Uncommon Descent Serving The Intelligent Design Community

Rethinking biology: What role does physical structure play in the development of cells?

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

That’s structuralism, in part. Further to Evelyn Fox Keller’s comment that the landscape of biological thought is being “radically reconfigured,” a cancer geneticist writes to say that a tumor’s physical environment fuels its growth and causes treatment resistance:

The forces of cancer

In vitro experiments showing that cancer cells actively migrate in response to fluid flow have supported the hypothesis that fluid escaping from the boundary of a tumor may guide the invasive migration of cancer cells toward lymphatic or blood vessels, potentially encouraging metastasis. There remains controversy over how the fluid forces induce the migration; the cells may respond to chemical gradients created by the cells and distorted by the flowing fluid,8 or the fluid may activate cell mechanosensors. Because of the potential for new therapeutic interventions, the transduction of mechanical fluid forces into biochemical signals by cell mechanosensors is an active area of investigation. In a more direct manner, the fluid flow can physically carry cancer cells to lymph nodes.

And fluid pressure is just one of the many forces in a tumor that can influence its development and progression. Tumors also develop increased solid pressure, as compared with normal tissue, stemming from the uncontrolled division of cancer cells and from the infiltration and proliferation of stromal and immune cells from the surrounding tissue and circulation. High-molecular-weight polysaccharides known as hydrogels found in the extracellular matrix (ECM) also add pressure on a tumor. The most well-studied of these hydrogels is hyaluronan; when the polysaccharide absorbs water, it swells, pressing on surrounding cells and structural elements of the tissue. More. (The Scientist, April 1, 2016)

and

May the Force be with you

The dissection of how cells sense and propagate physical forces is leading to exciting new tools and discoveries in mechanobiology and mechanomedicine.

Of course, mechanical properties and forces aren’t just important in disease, but in health as well. Almost all living cells and tissues exert and experience physical forces that influence biological function. The magnitudes of those forces vary among different cell and tissue types, as do cells’ sensitivities to changes in magnitudes, frequencies, and durations of the forces. Touch, hearing, proprioception, and certain other senses are well-known examples of specialized force sensors. But force detection and sensing are not limited to these special cases; rather, they are shared by all living cells in all tissues and organs. The underlying mechanisms of force generation and detection are not well understood, however, leaving many open questions about force dynamics; the distance over which a force exerts its impact; and how cells convert mechanical signals into biochemical signals and changes in gene expression (The Scientist, February 1, 2017)More.

We may come to understand evolution better if we see what can and can’t happen in physics terms.

See also: Keller: Landscape of biological thought is being “radically reconfigured”

Comments
Background In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to target questions like genome wide gene expression analysis, a reference genome or transcriptome is needed. Methods Therefore, in this study two Common Blackbirds were sacrificed, their mRNA was isolated and analyzed by RNA-Seq to de novo assemble a transcriptome and characterize it. Illumina reads (125 bp paired-end) and a Velvet/Oases pipeline led to 162,158 transcripts. For the annotation (using Blast+), an unfiltered protein database was used. SNPs were identified using SAMtools and BCFtools. Furthermore, mRNA from three single tissues (brain, heart and liver) of the same two Common Blackbirds were sequenced by Illumina (75 bp single-end reads). The draft transcriptome and the three single tissues were compared by their BLAST hits with the package VennDiagram in R. Results Following the annotation against protein databases, we found evidence for 15,580 genes in the transcriptome (all well characterized hits after annotation). On 18% of the assembled transcripts, 144,742 SNPs were identified which are, consequently, 0.09% of all nucleotides in the assembled transcriptome. In the transcriptome and in the single tissues (brain, heart and liver), 10,182 shared genes were found. Discussion Using a next-generation technology and bioinformatics tools, we made a first step towards the genomic investigation of the Common Blackbird. The de novo assembled transcriptome is usable for downstream analyses such as differential gene expression analysis and SNP identification. This study shows the importance of the approach to sequence single tissues to understand functions of tissues, proteins and the phenotype. Koglin, Sven & Trense, Daronja & Wink, Michael & Sauer?Gürth, Hedwig & Tietze, Thomas. (2017). Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula). PeerJ. 5. . 10.7717/peerj.4045. https://www.researchgate.net/profile/Sven_Koglin/publication/321778940_Characterization_of_a_de_novo_assembled_transcriptome_of_the_Common_Blackbird_Turdus_merula/links/5a315e44a6fdcc9b2d34c843/Characterization-of-a-de-novo-assembled-transcriptome-of-the-Common-Blackbird-Turdus-merula.pdfDionisio
January 19, 2018
January
01
Jan
19
19
2018
02:41 AM
2
02
41
AM
PDT
