sensitivity

The relative dose response (RDR) test has been used as a functional measure of whole-body stores of vitamin A in humans. We have examined the reproducibility of the RDR procedure in a population of Guatemalan adult subjects who would be expected to show a moderate prevalence of hypovitaminosis A. Fifty-one subjects were administered a standard RDR test, and the plasma samples were analyzed for retinol, tocopherol, retinol binding protein (RBP) and prealbumin (PAL). Thirty-four of the subjects underwent repeat RDR tests 7 d later. Plasma levels in fasted subjects were as follows: retinol, 1.35 +/- 0.30 mumol/L; RBP, 37.8 +/- 7.7 mg/L; PAL, 187.0 +/- 39.0 mg/L; and tocopherol, 16.6 +/- 6.2 mumol/L. RDRs ranged from -35.2% to +63.1%, with a mean of 2.6 +/- 10.4%. Overall, we observed poor within-subject reproducibility of the RDR procedure whether expressed numerically or by diagnostic classification. Moreover, in contrast to previous studies in children, we observed fewer positive RDR tests than would be expected for the population studied. Nevertheless, the mean RDR was inversely proportional to fasting retinol levels, thus confirming the validity of the biological basis of the RDR procedure in humans. Because of high intra-individual variability with this test, investigators should be cautious when using the RDR procedure in serial studies to monitor the efficacy of therapeutic interventions or subject compliance to dietary regimens.

Test-retest reproducibility of the relative dose response for vitamin A status in Guatemalan adults: issues of diagnostic specificity

The relative dose response (RDR) test was examined with regard to specificity and reproducibility in subjects with adequate dietary intake and normal liver reserves of vitamin A. Twelve subjects were administered an RDR test four times over 22 d, including one placebo test in which the oral dose of vitamin A was omitted. Additionally, static measures of retinol, tocopherol, retinol binding protein (RBP) and prealbumin (PAL) were taken to determine the intra- and inter-individual coefficient of variation for these blood constituents. Intra-individual coefficients of variation were as follows: retinol, 8.8%; RBP, 11.5%; PAL, 7.6%; and alpha-tocopherol, 8.8%. The mean RDR in vitamin A-replete subjects was 1.2% and ranged from approximately -25% to 11%. No differences were observed between placebo and true RDR (i.e., with vitamin A) test responses, and there was no difference among the three true RDRs over a period of 22 d. Consistent with the hypothesis upon which the RDR test is based, nascently absorbed vitamin A evidently entered a storage pool in the liver of vitamin A-replete subjects without immediate release to peripheral sites of utilization. Because the RDR test results were normal in all subjects, the procedure appears to offer high test specificity and does not falsely diagnose hypovitaminosis A. Nevertheless, the magnitude and direction of the RDR within an individual over 22 d were highly variable, and this variability may preclude the use of a single measure of the RDR to grade the relative vitamin A nutriture of an individual subject.

Dietary manipulation of postprandial colonic lactose fermentation: II. Addition of exogenous, microbial beta-galactosidases at mealtime

The feasibility and efficacy of adding microbial beta-galactosidase enzymes directly to milk at the time of consumption was explored in adult lactose-malabsorbers. The hydrogen breath test, and on one occasion, the rise in blood glucose, were used as indices of the completeness of intraintestinal hydrolysis and absorption of milk lactose. When added to 360 ml of cow milk containing 18 g of lactose, empirical dosages of three beta-galactosidases--one from Kluyveromyces (yeast) and two from Aspergillus (fungal)--had some effectiveness in reducing postprandial H2 excretion, although no in vivo treatment at the dosages chosen was as effective as pre-incubation of the milk in vitro. The yeast enzyme also reduced symptom frequency as compared to intact milk and enhanced postprandial rises in blood glucose. The replacement therapy with exogenous, food-grade beta-galactosidases may provide a useful intervention to reduce lactose malabsorption and milk intolerance in individuals with primary lactase deficiency.

Effective in vivo hydrolysis of milk lactose by beta-galactosidases in the presence of solid foods

The feasibility of enzyme replacement therapy with exogenous, food-grade, microbial enzymes at mealtime to effect intragastrointestinal hydrolysis of the lactose from 360 ml of cow's milk consumed with a solid food meal (breakfast cereals) was investigated in adult Guatemalan lactose-malabsorbers using a hydrogen breath-analysis procedure to quantify the completeness of postprandial carbohydrate absorption. Adding 2 g of a commercial preparation of beta-galactosidase from Kluyveromyces lactis at mealtime to milk taken with a refined cereal (cornflakes) and an unrefined cereal (bran) reduced the production of excess breath H2 attributable to lactose maldigestion to a level not significantly different from that achieved with lactose-prehydrolyzed milk. Sucrase, as expected, had no effect on H2 production. A beta-galactosidase from Aspergillus niger was less effective that the K. lactis enzyme for in vivo hydrolysis. Thus, exogenous betagalactosidases can eliminate lactose malabsorption in lactase-deficient individuals even in the presence of solid foods, allowing lactose intolerant persons to consume milk and dairy products without gastrointestinal discomfort.

Dietary manipulation of postprandial colonic lactose fermentation: I. Effect of solid foods in a meal

The effect of adding solid foods--cornflakes, banana and hard-boiled egg--to a meal with 360 ml of intact milk containing 18 g of lactose was investigated in 13 lactose-malabsorbers and 10 lactose-absorbers chosen from 36 Guatemalan adults screened for their capacity to digest and absorb completely the lactose in this volume of milk. A six-hour hydrogen breath test was used as the index of carbohydrate absorption. Minimal breath H2 was excreted by lactose-absorbers with either the intact milk alone, the intact milk with solid foods, or lactose-prehydrolyzed milk with solids. In lactose-malabsorbers, however, the 6-h excretion of H2 with intact milk plus solid food was intermediary between milk alone and prehydrolyzed milk with solids. A relative net reduction of 47% in lactose malabsorption was produced by adding food, and the peak-rise in breath H2 was delayed by 2 hours. A physiological consequence of taking solid foods along with milk is a slower rate of colonic fermentation, and this may be the basis for reducing gastro-intestinal symptoms in lactose-intolerant malabsorbers.

Application of a rapid dark adaptation test in children

The rapid dark adaptation test (after Thornton) has been shown to correlate with classical dark adaptation test results and vitamin A nutriture in adults. Using this test, 27 children in Guatemala (aged 5-12 years) and 18 children in Baltimore (aged 4 and 5 years) were studied. Plasma for vitamin A and zinc analysis was obtained from the Guatemalan children and dietary histories were obtained from the parents of the Baltimore children. All but two children (ages 4 and 5) were able to complete the study. For the Guatemalan group, the mean time to complete the test was 144 s, and for the Baltimore group, 171 s. Rapid dark adaptation test performance was significantly correlated to the dietary intake of vitamin A by a logarithmic model, p less than 0.05. The rapid dark adaptation test appears to be acceptable for use in childhood populations and could complement biochemical determination of vitamin A and/or zinc in clinical settings, field surveys, and research.