scholarly journals Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Patrick A. Leggieri ◽  
Yiyi Liu ◽  
Madeline Hayes ◽  
Bryce Connors ◽  
Susanna Seppälä ◽  
...  
Keyword(s):  
Biomedical Engineering ◽  
Ecological Factors ◽  
Annual Review ◽  
Publication Date ◽  
Control Points ◽  
Chemical Transformations ◽  
Modeling Tools ◽  
Microbiome Composition ◽  
Technology Gaps ◽  
And Function

Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review,we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Almut Heinken ◽  
Arianna Basile ◽  
Johannes Hertel ◽  
Cyrille Thinnes ◽  
Ines Thiele
Keyword(s):  
Human Microbiome ◽  
Metabolic Modeling ◽  
Therapeutic Interventions ◽  
Annual Review ◽  
Publication Date ◽  
Multivariate Statistical ◽  
Disease Etiology ◽  
Microbiome Composition ◽  
Complementary Approach ◽  
And Function

The human microbiome plays an important role in human health and disease. Meta-omics analyses provide indispensable data for linking changes in microbiome composition and function to disease etiology. Yet, the lack of a mechanistic understanding of, e.g., microbiome-metabolome links hampers the translation of these findings into effective, novel therapeutics. Here, we propose metabolic modeling of microbial communities through constraint-based reconstruction and analysis (COBRA) as a complementary approach to meta-omics analyses. First, we highlight the importance of microbial metabolism in cardiometabolic diseases, inflammatory bowel disease, colorectal cancer, Alzheimer disease, and Parkinson disease. Next, we demonstrate that microbial community modeling can stratify patients and controls, mechanistically link microbes with fecal metabolites altered in disease, and identify host pathways affected by the microbiome. Finally, we outline our vision for COBRA modeling combined with meta-omics analyses and multivariate statistical analyses to inform and guide clinical trials, yield testable hypotheses, and ultimately propose novel dietary and therapeutic interventions. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Biological Phase Separation and Biomolecular Condensates in Plants

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Ryan J. Emenecker ◽  
Alex S. Holehouse ◽  
Lucia C. Strader
Keyword(s):  
Phase Separation ◽  
Cell Biology ◽  
Condensed Matter ◽  
Annual Review ◽  
Publication Date ◽  
Nuclear Speckles ◽  
The Past ◽  
Shared Property ◽  
And Function ◽  
Physical Principles

A surge in research focused on understanding the physical principles governing the formation, properties, and function of membraneless compartments has occurred over the past decade. Compartments such as the nucleolus, stress granules, and nuclear speckles have been designated as biomolecular condensates to describe their shared property of spatially concentrating biomolecules. Although this research has historically been carried out in animal and fungal systems, recent work has begun to explore whether these same principles are relevant in plants. Effectively understanding and studying biomolecular condensates require interdisciplinary expertise that spans cell biology, biochemistry, and condensed matter physics and biophysics. As such, some involved concepts may be unfamiliar to any given individual. This review focuses on introducing concepts essential to the study of biomolecular condensates and phase separation for biologists seeking to carry out research in this area and further examines aspects of biomolecular condensates that are relevant to plant systems. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Extrachromosomal DNA: An Emerging Hallmark in Human Cancer

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Sihan Wu ◽  
Vineet Bafna ◽  
Howard Y. Chang ◽  
Paul S. Mischel
Keyword(s):  
Human Cancer ◽  
Regulatory Elements ◽  
Annual Review ◽  
Publication Date ◽  
Cancer Evolution ◽  
Form And Function ◽  
Current State ◽  
Human Genes ◽  
Cancer Tumor ◽  
And Function

Human genes are arranged on 23 pairs of chromosomes, but in cancer, tumor-promoting genes and regulatory elements can free themselves from chromosomes and relocate to circular, extrachromosomal pieces of DNA (ecDNA). ecDNA, because of its nonchromosomal inheritance, drives high-copy-number oncogene amplification and enables tumors to evolve their genomes rapidly. Furthermore, the circular ecDNA architecture fundamentally alters gene regulation and transcription, and the higher-order organization of ecDNA contributes to tumor pathogenesis. Consequently, patients whose cancers harbor ecDNA have significantly shorter survival. Although ecDNA was first observed more than 50 years ago, its critical importance has only recently come to light. In this review, we discuss the current state of understanding of how ecDNAs form and function as well as how they contribute to drug resistance and accelerated cancer evolution. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Mutant Allele Imbalance in Cancer