Migration is a widespread phenomenon across the animal kingdom as a response to seasonality in environmental conditions. Partially migratory populations are populations that consist of both migratory and residential individuals. Such populations are very common, yet their stability has long been debated. The inheritance of migratory activity is currently best described by the threshold model of quantitative genetics. The inclusion of such a genetic threshold model for migratory behavior leads to a stable zone in time and space of partially migratory populations under a wide range of demographic parameter values, when assuming stable environmental conditions and unlimited genetic diversity. Migratory species are expected to be particularly sensitive to global warming, as arrival at the breeding grounds might be increasingly mistimed as a result of the uncoupling of long-used cues and actual environmental conditions, with decreasing reproduction as a consequence. Here, we investigate the consequences for migratory behavior and the stability of partially migratory populations under five climate change scenarios and the assumption of a genetic threshold value for migratory behavior in an individual-based model. The results show a spatially and temporally stable zone of partially migratory populations after different lengths of time in all scenarios. In the scenarios in which the species expands its range from a particular set of starting populations, the genetic diversity and location at initialization determine the species’ colonization speed across the zone of partial migration and therefore across the entire landscape. Abruptly changing environmental conditions after model initialization never caused a qualitative change in phenotype distributions, or complete extinction. This suggests that climate change-induced shifts in species’ ranges as well as changes in survival probabilities and reproductive success can be met with flexibility in migratory behavior at the species level, which will reduce the risk of extinction. Cobben, Marleen & van Noordwijk, Arie. (2017). Consequences of the genetic threshold model for observing partial migration under climate change scenarios. Ecology and Evolution. 7. . 10.1002/ece3.3357. https://www.researchgate.net/publication/319612606_Consequences_of_the_genetic_threshold_model_for_observing_partial_migration_under_climate_change_scenarios/fulltext/59b4d9e0458515a5b4926f1f/319612606_Consequences_of_the_genetic_threshold_model_for_observing_partial_migration_under_climate_change_scenarios.pdfDionisio
January 19, 2018
January
01
Jan
19
19
2018
02:38 AM
2
02
38
AM
PDT
Project Ecological genomics of adaptation to environmental change Luciano B BeheregarayLuciano B Beheregaray · Chris BrauerChris Brauer · Michael P HammerMichael P Hammer · Show all 8 collaborators Goal: Rapid environmental and climatic change represents a clear and urgent challenge for conservation and evolutionary biologists – this is particularly so in aquatic ecosystems, which are experiencing some of the fastest rates of change. We are implementing a research program in ecological genomics to understand population adaptations and responses to environmental change in ecologically important aquatic organisms. Our program integrates comparative ecological genomics (in the wild and in the lab), phenotypic data and spatially-explicit modelling approaches to assess adaptation and vulnerability of aquatic biodiversity to environmental and climatic change. For details about this and other similar research programs please visit: http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/research-programs/Dionisio
January 19, 2018
January
01
Jan
19
19
2018
02:35 AM
2
02
35
AM
PDT
Epigenetics has attracted considerable attention with respect to its potential value in many areas of agricultural production, particularly under conditions where the environment can be manipulated or natural variation exists. Here we introduce key concepts and definitions of epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, review the current understanding of epigenetics in both fish and shellfish, and propose key areas of aquaculture where epigenetics could be applied. The first key area is environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either within or between generations to produce a desired phenotype. The second key area is epigenetic selection, which, alone or combined with genetic selection, may increase the reliability of producing animals with desired phenotypes. Based on aspects of life history and husbandry practices in aquaculture species, the application of epigenetic knowledge could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend traditional assumptions about selection practices. Ultimately, there are still many unanswered questions regarding how epigenetic mechanisms might be leveraged in aquaculture. Gavery, Mackenzie & Roberts, Steven. (2017). Epigenetic considerations in aquaculture. PeerJ. 5. e4147. 10.7717/peerj.4147. https://peerj.com/articles/4147.pdfDionisio
January 19, 2018
January
01
Jan
19
19
2018
02:32 AM
2
02
32
AM
PDT
Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented. Artificial selection in hatcheries has often been invoked as the most likely explanation for reduced fitness, and most studies to date have focused on finding signatures of hatchery-induced selection at the DNA level. We tested an alternative hypothesis, that captive rearing induces epigenetic reprogramming, by comparing genome-wide patterns of methylation and variation at the DNA level in hatchery-reared coho salmon (Oncorhynchus kisutch) with those of their wild counterparts in two geographically distant rivers. We found a highly significant proportion of epigenetic variation explained by the rearing environment that was as high as the one explained by the river of origin. The differentially methylated regions show enrichment for biological functions that may affect the capacity of hatchery-born smolts to migrate successfully in the ocean. Shared epigenetic variation between hatchery-reared salmon provides evidence for parallel epigenetic modifications induced by hatchery rearing in the absence of genetic differentiation between hatchery and natural-origin fish for each river. This study highlights epigenetic modifications induced by captive rearing as a potential explanatory mechanism for reduced fitness in hatchery-reared salmon. le luyer, Jeremy & Laporte, Martin & Beacham, Terry & Kaukinen, Karia & E Withler, Ruth & Leong, Jong & Rondeau, Eric & Koop, Ben & Bernatchez, Louis. (2017). Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon. Proceedings of the National Academy of Sciences. 114. . 10.1073/pnas.1711229114. https://www.researchgate.net/profile/Jeremy_Le_Luyer/publication/321197011_Parallel_epigenetic_modifications_induced_by_hatchery_rearing_in_a_Pacific_salmon/links/5a146931a6fdccd697bbe364/Parallel-epigenetic-modifications-induced-by-hatchery-rearing-in-a-Pacific-salmon.pdfDionisio
