Mechanical aspects of mesenchymal morphogenesis

Many embryonic cells generate substantial contractile forces as they spread and crawl.These forces mechanically deform each cell's local environment, and the resulting distortions can alter subsequent cell movements by convection and the mechanisms of contact guidance and haptotaxis. Here we develop a model for the cumulative effects of these cell-generated forces and show how they can lead to the formation of regular large-scale patterns in cell populations. This model leads to several predictions concerning the effects of cellular and matrix properties on the resulting patterns. We apply the model to two widely studied morphogenetic processes: (a) patterns of skin-organ primordia, especially feather germ formation, and (b) the condensation of cartilagenous skeletal rudiments in the developing vertebrate limb.

Download Full-text

Genetic and Molecular Analysis of Region 88E9;88F2 in Drosophila melanogaster, Including the ear Gene Related to Human Factors Involved in Lineage-Specific Leukemias

Genetics ◽

10.1093/genetics/160.3.1051 ◽

2002 ◽

Vol 160 (3) ◽

pp. 1051-1065

Author(s):

Claudia B Zraly ◽

Yun Feng ◽

Andrew K Dingwall

Keyword(s):

Large Scale ◽

Drosophila Genome ◽

Embryonic Cells ◽

Ems Mutagenesis ◽

Recessive Lethal ◽

Protein Levels ◽

Late Embryogenesis ◽

Complementation Groups ◽

Mammalian Genes ◽

Map Location

Abstract We identified and characterized the Drosophila gene ear (ENL/AF9-related), which is closely related to mammalian genes that have been implicated in the onset of acute lymphoblastic and myelogenous leukemias when their products are fused as chimeras with those of human HRX, a homolog of Drosophila trithorax. The ear gene product is present in all early embryonic cells, but becomes restricted to specific tissues in late embryogenesis. We mapped the ear gene to cytological region 88E11-13, near easter, and showed that it is deleted by Df(3R)ea5022rx1, a small, cytologically invisible deletion. Annotation of the completed Drosophila genome sequence suggests that this region might contain as many as 26 genes, most of which, including ear, are not represented by mutant alleles. We carried out a large-scale noncom-plementation screen using Df(3R)ea5022rx1 and chemical (EMS) mutagenesis from which we identified sevenc novel multi-allele recessive lethal complementation groups in this region. An overlapping deficiency, Df(3R)Po4, allowed us to map several of these groups to either the proximal or the distal regions of Df(3R)ea5022rx1. One of these complementation groups likely corresponds to the ear gene as judged by map location, terminal phenotype, and reduction of EAR protein levels.

Download Full-text

The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia

Scientific Reports ◽

10.1038/s41598-019-55490-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Camila D. Ritter ◽

Søren Faurby ◽

Dominic J. Bennett ◽

Luciano N. Naka ◽

Hans ter Steege ◽

...

Keyword(s):

Species Richness ◽

Large Scale ◽

Spatial Scales ◽

Local Environment ◽

Life Forms ◽

Taxonomic Group ◽

Diversity Gradients ◽

Richness Patterns ◽

Taxonomic Groups ◽

Micro Organisms

AbstractMost knowledge on biodiversity derives from the study of charismatic macro-organisms, such as birds and trees. However, the diversity of micro-organisms constitutes the majority of all life forms on Earth. Here, we ask if the patterns of richness inferred for macro-organisms are similar for micro-organisms. For this, we barcoded samples of soil, litter and insects from four localities on a west-to-east transect across Amazonia. We quantified richness as Operational Taxonomic Units (OTUs) in those samples using three molecular markers. We then compared OTU richness with species richness of two relatively well-studied organism groups in Amazonia: trees and birds. We find that OTU richness shows a declining west-to-east diversity gradient that is in agreement with the species richness patterns documented here and previously for birds and trees. These results suggest that most taxonomic groups respond to the same overall diversity gradients at large spatial scales. However, our results show a different pattern of richness in relation to habitat types, suggesting that the idiosyncrasies of each taxonomic group and peculiarities of the local environment frequently override large-scale diversity gradients. Our findings caution against using the diversity distribution of one taxonomic group as an indication of patterns of richness across all groups.