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Craig M. Bielski ◽  
Barry S. Taylor
Keyword(s):  
Cancer Biology ◽  
Mutant Allele ◽  
Tumor Biology ◽  
Cellular Level ◽  
Driver Mutations ◽  
Annual Review ◽  
Publication Date ◽  
Cancer Evolution ◽  
Allele Imbalance ◽  
And Function

The search for somatic mutations that drive the initiation and progression of human tumors has dominated recent cancer research. While much emphasis has been placed on characterizing the prevalence and function of driver mutations, comparatively less is known about their serial genetic evolution. Indeed, study of this phenomenon has largely focused on tumor-suppressor genes recessive at the cellular level or mechanisms of resistance in tumors with mutant oncogenes targeted by therapy. There is, however, a growing appreciation that despite a decades-old presumption of heterozygosity, changes in mutant oncogene zygosity are common and drive dosage and stoichiometry changes that lead to selective growth advantages. Here, we review the recent progress in understanding mutant allele imbalance and its implications for tumor biology, cancer evolution, and response to anticancer therapy. Expected final online publication date for the Annual Review of Cancer Biology, Volume 5 is March 4, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Critical Phenomena in Plasma Membrane Organization and Function

2020 ◽  
Vol 72 (1) ◽  
Author(s):  
Thomas R. Shaw ◽  
Subhadip Ghosh ◽  
Sarah L. Veatch
Keyword(s):  
Plasma Membrane ◽  
Critical Phenomena ◽  
Model Systems ◽  
Annual Review ◽  
Publication Date ◽  
Membrane Composition ◽  
Lipid Organization ◽  
And Function ◽  
Lateral Organization ◽  
Liquid Liquid Phase Separation

Lateral organization in the plane of the plasma membrane is an important driver of biological processes. The past dozen years have seen increasing experimental support for the notion that lipid organization plays an important role in modulating this heterogeneity. Various biophysical mechanisms rooted in the concept of liquid–liquid phase separation have been proposed to explain diverse experimental observations of heterogeneity in model and cell membranes with distinct but overlapping applicability. In this review, we focus on the evidence for and the consequences of the hypothesis that the plasma membrane is poised near an equilibrium miscibility critical point. Critical phenomena explain certain features of the heterogeneity observed in cells and model systems but also go beyond heterogeneity to predict other interesting phenomena, including responses to perturbations in membrane composition. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 20, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Simulating Outcomes of Cataract Surgery: Important Advances in Ophthalmology

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Susana Marcos ◽  
Eduardo Martinez-Enriquez ◽  
Maria Vinas ◽  
Alberto de Castro ◽  
Carlos Dorronsoro ◽  
...  
Keyword(s):  
Cataract Surgery ◽  
Biomedical Engineering ◽  
Quantitative Imaging ◽  
Crystalline Lens ◽  
Annual Review ◽  
Publication Date ◽  
Selection Methods ◽  
Active Elements ◽  
The World ◽  
Lens Opacities

As the human eye ages, the crystalline lens stiffens (presbyopia) and opacifies (cataract), requiring its replacement with an artificial lens [intraocular lens (IOL)]. Cataract surgery is the most frequently performed surgical procedure in the world. The increase in IOL designs has not been paralleled in practice by a sophistication in IOL selection methods, which rely on limited anatomical measurements of the eye and the surgeon's interpretation of the patient's needs and expectations. We propose that the future of IOL selection will be guided by 3D quantitative imaging of the crystalline lens to map lens opacities, anticipate IOL position, and develop fully customized eye models for ray-tracing-based IOL selection. Conversely, visual simulators (in which IOL designs are programmed in active elements) allow patients to experience prospective vision before surgery and to make more informed decisions about which IOL to choose. Quantitative imaging and optical and visual simulations of postsurgery outcomes will allow optimal treatments to be selected for a patient undergoing modern cataract surgery. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