January 19, 2018
January
01
Jan
19
19
2018
02:27 AM
2
02
27
AM
PDT
We examined spatio-temporal genetic variation at 53 single nucleotide polymorphisms in anadromous Arctic char populations from Western Greenland, a region experiencing pronounced climate change. The study was based on contemporary and historical samples, the latter represented by DNA extracted from otoliths and scales from the 1950s–1960s. We investigated whether genetic population structure was temporarily stable or unstable, the latter due to relatively small spawning and nursery areas combined with a harsh Arctic environment. Furthermore, in order to evaluate the potential for adaptive responses and local adaptation we estimated effective population size (Ne) and migration rate (m). Temporal stability of genetic population structure was suggested, based on a hierarchical analysis of genetic differentiation showing much higher differentiation among samples from different populations (FCT = 0.091) than among temporal samples from the same populations (FSC = 0.01). This was further supported by a neighbor-joining tree and assignment of individuals that showed high contingency between historical and contemporary samples. Estimates of Ne were high (> 500) in three out of four populations, with a lower estimate in one population potentially reflecting fishing pressure or suboptimal environmental conditions. Estimates of m were in most cases low, ? 0.01. Ne and m estimates suggest a potential for adaptive responses and local adaptation. However, long generation time may also cause adaptive responses by microevolution to be unable to track climate change, especially considering the low migration rates that reduce potential evolutionary rescue by gene flow from populations better adapted to the altered environments. Christensen, Camilla & Jacobsen, Magnus & Nygaard, Rasmus & Hansen, Michael. (2018). Spatiotemporal genetic structure of anadromous Arctic char (Salvelinus alpinus) populations in a region experiencing pronounced climate change. Conservation Genetics. 1-14. 10.1007/s10592-018-1047-x.Dionisio
January 19, 2018
January
01
Jan
19
19
2018
02:25 AM
2
02
25
AM
PDT
Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of non-model organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic. Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large proportion of fish (72%) tagged in three different rivers migrating up the same short river in the fall. Population genomics data from 6,136 SNP markers revealed weak, albeit significant, population differentiation (average pairwise FST = 0.011) and asymmetric dispersal was also revealed by population assignments. Approximate Bayesian Computation simulations suggested the presence of asymmetric gene flow, although in the opposite direction to that observed from the telemetry data, suggesting that dispersal does not necessarily lead to gene flow. These observations suggested that Arctic Char home to their natal river to spawn, but may overwinter in rivers with the shortest migratory route to minimize the costs of migration in non-breeding years. Genome scans and genetic-environment associations identified 90 outlier markers putatively under selection, 23 of which were in or near a gene. Of these, at least four were involved in muscle and cardiac function, consistent with the hypothesis that migratory harshness could drive local adaptation. Our study illustrates the power of integrating genomics and telemetry to study migrations in non-model organisms in logistically challenging environments such as the Arctic. Moore, Jean-Sébastien & Harris, Les & le luyer, Jeremy & Sutherland, Ben & Rougemont, Quentin & Tallman, Ross & Fisk, Aaron & Bernatchez, Louis. (2017). Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char. Molecular Ecology. 26. . 10.1111/mec.14393. https://www.researchgate.net/profile/Jean-Sebastien_Moore/publication/320738125_Genomics_and_telemetry_suggest_a_role_for_migration_harshness_in_determining_overwintering_habitat_choice_but_not_gene_flow_in_anadromous_Arctic_Char/links/59fc6afc0f7e9b9968bd7c47/Genomics-and-telemetry-suggest-a-role-for-migration-harshness-in-determining-overwintering-habitat-choice-but-not-gene-flow-in-anadromous-Arctic-Char.pdfDionisio
January 19, 2018
January
01
Jan
19
19
2018
02:20 AM
2
02
20
AM
PDT
The colonization of urban environments by animals is often accompanied by earlier breeding and associated changes in seasonal schedules. Accelerated timing of seasonal reproduction in derived urban populations is a potential cause of evolutionary divergence from ancestral populations if differences in physiological processes that regulate reproductive timing become fixed over time. We compared reproductive development in free-living and captive male dark-eyed juncos deriving from a population that recently colonized a city (~35 years) and ceased migrating to that of conspecifics that live in sympatry with the urban population during winter and spring but migrate elsewhere to breed. We predicted that the earlier breeding sedentary urban birds would exhibit accelerated reproductive development in the spring along the hypothalamic-pituitary-gonadal (HPG) axis as compared to migrants. We found that free-living sedentary urban and migrant juncos differed at the level of the pituitary when measured as baseline luteinizing hormone (LH) levels, but not in increased LH when challenged with Gonadotropin-Releasing Hormone (GnRH). Among captives held in a common garden, and at the level of the gonad, we found that sedentary urban birds produced more testosterone in response to GnRH than migrants living in the same common environment, suggesting greater gonadal sensitivity in the derived urban population. Greater gonadal sensitivity could arise from greater upstream activation by LH or FSH or from reduced suppression of gonadal development by the adrenal axis. We compared abundance of gonadal transcripts for LH receptor (LHR), follicle stimulating hormone receptor (FSHR), glucocorticoid receptor (GR), and mineralocorticoid receptor (MR) in the common-garden, predicting either more abundant transcripts for LHR and FSHR or fewer transcripts for GR and MR in the earlier breeding sedentary urban breeders, as compared to the migrants. We found no difference in the expression of these genes. Together these data suggest that advanced timing of reproduction in a recently derived urban population is facilitated by earlier increase in upstream baseline activity of the HPG and earlier release from gonadal suppression by yet-to-be-discovered mechanisms. Evolutionarily, our results suggest that potential for gene flow between seasonally sympatric populations may be limited due to urban-induced advances in the timing of reproduction and resulting allochrony with ancestral forms. Fudickar, Adam & J. Greives, Timothy & Abolins-Abols, Mikus & Atwell, Jonathan & Meddle, Simone & Friis, Guillermo & Stricker, Craig & Ketterson, Ellen. (2017). Mechanisms Associated with an Advance in the Timing of Seasonal Reproduction in an Urban Songbird. Frontiers in Ecology and Evolution. 