Download Full-text

Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2005990117 ◽

2020 ◽

Vol 117 (46) ◽

pp. 28784-28794

Author(s):

Sisi Chen ◽

Paul Rivaud ◽

Jong H. Park ◽

Tiffany Tsou ◽

Emeric Charles ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Large Scale ◽

Probabilistic Models ◽

Single Cells ◽

Measurement Techniques ◽

Patient Specific ◽

Cell Populations ◽

Cell Measurement ◽

The Impact

Single-cell measurement techniques can now probe gene expression in heterogeneous cell populations from the human body across a range of environmental and physiological conditions. However, new mathematical and computational methods are required to represent and analyze gene-expression changes that occur in complex mixtures of single cells as they respond to signals, drugs, or disease states. Here, we introduce a mathematical modeling platform, PopAlign, that automatically identifies subpopulations of cells within a heterogeneous mixture and tracks gene-expression and cell-abundance changes across subpopulations by constructing and comparing probabilistic models. Probabilistic models provide a low-error, compressed representation of single-cell data that enables efficient large-scale computations. We apply PopAlign to analyze the impact of 40 different immunomodulatory compounds on a heterogeneous population of donor-derived human immune cells as well as patient-specific disease signatures in multiple myeloma. PopAlign scales to comparisons involving tens to hundreds of samples, enabling large-scale studies of natural and engineered cell populations as they respond to drugs, signals, or physiological change.

Download Full-text

Effect of a Dipole Magnetic Field on Stellar Mass-Loss

Proceedings of the International Astronomical Union ◽

10.1017/s1743921317002587 ◽

2016 ◽

Vol 12 (S329) ◽

pp. 242-245

Author(s):

Chris Bard ◽

Richard Townsend

Keyword(s):

Magnetic Fields ◽

Mass Loss ◽

Large Scale ◽

Massive Star ◽

Loss Rate ◽

Mass Loss Rate ◽

Local Environment ◽

Surface Mass ◽

B Stars ◽

Dipole Magnetic Field

AbstractMassive star winds greatly influence the evolution of both their host star and local environment though their mass-loss rates, but current radiative line-driven wind models do not incorporate any magnetic effects. Recent surveys of O and B stars have found that about ten percent have large-scale, organized magnetic fields. These massive-star magnetic fields, which are thousands of times stronger than the Sun’s, affect the inherent properties of their own winds by changing the mass-loss rate. To quantify this, we present a simple surface mass-flux scaling over the stellar surface which can be easily integrated to get an estimate of the mass-loss rate for a magnetic massive star. The overall mass-loss rate is found to decrease by factors of 2-5 relative to the non-magnetic CAK mass-loss rate.

Download Full-text

Mapping Environmental Conflicts Using Spatial Text Mining

Land ◽

10.3390/land9090287 ◽

2020 ◽

Vol 9 (9) ◽

pp. 287 ◽

Cited By ~ 2

Author(s):

Jae-hyuck Lee ◽

Do-kyun Kim

Keyword(s):

Text Mining ◽

South Korea ◽

Large Scale ◽

Local Environment ◽

Environmental Conflict ◽

Current Status ◽

Environmental Conflicts ◽

Mining Technique ◽

Management Policies ◽

Definition Of

Mapping the characteristics and extent of environmental conflicts related to land use is important for developing regionally specific policies. However, because it is only possible to verify the frequency of conflicts on a specific predetermined subject, it is difficult to determine the various reasons for conflicts in a region. Therefore, this study mapped the current status of regional environmental conflicts in South Korea using a spatial text mining technique, then proposed relevant management policies. The results were obtained by analyzing environmental conflict data extracted from the online agendas of regional environmental organizations. Air quality-related conflicts in South Korea are concentrated in western municipalities; development-related conflicts are concentrated in the southern region of Jeju Island; and intensive safety-related conflicts occur in metropolitan areas, particularly Ulsan. Thus, the type of conflict is determined by the local environment, in accordance with the definition of environmental conflict, and the distribution is determined by the location of the stakeholder population. This study reveals the issues and locations related to local environmental conflict that require further attention, and proposes more wide-ranging methods for managing the links between conflicts by mapping environmental conflicts on a large scale rather than on an individual basis.

