Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Daphne Perlman ◽  
Marina Martínez-Álvaro ◽  
Sarah Moraïs ◽  
Ianina Altshuler ◽  
Live H. Hagen ◽  
...  
Keyword(s):  
Growth And Development ◽  
Annual Review ◽  
Publication Date ◽  
Core Microbiome ◽  
Host Environment ◽  
The Core ◽  
Genomic Architecture ◽  
Animal Growth ◽  
Potential Factors

Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host–core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Perspective on Data Science

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Roger D. Peng ◽  
Hilary S. Parker
Keyword(s):  
Iterative Process ◽  
Data Science ◽  
Annual Review ◽  
Publication Date ◽  
Broad Definition ◽  
The Core ◽  
Fields Of Study ◽  
Points Of Interest ◽  
New Knowledge

The field of data science currently enjoys a broad definition that includes a wide array of activities which borrow from many other established fields of study. Having such a vague characterization of a field in the early stages might be natural, but over time maintaining such a broad definition becomes unwieldy and impedes progress. In particular, the teaching of data science is hampered by the seeming need to cover many different points of interest. Data scientists must ultimately identify the core of the field by determining what makes the field unique and what it means to develop new knowledge in data science. In this review we attempt to distill some core ideas from data science by focusing on the iterative process of data analysis and develop some generalizations from past experience. Generalizations of this nature could form the basis of a theory of data science and would serve to unify and scale the teaching of data science to large audiences. Expected final online publication date for the Annual Review of Statistics, Volume 9 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The Yin and Yang of Histone Marks in Transcription

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Paul B. Talbert ◽  
Steven Henikoff
Keyword(s):  
Posttranslational Modifications ◽  
Human Genetics ◽  
Annual Review ◽  
Publication Date ◽  
Histone Marks ◽  
The Core ◽  
Core Histones ◽  
Yin And Yang ◽  
Transcriptional State ◽  
Histone Core

Nucleosomes wrap DNA and impede access for the machinery of transcription. The core histones that constitute nucleosomes are subject to a diversity of posttranslational modifications, or marks, that impact the transcription of genes. Their functions have sometimes been difficult to infer because the enzymes that write and read them are complex, multifunctional proteins. Here, we examine the evidence for the functions of marks and argue that the major marks perform a fairly small number of roles in either promoting transcription or preventing it. Acetylations and phosphorylations on the histone core disrupt histone-DNA contacts and/or destabilize nucleosomes to promote transcription. Ubiquitylations stimulate methylations that provide a scaffold for either the formation of silencing complexes or resistance to those complexes, and carry a memory of the transcriptional state. Tail phosphorylations deconstruct silencing complexes in particular contexts. We speculate that these fairly simple roles form the basis of transcriptional regulation by histone marks. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Hydration and Dehydration in Earth's Interior

2020 ◽  
Vol 49 (1) ◽  
Author(s):  
Eiji Ohtani
Keyword(s):  
Upper Mantle ◽  
Water Distribution ◽  
Annual Review ◽  
Publication Date ◽  
Mineral Physics ◽  
The Core ◽  
Water Influx ◽  
Terrestrial Water ◽  
Large Water ◽  
Hydration And Dehydration

Hydrogen and deuterium isotopic evidence indicates that the source of terrestrial water was mostly meteorites, with additional influx from nebula gas during accretion. There are two Earth models, with large (7–12 ocean masses) and small (1–4 ocean masses) water budgets that can explain the geochemical, cosmochemical, and geological observations. Geophysical and mineral physics data indicate that the upper and lower mantles are generally dry, whereas the mantle transition zone is wetter, with heterogeneous water distribution. Subducting slabs are a source of water influx, and there are three major sites of deep dehydration: the base of the upper mantle, and the top and bottom of the lower mantle in addition to slabs in the shallow upper mantle. Hydrated regions surround these dehydration sites. The core may be a hidden reservoir of hydrogen under the large water budget model. ▪ Earth is a water planet. Where and when was water delivered, and how much? How does water circulate in Earth? This review looks at the current answers to these fundamental questions. Expected final online publication date for the Annual Review of Earth and Planetary Sciences, Volume 49 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Markov Chain Monte Carlo in Practice

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Galin L. Jones ◽  
Qian Qin
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Online Publication ◽  
Probability Distributions ◽  
Annual Review ◽  
Publication Date ◽  
Mcmc Simulation ◽  
Essential Set

Markov chain Monte Carlo (MCMC) is an essential set of tools for estimating features of probability distributions commonly encountered in modern applications. For MCMC simulation to produce reliable outcomes, it needs to generate observations representative of the target distribution, and it must be long enough so that the errors of Monte Carlo estimates are small. We review methods for assessing the reliability of the simulation effort, with an emphasis on those most useful in practically relevant settings. Both strengths and weaknesses of these methods are discussed. The methods are illustrated in several examples and in a detailed case study. Expected final online publication date for the Annual Review of Statistics, Volume 9 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

From Cell Types to an Integrated Understanding of Brain Evolution: The Case of the Cerebral Cortex

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Maria Antonietta Tosches
Keyword(s):  
Developmental Biology ◽  
Cerebral Cortex ◽  
High Throughput ◽  
Neural Development ◽  
Brain Evolution ◽  
Cell Types ◽  
Annual Review ◽  
Publication Date ◽  
Structural Units