5. 85. 10.3389/fevo.2017.00085. https://www.researchgate.net/profile/Simone_Meddle/publication/318871742_Mechanisms_Associated_with_an_Advance_in_the_Timing_of_Seasonal_Reproduction_in_an_Urban_Songbird/links/5983202da6fdcca7b66e2e2c/Mechanisms-Associated-with-an-Advance-in-the-Timing-of-Seasonal-Reproduction-in-an-Urban-Songbird.PDFDionisio
January 19, 2018
January
01
Jan
19
19
2018
02:16 AM
2
02
16
AM
PDT
Seasonal migration is a widespread phenomenon, which is found in many different lineages of animals. This spectacular behaviour allows animals to avoid seasonally adverse environmental conditions to exploit more favourable habitats. Migration has been intensively studied in birds, which display astonishing variation in migration strategies, thus providing a powerful system for studying the ecological and evolutionary processes that shape migratory behaviour. Despite intensive research, the genetic basis of migration remains largely unknown. Here we used state-of-the-art radio-tracking technology to characterize the migratory behaviour of a partially migratory population of European blackbirds (Turdus merula) in southern Germany. We compared gene expression of resident and migrant individuals using high-throughput transcriptomics in blood samples. Analyses of sequence variation revealed a non-significant genetic structure between blackbirds differing by their migratory phenotype. We detected only four differentially expressed genes between migrants and residents, which might be associated with hyperphagia, moulting, and enhanced DNA replication and transcription. The most pronounced changes in gene expression occurred between migratory birds depending on when, in relation to their date of departure, blood was collected. Overall, the differentially expressed genes detected in this analysis may play crucial roles in determining the decision to migrate, or in controlling the physiological processes required for the onset of migration. These results provide new insights into, and testable hypotheses for, the molecular mechanisms controlling the migratory phenotype and its underlying physiological mechanisms in blackbirds and other migratory bird species. This article is protected by copyright. All rights reserved. Franchini, Paolo & Irisarri, Iker & Fudickar, Adam & Schmidt, Andreas & Meyer, Axel & Wikelski, Martin & Partecke, Jesko. (2017). Animal tracking meets migration genomics: Transcriptomic analysis of a partially migratory bird species. Molecular Ecology. . 10.1111/mec.14108. https://www.researchgate.net/profile/Adam_Fudickar/publication/315434379_Animal_tracking_meets_migration_genomics_Transcriptomic_analysis_of_a_partially_migratory_bird_species/links/59df800fa6fdccfcfda38457/Animal-tracking-meets-migration-genomics-Transcriptomic-analysis-of-a-partially-migratory-bird-species.pdfDionisio
January 19, 2018
January
01
Jan
19
19
2018
02:12 AM
2
02
12
AM
PDT
Myrosin cells accumulate myrosinases in their vacuoles to catalyze the production of toxic compounds when tissues are damaged by herbivores. Myrosin cells are positioned adjacent to the abaxial side of the vasculature but their origin is unclear. To determine whether the myrosin cells are differentiated from vascular precursor cells, we generated a transgenic Arabidopsis line that expressed a myrosin cell reporter together with one of three vascular precursor cell reporters. The myrosin-positive cells were discontinuously distributed while the vascular precursor-positive cells were continuously distributed. The fluorescent signals of the myosin and vascular reporters did not overlap. Furthermore, the shape of myrosin-positive cells was different from the shape of vascular precursor-positive cells. These results indicate that myosin cells develop independently of the vasculature. Shirakawa, Makoto & Ueda, Haruko & Shimada, Tomoo & Hara-Nishimura, Ikuko. (2016). Myrosin cells are differentiated directly from ground meristem cells and are developmentally independent of the vasculature in Arabidopsis leaves. Plant Signaling & Behavior. 11. 00-00. 10.1080/15592324.2016.1150403. https://www.researchgate.net/profile/Makoto_Shirakawa/publication/297891491_Myrosin_cells_are_differentiated_directly_from_ground_meristem_cells_and_are_developmentally_independent_of_the_vasculature_in_Arabidopsis_leaves/links/59dcd8e30f7e9bdd752dd0b8/Myrosin-cells-are-differentiated-directly-from-ground-meristem-cells-and-are-developmentally-independent-of-the-vasculature-in-Arabidopsis-leaves.pdfDionisio
January 18, 2018
January
01
Jan
18
18
2018
04:45 AM
4
04
45
AM
PDT