New Advances and Applications in Field-Flow Fractionation

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Christine L. Plavchak ◽  
William C. Smith ◽  
Carmen R.M. Bria ◽  
S. Kim Ratanathanawongs Williams
Keyword(s):  
Food Systems ◽  
Coming Of Age ◽  
Size Composition ◽  
Annual Review ◽  
Publication Date ◽  
Field Flow Fractionation ◽  
Multiple Components ◽  
Flow Fractionation ◽  
And Function ◽  
Size Scales

Field-flow fractionation (FFF) is a family of techniques that was created especially for separating and characterizing macromolecules, nanoparticles, and micrometer-sized analytes. It is coming of age as new nanomaterials, polymers, composites, and biohybrids with remarkable properties are introduced and new analytical challenges arise due to synthesis heterogeneities and the motivation to correlate analyte properties with observed performance. Appreciation of the complexity of biological, pharmaceutical, and food systems and the need to monitor multiple components across many size scales have also contributed to FFF's growth. This review highlights recent advances in FFF capabilities, instrumentation, and applications that feature the unique characteristics of different FFF techniques in determining a variety of information, such as averages and distributions in size, composition, shape, architecture, and microstructure and in investigating transformations and function. Expected final online publication date for the Annual Review of Analytical Chemistry, Volume 14 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Native Mass Spectrometry: Recent Progress and Remaining Challenges

2022 ◽  
Vol 51 (1) ◽  
Author(s):  
Kelly R. Karch ◽  
Dalton T. Snyder ◽  
Sophie R. Harvey ◽  
Vicki H. Wysocki
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Structural Biology ◽  
Recent Progress ◽  
Native Mass Spectrometry ◽  
Structure And Function ◽  
Annual Review ◽  
Publication Date ◽  
Analysis Software ◽  
And Function

Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Dendritic Cell Regulation of T Helper Cells

2021 ◽  
Vol 39 (1) ◽  
Author(s):  
Xiangyun Yin ◽  
Shuting Chen ◽  
Stephanie C. Eisenbarth
Keyword(s):  
Cell Differentiation ◽  
T Regulatory Cells ◽  
Adaptive Immune Response ◽  
Annual Review ◽  
Publication Date ◽  
T Helper ◽  
Follicular Helper ◽  
Th Cell ◽  
And Function ◽  
Antigen Presenting

As the professional antigen-presenting cells of the immune system, dendritic cells (DCs) sense the microenvironment and shape the ensuing adaptive immune response. DCs can induce both immune activation and immune tolerance according to the peripheral cues. Recent work has established that DCs comprise of several phenotypically and functionally heterogeneous subsets that differentially regulate T lymphocyte differentiation. This review summarizes both mouse and human DC subset phenotypes, development, diversification, and function. We focus on advances in our understanding of how different DC subsets regulate distinct CD4+ T helper (Th) cell differentiation, including Th1, Th2, Th17, T follicular helper, and T regulatory cells. We review DC subset intrinsic properties, local tissue microenvironments, and other immune cells that together determine Th cell differentiation during homeostasis and inflammation. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Solid-Binding Proteins: Bridging Synthesis, Assembly, and Function in Hybrid and Hierarchical Materials Fabrication

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karthik Pushpavanam ◽  
Jinrong Ma ◽  
Yifeng Cai ◽  
Nada Y. Naser ◽  
François Baneyx
Keyword(s):  
Binding Proteins ◽  
Functional Materials ◽  
Inorganic Materials ◽  
Annual Review ◽  
Chemical Information ◽  
Publication Date ◽  
Materials Synthesis ◽  
Hierarchical Materials ◽  
The Many ◽  
And Function

There is considerable interest in the development of hybrid organic–inorganic materials because of the potential for harvesting the unique capabilities that each system has to offer. Proteins are an especially attractive organic component owing to the high amount of chemical information encoded in their amino acid sequence, their amenability to molecular and computational (re)design, and the many structures and functions they specify. Genetic installation of solid-binding peptides (SBPs) within protein frameworks affords control over the position and orientation of adhesive and morphogenetic segments, and a path toward predictive synthesis and assembly of functional materials and devices, all while harnessing the built-in properties of the host scaffold. Here, we review the current understanding of the mechanisms through which SBPs bind to technologically relevant interfaces, with an emphasis on the variables that influence the process, and highlight the last decade of progress in the use of solid-binding proteins for hybrid and hierarchical materials synthesis. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 12 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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