Download Full-text

Copper-Adapted Suillus luteus, a Symbiotic Solution for Pines Colonizing Cu Mine Spoils

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.7279-7284.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 7279-7284 ◽

Cited By ~ 81

Author(s):

K. Adriaensen ◽

T. Vrålstad ◽

J.-P. Noben ◽

J. Vangronsveld ◽

J. V. Colpaert

Keyword(s):

Large Scale ◽

Land Reclamation ◽

Natural Populations ◽

Local Environment ◽

Ectomycorrhizal Fungus ◽

Suillus Luteus ◽

Cu Toxicity ◽

Pine Trees ◽

Cu Tolerance

ABSTRACT Natural populations thriving in heavy-metal-contaminated ecosystems are often subjected to selective pressures for increased resistance to toxic metals. In the present study we describe a population of the ectomycorrhizal fungus Suillus luteus that colonized a toxic Cu mine spoil in Norway. We hypothesized that this population had developed adaptive Cu tolerance and was able to protect pine trees against Cu toxicity. We also tested for the existence of cotolerance to Cu and Zn in S. luteus. Isolates from Cu-polluted, Zn-polluted, and nonpolluted sites were grown in vitro on Cu- or Zn-supplemented medium. The Cu mine isolates exhibited high Cu tolerance, whereas the Zn-tolerant isolates were shown to be Cu sensitive, and vice versa. This indicates the evolution of metal-specific tolerance mechanisms is strongly triggered by the pollution in the local environment. Cotolerance does not occur in the S. luteus isolates studied. In a dose-response experiment, the Cu sensitivity of nonmycorrhizal Pinus sylvestris seedlings was compared to the sensitivity of mycorrhizal seedlings colonized either by a Cu-sensitive or Cu-tolerant S. luteus isolate. In nonmycorrhizal plants and plants colonized by the Cu-sensitive isolate, root growth and nutrient uptake were strongly inhibited under Cu stress conditions. In contrast, plants colonized by the Cu-tolerant isolate were hardly affected. The Cu-adapted S. luteus isolate provided excellent insurance against Cu toxicity in pine seedlings exposed to elevated Cu levels. Such a metal-adapted Suillus-Pinus combination might be suitable for large-scale land reclamation at phytotoxic metalliferous and industrial sites.

Download Full-text

Nest size is predicted by female identity and the local environment in the blue tit ( Cyanistes caeruleus ), but is not related to the nest size of the genetic or foster mother

Royal Society Open Science ◽

10.1098/rsos.172036 ◽

2018 ◽

Vol 5 (4) ◽

pp. 172036

Author(s):

Louis G. O'Neill ◽

Timothy H. Parker ◽

Simon C. Griffith

Keyword(s):

Large Scale ◽

Environmental Variability ◽

Spatial Scales ◽

Local Environment ◽

Nest Size ◽

Foster Mother ◽

Nest Structure ◽

Blue Tit ◽

Cyanistes Caeruleus ◽

Nest Microclimate

The potential for animals to respond to changing climates has sparked interest in intraspecific variation in avian nest structure since this may influence nest microclimate and protect eggs and offspring from inclement weather. However, there have been relatively few large-scale attempts to examine variation in nests or the determinates of individual variation in nest structure within populations. Using a set of mostly pre-registered analyses, we studied potential predictors of variation in the size of a large sample (803) of blue tit ( Cyanistes caeruleus ) nests across three breeding seasons at Wytham Woods, UK. While our pre-registered analyses found that individual females built very similar nests across years, there was no evidence in follow-up ( post hoc ) analyses that their nest size correlated to that of their genetic mother or, in a cross-fostering experiment, to the nest where they were reared. In further pre-registered analyses, spatial environmental variability explained nest size variability at relatively broad spatial scales, and especially strongly at the scale of individual nest boxes. Our study indicates that nest structure is a characteristic of individuals, but is not strongly heritable, indicating that it will not respond rapidly to selection. Explaining the within-individual and within-location repeatability we observed requires further study.