The co-ordinated positioning of veins, mesophyll cells and stomata across a leaf is crucial for efficient gas exchange and transpiration, and therefore for overall function. In monocot leaves, stomatal cell files are positioned at the flanks of underlying longitudinal leaf veins, rather than directly above or below. This pattern suggests either that stomatal formation is inhibited in epidermal cells directly in contact with the vein, or that specification is induced in cells files beyond the vein. The SHORTROOT pathway specifies distinct cell-types around the vasculature in sub-epidermal layers of both root and shoots, with cell-type identity determined by distance from the vein. To test whether the pathway has the potential to similarly pattern epidermal cell-types, we expanded the expression domain of the rice OsSHR2 gene, which we show is restricted to developing leaf veins, to include bundle sheath cells encircling the vein. In transgenic lines, which were generated using the orthologous ZmSHR1 gene to avoid potential silencing of OsSHR2, stomatal cell files were observed both in the normal position and in more distant positions from the vein. Contrary to theoretical predictions, and to phenotypes observed in eudicot leaves, the increase in stomatal density did not enhance photosynthetic capacity or increase mesophyll cell density. Collectively these results suggest that the SHORTROOT pathway may co-ordinate the positioning of veins and stomata in monocot leaves, and that distinct mechanisms may operate in monocot and eudicot leaves to co-ordinate stomatal patterning with the development of underlying mesophyll cells. Schuler, Mara & V. Sedelnikova, Olga & Walker, Berkley & Westhoff, Peter & A. Langdale, Jane. (2017). SHORTROOT-Mediated Increase in Stomatal Density Has No Impact on Photosynthetic Efficiency. Plant Physiology. 176. pp.01005.2017. 10.1104/pp.17.01005. https://www.researchgate.net/profile/Berkley_Walker/publication/320995365_SHORTROOT-Mediated_Increase_in_Stomatal_Density_Has_No_Impact_on_Photosynthetic_Efficiency/links/5a13333c0f7e9b1e572e88f5/SHORTROOT-Mediated-Increase-in-Stomatal-Density-Has-No-Impact-on-Photosynthetic-Efficiency.pdfDionisio
January 18, 2018
January
01
Jan
18
18
2018
01:40 AM
1
01
40
AM
PDT
Stomata are simultaneously tasked with permitting the uptake of carbon dioxide for photosynthesis while limiting water loss from the plant. This process is mainly regulated by guard cell control of the stomatal aperture, but recent advancements have highlighted the importance of several genes that control stomatal development. Using targeted genetic manipulations of the stomatal lineage and a combination of gas exchange and microscopy techniques, we show that changes in stomatal development of the epidermal layer lead to coupled changes in the underlying mesophyll tissues. This coordinated response tends to match leaf photosynthetic potential (Vcmax) with gas?exchange capacity (gsmax), and hence the uptake of carbon dioxide for water lost. We found that different genetic regulators systematically altered tissue coordination in separate ways: the transcription factor SPEECHLESS (SPCH) primarily affected leaf size and thickness, whereas peptides in the EPIDERMAL PATTERNING FACTOR (EPF) family altered cell density in the mesophyll. It was also determined that interlayer coordination required the cell?surface receptor TOO MANY MOUTHS (TMM). These results demonstrate that stomata?specific regulators can alter mesophyll properties, which provides insight into how molecular pathways can organize leaf tissues to coordinate gas exchange and suggests new strategies for improving plant water?use efficiency. J. Dow, Graham & Berry, Joseph & C. Bergmann, Dominique. (2017). Disruption of stomatal lineage signaling or transcriptional regulators has differential effects on mesophyll development, but maintains coordination of gas exchange. New Phytologist. 216. . 10.1111/nph.14746. https://www.researchgate.net/publication/319204070_Disruption_of_stomatal_lineage_signaling_or_transcriptional_regulators_has_differential_effects_on_mesophyll_development_but_maintains_coordination_of_gas_exchange/fulltext/599b0125aca272dff128d5f8/319204070_Disruption_of_stomatal_lineage_signaling_or_transcriptional_regulators_has_differential_effects_on_mesophyll_development_but_maintains_coordination_of_gas_exchange.pdfDionisio
January 18, 2018
January
01
Jan
18
18
2018
01:29 AM
1
01
29
AM
PDT
The development and patterning of stomata in the plant epidermis has emerged as an ideal system for studying fundamental plant developmental processes. Over the past twenty years most studies of stomata have used the model dicotyledonous plant Arabidopsis thaliana. However, cultivated monocotyledonous grass (or Gramineae) varieties provide the majority of human nutrition, and future research into grass stomata could be of critical importance for improving food security. Recent studies using Brachypodium distachyon, Hordeum vulgare (barley) and Oryza sativa (rice) have led to the identification of the core transcriptional regulators essential for stomatal initiation and progression in grasses, and begun to unravel the role of secretory signaling peptides in controlling stomatal developmental. This review revisits how stomatal developmental unfolds in grasses, and identifies key ontogenetic steps for which knowledge of the underpinning molecular mechanisms remains outstanding. Hepworth, Christopher & Caine, Robert & Harrison, Emily & Sloan, Jennifer & Gray, Julie. (2017). Stomatal development: focusing on the grasses. Current opinion in plant biology. 41. 1-7. 10.1016/j.pbi.2017.07.009.Dionisio
January 18, 2018
January
01
Jan
18
18
2018
01:26 AM
1
01
26
AM
PDT
Stem cell regeneration is crucial for both cell turnover and tissue healing in multicellular organisms. In Arabidopsis roots, a reduced group of cells known as the quiescent center (QC) acts as a cell reservoir for surrounding stem cells during both normal growth and in response to external damage. Although cells of the QC have a very low mitotic activity, plant hormones such as brassinosteroids (BR) can promote QC divisions. Here, we used a tissue-specific strategy to investigate the spatial signaling requirements of BR-mediated QC divisions. We generated stem cell niche-specific receptor knockout lines by placing an artificial microRNA against BRI1 (BRASSINOSTEROID RESPONSE INSENSITIVE 1) under the control of the QC-specific promoter WOX5. Additionally, QC-specific knock-in lines for BRI1 and its downstream transcription factor BES1 (BRI1-EMS-SUPPRESOR1) were also created using the WOX5 promoter. By analyzing the roots of these lines, we uncover that BES1-mediated signaling cell-autonomously promotes QC divisions, that BRI1 is essential for sensing nearby inputs and triggering QC divisions, and that DNA damage promotes BR-dependent paracrine signaling in the stem cell niche as a prerequisite to stem cell replenishment. Lozano-Elena, Fidel & Planas Riverola, Ainoa & Vilarrasa-Blasi, Josep & Schwab, Rebecca & Caño-Delgado, Ana. (2017). Paracrine brassinosteroid signaling at the stem cell niche controls cellular regeneration. Journal of Cell Science. jcs.204065. 10.1242/jcs.204065. http://jcs.biologists.org/content/early/2017/12/13/jcs.204065.full.pdfDionisio
