ALBERT

Description: Background: Total parenteral nutrition (TPN) provides all nutritional needs intravenously. Although lifesaving, enthusiasm is significantly tempered due to side effects of liver and gut injury, as well as lack of mechanistic understanding into drivers of TPN injury. We hypothesized that the state of luminal nutritional deprivation with TPN drives alterations in gut–systemic signaling, contributing to injury, and tested this hypothesis using our ambulatory TPN model. Methods: A total of 16 one-week-old piglets were allocated randomly to TPN (n = 8) or enteral nutrition (EN, n = 8) for 3 weeks. Liver, gut, and serum were analyzed. All tests were two-sided, with a significance level of 0.05. Results: TPN resulted in significant hyperbilirubinemia and cholestatic liver injury, p = 0.034. Hepatic inflammation (cluster of differentiation 3 (CD3) immunohistochemistry) was higher with TPN (p = 0.021). No significant differences in alanine aminotransferase (ALT) or bile ductular proliferation were noted. TPN resulted in reduction of muscularis mucosa thickness and marked gut atrophy. Median and interquartile range for gut mass was 0.46 (0.30–0.58) g/cm in EN, and 0.19 (0.11–0.29) g/cm in TPN (p = 0.024). Key gut–systemic signaling regulators, liver farnesoid X receptor (FXR; p = 0.021), liver constitutive androstane receptor (CAR; p = 0.014), gut FXR (p = 0.028), G-coupled bile acid receptor (TGR5) (p = 0.003), epidermal growth factor (EGF; p = 0.016), organic anion transporter (OAT; p = 0.028), Mitogen-activated protein kinases-1 (MAPK1) (p = 0.037), and sodium uptake transporter sodium glucose-linked transporter (SGLT-1; p = 0.010) were significantly downregulated in TPN animals, whereas liver cholesterol 7 alpha-hydroxylase (CyP7A1) was substantially higher with TPN (p = 0.011). Conclusion: We report significant alterations in key hepatobiliary receptors driving gut–systemic signaling in a TPN piglet model. This presents a major advancement to our understanding of TPN-associated injury and suggests opportunities for strategic targeting of the gut–systemic axis, specifically, FXR, TGR5, and EGF in developing ameliorative strategies.

Description: Clubroot is a disease of cruciferous crops that causes significant economic losses to vegetable production worldwide. We applied high-throughput amplicon sequencing technology to quantify the effect of Trichodermaharzianum LTR-2 inoculation on the rhizosphere community of Chinese cabbage (Brassica rapa subsp. pekinensis cv. Jiaozhou) in a commercial production area. T. harzianum inoculation of cabbage reduced the incidence of clubroot disease by 45.4% (p 〈 0.05). The disease control efficacy (PDIDS) was 63%. This reduction in disease incidence and severity coincided with a drastic reduction in both the relative abundance of Plasmodiaphora brassicae, the causative pathogen of cabbage clubroot disease, and its copy number in rhizosphere soil. Pathogenic fungi Alternaria and Fusarium were also negatively associated with Trichoderma inoculation according to co-occurrence network analysis. Inoculation drastically reduced the relative abundance of the dominant bacterial genera Delftia and Pseudomonas, whilst increasing others including Bacillus. Our results demonstrate that T. harzianum LTR-2 is an effective biological control agent for cabbage clubroot, which acts through modulation of the soil and rhizosphere microbial community.

Description: As aberrant activity of protein kinases is observed in many disease states, these enzymes are common targets for therapeutics and detection of activity levels. The development of non-natural protein kinase substrates offers an approach to protein substrate competitive inhibitors, a class of kinase inhibitors with promise for improved specificity. Also, kinase activity detection approaches would benefit from substrates with improved activity and specificity. Here, we apply a substrate-mediated selection to a peptidomimetic DNA-encoded chemical library for enrichment of molecules that can be phosphorylated by the protein tyrosine kinase, c-Src. Several substrates were identified and characterized for activity. A lead compound (SrcDEL10) showed both the ability to serve as a substrate and to promote ATP hydrolysis by the kinase. In inhibition assays, compounds displayed IC50′s ranging from of 8–100 µM. NMR analysis of SrcDEL10 bound to the c-Src:ATP complex was conducted to characterize the binding mode. An ester derivative of the lead compound demonstrated cellular activity with inhibition of Src-dependent signaling in cell culture. Together, the results show the potential for substrate-mediated selections of DNA-encoded libraries to discover molecules with functions other than simple protein binding and offer a new discovery method for development of synthetic tyrosine kinase substrates.