Download Full-text

Shh induces symmetry breaking in the presomitic mesoderm by inducing tissue shear and orientated cell rearrangements

10.1101/589549 ◽

2019 ◽

Author(s):

J. Yin ◽

T. E. Saunders

Keyword(s):

Skeletal Muscle ◽

Symmetry Breaking ◽

Cell Mechanics ◽

Large Scale ◽

Cell Layer ◽

Cell Populations ◽

Presomitic Mesoderm ◽

Cellular Changes ◽

Muscle Myosin ◽

Adaxial Cells

AbstractFuture boundaries of skeletal muscle segments are determined in the presomitic mesoderm (PSM). Within the PSM, future somitic cells undergo significant changes in both morphology and position. How such large-scale cellular changes are coordinated and the effect on the future border formation is unknown. We find that cellular rearrangements differ between cell populations within the PSM. In contrast to lateral somitic cells, which display less organized rearrangement, the adaxial cell layer undergoes significant tissue shearing with dorsal and ventral cells sliding posteriorly. This shear is generated by orientated intercalations of dorsally and ventrally located adaxial cells, which induces a chevron-like pattern. We find Shh signaling is required for the tissue shear and morphogenesis of adaxial cells. In particular, we observe Shh-dependent polarized recruitment of non-muscle myosin IIA drives apical constrictions, and thus the intercalations and shear. This reveals a novel role for Shh in regulating cell mechanics in the PSM.

Download Full-text

Synthesis of polypeptides via bioinspired polymerization of in situ purified N-carboxyanhydrides

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1901442116 ◽

2019 ◽

Vol 116 (22) ◽

pp. 10658-10663 ◽

Cited By ~ 23

Author(s):

Ziyuan Song ◽

Hailin Fu ◽

Jiang Wang ◽

Jingshu Hui ◽

Tianrui Xue ◽

...

Keyword(s):

Large Scale ◽

Low Cost ◽

Local Environment ◽

Side Reactions ◽

Scale Production ◽

Competing Species ◽

Natural Protein ◽

Large Scale Production ◽

Synthetic Polypeptides

Ribozymes synthesize proteins in a highly regulated local environment to minimize side reactions caused by various competing species. In contrast, it is challenging to prepare synthetic polypeptides from the polymerization of N-carboxyanhydrides (NCAs) in the presence of water and impurities, which induce monomer degradations and chain terminations, respectively. Inspired by natural protein synthesis, we herein report the preparation of well-defined polypeptides in the presence of competing species, by using a water/dichloromethane biphasic system with macroinitiators anchored at the interface. The impurities are extracted into the aqueous phase in situ, and the localized macroinitiators allow for NCA polymerization at a rate which outpaces water-induced side reactions. Our polymerization strategy streamlines the process from amino acids toward high molecular weight polypeptides with low dispersity by circumventing the tedious NCA purification and the demands for air-free conditions, enabling low-cost, large-scale production of polypeptides that has potential to change the paradigm of polypeptide-based biomaterials.

Download Full-text

High-Throughput Selection of Retrovirus Producer Cell Lines Leads to Markedly Improved Efficiency of Germ Line-Transmissible Insertions in Zebra Fish

Journal of Virology ◽

10.1128/jvi.76.5.2192-2198.2002 ◽

2002 ◽

Vol 76 (5) ◽

pp. 2192-2198 ◽

Cited By ~ 51

Author(s):

Wenbiao Chen ◽

Shawn Burgess ◽

Greg Golling ◽

Adam Amsterdam ◽

Nancy Hopkins

Keyword(s):

Cell Lines ◽

Large Scale ◽

Insertional Mutagenesis ◽

Germ Line ◽

High Titer ◽

Retroviral Vectors ◽

Embryonic Cells ◽

Zebra Fish ◽

Glycoprotein G ◽

Producer Cell

ABSTRACT Vesicular stomatitis virus glycoprotein G-pseudotyped mouse retroviral vectors have been used as mutagens for a large-scale insertional mutagenesis screen in the zebra fish. To reproducibly generate high-titer virus stocks, we devised a method for rapidly selecting cell lines that can yield high-titer viruses and isolated a producer cell line that yields virus at a high titer on zebra fish embryos. Virus produced from this line, designated GT virus, is nontoxic following injection of zebra fish blastulae and efficiently infects embryonic cells that give rise to the future germ line. Using GT virus preparations we generated roughly 500,000 germ line-transmissible proviral insertions in a population of 25,000 founder fish in about 2 months. The GT virus contains a gene trap, and trap events can be detected in the offspring of almost every founder fish. We discuss potential applications of this highly efficient method for generating germ line-transmissible insertions in a vertebrate

Download Full-text