January 18, 2018
January
01
Jan
18
18
2018
01:23 AM
1
01
23
AM
PDT
Development of stomata, valves on the plant epidermis for optimal gas exchange and water control, is fine-tuned by multiple signaling peptides with unique, overlapping, or antagonistic activities. EPIDERMAL PATTERNING FACTOR1 (EPF1) is a founding member of the secreted peptide ligands enforcing stomatal patterning. Yet, its exact role remains unclear. Here, we report that EPF1 and its primary receptor ERECTA-LIKE1 (ERL1) target MUTE, a transcription factor specifying the proliferation-to-differentiation switch within the stomatal cell lineages. In turn, MUTE directly induces ERL1. The absolute co-expression of ERL1 and MUTE, with the co-presence of EPF1, triggers autocrine inhibition of stomatal fate. During normal stomatal development, this autocrine inhibition prevents extra symmetric divisions of stomatal precursors likely owing to excessive MUTE activity. Our study reveals the unexpected role of self-inhibition as a mechanism for ensuring proper stomatal development and suggests an intricate signal buffering mechanism underlying plant tissue patterning. Qi, Xingyun & Han, Soon-Ki & H Dang, Jonathan & M Garrick, Jaqueline & Ito, Masaki & K. Hofstetter, Alex & Torii, Keiko. (2017). Autocrine regulation of stomatal differentiation potential by EPF1 and ERECTA-LIKE1 ligand-receptor signaling. eLife Sciences. 6. e24102. 10.7554/eLife.24102. https://www.researchgate.net/profile/Keiko_Torii/publication/322116826_Autocrine_regulation_of_stomatal_differentiation_potential_by_EPF1_and_ERECTA-LIKE1_ligand-receptor_signaling/links/5a45df75a6fdcce1971a91f2/Autocrine-regulation-of-stomatal-differentiation-potential-by-EPF1-and-ERECTA-LIKE1-ligand-receptor-signaling.pdfDionisio
January 18, 2018
January
01
Jan
18
18
2018
01:18 AM
1
01
18
AM
PDT
The development and patterning of stomata in the plant epidermis has emerged as an ideal system for studying fundamental plant developmental processes. Over the past twenty years most studies of stomata have used the model dicotyledonous plant Arabidopsis thaliana. However, cultivated monocotyledonous grass (or Gramineae) varieties provide the majority of human nutrition, and future research into grass stomata could be of critical importance for improving food security. Recent studies using Brachypodium distachyon, Hordeum vulgare (barley) and Oryza sativa (rice) have led to the identification of the core transcriptional regulators essential for stomatal initiation and progression in grasses, and begun to unravel the role of secretory signaling peptides in controlling stomatal developmental. This review revisits how stomatal developmental unfolds in grasses, and identifies key ontogenetic steps for which knowledge of the underpinning molecular mechanisms remains outstanding. Hepworth, Christopher & Caine, Robert & Harrison, Emily & Sloan, Jennifer & Gray, Julie. (2017). Stomatal development: focusing on the grasses. Current opinion in plant biology. 41. 1-7. 10.1016/j.pbi.2017.07.009.Dionisio
January 18, 2018
January
01
Jan
18
18
2018
01:14 AM
1
01
14
AM
PDT
@305 addendum
In plants, extracellular signals are primarily sensed by plasma membrane-localized receptor-like kinases (RLKs). ERECTA is a leucine-rich repeat RLK that together with its paralogs ERECTA-like 1 (ERL1) and ERL2 regulates multiple aspects of plant development. ERECTA forms complexes with a range of co-receptors and senses secreted cysteine-rich small proteins from the EPF/EPFL family. Currently the mechanism of the cytoplasmic domain activation and transmission of the signal by ERECTA is unclear. To gain a better understanding we performed a structure–function analysis by introducing altered ERECTA genes into erecta and erecta erl1 erl2 mutants. These experiments indicated that ERECTA’s ability to phosphorylate is functionally significant, and that while the cytoplasmic juxtamembrane domain is important for ERECTA function, the C-terminal tail is not. An analysis of multiple putative phosphorylation sites identified four amino acids in the activation segment of the kinase domain as functionally important. Homology of those residues to functionally significant amino acids in multiple other plant RLKs emphasizes similarities in RLK function. Specifically, our data predicts Thr812 as a primary site of phosphor-activation and potential inhibitory phosphorylation of Tyr815 and Tyr820. In addition, our experiments suggest that there are differences in the molecular mechanism of ERECTA function during regulation of stomata development and in elongation of above-ground organs.
Z Kosentka, Pawel & Zhang, Liang & A Simon, Yonas & Satpathy, Binita & Maradiaga, Richard & Mitoubsi, Omar & Shpak, Elena. (2017). Identification of critical functional residues of receptor-like kinase ERECTA. Journal of experimental botany. 68. . 10.1093/jxb/erx022.
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 18, 2018
January
01
Jan
18
18
2018
01:07 AM
1
01
07
AM
PDT
Stomata are dispersed pores found in the epidermis of land plants that facilitate gas exchange for photosynthesis while minimizing water loss. Stomata are formed from progenitor cells, which execute a series of differentiation events and stereotypical cell divisions. The sequential activation of master regulatory basic-helix-loop-helix (bHLH) transcription factors controls the initiation, proliferation and differentiation of stomatal cells. Cell-cell communication mediated by secreted peptides, receptor kinases, and downstream mitogen- activated kinase cascades enforces proper stomatal patterning, and an intrinsic polarity mechanism ensures asymmetric cell divisions. As we review here, recent studies have provided insights into the intrinsic and extrinsic factors that control stomatal development. These findings have also highlighted striking similarities between plants and animals with regards to their mechanisms of specialized cell differentiation.