Description: An in-depth assessment of plant nutrient resorption can offer insights into understanding ecological processes and functional responses to biotic and abiotic changes in the environment. The legume proportion in a mixed grassland can drive changes in the soil environment and plant relationships, but little information is available regarding how the legume proportion influences plant nutrient resorption in mixed grasslands. In this study, three mixed communities of Leymus chinensis (Trin.) Tzvel. and Medicago sativa L. differing in legume proportion (Low-L, with 25% legume composition; Mid-L, with 50% legume composition; High-L, with 75% legume composition) were established with four replicates in a degraded grassland. Four years after establishing the mixed grassland, the quantity of biological N2 fixation by M. sativa, the availabilities of water and nitrogen (N) and phosphorus (P) in soil were examined, and the concentrations and resorption of leaf N and P for both species were measured during forage maturation and senescence. The results showed Mid-L had greater biological N2 fixation and soil N availability than Low-L and High-L, while the High-L had lower soil water and P availability, but a greater soil available N:P ratio compared with Low-L and Mid-L. Legume proportion did not alter N or P concentrations of mature leaves. However, in Mid-L N resorption was reduced by 8 to 16% for the two mixed-species compared with Low-L and High-L. High-L enhanced P resorption by 20 to 24% in both plant species compared with Low-L. The L. chinensis and M. sativa responded differently to varied legume proportion in terms of P resorption. It was concluded that legume proportion drove changes in soil nutrient availability of mixed communities, which primarily altered plant nutrient resorption during senescence, but had no influence on the nutrient concentrations of mature plants. A moderate legume proportion reduced N resorption, and increased senesced leaf N concentration of grass and legume species. The difference in P resorption by two mixed-species significantly changed the interspecific difference of senesced leaf P concentration and the N:P ratio with varied legume proportion.

Description: Ecosystems are complex networks of interacting individuals co-evolving with their environment. As such, changes to an interaction can influence the whole ecosystem. However, to predict the outcome of these changes, considerable understanding of processes driving the system is required. Synthetic biology provides powerful tools to aid this understanding, but these developments also allow us to change specific interactions. Of particular interest is the ecological importance of mutualism, a subset of cooperative interactions. Mutualism occurs when individuals of different species provide a reciprocal fitness benefit. We review available experimental techniques of synthetic biology focused on engineered synthetic mutualistic systems. Components of these systems have defined interactions that can be altered to model naturally occurring relationships. Integrations between experimental systems and theoretical models, each informing the use or development of the other, allow predictions to be made about the nature of complex relationships. The predictions range from stability of microbial communities in extreme environments to the collapse of ecosystems due to dangerous levels of human intervention. With such caveats, we evaluate the promise of synthetic biology from the perspective of ethics and laws regarding biological alterations, whether on Earth or beyond. Just because we are able to change something, should we?

Description: The inward rectifier potassium (Kir) channels play key roles in the physiology of mosquitoes and other insects. Our group, among others, previously demonstrated that small molecule inhibitors of Kir channels are promising lead molecules for developing new insecticides to control adult female mosquitoes. However, the potential use of Kir channel inhibitors as larvicidal agents is unknown. Here we tested the hypothesis that pharmacological inhibition of Kir channels in the larvae of Aedes aegypti, the vector of several medically important arboviruses, induces lethality. We demonstrated that adding barium, a non-specific blocker of Kir channels, or VU041, a specific small-molecule inhibitor of mosquito Kir1 channels, to the rearing water (deionized H2O) of first instar larvae killed them within 48 h. We further showed that the toxic efficacy of VU041 within 24 h was significantly enhanced by increasing the osmolality of the rearing water to 100 mOsm/kg H2O with NaCl, KCl or mannitol; KCl provided the strongest enhancement compared to NaCl and mannitol. These data suggest: (1) the important role of Kir channels in the acclimation of larvae to elevated ambient osmolality and KCl concentrations; and (2) the disruption of osmoregulation as a potential mechanism of the toxic action of VU041. The present study provides the first evidence that inhibition of Kir channels is lethal to larval mosquitoes and broadens the potential applications of our existing arsenal of small molecule inhibitors of Kir channels, which have previously only been considered for developing adulticides.

Description: Soil nitrification (microbial oxidation of ammonium to nitrate) can lead to nitrogen leaching and environmental pollution. A number of plant species are able to suppress soil nitrifiers by exuding inhibitors from roots, a process called biological nitrification inhibition (BNI). However, the BNI activity of perennial grasses in the nutrient-poor soils of Australia and the effects of BNI activity on nitrifying microbes in the rhizosphere microbiome have not been well studied. Here we evaluated the BNI capacity of bermudagrass (Cynodon dactylon L.), St. Augustinegrass (Stenotaphrum secundatum (Walt.) Kuntze), saltwater couch (Sporobolus virginicus), seashore paspalum (Paspalum vaginatum Swartz.), and kikuyu grass (Pennisetum clandestinum) compared with the known positive control, koronivia grass (Brachiaria humidicola). The microbial communities were analysed by sequencing 16S rRNA genes. St. Augustinegrass and bermudagrass showed high BNI activity, about 80 to 90% of koronivia grass. All the three grasses with stronger BNI capacities suppressed the populations of Nitrospira in the rhizosphere, a bacteria genus with a nitrite-oxidizing function, but not all of the potential ammonia-oxidizing archaea. The rhizosphere of saltwater couch and seashore paspalum exerted a weak recruitment effect on the soil microbiome. Our results demonstrate that BNI activity of perennial grasses played a vital role in modulating nitrification-associated microbial populations.