With the discovery of the incredible diversity of neurons, Cajal and coworkers laid the foundation of modern neuroscience. Neuron types are not only structural units of nervous systems but also evolutionary units, because their identities are encoded in the genome. With the advent of high-throughput cellular transcriptomics, neuronal identities can be characterized and compared systematically across species. The comparison of neurons in mammals, reptiles, and birds indicates that the mammalian cerebral cortex is a mosaic of deeply conserved and recently evolved neuron types. Using the cerebral cortex as a case study, this review illustrates how comparing neuron types across species is key to reconciling observations on neural development, neuroanatomy, circuit wiring, and physiology for an integrated understanding of brain evolution. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals COREMIC: a web-tool to search for a niche associated CORE MICrobiome

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4395 ◽  
Author(s):  
Richard R. Rodrigues ◽  
Nyle C. Rodgers ◽  
Xiaowei Wu ◽  
Mark A. Williams
Keyword(s):  
Growth Promotion ◽  
Niche Partitioning ◽  
Web Tool ◽  
Core Microbiome ◽  
Exact Test ◽  
The Core ◽  
Link Type ◽  
Using Data ◽  
User Friendly

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val <0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.

scholarly journals Biophysics of Chromatin Remodeling

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Ilana M. Nodelman ◽  
Gregory D. Bowman
Keyword(s):  
Chromatin Remodeling ◽  
Growth And Development ◽  
Genomic Dna ◽  
Eukaryotic Cells ◽  
Annual Review ◽  
Publication Date ◽  
Chromatin Remodelers ◽  
Experimental Findings ◽  
Histone Core ◽  
Standing Question

As primary carriers of epigenetic information and gatekeepers of genomic DNA, nucleosomes are essential for proper growth and development of all eukaryotic cells. Although they are intrinsically dynamic, nucleosomes are actively reorganized by ATP-dependent chromatin remodelers. Chromatin remodelers contain helicase-like ATPase motor domains that can translocate along DNA, and a long-standing question in the field is how this activity is used to reposition or slide nucleosomes. In addition to ratcheting along DNA like their helicase ancestors, remodeler ATPases appear to dictate specific alternating geometries of the DNA duplex, providing an unexpected means for moving DNA past the histone core. Emerging evidence supports twist-based mechanisms for ATP-driven repositioning of nucleosomes along DNA. In this review, we discuss core experimental findings and ideas that have shaped the view of how nucleosome sliding may be achieved. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome

2017 ◽  
Author(s):  
Richard R. Rodrigues ◽  
Nyle C. Rodgers ◽  
Xiaowei Wu ◽  
Mark A. Williams
Keyword(s):  
Root Zone ◽  
Growth Promotion ◽  
Niche Partitioning ◽  
Web Tool ◽  
Core Microbiome ◽  
Exact Test ◽  
The Core ◽  
Using Data ◽  
User Friendly

AbstractMicrobial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (5 environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val < 0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.

Grappling Spacecraft

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Carl Glen Henshaw ◽  
Samantha Glassner ◽  
Bo Naasz ◽  
Brian Roberts
Keyword(s):  
Autonomous Systems ◽  
Space Station ◽  
Complex Problem ◽  
Robotic Systems ◽  
Robotic Arm ◽  
Annual Review ◽  
Publication Date ◽  
Reliable Operation ◽  
New Techniques ◽  
The Core

This article provides a survey overview of the techniques, mechanisms, algorithms, and test and validation strategies required for the design of robotic grappling vehicles intended to approach and grapple free-flying client satellites. We concentrate on using a robotic arm to grapple a free-floating spacecraft, as distinct from spacecraft docking and berthing, where two spacecraft directly mate with each other. Robotic grappling of client spacecraft is a deceptively complex problem: It entails designing a robotic system that functions robustly in the visually stark, thermally extreme orbital environment, operating near massive and extremely expensive yet fragile client hardware, using relatively slow flight computers with limited and laggy communications. Spaceflight robotic systems are challenging to test and validate prior to deployment and extremely expensive to launch, which significantly limits opportunities to experiment with new techniques. These factors make the design and operation of orbital robotic systems significantly different from those of their terrestrial counterparts, and as a result, only a relative handful of systems have been demonstrated on orbit. Nevertheless, there is increasing interest in on-orbit robotic servicing and assembly missions, and grappling is the core requirement for these systems. Although existing systems such as the Space Station Remote Manipulator System have demonstrated extremely reliable operation, upcoming missions will attempt to expand the types of spacecraft that can be safely and dependably grappled and berthed. Expected final online publication date for the Annual Review of Control, Robotics, and Autonomous Systems, Volume 5 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Shifty Attitudes: Indexical Shift Versus Perspectival Anaphora

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Sandhya Sundaresan
Keyword(s):  
Online Publication ◽  
Unified Model ◽  
Future Research ◽  
Annual Review ◽  
Publication Date ◽  
The Core ◽  
Attitude Shift

In cases of indexical shift, so-called indexical pronouns like I, you, here, and now refer to the speaker, addressee, location, and time of some context other than the utterance context. In cases of perspectival anaphora, an anaphor tracks the perspective of some individual other than the utterance speaker [or addressee(s)]. Thus, both phenomena involve referential obviation of a pronoun or anaphor from the utterance context. Such obviation also occurs under strikingly similar grammatical conditions—for instance, in the scope of an attitude predicate (e.g., say, think, perceive). In this review, I introduce the core properties of both phenomena and show that they actually stand in a subset–superset relation. The availability of indexical shift in a given environment entails that of perspectival anaphora, but not vice-versa. I describe a plausible way to make sense of these insights within a unified model of attitude shift, which in turn helps chart out clear avenues for future research. Expected final online publication date for the Annual Review of Linguistics, Volume 7 is January 14, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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