Han, S.-K & Torii, Keiko. (2016). Lineage-specific stem cells, signals and asymmetries during stomatal development. Development. 143. 1259-1270. 10.1242/dev.127712. https://www.researchgate.net/profile/Keiko_Torii/publication/301536187_Lineage-specific_stem_cells_signals_and_asymmetries_during_stomatal_development/links/571e93d308aefa648899a376/Lineage-specific-stem-cells-signals-and-asymmetries-during-stomatal-development.pdf
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 18, 2018
January
01
Jan
18
18
2018
12:58 AM
12
12
58
AM
PDT
@305 addendum https://www.researchgate.net/profile/Elena_Shpak/publication/313819497_Identification_of_critical_functional_residues_of_receptor-like_kinase_ERECTA/links/58ad973645851503be91cb07/Identification-of-critical-functional-residues-of-receptor-like-kinase-ERECTA.pdfDionisio
January 17, 2018
January
01
Jan
17
17
2018
06:09 PM
6
06
09
PM
PDT
These results suggest that there are distinct signaling requirements for ERECTA in different developmental processes and imply that ERECTA might transmit the signal to downstream targets in different ways. The receptor-like kinases BAK1 and SCRAMBLED have also been shown to control multiple pathways using distinct signaling mechanisms with different requirements for their kinase domain function [...]
Identification of critical functional residues of receptor-like kinase ERECTA Pawel Z. Kosentka, Liang Zhang, Yonas A. Simon, Binita Satpathy, Richard Maradiaga, Omar Mitoubsi and Elena D. Shpak Journal of Experimental Botany doi:10.1093/jxb/erx022
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 17, 2018
January
01
Jan
17
17
2018
03:44 PM
3
03
44
PM
PDT
It has been argued here that the discontent is better understood as stemming from a few inescapable properties of living things, which lead to disappointment with evolutionary biology, and a nagging feeling that reform must be overdue. Evolutionary biology, like history, but unlike other natural sciences, raises issues of purpose and agency, alongside those of complexity and generality [...] It is remarkable, for example, that much of the funding for challenging current practice in evolutionary biology comes from The John Templeton Foundation (Pennisi 2016), which is committed to using science to reveal underlying purpose, and rejecting what Nagel (2012) calls “the Materialist Neo-Darwinian Conception of Nature”. [...] claims that evolutionary biology is misguided or importantly incomplete are not harmless, but actively hinder progress in the field. [...] a field that urgently needs reform is a field “in crisis” (Mazur 2010), and when it fails to reform, this lends credibility to claims that scientists are, at best, hidebound and foolish, and at worst, guilty of ideologically-motivated deception (Mazur 2010; Teresi 2011).
What’s wrong with evolutionary biology? John J. Welch Biology & Philosophy March 2017, Volume 32, Issue 2, pp 263–279
Dionisio
January 16, 2018
January
01
Jan
16
16
2018
12:47 AM
12
12
47
AM
PDT
[...] one research programme: the study of adaptive function. [...] traits of all kinds might be adaptations [...] Such research uses ideas related to optimization, including tools from engineering and economics, and often represents evolution in terms of (imaginary) agents with (imaginary) agendas. Hypothesizing about adaptive rationales is easy to do badly, and difficult to do well.
What’s wrong with evolutionary biology? John J. Welch Biology & Philosophy March 2017, Volume 32, Issue 2, pp 263–279
Dionisio
January 16, 2018
January
01
Jan
16
16
2018
12:28 AM
12
12
28
AM
PDT
[...] the theory of natural selection causes additional problems. One problem is its deceptive simplicity [...] [...] it is an idea that we all think we understand, but which continues to divide experts [...] [...] natural selection causes problems, not only because it is mindless and amoral, but because it can seem downright immoral. [...] Darwinist explanations inherently invoke selfishness and greed as the most important driving forces [...] [...] Darwin’s own emphasis on “struggle” probably rests on a mistake [...]
What’s wrong with evolutionary biology? John J. Welch Biology & Philosophy March 2017, Volume 32, Issue 2, pp 263–279
Dionisio
January 16, 2018
January
01
Jan
16
16
2018
12:15 AM
12
12
15
AM
PDT
The characteristics of life also guarantee that the explanatory frameworks of evolutionary biology will be disappointing to some. Disappointment is caused partly by the sheer complexity of life’s dynamical processes. This means that our predictive power will always be weak in certain ways, and that our descriptions of evolution will always be enormous simplifications.
What’s wrong with evolutionary biology? John J. Welch Biology & Philosophy March 2017, Volume 32, Issue 2, pp 263–279 https://link.springer.com/content/pdf/10.1007%2Fs10539-016-9557-8.pdf
Dionisio
January 15, 2018
January
01
Jan
15
15
2018
11:53 PM
11
11
53
PM
PDT
Some problems for evolutionary biology are caused by the basic characteristics of life. Some banal practical problems are caused by the sheer scope of evolutionary biology. [...] new data appear at a very rapid rate, particularly, in recent years, from molecular biology.
What’s wrong with evolutionary biology? John J. Welch Biology & Philosophy March 2017, Volume 32, Issue 2, pp 263–279 https://link.springer.com/content/pdf/10.1007%2Fs10539-016-9557-8.pdf
Dionisio
January 15, 2018
January
01
Jan
15
15
2018
11:48 PM
11
11
48
PM
PDT
Evo-devo despacito? :)
Usually, evolutionary economists equate evolutionary theory with modern Darwinism. However, the rise of evolutionary developmental biology (Evo-Devo) puts into question the monopoly of Darwinism in evolutionary biology. The major divergences between the two paradigms in evolutionary biology are drawn in the analysis of three trade-offs: population vs. typological thinking, creative role of natural selection vs. internal (inherent) change, and microevolution vs. macroevolution. It is argued here that the Evo-Devo breakthrough helps us to understand better the limits to Darwinism in the social realm and outline the contours of an alternative paradigm in evolutionary economics that favors structural macroevolution and what Schumpeter called “change from within”.