Description: Background: In many parts of the world, stark racial disparities in human immunodeficiency virus (HIV) prevalence, incidence, prevention, and care outcomes persist among gay, bisexual, and other men who have sex with men (MSM), with Black MSM significantly impacted in the United States (U.S.). Individual-level characteristics, including sexual behaviors and socioeconomic status, do not fully account for racial/ethnic disparities in HIV among MSM. We hypothesize that neighborhood contexts and network characteristics influence risk for HIV infection as well as HIV-related prevention and care behaviors. As such, the study design includes the use of real-time geospatial methods and in-depth assessments of multiple network typologies to investigate the impact of neighborhood and network-level factors on HIV prevention and treatment among Black MSM residing in longstanding priority HIV elimination areas in the U.S., namely Chicago, Illinois and in the Deep South (Jackson, Mississippi and New Orleans, Louisiana) (n = 450, n = 50, and n = 100, respectively). We describe the design, sampling methods, data collection, data management methods, and preliminary findings of the ongoing ‘Neighborhoods and Networks (N2) Cohort Study’. Methods/Design: N2 employs a prospective longitudinal design. The sample includes Black MSM participants in Chicago recruited via respondent-driven sampling and assessed every six months over two years of follow-up. Participants enrolled in Jackson and New Orleans are being recruited through existing health and community services and assessed every six months over one year of follow-up. Mobility within and between neighborhoods is being assessed using global positioning system (GPS) technology. Social and sexual networks among Black MSM are being studied through egocentric network inventories as well as newer methods of creating meso-level networks that involve social media (Facebook) and mobile phone contacts. Key HIV prevention outcomes such as pre-exposure prophylaxis (PrEP) care engagement, and HIV/STI (sexually transmitted infections) biomarkers will be examined at baseline and follow-up. Results: As of 31 December 2018, a total of 361 men were enrolled across all study sites: 259 in Chicago and 102 in the Deep South (75 in New Orleans and 27 in Jackson). At baseline, participants ranged in age from 17 to 65 years old (mean = 34.3, standard deviation = 5.1) with 123 men (34.1%) self-reported as HIV positive. While HIV treatment levels were similar between sites, men in the Deep South reported higher rates of adherence than men in Chicago (63.3% versus 49.4%, p = 0.03). Sexual risk profiles were mainly the same between men from different study sites, with 22.9% of men in Chicago and 28.9% in the Deep South reporting consistent condom use during vaginal and anal sex (p = 0.26). Regarding their home neighborhoods, men in the Deep South were more likely than those in Chicago to characterize theirs as having a good reputation (43.1% versus 24.7%, p 〈 0.001) and as being safe (37.3% versus 21.2%, p = 0.002). Conclusions: The focus on Black MSM in the N2 Study will allow for a nuanced exploration of the attitudes, beliefs, behaviors, and practices of a diverse group of Black MSM. The study is also positioned to provide novel insight about neighborhood and network characteristics that influence HIV-related behaviors. A health equity framework ensures that Black MSM are not explicitly or implicitly deemed as deviant, disordered, or the non-reference group. Findings from N2 will provide guidance for the implementation of more impactful HIV prevention interventions that engage a diverse population of Black MSM as we work toward HIV elimination in the U.S.

Description: Sample entropy (SE) has relative consistency using biologically-derived, discrete data 〉500 data points. For certain populations, collecting this quantity is not feasible and continuous data has been used. The effect of using continuous versus discrete data on SE is unknown, nor are the relative effects of sampling rate and input parameters m (comparison vector length) and r (tolerance). Eleven subjects walked for 10-minutes and continuous joint angles (480 Hz) were calculated for each lower-extremity joint. Data were downsampled (240, 120, 60 Hz) and discrete range-of-motion was calculated. SE was quantified for angles and range-of-motion at all sampling rates and multiple combinations of parameters. A differential relationship between joints was observed between range-of-motion and joint angles. Range-of-motion SE showed no difference; whereas, joint angle SE significantly decreased from ankle to knee to hip. To confirm findings from biological data, continuous signals with manipulations to frequency, amplitude, and both were generated and underwent similar analysis to the biological data. In general, changes to m, r, and sampling rate had a greater effect on continuous compared to discrete data. Discrete data was robust to sampling rate and m. It is recommended that different data types not be compared and discrete data be used for SE.