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New Computational Tool provides 3-D Views of Molecular Processes Affecting Human Metabolism

Researchers recently created a novel virtual resource called Recon3D to provide biologists with 3-D perspectives of spatially linked genes, proteins, and metabolites for analyzing molecular processes affecting human metabolism. Recon3D is currently available online through two databases: Bigg Models and the Virtual Metabolic Human database. 

The tool can offer insights into the mechanisms of action for disease-related mutations and reveal how genes, proteins, and metabolic reactions respond to drugs. It has been used to analyze human sequencing data to map mutation hotspots in 3D as well as to show that drugs with different molecular structures can exert similar metabolic responses.

This first resource of its kind provides the most comprehensive human metabolic map to date and accounts for 17 percent of the known functional genes in the human genome. It will help break research ground on the molecular mechanisms of human metabolism and offer a new human-based approach towards understanding diseases affected by metabolism.

Reference Link: https://www.nature.com/articles/nbt.4072

According to data presented by the American Heart Association, certain cooking methods for meat, fish and chicken increase risk for high blood pressure.

Researchers compared meat consumed after high-temperature cooking methods and tracked hypertension incidence rates from more that 100,000 disease-free participants.

Increased consumption of red meat, fish and chicken prepared on an open-flame, and cooked longer at higher temperatures, increased the risk for high blood pressure.

Liu G. Meat cooking methods and risk of hypertension: results from three prospective cohort studies. Abstract presented at EPI|LIFESTYLE 2018 Scientific Sessions; March 20-23, 2018; New Orleans, LA.

 

 

 

According to a study published in the International Journal of Cancer, a diet high in red meat increases risk of colon cancer in women.

Researchers compared cancer incidence rates for dietary patterns centered on red meat, fish, poultry, or no meat in 32,147 women. Those who consumed red meat were more likely to develop distal colon cancer than those who consumed no red meat.

The authors note that higher intakes of dietary fiber, vitamins, and minerals associated with meat-free diets may protect against cancer.

Rada‐Fernandez de Jauregui D, Evans CEL, Jones P, Greenwood DC, Hancock N, Cade JE. Common dietary patterns and risk of cancers of the colon and rectum: Analysis from the United Kingdom Women’s Cohort Study (UKWCS). Intl J Cancer. Published online April 1, 2018.

Vegetarian diets help prevent diabetes, according to a study published in Nutrition and Diabetes.

Plant-based diets increase fiber and magnesium intake associated with improved insulin signaling via whole grains, vegetables, and soy products and eliminate saturated fat intake from meat products.

Researchers assessed dietary patterns for 2,918 Taiwanese participants over five years and tracked diabetes incidence rates. Those who followed a vegetarian diet had a lower risk for developing diabetes by 35 percent, compared with non-vegetarians.

Researchers observed a 53 percent reduction in risk in participants who converted to a vegetarian diet.

The authors recommend clinicians employ plant-based diets into lifestyle interventions to combat increased risk factors associated with Western dietary patterns.

Researchers examined data for 190,672 participants from The Cardiovascular Disease Lifetime Risk Pooling Project. They tracked BMI, cardiovascular disease incidence rates, and mortality. Those with BMIs higher than 24.9 increased their risk for heart disease, developed heart disease earlier in life, and were more likely to die from a cardiovascular event when compared to those with lower BMIs.

Researchers observed a higher average number of years spent living with cardiovascular disease in overweight and obese individuals and note that overweight individuals appear to live longer due to earlier onset of the disease.

Obese and overweight people live shorter lives and live with more chronic diseases, according to a study published in JAMA Cardiology

Khan SS, Ning H, Wilkins JT, et al. Association of body mass index with lifetime risk of cardiovascular disease and compression of morbidity. JAMA Cardiol. Published online February 28, 2018.

Scientists recently infected the first human liver-on-a-chip model with hepatitis B and unraveled biological and immune responses to the virus similar to that found in real human livers.

This 3-D human-based model reproduced the viral infection at infection doses similar to that found in humans. Because it is physiologically relevant to humans, (vs animals), it is likely to reduce the time and cost traditionally required for drug development for hepatitis B.

Ortega-Prieto AM, Skelton JK, Wai SN, et al. 3D microfluidic liver cultures as a physiological preclinical tool for hepatitis B virus infection. Nat Commun. 2018;9:682. doi: 10.1038/s41467-018-02969-8.

Biomedical engineers recently created a miniature device composed of blood vessels, a valve that induces a “wound,” and the flow of blood to recapitulate the wound healing process seen during injury in humans. They used the human-based system to understand the role of several key-clotting factors for blood clot formation.

The system helped the scientists to determine the defects causing excessive bleeding in hemophilia-A patients, as well as, to assess the specific effects of blood clotting drugs. Thus, the model can be used:1. as a screening tool for drugs to modulate human wound healing, 2. a diagnostic tool to identify patients with bleeding disorders, and 3. a personalized medicine tool to determine the optimal individualized drug treatments to modulate clotting.

Unlike previous models which only simulate one aspect of the wound healing process, this system reproduces all components of the human small blood vessel injury and repair process.

 

Sakurai Y, Hardy ET, Ahn B, et al. A microengineered vascularized bleeding model that integrates the principal components of hemostasis. Nat Commun. 2018;9:509. doi: 10.1038/s41467-018-02990-x.

Virtual Brain:

Researchers used a brain modeling platform called The Virtual Brain to incorporate individual patient brain measurements to produce personalized models simulating six features of patient brain activity. The tool allowed the researchers to assess the neuron interactions involved, which cannot be directly measured in humans, and enables the data from patient’s brain signals to predict neuronal network interactions.

This method advances personalized medicine by producing individualized models that can be used to optimize brain surgical procedures to improve outcomes prior to execution. It can also be used to uncover individual differences in brain networks and functions as well as underlying mechanisms of brain disorders.

Improving Research: Unlike other computational models, this mathematical platform can incorporate real-time human data to make better predictions about brain processes relevant to each individual patient and with greater resolution than previous attempts in invasive animal studies.

 

Schirner M, McIntosh AR, Jirsa V, Deco G, Ritter P. Inferring multi-scale neural mechanisms with brain network modelling. Elife. 2018;7. doi: 10.7554/eLife.28927.