The challenge of Evo-Devo: implications for evolutionary economists George Liagouras https://doi.org/10.1007/s00191-017-0525-5 Journal of Evolutionary Economics September 2017, Volume 27, Issue 4, pp 795–823
Dionisio
January 15, 2018
January
01
Jan
15
15
2018
11:19 PM
11
11
19
PM
PDT
The epidermis of aerial plant organs is thought to be limiting for growth, because it acts as a continuous load-bearing layer, resisting tension. Leaf epidermis contains jigsaw puzzle piece-shaped pavement cells whose shape has been proposed to be a result of subcellular variations in expansion rate that induce local buckling events. Paradoxically, such local compressive buckling should not occur given the tensile stresses across the epidermis. Using computational modeling, we show that the simplest scenario to explain pavement cell shapes within an epidermis under tension must involve mechanical wall heterogeneities across and along the anticlinal pavement cell walls between adjacent cells. Combining genetics, atomic force microscopy, and immunolabeling, we demonstrate that contiguous cell walls indeed exhibit hybrid mechanochemical properties. Such biochemical wall heterogeneities precede wall bending. Altogether, this provides a possible mechanism for the generation of complex plant cell shapes.
Mechanochemical Polarization of Contiguous Cell Walls Shapes Plant Pavement Cells Mateusz Majda, Peter Grones, Ida-Maria Sintorn, Thomas Vain, Pascale Milani, Pawel Krupinski, Beata Zagórska-Marek, Corrado Viotti, Henrik Jönsson, Ewa J. Mellerowicz, Olivier Hamant, Stéphanie Robert DOI: http://dx.doi.org/10.1016/j.devcel.2017.10.017 Volume 43, Issue 3, p290–304.e4, Developmental Cell
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 15, 2018
January
01
Jan
15
15
2018
12:54 PM
12
12
54
PM
PDT
Coordinated development of multicellular organisms depends on the ability of cells to assess their relative positions within the growing organism. This is achieved through intercellular communication, commonly based on the production and perception of mobile signaling molecules. [...] the mobile signals used by plants to instruct cell-fate decisions, such as hormones and peptide ligands, are distinct from those of animals [...]
Boundary Formation through a Direct Threshold-Based Readout of Mobile Small RNA Gradients Damianos S.Skopelitis, Anna H.Benkovics, Aman Y.Husbands, Marja C.P.Timmermans Developmental Cell 43, 1–9 Volume 43, Issue 3, Pages 265-273.e6 https://doi.org/10.1016/j.devcel.2017.10.003 https://www.researchgate.net/profile/Aman_Husbands/publication/320639868_Boundary_Formation_through_a_Direct_Threshold-Based_Readout_of_Mobile_Small_RNA_Gradients/links/5a1ec9c4a6fdccc6b7f8b6bc/Boundary-Formation-through-a-Direct-Threshold-Based-Readout-of-Mobile-Small-RNA-Gradients.pdf
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 15, 2018
January
01
Jan
15
15
2018
12:40 PM
12
12
40
PM
PDT
Small RNAs have emerged as a new class of mobile signals. Here, we investigate their mechanism of action and show that mobile small RNAs generate sharply defined domains of target gene expression through an intrinsic and direct threshold-based readout of their mobility gradients. This readout is highly sensitive to small RNA levels at the source, allowing plasticity in the positioning of a target gene expression boundary. Besides patterning their immediate targets, the readouts of opposing small RNA gradients enable specification of robust, uniformly positioned developmental boundaries. These patterning properties of small RNAs are reminiscent of those of animal morphogens. However, their mode of action and the intrinsic nature of their gradients distinguish mobile small RNAs from classical morphogens and present a unique direct mechanism through which to relay positional information. Mobile small RNAs and their targets thus emerge as highly portable, evolutionarily tractable regulatory modules through which to create pattern.
Boundary Formation through a Direct Threshold-Based Readout of Mobile Small RNA Gradients Damianos S.Skopelitis, Anna H.Benkovics, Aman Y.Husbands, Marja C.P.Timmermans Developmental Cell 43, 1–9 Volume 43, Issue 3, Pages 265-273.e6 https://doi.org/10.1016/j.devcel.2017.10.003
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 15, 2018
January
01
Jan
15
15
2018
12:26 PM
12
12
26
PM
PDT
Exploring biogenic amine receptors and downstream regulatory pathways involved in insect behavior and derived social functions will advance our understanding of how the eusocial insect brain evolved perceptual and cognitive capacities in association with sociality. Broader sampling is required to gain phylogenetic insight into the evolution of aminergic control systems. Determining patterns of conservation and/or diversification of aminergic regulatory mechanisms of social behavior will benefit from studies of insect genera that include solitary and eusocial species. Despite the widespread activity of biogenic amines, functional patterns appear. 5-HT may control energy expenditure through feeding behavior and circadian rhythms, DA regulates fertility, thus modulating task performance in eusocial species, and OA modulates appetitive learning associated with feeding and nestmate recognition. Advances in epigenetics (Libbrecht et al., 2016), neurogenetics (Friedman and Gordon, 2016), and the integration of sociobiology and neurochemistry (Kamhi and Traniello, 2013) will aid in future research.
Origins of Aminergic Regulation of Behavior in Complex Insect Social Systems J. Frances Kamhi,1,* Sara Arganda,2,3 Corrie S. Moreau,4 and James F. A. Traniello Front Syst Neurosci. 2017; 11: 74. doi: 10.3389/fnsys.2017.00074
Parole, parole, parole… Where’s the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 15, 2018
January
01
Jan
15
15
2018
11:31 AM
11
11
31
AM
PDT
1 2 3 4 12

Leave a Reply